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Benedetti F, Mongodin EF, Badger JH, Munawwar A, Cellini A, Yuan W, Silvestri G, Kraus CN, Marini S, Rathinam CV, Salemi M, Tettelin H, Gallo RC, Zella D. Bacterial DnaK reduces the activity of anti-cancer drugs cisplatin and 5FU. J Transl Med 2024; 22:269. [PMID: 38475767 DOI: 10.1186/s12967-024-05078-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 03/07/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Chemotherapy is a primary treatment for cancer, but its efficacy is often limited by cancer-associated bacteria (CAB) that impair tumor suppressor functions. Our previous research found that Mycoplasma fermentans DnaK, a chaperone protein, impairs p53 activities, which are essential for most anti-cancer chemotherapeutic responses. METHODS To investigate the role of DnaK in chemotherapy, we treated cancer cell lines with M. fermentans DnaK and then with commonly used p53-dependent anti-cancer drugs (cisplatin and 5FU). We evaluated the cells' survival in the presence or absence of a DnaK-binding peptide (ARV-1502). We also validated our findings using primary tumor cells from a novel DnaK knock-in mouse model. To provide a broader context for the clinical significance of these findings, we investigated human primary cancer sequencing datasets from The Cancer Genome Atlas (TCGA). We identified F. nucleatum as a CAB carrying DnaK with an amino acid composition highly similar to M. fermentans DnaK. Therefore, we investigated the effect of F. nucleatum DnaK on the anti-cancer activity of cisplatin and 5FU. RESULTS Our results show that both M. fermentans and F. nucleatum DnaKs reduce the effectiveness of cisplatin and 5FU. However, the use of ARV-1502 effectively restored the drugs' anti-cancer efficacy. CONCLUSIONS Our findings offer a practical framework for designing and implementing novel personalized anti-cancer strategies by targeting specific bacterial DnaKs in patients with poor response to chemotherapy, underscoring the potential for microbiome-based personalized cancer therapies.
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Affiliation(s)
- Francesca Benedetti
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Emmanuel F Mongodin
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Jonathan H Badger
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Arshi Munawwar
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ashley Cellini
- Pathology Biorepository Shared Service, University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, MD, 21201, USA
| | - Weirong Yuan
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Giovannino Silvestri
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Simone Marini
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- Department of Epidemiology, University of Florida, Gainesville, FL, USA
| | - Chozha V Rathinam
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- Department of Pathology, University of Florida, Gainesville, FL, USA
| | - Hervé Tettelin
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Robert C Gallo
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Davide Zella
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA.
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Badger JH, Giordano R, Zimin A, Wappel R, Eskipehlivan SM, Muller S, Donthu R, Soto-Adames F, Vieira P, Zasada I, Goodwin S. Direct sequencing of insect symbionts via nanopore adaptive sampling. Curr Opin Insect Sci 2024; 61:101135. [PMID: 37926187 DOI: 10.1016/j.cois.2023.101135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/07/2023]
Abstract
Insect symbionts can alter their host phenotype and their effects can range from beneficial to pathogenic. Moreover, many insects exhibit co-infections, making their study more challenging. Less than 1% of insect species have high-quality referenced genomes available and fewer still also have their symbionts sequenced. Two methods are commonly used to sequence symbionts: whole-genome sequencing to concomitantly capture the host and bacterial genomes, or isolation of the symbiont's genome before sequencing. These methods are limited when dealing with rare or poorly characterized symbionts. Long-read technology is an important tool to generate high-quality genomes as they can overcome high levels of heterozygosity, repeat content, and transposable elements that confound short-read methods. Oxford Nanopore (ONT) adaptive sampling allows a sequencing instrument to select or reject sequences in real time. We describe a method based on ONT adaptive sampling (subtractive) approach that readily permitted the sequencing of the complete genomes of mitochondria, Buchnera and its plasmids (pLeu, pTrp), and Wolbachia genomes in two aphid species, Aphis glycines and Pentalonia nigronervosa. Adaptive sampling is able to retrieve organelles such as mitochondria and symbionts that have high representation in their hosts such as Buchnera and Wolbachia, but is less successful at retrieving symbionts in low concentrations.
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Affiliation(s)
- Jonathan H Badger
- Genetics and Microbiome Core, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Rosanna Giordano
- Institute of Environment, Florida International University, Miami, FL, USA
| | - Aleksey Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Robert Wappel
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | | | - Ravikiran Donthu
- Centre for Life Sciences, Mahindra University, Bahadurpally, Hyderabad 500043, India
| | - Felipe Soto-Adames
- Florida Department of Agriculture and Consumer Services, Department of Plant Industry, Gainesville, FL 32614, USA
| | - Paulo Vieira
- USDA-ARS Agricultural Research Center, Mycology & Nematology Genetic Diversity & Biology Laboratory, Beltsville, MD, USA
| | - Inga Zasada
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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3
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Soares NR, Huguet-Tapia JC, Guan D, Clark CA, Yang KT, Kluchka OR, Thombal RS, Kartika R, Badger JH, Pettis GS. Comparative genomics of the niche-specific plant pathogen Streptomyces ipomoeae reveal novel genome content and organization. Appl Environ Microbiol 2023; 89:e0030823. [PMID: 38009923 PMCID: PMC10734452 DOI: 10.1128/aem.00308-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/28/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE While most plant-pathogenic Streptomyces species cause scab disease on a variety of plant hosts, Streptomyces ipomoeae is the sole causative agent of soil rot disease of sweet potato and closely related plant species. Here, genome sequencing of virulent and avirulent S. ipomoeae strains coupled with comparative genomic analyses has identified genome content and organization features unique to this streptomycete plant pathogen. The results here will enable future research into the mechanisms used by S. ipomoeae to cause disease and to persist in its niche environment.
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Affiliation(s)
- Natasha R. Soares
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | | | - Dongli Guan
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Christopher A. Clark
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Kuei-Ting Yang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Olivia R. Kluchka
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Raju S. Thombal
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Rendy Kartika
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Jonathan H. Badger
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gregg S. Pettis
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
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4
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McCulloch JA, Davar D, Rodrigues RR, Badger JH, Fang JR, Cole AM, Balaji AK, Vetizou M, Prescott SM, Fernandes MR, Costa RGF, Yuan W, Salcedo R, Bahadiroglu E, Roy S, DeBlasio RN, Morrison RM, Chauvin JM, Ding Q, Zidi B, Lowin A, Chakka S, Gao W, Pagliano O, Ernst SJ, Rose A, Newman NK, Morgun A, Zarour HM, Trinchieri G, Dzutsev AK. Intestinal microbiota signatures of clinical response and immune-related adverse events in melanoma patients treated with anti-PD-1. Nat Med 2022; 28:545-556. [PMID: 35228752 DOI: 10.1038/s41591-022-01698-2] [Citation(s) in RCA: 145] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 01/13/2022] [Indexed: 12/12/2022]
Abstract
Ample evidence indicates that the gut microbiome is a tumor-extrinsic factor associated with antitumor response to anti-programmed cell death protein-1 (PD-1) therapy, but inconsistencies exist between published microbial signatures associated with clinical outcomes. To resolve this, we evaluated a new melanoma cohort, along with four published datasets. Time-to-event analysis showed that baseline microbiota composition was optimally associated with clinical outcome at approximately 1 year after initiation of treatment. Meta-analysis and other bioinformatic analyses of the combined data show that bacteria associated with favorable response are confined within the Actinobacteria phylum and the Lachnospiraceae/Ruminococcaceae families of Firmicutes. Conversely, Gram-negative bacteria were associated with an inflammatory host intestinal gene signature, increased blood neutrophil-to-lymphocyte ratio, and unfavorable outcome. Two microbial signatures, enriched for Lachnospiraceae spp. and Streptococcaceae spp., were associated with favorable and unfavorable clinical response, respectively, and with distinct immune-related adverse effects. Despite between-cohort heterogeneity, optimized all-minus-one supervised learning algorithms trained on batch-corrected microbiome data consistently predicted outcomes to programmed cell death protein-1 therapy in all cohorts. Gut microbial communities (microbiotypes) with nonuniform geographical distribution were associated with favorable and unfavorable outcomes, contributing to discrepancies between cohorts. Our findings shed new light on the complex interaction between the gut microbiome and response to cancer immunotherapy, providing a roadmap for future studies.
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Affiliation(s)
- John A McCulloch
- Genetics and Microbiome Core, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Diwakar Davar
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Richard R Rodrigues
- Genetics and Microbiome Core, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.,Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jonathan H Badger
- Genetics and Microbiome Core, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Jennifer R Fang
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Alicia M Cole
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Ascharya K Balaji
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Marie Vetizou
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Stephanie M Prescott
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Miriam R Fernandes
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Raquel G F Costa
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Wuxing Yuan
- Genetics and Microbiome Core, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.,Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Rosalba Salcedo
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Erol Bahadiroglu
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Soumen Roy
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Richelle N DeBlasio
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert M Morrison
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joe-Marc Chauvin
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Quanquan Ding
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bochra Zidi
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ava Lowin
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Saranya Chakka
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wentao Gao
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ornella Pagliano
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Scarlett J Ernst
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Amy Rose
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nolan K Newman
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Andrey Morgun
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Hassane M Zarour
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA. .,Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Giorgio Trinchieri
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| | - Amiran K Dzutsev
- Cancer Immunobiology Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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5
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Spencer CN, McQuade JL, Gopalakrishnan V, McCulloch JA, Vetizou M, Cogdill AP, Khan AW, Zhang X, White MG, Peterson CB, Wong MC, Morad G, Rodgers T, Badger JH, Helmink BA, Andrews MC, Rodrigues RR, Morgun A, Kim YS, Roszik J, Hoffman KL, Zheng J, Zhou Y, Medik YB, Kahn LM, Johnson S, Hudgens CW, Wani K, Gaudreau PO, Harris AL, Jamal MA, Baruch EN, Perez-Guijarro E, Day CP, Merlino G, Pazdrak B, Lochmann BS, Szczepaniak-Sloane RA, Arora R, Anderson J, Zobniw CM, Posada E, Sirmans E, Simon J, Haydu LE, Burton EM, Wang L, Dang M, Clise-Dwyer K, Schneider S, Chapman T, Anang NAAS, Duncan S, Toker J, Malke JC, Glitza IC, Amaria RN, Tawbi HA, Diab A, Wong MK, Patel SP, Woodman SE, Davies MA, Ross MI, Gershenwald JE, Lee JE, Hwu P, Jensen V, Samuels Y, Straussman R, Ajami NJ, Nelson KC, Nezi L, Petrosino JF, Futreal PA, Lazar AJ, Hu J, Jenq RR, Tetzlaff MT, Yan Y, Garrett WS, Huttenhower C, Sharma P, Watowich SS, Allison JP, Cohen L, Trinchieri G, Daniel CR, Wargo JA. Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response. Science 2021; 374:1632-1640. [PMID: 34941392 PMCID: PMC8970537 DOI: 10.1126/science.aaz7015] [Citation(s) in RCA: 318] [Impact Index Per Article: 106.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Gut bacteria modulate the response to immune checkpoint blockade (ICB) treatment in cancer, but the effect of diet and supplements on this interaction is not well studied. We assessed fecal microbiota profiles, dietary habits, and commercially available probiotic supplement use in melanoma patients and performed parallel preclinical studies. Higher dietary fiber was associated with significantly improved progression-free survival in 128 patients on ICB, with the most pronounced benefit observed in patients with sufficient dietary fiber intake and no probiotic use. Findings were recapitulated in preclinical models, which demonstrated impaired treatment response to anti–programmed cell death 1 (anti–PD-1)–based therapy in mice receiving a low-fiber diet or probiotics, with a lower frequency of interferon-γ–positive cytotoxic T cells in the tumor microenvironment. Together, these data have clinical implications for patients receiving ICB for cancer.
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Affiliation(s)
- Christine N. Spencer
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer L. McQuade
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - John A. McCulloch
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Marie Vetizou
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Alexandria P. Cogdill
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - A. Wadud Khan
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaotao Zhang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael G. White
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christine B. Peterson
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matthew C. Wong
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Golnaz Morad
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Theresa Rodgers
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jonathan H. Badger
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Beth A. Helmink
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Miles C. Andrews
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Richard R. Rodrigues
- Frederick National Laboratory for Cancer Research, and Microbiome and Genetics Core, Laboratory of Integrative Cancer Immunology, CCR, NCI, NIH, Bethesda, MD 20852, USA
| | - Andrey Morgun
- Department of Pharmaceutical Science, Oregon State University, Corvallis, OR 97331, USA
| | - Young S. Kim
- Nutritional Science Research Group, Division of Cancer Prevention, NCI, NIH, Rockville, MD 20850, USA
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kristi L. Hoffman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jiali Zheng
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yifan Zhou
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yusra B. Medik
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Laura M. Kahn
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- MD Anderson University of Texas Health Graduate School, Houston, TX 77030, USA
| | - Sarah Johnson
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Courtney W. Hudgens
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Khalida Wani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pierre-Olivier Gaudreau
- Canadian Cancer Trials Group and Department of Oncology, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Angela L. Harris
- Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mohamed A. Jamal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Erez N. Baruch
- Department of Internal Medicine, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Eva Perez-Guijarro
- Laboratory of Cancer Biology and Genetics, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Glenn Merlino
- Laboratory of Cancer Biology and Genetics, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Barbara Pazdrak
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Brooke S. Lochmann
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Reetakshi Arora
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jaime Anderson
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chrystia M. Zobniw
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Eliza Posada
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Elizabeth Sirmans
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Julie Simon
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lauren E. Haydu
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Elizabeth M. Burton
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Minghao Dang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Karen Clise-Dwyer
- Advanced Cytometry and Sorting Facility at South Campus, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Hematopoietic Biology and Malignancy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sarah Schneider
- Advanced Cytometry and Sorting Facility at South Campus, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Thomas Chapman
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nana-Ama A. S. Anang
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sheila Duncan
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Joseph Toker
- Department of Neurosurgery, Harvard University, Cambridge, MA 02138, USA
- Department of Oncology, University of Cambridge, Cambridge CB2 1TN, UK
| | - Jared C. Malke
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Isabella C. Glitza
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rodabe N. Amaria
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hussein A. Tawbi
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Adi Diab
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael K. Wong
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sapna P. Patel
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Scott E. Woodman
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael A. Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Merrick I. Ross
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeffrey E. Gershenwald
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeffrey E. Lee
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Vanessa Jensen
- Department of Veterinary Medicine and Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Ravid Straussman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Nadim J. Ajami
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kelly C. Nelson
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Luigi Nezi
- Dipartimento di Oncologia Sperimentale, Instituto Europeo di Oncologia, Milan, P.I. 08691440153, Italy
| | - Joseph F. Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - P. Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alexander J. Lazar
- MD Anderson University of Texas Health Graduate School, Houston, TX 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianhua Hu
- Department of Biostatistics, Columbia University, New York, NY 10032, USA
| | - Robert R. Jenq
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Stem Cell Transplant, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael T. Tetzlaff
- Departments of Pathology and Dermatology, Dermatopathology and Oral Pathology Unit, University of California San Francisco, San Francisco, CA 94115, USA
| | - Yan Yan
- Department of Biostatistics and the Harvard T.H. Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Wendy S. Garrett
- Department of Molecular Metabolism, T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Curtis Huttenhower
- Department of Biostatistics and the Harvard T.H. Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Padmanee Sharma
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Parker Institute for Cancer Immunotherapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Stephanie S. Watowich
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - James P. Allison
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Parker Institute for Cancer Immunotherapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lorenzo Cohen
- Department of Palliative, Rehabilitation, and Integrative Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Giorgio Trinchieri
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Carrie R. Daniel
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer A. Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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6
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Hild B, Dreier MS, Oh JH, McCulloch JA, Badger JH, Guo J, Thefaine CE, Umarova R, Hall KD, Gavrilova O, Rosshart SP, Trinchieri G, Rehermann B. Neonatal exposure to a wild-derived microbiome protects mice against diet-induced obesity. Nat Metab 2021; 3:1042-1057. [PMID: 34417593 PMCID: PMC9969744 DOI: 10.1038/s42255-021-00439-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 07/13/2021] [Indexed: 02/07/2023]
Abstract
Obesity and its consequences are among the greatest challenges in healthcare. The gut microbiome is recognized as a key factor in the pathogenesis of obesity. Using a mouse model, we show here that a wild-derived microbiome protects against excessive weight gain, severe fatty liver disease and metabolic syndrome during a 10-week course of high-fat diet. This phenotype is transferable only during the first weeks of life. In adult mice, neither transfer nor severe disturbance of the wild-type microbiome modifies the metabolic response to a high-fat diet. The protective phenotype is associated with increased secretion of metabolic hormones and increased energy expenditure through activation of brown adipose tissue. Thus, we identify a microbiome that protects against weight gain and its negative consequences through metabolic programming in early life. Translation of these results to humans may identify early-life therapeutics that protect against obesity.
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Affiliation(s)
- Benedikt Hild
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, USA
- Department of Gastroenterology and Hepatology, University Hospital Essen, Essen, Germany
| | - Matthew S Dreier
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Ji Hoon Oh
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - John A McCulloch
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Jonathan H Badger
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Juen Guo
- Integrative Physiology Section, Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Claire E Thefaine
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Regina Umarova
- Liver Diseases Virology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Kevin D Hall
- Integrative Physiology Section, Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Oksana Gavrilova
- Mouse Metabolism Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Stephan P Rosshart
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, USA
- Translational Microbiome Research Laboratory, Department of Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, Medical Center - University of Freiburg, Freiburg, Germany
| | - Giorgio Trinchieri
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Barbara Rehermann
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, USA.
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7
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Davar D, Dzutsev A, McCulloch JA, Rodrigues RR, Chauvin JM, Morrison RM, Deblasio RN, Menna C, Ding Q, Pagliano O, Zidi B, Zhang S, Badger JH, Vetizou M, Cole AM, Fernandes MR, Prescott S, Costa RG, Balaji AK, Morgun A, Vujkovic-Cvijin I, Wang H, Borhani AA, Schwartz MB, Dubner HM, Ernst SJ, Rose A, Najjar YG, Belkaid Y, Kirkwood JM, Trinchieri G, Zarour HM. Abstract LB062: Efficacy of Responder-derived Fecal Microbiota Transplant (R-FMT) and Pembrolizumab in Anti-PD-1 Refractory Patients with Advanced Melanoma. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-lb062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Monoclonal antibodies (mAb) targeting the programmed cell death protein 1 (PD-1) receptor provide durable long-term benefit in a subset of patients (pts) with advanced melanoma with response rates of 35-42% and 4-year progression-free survival (PFS) rate of 27%. Separately, the composition of the gut microbiota has been shown to correlate with anti-PD-1 efficacy in human cancer pts with melanoma, renal cell cancer and non-small cell lung cancer (NSCLC) although the precise organisms differ considerably across various studies. In preclinical models, responder-derived fecal microbiome and microbiome consortia produce anti-tumor responses. The effect of microbiome modulation in pts with anti-PD-1 refractory melanoma has not been evaluated. Methods: To evaluate whether primary resistance to anti-PD-1 immunotherapy could be overcome by intestinal microbiome modulation, we designed and conducted a phase II study (NCT03341143). We enrolled pts with primary refractory metastatic melanoma with best response of short-term stable disease (≤6 months) or progressive disease (PD) to prior anti-PD-1 based immunotherapy. Pts received single-administration of responder-derived fecal microbiota transplantation (R-FMT) together with pembrolizumab. Candidate donors were pts with advanced melanoma treated with anti-PD-1 immunotherapy with durable partial or complete response (PR, CR). Pembrolizumab was continued till intolerable toxicity or disease progression. Safety and clinical activity (based on RECIST v1.1) were main objectives; while progression-free survival (PFS) was a key secondary endpoint. Results: As of December 1, 2020, 16 pts with primary refractory melanoma were enrolled, of whom 15 were evaluable. LDH was elevated in 14/15 pts; and the median number of prior therapies was 2. Recipient pts were seromatched to receive a single R-FMT from one of eight candidate donors (5 CR; 3 PR; median PFS 58 months, range 43-70). R-FMT was administered via colonoscopy after bowel preparation with no use of antibiotics. Pembrolizumab was administered IV per label. R-FMT/pembrolizumab was well-tolerated, with no unusual toxicity signals. R-FMT induced rapid and durable microbiota perturbation in most pts; while 6 of 15 evaluable pts had evidence of clinical benefit. Response to R-FMT/pembrolizumab was associated with an increased abundance of taxa previously shown to be associated with response to anti-PD-1, increased CD8+ T cell activation, and decreased frequency of IL-8 expressing myeloid cells. Responders had distinct proteomic and metabolomic signatures, and transkingdom network analyses confirmed that the gut microbiome regulated these changes. Conclusions: In pts with anti-PD-1 primary refractory melanoma, R-FMT/pembrolizumab changed the gut microbiome and reprogrammed the tumor microenvironment to overcome resistance to anti-PD-1 immunotherapy. Response was associated with CD8 T cell induction and reduction of IL-8 expressing myeloid cells.
Citation Format: Diwakar Davar, Amiran Dzutsev, John A. McCulloch, Richard R. Rodrigues, Joe-Marc Chauvin, Robert M. Morrison, Richelle N. Deblasio, Carmine Menna, Quanquan Ding, Ornella Pagliano, Bochra Zidi, Shuowen Zhang, Jonathan H. Badger, Marie Vetizou, Alicia M. Cole, Miriam R. Fernandes, Stephanie Prescott, Raquel G. Costa, Ascharya K. Balaji, Andrey Morgun, Ivan Vujkovic-Cvijin, Hong Wang, Amir A. Borhani, Marc B. Schwartz, Howard M. Dubner, Scarlett J. Ernst, Amy Rose, Yana G. Najjar, Yasmine Belkaid, John M. Kirkwood, Giorgio Trinchieri, Hassane M. Zarour. Efficacy of Responder-derived Fecal Microbiota Transplant (R-FMT) and Pembrolizumab in Anti-PD-1 Refractory Patients with Advanced Melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB062.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Hong Wang
- 1University of Pittsburgh, Pittsburgh, PA
| | - Amir A. Borhani
- 6Northwestern University - The Feinberg School of Medicine, Chicago, IL
| | | | | | | | - Amy Rose
- 1University of Pittsburgh, Pittsburgh, PA
| | | | - Yasmine Belkaid
- 7National Institute of Allergy and Infectious Diseases, Bethesda, DC
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8
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Davar D, Dzutsev AK, McCulloch JA, Rodrigues RR, Chauvin JM, Morrison RM, Deblasio RN, Menna C, Ding Q, Pagliano O, Zidi B, Zhang S, Badger JH, Vetizou M, Cole AM, Fernandes MR, Prescott S, Costa RGF, Balaji AK, Morgun A, Vujkovic-Cvijin I, Wang H, Borhani AA, Schwartz MB, Dubner HM, Ernst SJ, Rose A, Najjar YG, Belkaid Y, Kirkwood JM, Trinchieri G, Zarour HM. Fecal microbiota transplant overcomes resistance to anti-PD-1 therapy in melanoma patients. Science 2021; 371:595-602. [PMID: 33542131 DOI: 10.1126/science.abf3363] [Citation(s) in RCA: 663] [Impact Index Per Article: 221.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022]
Abstract
Anti-programmed cell death protein 1 (PD-1) therapy provides long-term clinical benefits to patients with advanced melanoma. The composition of the gut microbiota correlates with anti-PD-1 efficacy in preclinical models and cancer patients. To investigate whether resistance to anti-PD-1 can be overcome by changing the gut microbiota, this clinical trial evaluated the safety and efficacy of responder-derived fecal microbiota transplantation (FMT) together with anti-PD-1 in patients with PD-1-refractory melanoma. This combination was well tolerated, provided clinical benefit in 6 of 15 patients, and induced rapid and durable microbiota perturbation. Responders exhibited increased abundance of taxa that were previously shown to be associated with response to anti-PD-1, increased CD8+ T cell activation, and decreased frequency of interleukin-8-expressing myeloid cells. Responders had distinct proteomic and metabolomic signatures, and transkingdom network analyses confirmed that the gut microbiome regulated these changes. Collectively, our findings show that FMT and anti-PD-1 changed the gut microbiome and reprogrammed the tumor microenvironment to overcome resistance to anti-PD-1 in a subset of PD-1 advanced melanoma.
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Affiliation(s)
- Diwakar Davar
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Amiran K Dzutsev
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - John A McCulloch
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Richard R Rodrigues
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.,Genetics and Microbiome Core, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Joe-Marc Chauvin
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Robert M Morrison
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Richelle N Deblasio
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Carmine Menna
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Quanquan Ding
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Ornella Pagliano
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Bochra Zidi
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Shuowen Zhang
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jonathan H Badger
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Marie Vetizou
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Alicia M Cole
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Miriam R Fernandes
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Stephanie Prescott
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Raquel G F Costa
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ascharya K Balaji
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Andrey Morgun
- College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA
| | - Ivan Vujkovic-Cvijin
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Bethesda, MD 20892, USA
| | - Hong Wang
- Biostatistics Facility, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Amir A Borhani
- Division of Abdominal Imaging, Department of Radiology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Marc B Schwartz
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Howard M Dubner
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Scarlett J Ernst
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Amy Rose
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Yana G Najjar
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Yasmine Belkaid
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Bethesda, MD 20892, USA
| | - John M Kirkwood
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Giorgio Trinchieri
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
| | - Hassane M Zarour
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA. .,Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA
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9
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Giordano R, Donthu RK, Zimin AV, Julca Chavez IC, Gabaldon T, van Munster M, Hon L, Hall R, Badger JH, Nguyen M, Flores A, Potter B, Giray T, Soto-Adames FN, Weber E, Marcelino JAP, Fields CJ, Voegtlin DJ, Hill CB, Hartman GL. Soybean aphid biotype 1 genome: Insights into the invasive biology and adaptive evolution of a major agricultural pest. Insect Biochem Mol Biol 2020; 120:103334. [PMID: 32109587 DOI: 10.1016/j.ibmb.2020.103334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/07/2020] [Accepted: 02/10/2020] [Indexed: 05/12/2023]
Abstract
The soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae) is a serious pest of the soybean plant, Glycine max, a major world-wide agricultural crop. We assembled a de novo genome sequence of Ap. glycines Biotype 1, from a culture established shortly after this species invaded North America. 20.4% of the Ap. glycines proteome is duplicated. These in-paralogs are enriched with Gene Ontology (GO) categories mostly related to apoptosis, a possible adaptation to plant chemistry and other environmental stressors. Approximately one-third of these genes show parallel duplication in other aphids. But Ap. gossypii, its closest related species, has the lowest number of these duplicated genes. An Illumina GoldenGate assay of 2380 SNPs was used to determine the world-wide population structure of Ap. Glycines. China and South Korean aphids are the closest to those in North America. China is the likely origin of other Asian aphid populations. The most distantly related aphids to those in North America are from Australia. The diversity of Ap. glycines in North America has decreased over time since its arrival. The genetic diversity of Ap. glycines North American population sampled shortly after its first detection in 2001 up to 2012 does not appear to correlate with geography. However, aphids collected on soybean Rag experimental varieties in Minnesota (MN), Iowa (IA), and Wisconsin (WI), closer to high density Rhamnus cathartica stands, appear to have higher capacity to colonize resistant soybean plants than aphids sampled in Ohio (OH), North Dakota (ND), and South Dakota (SD). Samples from the former states have SNP alleles with high FST values and frequencies, that overlap with genes involved in iron metabolism, a crucial metabolic pathway that may be affected by the Rag-associated soybean plant response. The Ap. glycines Biotype 1 genome will provide needed information for future analyses of mechanisms of aphid virulence and pesticide resistance as well as facilitate comparative analyses between aphids with differing natural history and host plant range.
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Affiliation(s)
- Rosanna Giordano
- Puerto Rico Science, Technology and Research Trust, San Juan, PR, USA; Know Your Bee, Inc. San Juan, PR, USA.
| | - Ravi Kiran Donthu
- Puerto Rico Science, Technology and Research Trust, San Juan, PR, USA; Know Your Bee, Inc. San Juan, PR, USA.
| | - Aleksey V Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Irene Consuelo Julca Chavez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain; Institute for Research in Biomedicine, Barcelona, Spain
| | - Toni Gabaldon
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain; Institute for Research in Biomedicine, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Manuella van Munster
- CIRAD-INRA-Montpellier SupAgro, TA A54/K, Campus International de Baillarguet, Montpellier, France
| | | | | | - Jonathan H Badger
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institute of Health, DHHS, Bethesda, MD, USA
| | - Minh Nguyen
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Alejandra Flores
- College of Liberal Arts and Sciences, School of Molecular and Cellular Biology, University of Illinois, Urbana, IL, USA
| | - Bruce Potter
- University of Minnesota, Southwest Research and Outreach Center, Lamberton, MN, USA
| | - Tugrul Giray
- Department of Biology, University of Puerto Rico, San Juan, PR, USA
| | - Felipe N Soto-Adames
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry, Entomology, Gainesville, FL, USA
| | | | - Jose A P Marcelino
- Puerto Rico Science, Technology and Research Trust, San Juan, PR, USA; Know Your Bee, Inc. San Juan, PR, USA; Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
| | - Christopher J Fields
- HPCBio, Roy J. Carver Biotechnology Center, University of Illinois, Urbana, IL, USA
| | - David J Voegtlin
- Illinois Natural History Survey, University of Illinois, Urbana, IL, USA
| | | | - Glen L Hartman
- USDA-ARS and Department of Crop Sciences, University of Illinois, Urbana, IL, USA
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10
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Song NY, Li X, Badger JH, Brown JW, Sun X, Shi G, Zhu F, Jiang C, O'hUigin C, Wu X, Trinchieri G, Hu Y. Abstract B17: IKKα/STAT3 antagonistic signaling regulates fungi-bacteria endosymbiosis-associated carcinogenesis. Cancer Res 2020. [DOI: 10.1158/1538-7445.mvc2020-b17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Clinically, oral fungating lesions frequently occur in cancer patients following radiation and chemotherapy. However, their role in carcinogenesis has not been fully understood. Our previous finding showed that defective IKKα-mediated autoreactive T cells promote fungal infection and esophageal malignancy, but whether IKKα-mediated altered epithelial properties regulate fungal colonization and carcinogenesis remains to be tested. To investigate whether IKKα-mediated altered epithelial properties regulate fungal colonization and carcinogenesis, we orally infected mice lacking Ikkα (IkkαΔSOE) or both Ikkα and Stat3 (IkkαΔSOEStat3ΔSOE) in the stem cells of the skin and mouth with fungi. We found that oral fungal infection enhanced Ikkα ablation-mediated skin and oral carcinogenesis in association with increased oral and skin bacteria counts and altered oral bacteria phylum from gram-positive to gram-negative. Enhanced oral fungal/bacterial infection increased inflammasome activities and systemic IL-17A/IL-1β signals. Surprisingly, Stat3 ablation rescued these phenotypes in IkkαΔSOEStat3ΔSOE mice. In addition, amoxicillin treatment inhibited skin carcinogenesis and oral/skin bacteria counts and reversed oral bacteria phyla in fungal-inoculated IkkαΔSOE mice. These findings highlight that cancer cell IKKα/STAT3 antagonizing pathways determine susceptibility to fungal and bacterial colonization, which impacts carcinogenesis. Human head and neck squamous cell carcinomas also share oncogenic pathways and bacteria sequences/counts with mice, suggesting that oral fungating/ulcerating lesions enhance local and distal tumorigenesis in humans.
Citation Format: Na-Young Song, Xin Li, Jonathan H. Badger, Jami Willette Brown, Xhonghe Sun, Gongping Shi, Feng Zhu, Chengfei Jiang, Colum O'hUigin, Xiaolin Wu, Giorgio Trinchieri, Yinling Hu. IKKα/STAT3 antagonistic signaling regulates fungi-bacteria endosymbiosis-associated carcinogenesis [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr B17.
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Affiliation(s)
| | - Xin Li
- 2National Institutes of Health, Frederick, MD,
| | | | | | - Xhonghe Sun
- 3Leidos Biomedical Research, Inc., Frederick, MD
| | | | - Feng Zhu
- 2National Institutes of Health, Frederick, MD,
| | | | | | - Xiaolin Wu
- 2National Institutes of Health, Frederick, MD,
| | | | - Yinling Hu
- 2National Institutes of Health, Frederick, MD,
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11
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Abstract
Humans are living ecosystems composed of human cells and microbes. The microbiome is the collection of microbes (microbiota) and their genes. Recent breakthroughs in the high-throughput sequencing technologies have made it possible for us to understand the composition of the human microbiome. Launched by the National Institutes of Health in USA, the human microbiome project indicated that our bodies harbor a wide array of microbes, specific to each body site with interpersonal and intrapersonal variabilities. Numerous studies have indicated that several factors influence the development of the microbiome including genetics, diet, use of antibiotics, and lifestyle, among others. The microbiome and its mediators are in a continuous cross talk with the host immune system; hence, any imbalance on one side is reflected on the other. Dysbiosis (microbiota imbalance) was shown in many diseases and pathological conditions such as inflammatory bowel disease, celiac disease, multiple sclerosis, rheumatoid arthritis, asthma, diabetes, and cancer. The microbial composition mirrors inflammation variations in certain disease conditions, within various stages of the same disease; hence, it has the potential to be used as a biomarker.
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Affiliation(s)
- Manoj Kumar
- Division of Translational Medicine, Research Department, Sidra Medicine, Doha, Qatar
| | - Parul Singh
- Division of Translational Medicine, Research Department, Sidra Medicine, Doha, Qatar
| | - Selvasankar Murugesan
- Division of Translational Medicine, Research Department, Sidra Medicine, Doha, Qatar
| | - Marie Vetizou
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - John McCulloch
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan H Badger
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Giorgio Trinchieri
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Souhaila Al Khodor
- Division of Translational Medicine, Research Department, Sidra Medicine, Doha, Qatar.
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12
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Song H, Donthu RK, Hall R, Hon L, Weber E, Badger JH, Giordano R. Description of soybean aphid (Aphis glycines Matsumura) mitochondrial genome and comparative mitogenomics of Aphididae (Hemiptera: Sternorrhyncha). Insect Biochem Mol Biol 2019; 113:103208. [PMID: 31422150 DOI: 10.1016/j.ibmb.2019.103208] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 06/26/2019] [Accepted: 07/25/2019] [Indexed: 06/10/2023]
Abstract
The complete mitochondrial genome of the soybean aphid (Aphis glycines Matsumura), a major agricultural pest in the world, is described for the first time, which consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, as well as a large repeat region between tRNA-Glu and tRNA-Phe, and an AT-rich control region. The 17,954 bp mtgenome is the largest reported from the family Aphididae, and its gene order follows the ancestral insect mtgenome except for the repeat region, which contains a 195 bp unit repeated 11.9 times, representing the highest reported repeats among the known aphid mtgenomes to date. A new molecular phylogeny of Aphidae is reconstructed based on all available aphid mtgenomes, and it is shown that the mtgenome data can robustly resolve relationships at the subfamily level, but do not have sufficient phylogenetic information to resolve deep relationships. A phylogeny-based comparative analysis of mtgenomes has been performed to investigate the evolution of the repeat region between tRNA-Glu and tRNA-Phe. So far, among aphids, 13 species are known to have this repeat region of variable lengths, and a phylogenetic analysis of the repeat region shows that a large proportion of the sequences are conserved across the phylogeny, suggesting that the repeat region evolved in the most recent common ancestor of Aphidinae and Eriosomatinae, and that it has gone through numerous episodes of lineage-specific losses and expansions. Combined together, this study provides novel insights into how the repeat regions have evolved within aphids.
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Affiliation(s)
- Hojun Song
- Department of Entomology, Texas A&M University, College Station, TX, USA.
| | - Ravi Kiran Donthu
- Puerto Rico, Science, Technology & Research Trust, San Juan, PR, USA; Know Your Bee, Inc, San Juan, PR, USA
| | | | | | - Everett Weber
- Puerto Rico, Science, Technology & Research Trust, San Juan, PR, USA; Know Your Bee, Inc, San Juan, PR, USA
| | - Jonathan H Badger
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institute of Health, DHHS, Bethesda, MD, USA
| | - Rosanna Giordano
- Puerto Rico, Science, Technology & Research Trust, San Juan, PR, USA; Know Your Bee, Inc, San Juan, PR, USA
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13
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Rosshart SP, Herz J, Vassallo BG, Hunter A, Wall MK, Badger JH, McCulloch JA, Anastasakis DG, Sarshad AA, Leonardi I, Collins N, Blatter JA, Han SJ, Tamoutounour S, Potapova S, Foster St Claire MB, Yuan W, Sen SK, Dreier MS, Hild B, Hafner M, Wang D, Iliev ID, Belkaid Y, Trinchieri G, Rehermann B. Laboratory mice born to wild mice have natural microbiota and model human immune responses. Science 2019; 365:365/6452/eaaw4361. [PMID: 31371577 DOI: 10.1126/science.aaw4361] [Citation(s) in RCA: 299] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 05/06/2019] [Accepted: 06/27/2019] [Indexed: 12/11/2022]
Abstract
Laboratory mouse studies are paramount for understanding basic biological phenomena but also have limitations. These include conflicting results caused by divergent microbiota and limited translational research value. To address both shortcomings, we transferred C57BL/6 embryos into wild mice, creating "wildlings." These mice have a natural microbiota and pathogens at all body sites and the tractable genetics of C57BL/6 mice. The bacterial microbiome, mycobiome, and virome of wildlings affect the immune landscape of multiple organs. Their gut microbiota outcompete laboratory microbiota and demonstrate resilience to environmental challenges. Wildlings, but not conventional laboratory mice, phenocopied human immune responses in two preclinical studies. A combined natural microbiota- and pathogen-based model may enhance the reproducibility of biomedical studies and increase the bench-to-bedside safety and success of immunological studies.
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Affiliation(s)
- Stephan P Rosshart
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA.
| | - Jasmin Herz
- Center for Brain Immunology and Glia, Department of Neuroscience, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Brian G Vassallo
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Ashli Hunter
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Morgan K Wall
- Center for Brain Immunology and Glia, Department of Neuroscience, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Jonathan H Badger
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - John A McCulloch
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Dimitrios G Anastasakis
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD 20892, USA
| | - Aishe A Sarshad
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD 20892, USA
| | - Irina Leonardi
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Nicholas Collins
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joshua A Blatter
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Seong-Ji Han
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Samira Tamoutounour
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Svetlana Potapova
- Laboratory of Animal Sciences Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Mark B Foster St Claire
- Laboratory of Animal Sciences Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Wuxing Yuan
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA.,Leidos Biomedical Research, Inc., Microbiome and Genetics Core, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shurjo K Sen
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA.,Leidos Biomedical Research, Inc., Microbiome and Genetics Core, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew S Dreier
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Benedikt Hild
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD 20892, USA
| | - David Wang
- Departments of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Iliyan D Iliev
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Yasmine Belkaid
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Giorgio Trinchieri
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Barbara Rehermann
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA.
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14
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Fatkhullina AR, Peshkova IO, Dzutsev A, Aghayev T, McCulloch JA, Thovarai V, Badger JH, Vats R, Sundd P, Tang HY, Kossenkov AV, Hazen SL, Trinchieri G, Grivennikov SI, Koltsova EK. An Interleukin-23-Interleukin-22 Axis Regulates Intestinal Microbial Homeostasis to Protect from Diet-Induced Atherosclerosis. Immunity 2018; 49:943-957.e9. [PMID: 30389414 PMCID: PMC6257980 DOI: 10.1016/j.immuni.2018.09.011] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 06/20/2018] [Accepted: 09/13/2018] [Indexed: 12/20/2022]
Abstract
Although commensal flora is involved in the regulation of immunity, the interplay between cytokine signaling and microbiota in atherosclerosis remains unknown. We found that interleukin (IL)-23 and its downstream target IL-22 restricted atherosclerosis by repressing pro-atherogenic microbiota. Inactivation of IL-23-IL-22 signaling led to deterioration of the intestinal barrier, dysbiosis, and expansion of pathogenic bacteria with distinct biosynthetic and metabolic properties, causing systemic increase in pro-atherogenic metabolites such as lipopolysaccharide (LPS) and trimethylamine N-oxide (TMAO). Augmented disease in the absence of the IL-23-IL-22 pathway was mediated in part by pro-atherogenic osteopontin, controlled by microbial metabolites. Microbiota transfer from IL-23-deficient mice accelerated atherosclerosis, whereas microbial depletion or IL-22 supplementation reduced inflammation and ameliorated disease. Our work uncovers the IL-23-IL-22 signaling as a regulator of atherosclerosis that restrains expansion of pro-atherogenic microbiota and argues for informed use of cytokine blockers to avoid cardiovascular side effects driven by microbiota and inflammation.
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Affiliation(s)
- Aliia R Fatkhullina
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Iuliia O Peshkova
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Amiran Dzutsev
- Cancer and Inflammation Program, Center for Cancer Research, NCI, NIH, Frederick National Laboratory for Cancer Research sponsored by the NCI, Bethesda, MD, 20892, USA
| | - Turan Aghayev
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - John A McCulloch
- Cancer and Inflammation Program, Center for Cancer Research, NCI, NIH, Frederick National Laboratory for Cancer Research sponsored by the NCI, Bethesda, MD, 20892, USA
| | - Vishal Thovarai
- Cancer and Inflammation Program, Center for Cancer Research, NCI, NIH, Frederick National Laboratory for Cancer Research sponsored by the NCI, Bethesda, MD, 20892, USA; Basic Science Program, Frederick National Laboratory for Cancer Research sponsored by the NCI, Bethesda, MD, 20892, USA
| | - Jonathan H Badger
- Cancer and Inflammation Program, Center for Cancer Research, NCI, NIH, Frederick National Laboratory for Cancer Research sponsored by the NCI, Bethesda, MD, 20892, USA
| | - Ravi Vats
- Pittsburgh Heart, Lung and Blood Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Prithu Sundd
- Pittsburgh Heart, Lung and Blood Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Hsin-Yao Tang
- Proteomics and Metabolomics, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Andrew V Kossenkov
- Bioinformatics Facilities, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Stanley L Hazen
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Giorgio Trinchieri
- Cancer and Inflammation Program, Center for Cancer Research, NCI, NIH, Frederick National Laboratory for Cancer Research sponsored by the NCI, Bethesda, MD, 20892, USA
| | - Sergei I Grivennikov
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Ekaterina K Koltsova
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
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15
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Yoshimura T, McLean MH, Dzutsev AK, Yao X, Chen K, Huang J, Gong W, Zhou J, Xiang Y, H Badger J, O'hUigin C, Thovarai V, Tessarollo L, Durum SK, Trinchieri G, Bian XW, Wang JM. The Antimicrobial Peptide CRAMP Is Essential for Colon Homeostasis by Maintaining Microbiota Balance. J Immunol 2018; 200:2174-2185. [PMID: 29440355 DOI: 10.4049/jimmunol.1602073] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 12/21/2017] [Indexed: 01/05/2023]
Abstract
Commensal bacteria are critical for physiological functions in the gut, and dysbiosis in the gut may cause diseases. In this article, we report that mice deficient in cathelin-related antimicrobial peptide (CRAMP) were defective in the development of colon mucosa and highly sensitive to dextran sulfate sodium (DSS)-elicited colitis, as well as azoxymethane-mediated carcinogenesis. Pretreatment of CRAMP-/- mice with antibiotics markedly reduced the severity of DSS-induced colitis, suggesting CRAMP as a limiting factor on dysbiosis in the colon. This was supported by observations that wild-type (WT) mice cohoused with CRAMP-/- mice became highly sensitive to DSS-induced colitis, and the composition of fecal microbiota was skewed by CRAMP deficiency. In particular, several bacterial species that are typically found in oral microbiota, such as Mogibacterium neglectum, Desulfovibrio piger, and Desulfomicrobium orale, were increased in feces of CRAMP-/- mice and were transferred to WT mice during cohousing. When littermates of CRAMP+/- parents were examined, the composition of the fecal microbiota of WT pups and heterozygous parents was similar. In contrast, although the difference in fecal microbiota between CRAMP-/- and WT pups was small early on after weaning and single mouse housing, there was an increasing divergence with prolonged single housing. These results indicate that CRAMP is critical in maintaining colon microbiota balance and supports mucosal homeostasis, anti-inflammatory responses, and protection from carcinogenesis.
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Affiliation(s)
- Teizo Yoshimura
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702; .,Department of Pathology and Experimental Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
| | - Mairi H McLean
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702.,School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom
| | - Amiran K Dzutsev
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702
| | - Xiaohong Yao
- Institute of Pathology and Southwest Cancer Center, Third Military Medical University, Chongqing 400038, China
| | - Keqiang Chen
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702
| | - Jiaqiang Huang
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702.,College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing 100044, China
| | - Wanghua Gong
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702; and
| | - Jiamin Zhou
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702
| | - Yi Xiang
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702
| | - Jonathan H Badger
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702
| | - Colm O'hUigin
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702
| | - Vishal Thovarai
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702; and
| | - Lino Tessarollo
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702
| | - Scott K Durum
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702
| | - Giorgio Trinchieri
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702
| | - Xiu-Wu Bian
- Institute of Pathology and Southwest Cancer Center, Third Military Medical University, Chongqing 400038, China
| | - Ji Ming Wang
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702;
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16
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Rosshart SP, Vassallo BG, Angeletti D, Hutchinson DS, Morgan AP, Takeda K, Hickman HD, McCulloch JA, Badger JH, Ajami NJ, Trinchieri G, Pardo-Manuel de Villena F, Yewdell JW, Rehermann B. Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance. Cell 2017; 171:1015-1028.e13. [PMID: 29056339 DOI: 10.1016/j.cell.2017.09.016] [Citation(s) in RCA: 487] [Impact Index Per Article: 69.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 06/12/2017] [Accepted: 09/09/2017] [Indexed: 12/14/2022]
Abstract
Laboratory mice, while paramount for understanding basic biological phenomena, are limited in modeling complex diseases of humans and other free-living mammals. Because the microbiome is a major factor in mammalian physiology, we aimed to identify a naturally evolved reference microbiome to better recapitulate physiological phenomena relevant in the natural world outside the laboratory. Among 21 distinct mouse populations worldwide, we identified a closely related wild relative to standard laboratory mouse strains. Its bacterial gut microbiome differed significantly from its laboratory mouse counterpart and was transferred to and maintained in laboratory mice over several generations. Laboratory mice reconstituted with natural microbiota exhibited reduced inflammation and increased survival following influenza virus infection and improved resistance against mutagen/inflammation-induced colorectal tumorigenesis. By demonstrating the host fitness-promoting traits of natural microbiota, our findings should enable the discovery of protective mechanisms relevant in the natural world and improve the modeling of complex diseases of free-living mammals. VIDEO ABSTRACT.
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Affiliation(s)
- Stephan P Rosshart
- Immunology Section, Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA.
| | - Brian G Vassallo
- Immunology Section, Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Davide Angeletti
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Diane S Hutchinson
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrew P Morgan
- Department of Genetics, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kazuyo Takeda
- Microscopy and Imaging Core Facility, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993-0002, USA
| | - Heather D Hickman
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - John A McCulloch
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Jonathan H Badger
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Nadim J Ajami
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Giorgio Trinchieri
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jonathan W Yewdell
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Barbara Rehermann
- Immunology Section, Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA.
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17
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Smith SR, Gillard JTF, Kustka AB, McCrow JP, Badger JH, Zheng H, New AM, Dupont CL, Obata T, Fernie AR, Allen AE. Correction: Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation. PLoS Genet 2017; 13:e1006688. [PMID: 28355217 PMCID: PMC5371279 DOI: 10.1371/journal.pgen.1006688] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pgen.1006490.].
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18
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Abstract
Commensal microorganisms (the microbiota) live on all the surface barriers of our body and are particularly abundant and diverse in the distal gut. The microbiota and its larger host represent a metaorganism in which the cross talk between microbes and host cells is necessary for health, survival, and regulation of physiological functions locally, at the barrier level, and systemically. The ancestral molecular and cellular mechanisms stemming from the earliest interactions between prokaryotes and eukaryotes have evolved to mediate microbe-dependent host physiology and tissue homeostasis, including innate and adaptive resistance to infections and tissue repair. Mostly because of its effects on metabolism, cellular proliferation, inflammation, and immunity, the microbiota regulates cancer at the level of predisposing conditions, initiation, genetic instability, susceptibility to host immune response, progression, comorbidity, and response to therapy. Here, we review the mechanisms underlying the interaction of the microbiota with cancer and the evidence suggesting that the microbiota could be targeted to improve therapy while attenuating adverse reactions.
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Affiliation(s)
- Amiran Dzutsev
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892,
| | - Jonathan H Badger
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892,
| | - Ernesto Perez-Chanona
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892,
| | - Soumen Roy
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892,
| | - Rosalba Salcedo
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892,
| | - Carolyne K Smith
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892,
| | - Giorgio Trinchieri
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892,
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19
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Smith SR, Gillard JTF, Kustka AB, McCrow JP, Badger JH, Zheng H, New AM, Dupont CL, Obata T, Fernie AR, Allen AE. Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation. PLoS Genet 2016; 12:e1006490. [PMID: 27973599 PMCID: PMC5156380 DOI: 10.1371/journal.pgen.1006490] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 11/16/2016] [Indexed: 11/23/2022] Open
Abstract
Environmental fluctuations affect distribution, growth and abundance of diatoms in nature, with iron (Fe) availability playing a central role. Studies on the response of diatoms to low Fe have either utilized continuous (24 hr) illumination or sampled a single time of day, missing any temporal dynamics. We profiled the physiology, metabolite composition, and global transcripts of the pennate diatom Phaeodactylum tricornutum during steady-state growth at low, intermediate, and high levels of dissolved Fe over light:dark cycles, to better understand fundamental aspects of genetic control of physiological acclimation to growth under Fe-limitation. We greatly expand the catalog of genes involved in the low Fe response, highlighting the importance of intracellular trafficking in Fe-limited diatoms. P. tricornutum exhibited transcriptomic hallmarks of slowed growth leading to prolonged periods of cell division/silica deposition, which could impact biogeochemical carbon sequestration in Fe-limited regions. Light harvesting and ribosome biogenesis transcripts were generally reduced under low Fe while transcript levels for genes putatively involved in the acquisition and recycling of Fe were increased. We also noted shifts in expression towards increased synthesis and catabolism of branched chain amino acids in P. tricornutum grown at low Fe whereas expression of genes involved in central core metabolism were relatively unaffected, indicating that essential cellular function is protected. Beyond the response of P. tricornutum to low Fe, we observed major coordinated shifts in transcript control of primary and intermediate metabolism over light:dark cycles which contribute to a new view of the significance of distinctive diatom pathways, such as mitochondrial glycolysis and the ornithine-urea cycle. This study provides new insight into transcriptional modulation of diatom physiology and metabolism across light:dark cycles in response to Fe availability, providing mechanistic understanding for the ability of diatoms to remain metabolically poised to respond quickly to Fe input and revealing strategies underlying their ecological success. Oceanic diatoms live in constantly fluctuating environments to which they must adapt in order to survive. During sunlit hours, photosynthesis occurs allowing diatoms to store energy used at night to sustain energy demands. Cellular and molecular mechanisms for regulation of phytoplankton growth are important to understand because of their environmental roles at the base of food webs and in regulating carbon flux out of the atmosphere. In ocean ecosystems, the availability of iron (Fe) commonly limits phytoplankton growth and diatoms typically outcompete other phytoplankton when Fe is added, indicating they have adaptations allowing them to both survive at low Fe and rapidly respond to Fe additions. These adaptations may be unique depending on isolation from coastal or oceanic locations. To identify adaptive strategies, we characterized the response of a model diatom, Phaeodactylum tricornutum, to limiting Fe conditions over day:night cycles using a combination of gene expression analyses, metabolite, and physiology measurements. Major coordinated shifts in metabolism and growth were documented over diel cycles, with peak expression of low Fe expressed genes in the dark phase. Diatoms respond to limiting Fe by increasing Fe acquisition, while decreasing growth rate through slowed cell cycle progression, reduced energy acquisition, and subtle metabolic remodeling.
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Affiliation(s)
- Sarah R. Smith
- Integrative Oceanography Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California, United States of America
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - Jeroen T. F. Gillard
- J. Craig Venter Institute, La Jolla, California, United States of America
- Department of Biology, CSU Bakersfield, Bakersfield, California, United States of America
| | - Adam B. Kustka
- Department of Earth and Environmental Sciences, Rutgers University, Newark, New Jersey, United States of America
| | - John P. McCrow
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - Jonathan H. Badger
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - Hong Zheng
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - Ashley M. New
- Department of Earth and Environmental Sciences, Rutgers University, Newark, New Jersey, United States of America
| | - Chris L. Dupont
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - Toshihiro Obata
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
| | - Andrew E. Allen
- Integrative Oceanography Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California, United States of America
- J. Craig Venter Institute, La Jolla, California, United States of America
- * E-mail: ,
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20
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Hamilton EP, Kapusta A, Huvos PE, Bidwell SL, Zafar N, Tang H, Hadjithomas M, Krishnakumar V, Badger JH, Caler EV, Russ C, Zeng Q, Fan L, Levin JZ, Shea T, Young SK, Hegarty R, Daza R, Gujja S, Wortman JR, Birren BW, Nusbaum C, Thomas J, Carey CM, Pritham EJ, Feschotte C, Noto T, Mochizuki K, Papazyan R, Taverna SD, Dear PH, Cassidy-Hanley DM, Xiong J, Miao W, Orias E, Coyne RS. Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome. eLife 2016; 5. [PMID: 27892853 PMCID: PMC5182062 DOI: 10.7554/elife.19090] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 11/14/2016] [Indexed: 12/30/2022] Open
Abstract
The germline genome of the binucleated ciliate Tetrahymena thermophila undergoes programmed chromosome breakage and massive DNA elimination to generate the somatic genome. Here, we present a complete sequence assembly of the germline genome and analyze multiple features of its structure and its relationship to the somatic genome, shedding light on the mechanisms of genome rearrangement as well as the evolutionary history of this remarkable germline/soma differentiation. Our results strengthen the notion that a complex, dynamic, and ongoing interplay between mobile DNA elements and the host genome have shaped Tetrahymena chromosome structure, locally and globally. Non-standard outcomes of rearrangement events, including the generation of short-lived somatic chromosomes and excision of DNA interrupting protein-coding regions, may represent novel forms of developmental gene regulation. We also compare Tetrahymena's germline/soma differentiation to that of other characterized ciliates, illustrating the wide diversity of adaptations that have occurred within this phylum.
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Affiliation(s)
- Eileen P Hamilton
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, United States
| | - Aurélie Kapusta
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Piroska E Huvos
- Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, United States
| | | | - Nikhat Zafar
- J. Craig Venter Institute, Rockville, United States
| | - Haibao Tang
- J. Craig Venter Institute, Rockville, United States
| | | | | | | | | | - Carsten Russ
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Qiandong Zeng
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Lin Fan
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Joshua Z Levin
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Terrance Shea
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Sarah K Young
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Ryan Hegarty
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Riza Daza
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Sharvari Gujja
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Jennifer R Wortman
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Bruce W Birren
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Chad Nusbaum
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Jainy Thomas
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Clayton M Carey
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Ellen J Pritham
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Tomoko Noto
- Institute of Molecular Biotechnology, Vienna, Austria
| | | | - Romeo Papazyan
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Sean D Taverna
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Paul H Dear
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Jie Xiong
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Wei Miao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Eduardo Orias
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, United States
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21
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Chen H, Brinkac LM, Mishra P, Li N, Lymperopoulou DS, Dickerson TL, Gordon-Bradley N, Williams HN, Badger JH. Draft genome sequences for the obligate bacterial predators Bacteriovorax spp. of four phylogenetic clusters. Stand Genomic Sci 2015. [PMID: 26203326 PMCID: PMC4511183 DOI: 10.1186/1944-3277-10-11] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Bacteriovorax is the halophilic genus of the obligate bacterial predators, Bdellovibrio and like organisms. The predators are known for their unique biphasic life style in which they search for and attack their prey in the free living phase; penetrate, grow, multiply and lyse the prey in the intraperiplasmic phase. Bacteriovorax isolates representing four phylogenetic clusters were selected for genomic sequencing. Only one type strain genome has been published so far from the genus Bacteriovorax. We report the genomes from non-type strains isolated from aquatic environments. Here we describe and compare the genomic features of the four strains, together with the classification and annotation.
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Affiliation(s)
- Huan Chen
- Florida A&M University, Tallahassee, USA ; National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310-4005, USA
| | | | | | - Nan Li
- Florida A&M University, Tallahassee, USA
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22
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Dupont CL, Larsson J, Yooseph S, Ininbergs K, Goll J, Asplund-Samuelsson J, McCrow JP, Celepli N, Allen LZ, Ekman M, Lucas AJ, Hagström Å, Thiagarajan M, Brindefalk B, Richter AR, Andersson AF, Tenney A, Lundin D, Tovchigrechko A, Nylander JAA, Brami D, Badger JH, Allen AE, Rusch DB, Hoffman J, Norrby E, Friedman R, Pinhassi J, Venter JC, Bergman B. Functional tradeoffs underpin salinity-driven divergence in microbial community composition. PLoS One 2014; 9:e89549. [PMID: 24586863 PMCID: PMC3937345 DOI: 10.1371/journal.pone.0089549] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 01/23/2014] [Indexed: 11/23/2022] Open
Abstract
Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.
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Affiliation(s)
- Chris L. Dupont
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, United States of America
- * E-mail: (CLD); (JL)
| | - John Larsson
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- * E-mail: (CLD); (JL)
| | - Shibu Yooseph
- Informatics Group, J. Craig Venter Institute, San Diego, California, United States of America
| | - Karolina Ininbergs
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Johannes Goll
- Informatics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | | | - John P. McCrow
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, United States of America
| | - Narin Celepli
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Lisa Zeigler Allen
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, United States of America
| | - Martin Ekman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Andrew J. Lucas
- Marine Physical Laboratory, Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States of America
| | - Åke Hagström
- Swedish Institute for the Marine Environment (SIME), University of Gothenburg, Gothenburg, Sweden
| | - Mathangi Thiagarajan
- Informatics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Björn Brindefalk
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Alexander R. Richter
- Informatics Group, J. Craig Venter Institute, San Diego, California, United States of America
| | - Anders F. Andersson
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Solna, Sweden
| | - Aaron Tenney
- Informatics Group, J. Craig Venter Institute, San Diego, California, United States of America
| | - Daniel Lundin
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Solna, Sweden
| | - Andrey Tovchigrechko
- Informatics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Johan A. A. Nylander
- Department of Biodiversity Informatics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Daniel Brami
- Informatics Group, J. Craig Venter Institute, San Diego, California, United States of America
| | - Jonathan H. Badger
- Informatics Group, J. Craig Venter Institute, San Diego, California, United States of America
| | - Andrew E. Allen
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, United States of America
| | - Douglas B. Rusch
- Informatics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Jeff Hoffman
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, United States of America
| | - Erling Norrby
- Center for History of Science, The Royal Swedish Academy of Sciences, Stockholm, Sweden
| | - Robert Friedman
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, United States of America
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - J. Craig Venter
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, United States of America
| | - Birgitta Bergman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
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McLean JS, Lombardo MJ, Badger JH, Edlund A, Novotny M, Yee-Greenbaum J, Vyahhi N, Hall AP, Yang Y, Dupont CL, Ziegler MG, Chitsaz H, Allen AE, Yooseph S, Tesler G, Pevzner PA, Friedman RM, Nealson KH, Venter JC, Lasken RS. Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. Proc Natl Acad Sci U S A 2013; 110:E2390-9. [PMID: 23754396 PMCID: PMC3696752 DOI: 10.1073/pnas.1219809110] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The "dark matter of life" describes microbes and even entire divisions of bacterial phyla that have evaded cultivation and have yet to be sequenced. We present a genome from the globally distributed but elusive candidate phylum TM6 and uncover its metabolic potential. TM6 was detected in a biofilm from a sink drain within a hospital restroom by analyzing cells using a highly automated single-cell genomics platform. We developed an approach for increasing throughput and effectively improving the likelihood of sampling rare events based on forming small random pools of single-flow-sorted cells, amplifying their DNA by multiple displacement amplification and sequencing all cells in the pool, creating a "mini-metagenome." A recently developed single-cell assembler, SPAdes, in combination with contig binning methods, allowed the reconstruction of genomes from these mini-metagenomes. A total of 1.07 Mb was recovered in seven contigs for this member of TM6 (JCVI TM6SC1), estimated to represent 90% of its genome. High nucleotide identity between a total of three TM6 genome drafts generated from pools that were independently captured, amplified, and assembled provided strong confirmation of a correct genomic sequence. TM6 is likely a Gram-negative organism and possibly a symbiont of an unknown host (nonfree living) in part based on its small genome, low-GC content, and lack of biosynthesis pathways for most amino acids and vitamins. Phylogenomic analysis of conserved single-copy genes confirms that TM6SC1 is a deeply branching phylum.
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Affiliation(s)
- Jeffrey S McLean
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, CA 92121, USA.
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24
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Konotchick T, Dupont CL, Valas RE, Badger JH, Allen AE. Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season. New Phytol 2013; 198:398-407. [PMID: 23488966 PMCID: PMC3644879 DOI: 10.1111/nph.12160] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 12/10/2012] [Indexed: 05/30/2023]
Abstract
To increase knowledge of transcript diversity for the giant kelp, Macrocystis pyrifera, and assess gene expression across naturally occurring depth gradients in light, temperature and nutrients, we sequenced four cDNA libraries created from blades collected at the sea surface and at 18 m depth during the winter and summer. Comparative genomics cluster analyses revealed novel gene families (clusters) in existing brown alga expressed sequence tag data compared with other related algal groups, a pattern also seen with the addition of M. pyrifera sequences. Assembly of 228 Mbp of sequence generated c. 9000 isotigs and c. 12,000 open reading frames. Annotations were assigned using families of hidden Markov models for c. 11% of open reading frames; M. pyrifera had highest similarity to other members of the Phaeophyceae, namely Ectocarpus siliculosus and Laminaria digitata. Quantitative polymerase chain reaction of transcript targets verified depth-related differences in gene expression; stress response and light-harvesting transcripts, especially members of the LI818 (also known as LHCSR) family, showed high expression in the surface compared with 18 m depth, while some nitrogen acquisition transcripts (e.g. nitrite reductase) were upregulated at depth compared with the surface, supporting a conceptual biological model of depth-dependent physiology.
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Affiliation(s)
- Talina Konotchick
- J. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA, USA
| | | | - Ruben E Valas
- J. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA, USA
| | - Jonathan H Badger
- J. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA, USA
| | - Andrew E Allen
- J. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA, USA
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25
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Fodor AA, DeSantis TZ, Wylie KM, Badger JH, Ye Y, Hepburn T, Hu P, Sodergren E, Liolios K, Huot-Creasy H, Birren BW, Earl AM. The "most wanted" taxa from the human microbiome for whole genome sequencing. PLoS One 2012; 7:e41294. [PMID: 22848458 PMCID: PMC3406062 DOI: 10.1371/journal.pone.0041294] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 06/19/2012] [Indexed: 11/24/2022] Open
Abstract
The goal of the Human Microbiome Project (HMP) is to generate a comprehensive catalog of human-associated microorganisms including reference genomes representing the most common species. Toward this goal, the HMP has characterized the microbial communities at 18 body habitats in a cohort of over 200 healthy volunteers using 16S rRNA gene (16S) sequencing and has generated nearly 1,000 reference genomes from human-associated microorganisms. To determine how well current reference genome collections capture the diversity observed among the healthy microbiome and to guide isolation and future sequencing of microbiome members, we compared the HMP's 16S data sets to several reference 16S collections to create a 'most wanted' list of taxa for sequencing. Our analysis revealed that the diversity of commonly occurring taxa within the HMP cohort microbiome is relatively modest, few novel taxa are represented by these OTUs and many common taxa among HMP volunteers recur across different populations of healthy humans. Taken together, these results suggest that it should be possible to perform whole-genome sequencing on a large fraction of the human microbiome, including the 'most wanted', and that these sequences should serve to support microbiome studies across multiple cohorts. Also, in stark contrast to other taxa, the 'most wanted' organisms are poorly represented among culture collections suggesting that novel culture- and single-cell-based methods will be required to isolate these organisms for sequencing.
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Affiliation(s)
- Anthony A. Fodor
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Todd Z. DeSantis
- Bioinformatics Department, Second Genome, Inc., San Bruno, California, United States of America
| | - Kristine M. Wylie
- Department of Genetics, The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jonathan H. Badger
- Microbial and Environmental Genomics Department. J. Craig Venter Institute, San Diego, California, United States of America
| | - Yuzhen Ye
- School of Informatics and Computing, Indiana University, Bloomington, Indiana, United States of America
| | - Theresa Hepburn
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Ping Hu
- Earth Science Division, Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Erica Sodergren
- Department of Genetics, The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Konstantinos Liolios
- Microbial Genomics and Metagenomics Program, Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Heather Huot-Creasy
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Bruce W. Birren
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Ashlee M. Earl
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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Coyne RS, Hannick L, Shanmugam D, Hostetler JB, Brami D, Joardar VS, Johnson J, Radune D, Singh I, Badger JH, Kumar U, Saier M, Wang Y, Cai H, Gu J, Mather MW, Vaidya AB, Wilkes DE, Rajagopalan V, Asai DJ, Pearson CG, Findly RC, Dickerson HW, Wu M, Martens C, Van de Peer Y, Roos DS, Cassidy-Hanley DM, Clark TG. Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control. Genome Biol 2011; 12:R100. [PMID: 22004680 PMCID: PMC3341644 DOI: 10.1186/gb-2011-12-10-r100] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 09/15/2011] [Accepted: 10/17/2011] [Indexed: 01/09/2023] Open
Abstract
Background Ichthyophthirius multifiliis, commonly known as Ich, is a highly pathogenic ciliate responsible for 'white spot', a disease causing significant economic losses to the global aquaculture industry. Options for disease control are extremely limited, and Ich's obligate parasitic lifestyle makes experimental studies challenging. Unlike most well-studied protozoan parasites, Ich belongs to a phylum composed primarily of free-living members. Indeed, it is closely related to the model organism Tetrahymena thermophila. Genomic studies represent a promising strategy to reduce the impact of this disease and to understand the evolutionary transition to parasitism. Results We report the sequencing, assembly and annotation of the Ich macronuclear genome. Compared with its free-living relative T. thermophila, the Ich genome is reduced approximately two-fold in length and gene density and three-fold in gene content. We analyzed in detail several gene classes with diverse functions in behavior, cellular function and host immunogenicity, including protein kinases, membrane transporters, proteases, surface antigens and cytoskeletal components and regulators. We also mapped by orthology Ich's metabolic pathways in comparison with other ciliates and a potential host organism, the zebrafish Danio rerio. Conclusions Knowledge of the complete protein-coding and metabolic potential of Ich opens avenues for rational testing of therapeutic drugs that target functions essential to this parasite but not to its fish hosts. Also, a catalog of surface protein-encoding genes will facilitate development of more effective vaccines. The potential to use T. thermophila as a surrogate model offers promise toward controlling 'white spot' disease and understanding the adaptation to a parasitic lifestyle.
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Affiliation(s)
- Robert S Coyne
- Genomic Medicine, J Craig Venter Institute, Rockville, MD 20850, USA.
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27
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Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo MJ, Dupont CL, Badger JH, Novotny M, Rusch DB, Fraser LJ, Gormley NA, Schulz-Trieglaff O, Smith GP, Evers DJ, Pevzner PA, Lasken RS. Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat Biotechnol 2011; 29:915-21. [PMID: 21926975 PMCID: PMC3558281 DOI: 10.1038/nbt.1966] [Citation(s) in RCA: 183] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 08/09/2011] [Indexed: 11/09/2022]
Abstract
Whole genome amplification by the multiple displacement amplification (MDA) method allows sequencing of DNA from single cells of bacteria that cannot be cultured. Assembling a genome is challenging, however, because MDA generates highly nonuniform coverage of the genome. Here we describe an algorithm tailored for short-read data from single cells that improves assembly through the use of a progressively increasing coverage cutoff. Assembly of reads from single Escherichia coli and Staphylococcus aureus cells captures >91% of genes within contigs, approaching the 95% captured from an assembly based on many E. coli cells. We apply this method to assemble a genome from a single cell of an uncultivated SAR324 clade of Deltaproteobacteria, a cosmopolitan bacterial lineage in the global ocean. Metabolic reconstruction suggests that SAR324 is aerobic, motile and chemotaxic. Our approach enables acquisition of genome assemblies for individual uncultivated bacteria using only short reads, providing cell-specific genetic information absent from metagenomic studies.
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Affiliation(s)
- Hamidreza Chitsaz
- Department of Computer Science, University of California, La Jolla, CA, USA
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Chen Y, Stine OC, Badger JH, Gil AI, Nair GB, Nishibuchi M, Fouts DE. Comparative genomic analysis of Vibrio parahaemolyticus: serotype conversion and virulence. BMC Genomics 2011; 12:294. [PMID: 21645368 PMCID: PMC3130711 DOI: 10.1186/1471-2164-12-294] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 06/06/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Vibrio parahaemolyticus is a common cause of foodborne disease. Beginning in 1996, a more virulent strain having serotype O3:K6 caused major outbreaks in India and other parts of the world, resulting in the emergence of a pandemic. Other serovariants of this strain emerged during its dissemination and together with the original O3:K6 were termed strains of the pandemic clone. Two genomes, one of this virulent strain and one pre-pandemic strain have been sequenced. We sequenced four additional genomes of V. parahaemolyticus in this study that were isolated from different geographical regions and time points. Comparative genomic analyses of six strains of V. parahaemolyticus isolated from Asia and Peru were performed in order to advance knowledge concerning the evolution of V. parahaemolyticus; specifically, the genetic changes contributing to serotype conversion and virulence. Two pre-pandemic strains and three pandemic strains, isolated from different geographical regions, were serotype O3:K6 and either toxin profiles (tdh+, trh-) or (tdh-, trh+). The sixth pandemic strain sequenced in this study was serotype O4:K68. RESULTS Genomic analyses revealed that the trh+ and tdh+ strains had different types of pathogenicity islands and mobile elements as well as major structural differences between the tdh pathogenicity islands of the pre-pandemic and pandemic strains. In addition, the results of single nucleotide polymorphism (SNP) analysis showed that 94% of the SNPs between O3:K6 and O4:K68 pandemic isolates were within a 141 kb region surrounding the O- and K-antigen-encoding gene clusters. The "core" genes of V. parahaemolyticus were also compared to those of V. cholerae and V. vulnificus, in order to delineate differences between these three pathogenic species. Approximately one-half (49-59%) of each species' core genes were conserved in all three species, and 14-24% of the core genes were species-specific and in different functional categories. CONCLUSIONS Our data support the idea that the pandemic strains are closely related and that recent South American outbreaks of foodborne disease caused by V. parahaemolyticus are closely linked to outbreaks in India. Serotype conversion from O3:K6 to O4:K68 was likely due to a recombination event involving a region much larger than the O-antigen- and K-antigen-encoding gene clusters. Major differences between pathogenicity islands and mobile elements are also likely driving the evolution of V. parahaemolyticus. In addition, our analyses categorized genes that may be useful in differentiating pathogenic Vibrios at the species level.
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Affiliation(s)
- Yuansha Chen
- The J. Craig Venter Institute, Rockville, MD, USA
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29
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Huguet-Tapia JC, Badger JH, Loria R, Pettis GS. Streptomyces turgidiscabies Car8 contains a modular pathogenicity island that shares virulence genes with other actinobacterial plant pathogens. Plasmid 2011; 65:118-24. [DOI: 10.1016/j.plasmid.2010.11.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 11/02/2010] [Accepted: 11/08/2010] [Indexed: 10/18/2022]
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Cock JM, Sterck L, Rouzé P, Scornet D, Allen AE, Amoutzias G, Anthouard V, Artiguenave F, Aury JM, Badger JH, Beszteri B, Billiau K, Bonnet E, Bothwell JH, Bowler C, Boyen C, Brownlee C, Carrano CJ, Charrier B, Cho GY, Coelho SM, Collén J, Corre E, Da Silva C, Delage L, Delaroque N, Dittami SM, Doulbeau S, Elias M, Farnham G, Gachon CMM, Gschloessl B, Heesch S, Jabbari K, Jubin C, Kawai H, Kimura K, Kloareg B, Küpper FC, Lang D, Le Bail A, Leblanc C, Lerouge P, Lohr M, Lopez PJ, Martens C, Maumus F, Michel G, Miranda-Saavedra D, Morales J, Moreau H, Motomura T, Nagasato C, Napoli CA, Nelson DR, Nyvall-Collén P, Peters AF, Pommier C, Potin P, Poulain J, Quesneville H, Read B, Rensing SA, Ritter A, Rousvoal S, Samanta M, Samson G, Schroeder DC, Ségurens B, Strittmatter M, Tonon T, Tregear JW, Valentin K, von Dassow P, Yamagishi T, Van de Peer Y, Wincker P. The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature 2010; 465:617-21. [PMID: 20520714 DOI: 10.1038/nature09016] [Citation(s) in RCA: 518] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Accepted: 03/15/2010] [Indexed: 01/05/2023]
Abstract
Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae, closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic approaches to explore these and other aspects of brown algal biology further.
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Affiliation(s)
- J Mark Cock
- UPMC Université Paris 6, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France.
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Inskeep WP, Rusch DB, Jay ZJ, Herrgard MJ, Kozubal MA, Richardson TH, Macur RE, Hamamura N, Jennings RD, Fouke BW, Reysenbach AL, Roberto F, Young M, Schwartz A, Boyd ES, Badger JH, Mathur EJ, Ortmann AC, Bateson M, Geesey G, Frazier M. Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function. PLoS One 2010; 5:e9773. [PMID: 20333304 PMCID: PMC2841643 DOI: 10.1371/journal.pone.0009773] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2009] [Accepted: 02/25/2010] [Indexed: 01/07/2023] Open
Abstract
The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14–15,000 Sanger reads per site) was obtained for five high-temperature (>65°C) chemotrophic microbial communities sampled from geothermal springs (or pools) in Yellowstone National Park (YNP) that exhibit a wide range in geochemistry including pH, dissolved sulfide, dissolved oxygen and ferrous iron. Metagenome data revealed significant differences in the predominant phyla associated with each of these geochemical environments. Novel members of the Sulfolobales are dominant in low pH environments, while other Crenarchaeota including distantly-related Thermoproteales and Desulfurococcales populations dominate in suboxic sulfidic sediments. Several novel archaeal groups are well represented in an acidic (pH 3) Fe-oxyhydroxide mat, where a higher O2 influx is accompanied with an increase in archaeal diversity. The presence or absence of genes and pathways important in S oxidation-reduction, H2-oxidation, and aerobic respiration (terminal oxidation) provide insight regarding the metabolic strategies of indigenous organisms present in geothermal systems. Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites. The distribution of functional genes involved in electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, Fe, O2) control microbial community structure and function in YNP geothermal springs.
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Affiliation(s)
- William P. Inskeep
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America
- * E-mail: (WPI); (DBR)
| | - Douglas B. Rusch
- J. Craig Venter Institute, Rockville, Maryland, United States of America
- * E-mail: (WPI); (DBR)
| | - Zackary J. Jay
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America
| | | | - Mark A. Kozubal
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America
| | | | - Richard E. Macur
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America
| | - Natsuko Hamamura
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Japan
| | - Ryan deM. Jennings
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America
| | - Bruce W. Fouke
- University of Illinois, Urbana, Illinois, United States of America
| | | | - Frank Roberto
- Idaho National Laboratory, Idaho Falls, Idaho, United States of America
| | - Mark Young
- Thermal Biology Institute and Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana, United States of America
| | - Ariel Schwartz
- Synthetic Genomics Inc., La Jolla, California, United States of America
| | - Eric S. Boyd
- Thermal Biology Institute and Department of Microbiology, Montana State University, Bozeman, Montana, United States of America
| | - Jonathan H. Badger
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Eric J. Mathur
- Synthetic Genomics Inc., La Jolla, California, United States of America
| | - Alice C. Ortmann
- Department of Marine Science, University of South Alabama, Mobile, Alabama, United States of America
| | - Mary Bateson
- Thermal Biology Institute and Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana, United States of America
| | - Gill Geesey
- Thermal Biology Institute and Department of Microbiology, Montana State University, Bozeman, Montana, United States of America
| | - Marvin Frazier
- J. Craig Venter Institute, Rockville, Maryland, United States of America
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Hartman AL, Norais C, Badger JH, Delmas S, Haldenby S, Madupu R, Robinson J, Khouri H, Ren Q, Lowe TM, Maupin-Furlow J, Pohlschroder M, Daniels C, Pfeiffer F, Allers T, Eisen JA. The complete genome sequence of Haloferax volcanii DS2, a model archaeon. PLoS One 2010; 5:e9605. [PMID: 20333302 PMCID: PMC2841640 DOI: 10.1371/journal.pone.0009605] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Accepted: 02/11/2010] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Haloferax volcanii is an easily culturable moderate halophile that grows on simple defined media, is readily transformable, and has a relatively stable genome. This, in combination with its biochemical and genetic tractability, has made Hfx. volcanii a key model organism, not only for the study of halophilicity, but also for archaeal biology in general. METHODOLOGY/PRINCIPAL FINDINGS We report here the sequencing and analysis of the genome of Hfx. volcanii DS2, the type strain of this species. The genome contains a main 2.848 Mb chromosome, three smaller chromosomes pHV1, 3, 4 (85, 438, 636 kb, respectively) and the pHV2 plasmid (6.4 kb). CONCLUSIONS/SIGNIFICANCE The completed genome sequence, presented here, provides an invaluable tool for further in vivo and in vitro studies of Hfx. volcanii.
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Affiliation(s)
- Amber L. Hartman
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
- UC Davis Genome Center, University of California Davis, Davis, California, United States of America
| | - Cédric Norais
- Institut de Génétique et Microbiologie, Université Paris-Sud, Paris, France
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jonathan H. Badger
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
| | - Stéphane Delmas
- Institute of Genetics, University of Nottingham, Nottingham, United Kingdom
| | - Sam Haldenby
- Institute of Genetics, University of Nottingham, Nottingham, United Kingdom
| | - Ramana Madupu
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
| | - Jeffrey Robinson
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
| | - Hoda Khouri
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
| | - Qinghu Ren
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
| | - Todd M. Lowe
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Julie Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Mecky Pohlschroder
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Charles Daniels
- Department of Microbiology, Ohio State University, Columbus, Ohio, United States of America
| | - Friedhelm Pfeiffer
- Department of Membrane Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Thorsten Allers
- Institute of Genetics, University of Nottingham, Nottingham, United Kingdom
| | - Jonathan A. Eisen
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
- UC Davis Genome Center, University of California Davis, Davis, California, United States of America
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, California, United States of America
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
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Yang JC, Madupu R, Durkin AS, Ekborg NA, Pedamallu CS, Hostetler JB, Radune D, Toms BS, Henrissat B, Coutinho PM, Schwarz S, Field L, Trindade-Silva AE, Soares CAG, Elshahawi S, Hanora A, Schmidt EW, Haygood MG, Posfai J, Benner J, Madinger C, Nove J, Anton B, Chaudhary K, Foster J, Holman A, Kumar S, Lessard PA, Luyten YA, Slatko B, Wood N, Wu B, Teplitski M, Mougous JD, Ward N, Eisen JA, Badger JH, Distel DL. The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms). PLoS One 2009; 4:e6085. [PMID: 19568419 PMCID: PMC2699552 DOI: 10.1371/journal.pone.0006085] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Accepted: 05/06/2009] [Indexed: 12/02/2022] Open
Abstract
Here we report the complete genome sequence of Teredinibacter turnerae T7901. T. turnerae is a marine gamma proteobacterium that occurs as an intracellular endosymbiont in the gills of wood-boring marine bivalves of the family Teredinidae (shipworms). This species is the sole cultivated member of an endosymbiotic consortium thought to provide the host with enzymes, including cellulases and nitrogenase, critical for digestion of wood and supplementation of the host's nitrogen-deficient diet. T. turnerae is closely related to the free-living marine polysaccharide degrading bacterium Saccharophagus degradans str. 2–40 and to as yet uncultivated endosymbionts with which it coexists in shipworm cells. Like S. degradans, the T. turnerae genome encodes a large number of enzymes predicted to be involved in complex polysaccharide degradation (>100). However, unlike S. degradans, which degrades a broad spectrum (>10 classes) of complex plant, fungal and algal polysaccharides, T. turnerae primarily encodes enzymes associated with deconstruction of terrestrial woody plant material. Also unlike S. degradans and many other eubacteria, T. turnerae dedicates a large proportion of its genome to genes predicted to function in secondary metabolism. Despite its intracellular niche, the T. turnerae genome lacks many features associated with obligate intracellular existence (e.g. reduced genome size, reduced %G+C, loss of genes of core metabolism) and displays evidence of adaptations common to free-living bacteria (e.g. defense against bacteriophage infection). These results suggest that T. turnerae is likely a facultative intracellular ensosymbiont whose niche presently includes, or recently included, free-living existence. As such, the T. turnerae genome provides insights into the range of genomic adaptations associated with intracellular endosymbiosis as well as enzymatic mechanisms relevant to the recycling of plant materials in marine environments and the production of cellulose-derived biofuels.
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Affiliation(s)
- Joyce C. Yang
- Ocean Genome Legacy, Inc., Ipswich, Massachusetts, United States of America
| | - Ramana Madupu
- J. Craig Venter Institute, San Diego, California, United States of America
| | - A. Scott Durkin
- J. Craig Venter Institute, San Diego, California, United States of America
| | - Nathan A. Ekborg
- Ocean Genome Legacy, Inc., Ipswich, Massachusetts, United States of America
| | | | | | - Diana Radune
- J. Craig Venter Institute, San Diego, California, United States of America
| | - Bradley S. Toms
- J. Craig Venter Institute, San Diego, California, United States of America
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universités Aix-Marseille I & II, Case 932, Marseille, France
| | - Pedro M. Coutinho
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universités Aix-Marseille I & II, Case 932, Marseille, France
| | - Sandra Schwarz
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Lauren Field
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Amaro E. Trindade-Silva
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Ilha do Fundao, CCS, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos A. G. Soares
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Ilha do Fundao, CCS, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sherif Elshahawi
- Department of Environmental and Biomolecular Systems, OGI School of Science & Engineering, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Amro Hanora
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Eric W. Schmidt
- College of Pharmacy, University of Utah, Salt Lake City, Utah, United States of America
| | - Margo G. Haygood
- Department of Environmental and Biomolecular Systems, OGI School of Science & Engineering, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Janos Posfai
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Jack Benner
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | | | - John Nove
- Ocean Genome Legacy, Inc., Ipswich, Massachusetts, United States of America
| | - Brian Anton
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Kshitiz Chaudhary
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Jeremy Foster
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Alex Holman
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Sanjay Kumar
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Philip A. Lessard
- Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Yvette A. Luyten
- Ocean Genome Legacy, Inc., Ipswich, Massachusetts, United States of America
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Barton Slatko
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Nicole Wood
- Ocean Genome Legacy, Inc., Ipswich, Massachusetts, United States of America
| | - Bo Wu
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Max Teplitski
- University of Florida, Gainesville, Florida, United States of America
| | - Joseph D. Mougous
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Naomi Ward
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, United States of America
| | - Jonathan A. Eisen
- UC Davis Genome Center, University of California Davis, Davis, California, United States of America
| | - Jonathan H. Badger
- J. Craig Venter Institute, San Diego, California, United States of America
| | - Daniel L. Distel
- Ocean Genome Legacy, Inc., Ipswich, Massachusetts, United States of America
- * E-mail:
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Worden AZ, Lee JH, Mock T, Rouzé P, Simmons MP, Aerts AL, Allen AE, Cuvelier ML, Derelle E, Everett MV, Foulon E, Grimwood J, Gundlach H, Henrissat B, Napoli C, McDonald SM, Parker MS, Rombauts S, Salamov A, Von Dassow P, Badger JH, Coutinho PM, Demir E, Dubchak I, Gentemann C, Eikrem W, Gready JE, John U, Lanier W, Lindquist EA, Lucas S, Mayer KFX, Moreau H, Not F, Otillar R, Panaud O, Pangilinan J, Paulsen I, Piegu B, Poliakov A, Robbens S, Schmutz J, Toulza E, Wyss T, Zelensky A, Zhou K, Armbrust EV, Bhattacharya D, Goodenough UW, Van de Peer Y, Grigoriev IV. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science 2009; 324:268-72. [PMID: 19359590 DOI: 10.1126/science.1167222] [Citation(s) in RCA: 416] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Picoeukaryotes are a taxonomically diverse group of organisms less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from tropical to polar and could serve as sentinel organisms for biogeochemical fluxes of modern oceans during climate change. These broadly distributed primary producers belong to an anciently diverged sister clade to land plants. Although Micromonas isolates have high 18S ribosomal RNA gene identity, we found that genomes from two isolates shared only 90% of their predicted genes. Their independent evolutionary paths were emphasized by distinct riboswitch arrangements as well as the discovery of intronic repeat elements in one isolate, and in metagenomic data, but not in other genomes. Divergence appears to have been facilitated by selection and acquisition processes that actively shape the repertoire of genes that are mutually exclusive between the two isolates differently than the core genes. Analyses of the Micromonas genomes offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution.
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Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham JE, Bryant DA, Robb F, Colman A, Tallon LJ, Badger JH, Madupu R, Ward NL, Eisen JA. Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS One 2009; 4:e4207. [PMID: 19148287 PMCID: PMC2615216 DOI: 10.1371/journal.pone.0004207] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2008] [Accepted: 11/07/2008] [Indexed: 12/02/2022] Open
Abstract
In order to enrich the phylogenetic diversity represented in the available sequenced bacterial genomes and as part of an “Assembling the Tree of Life” project, we determined the genome sequence of Thermomicrobium roseum DSM 5159. T. roseum DSM 5159 is a red-pigmented, rod-shaped, Gram-negative extreme thermophile isolated from a hot spring that possesses both an atypical cell wall composition and an unusual cell membrane that is composed entirely of long-chain 1,2-diols. Its genome is composed of two circular DNA elements, one of 2,006,217 bp (referred to as the chromosome) and one of 919,596 bp (referred to as the megaplasmid). Strikingly, though few standard housekeeping genes are found on the megaplasmid, it does encode a complete system for chemotaxis including both chemosensory components and an entire flagellar apparatus. This is the first known example of a complete flagellar system being encoded on a plasmid and suggests a straightforward means for lateral transfer of flagellum-based motility. Phylogenomic analyses support the recent rRNA-based analyses that led to T. roseum being removed from the phylum Thermomicrobia and assigned to the phylum Chloroflexi. Because T. roseum is a deep-branching member of this phylum, analysis of its genome provides insights into the evolution of the Chloroflexi. In addition, even though this species is not photosynthetic, analysis of the genome provides some insight into the origins of photosynthesis in the Chloroflexi. Metabolic pathway reconstructions and experimental studies revealed new aspects of the biology of this species. For example, we present evidence that T. roseum oxidizes CO aerobically, making it the first thermophile known to do so. In addition, we propose that glycosylation of its carotenoids plays a crucial role in the adaptation of the cell membrane to this bacterium's thermophilic lifestyle. Analyses of published metagenomic sequences from two hot springs similar to the one from which this strain was isolated, show that close relatives of T. roseum DSM 5159 are present but have some key differences from the strain sequenced.
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Affiliation(s)
- Dongying Wu
- University of California Davis Genome Center, Davis, California, United States of America
| | - Jason Raymond
- Microbial Systems Division, Biosciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Martin Wu
- University of California Davis Genome Center, Davis, California, United States of America
| | - Sourav Chatterji
- University of California Davis Genome Center, Davis, California, United States of America
| | - Qinghu Ren
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Joel E. Graham
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Frank Robb
- University of Maryland Biotechnology Institute, Baltimore, Maryland, United States of America
| | - Albert Colman
- University of Maryland Biotechnology Institute, Baltimore, Maryland, United States of America
| | - Luke J. Tallon
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Jonathan H. Badger
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Ramana Madupu
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Naomi L. Ward
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Jonathan A. Eisen
- University of California Davis Genome Center, Davis, California, United States of America
- Section of Evolution and Ecology, University of California Davis, Davis, California, United States of America
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, California, United States of America
- * E-mail:
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Egan A, Mahurkar A, Crabtree J, Badger JH, Carlton JM, Silva JC. IDEA: Interactive Display for Evolutionary Analyses. BMC Bioinformatics 2008; 9:524. [PMID: 19061522 PMCID: PMC2655098 DOI: 10.1186/1471-2105-9-524] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Accepted: 12/08/2008] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of interest an increasingly important approach to addressing broad evolutionary questions. Two of the programs most widely used for this purpose are codeml and baseml, parts of the PAML (Phylogenetic Analysis by Maximum Likelihood) suite. A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency. RESULTS We have developed IDEA (Interactive Display for Evolutionary Analyses), an intuitive graphical input and output interface which interacts with PHYLIP for phylogeny reconstruction and with codeml and baseml for molecular evolution analyses. IDEA's graphical input and visualization interfaces eliminate the need to edit and parse text input and output files, reducing the likelihood of errors and improving processing time. Further, its interactive output display gives the user immediate access to results. Finally, IDEA can process data in parallel on a local machine or computing grid, allowing genome-wide analyses to be completed quickly. CONCLUSION IDEA provides a graphical user interface that allows the user to follow a codeml or baseml analysis from parameter input through to the exploration of results. Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results. The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data.
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Affiliation(s)
- Amy Egan
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Anup Mahurkar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jonathan Crabtree
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | | | - Jane M Carlton
- Department of Medical Parasitology, New York University School of Medicine, New York, NY 10010, USA
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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van den Berg MA, Albang R, Albermann K, Badger JH, Daran JM, Driessen AJM, Garcia-Estrada C, Fedorova ND, Harris DM, Heijne WHM, Joardar V, Kiel JAKW, Kovalchuk A, Martín JF, Nierman WC, Nijland JG, Pronk JT, Roubos JA, van der Klei IJ, van Peij NNME, Veenhuis M, von Döhren H, Wagner C, Wortman J, Bovenberg RAL. Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum. Nat Biotechnol 2008; 26:1161-8. [PMID: 18820685 DOI: 10.1038/nbt.1498] [Citation(s) in RCA: 344] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Accepted: 08/27/2008] [Indexed: 11/09/2022]
Abstract
Industrial penicillin production with the filamentous fungus Penicillium chrysogenum is based on an unprecedented effort in microbial strain improvement. To gain more insight into penicillin synthesis, we sequenced the 32.19 Mb genome of P. chrysogenum Wisconsin54-1255 and identified numerous genes responsible for key steps in penicillin production. DNA microarrays were used to compare the transcriptomes of the sequenced strain and a penicillinG high-producing strain, grown in the presence and absence of the side-chain precursor phenylacetic acid. Transcription of genes involved in biosynthesis of valine, cysteine and alpha-aminoadipic acid-precursors for penicillin biosynthesis-as well as of genes encoding microbody proteins, was increased in the high-producing strain. Some gene products were shown to be directly controlling beta-lactam output. Many key cellular transport processes involving penicillins and intermediates remain to be characterized at the molecular level. Genes predicted to encode transporters were strongly overrepresented among the genes transcriptionally upregulated under conditions that stimulate penicillinG production, illustrating potential for future genomics-driven metabolic engineering.
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38
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Fouts DE, Tyler HL, DeBoy RT, Daugherty S, Ren Q, Badger JH, Durkin AS, Huot H, Shrivastava S, Kothari S, Dodson RJ, Mohamoud Y, Khouri H, Roesch LFW, Krogfelt KA, Struve C, Triplett EW, Methé BA. Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice. PLoS Genet 2008; 4:e1000141. [PMID: 18654632 PMCID: PMC2453333 DOI: 10.1371/journal.pgen.1000141] [Citation(s) in RCA: 208] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Accepted: 06/24/2008] [Indexed: 12/25/2022] Open
Abstract
We report here the sequencing and analysis of the genome of the nitrogen-fixing endophyte, Klebsiella pneumoniae 342. Although K. pneumoniae 342 is a member of the enteric bacteria, it serves as a model for studies of endophytic, plant-bacterial associations due to its efficient colonization of plant tissues (including maize and wheat, two of the most important crops in the world), while maintaining a mutualistic relationship that encompasses supplying organic nitrogen to the host plant. Genomic analysis examined K. pneumoniae 342 for the presence of previously identified genes from other bacteria involved in colonization of, or growth in, plants. From this set, approximately one-third were identified in K. pneumoniae 342, suggesting additional factors most likely contribute to its endophytic lifestyle. Comparative genome analyses were used to provide new insights into this question. Results included the identification of metabolic pathways and other features devoted to processing plant-derived cellulosic and aromatic compounds, and a robust complement of transport genes (15.4%), one of the highest percentages in bacterial genomes sequenced. Although virulence and antibiotic resistance genes were predicted, experiments conducted using mouse models showed pathogenicity to be attenuated in this strain. Comparative genomic analyses with the presumed human pathogen K. pneumoniae MGH78578 revealed that MGH78578 apparently cannot fix nitrogen, and the distribution of genes essential to surface attachment, secretion, transport, and regulation and signaling varied between each genome, which may indicate critical divergences between the strains that influence their preferred host ranges and lifestyles (endophytic plant associations for K. pneumoniae 342 and presumably human pathogenesis for MGH78578). Little genome information is available concerning endophytic bacteria. The K. pneumoniae 342 genome will drive new research into this less-understood, but important category of bacterial-plant host relationships, which could ultimately enhance growth and nutrition of important agricultural crops and development of plant-derived products and biofuels.
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Fedorova ND, Khaldi N, Joardar VS, Maiti R, Amedeo P, Anderson MJ, Crabtree J, Silva JC, Badger JH, Albarraq A, Angiuoli S, Bussey H, Bowyer P, Cotty PJ, Dyer PS, Egan A, Galens K, Fraser-Liggett CM, Haas BJ, Inman JM, Kent R, Lemieux S, Malavazi I, Orvis J, Roemer T, Ronning CM, Sundaram JP, Sutton G, Turner G, Venter JC, White OR, Whitty BR, Youngman P, Wolfe KH, Goldman GH, Wortman JR, Jiang B, Denning DW, Nierman WC. Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genet 2008; 4:e1000046. [PMID: 18404212 PMCID: PMC2289846 DOI: 10.1371/journal.pgen.1000046] [Citation(s) in RCA: 357] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Accepted: 03/04/2008] [Indexed: 01/23/2023] Open
Abstract
We present the genome sequences of a new clinical isolate of the important human pathogen, Aspergillus fumigatus, A1163, and two closely related but rarely pathogenic species, Neosartorya fischeri NRRL181 and Aspergillus clavatus NRRL1. Comparative genomic analysis of A1163 with the recently sequenced A. fumigatus isolate Af293 has identified core, variable and up to 2% unique genes in each genome. While the core genes are 99.8% identical at the nucleotide level, identity for variable genes can be as low 40%. The most divergent loci appear to contain heterokaryon incompatibility (het) genes associated with fungal programmed cell death such as developmental regulator rosA. Cross-species comparison has revealed that 8.5%, 13.5% and 12.6%, respectively, of A. fumigatus, N. fischeri and A. clavatus genes are species-specific. These genes are significantly smaller in size than core genes, contain fewer exons and exhibit a subtelomeric bias. Most of them cluster together in 13 chromosomal islands, which are enriched for pseudogenes, transposons and other repetitive elements. At least 20% of A. fumigatus-specific genes appear to be functional and involved in carbohydrate and chitin catabolism, transport, detoxification, secondary metabolism and other functions that may facilitate the adaptation to heterogeneous environments such as soil or a mammalian host. Contrary to what was suggested previously, their origin cannot be attributed to horizontal gene transfer (HGT), but instead is likely to involve duplication, diversification and differential gene loss (DDL). The role of duplication in the origin of lineage-specific genes is further underlined by the discovery of genomic islands that seem to function as designated “gene dumps” and, perhaps, simultaneously, as “gene factories”. Aspergillus is an extremely diverse genus of filamentous ascomycetous fungi (molds) found ubiquitously in soil and decomposing vegetation. Being supreme opportunists, aspergilli have adapted to overcome various chemical, physical, and biological stresses found in heterogeneous environments. While most species in the genus are saprophytes, a surprising number are able to infect wounded plants and animals. Remarkably, the allergic human host also responds abnormally to the aspergilli with lung and sinus disease. The advent of immunosuppressive agents and other medical advances have created a large worldwide pool of human hosts susceptible to some Aspergillus species, including the world's most harmful mold and the causative agent of invasive aspergillosis, Aspergillus fumigatus. In this study, we have used the power of comparative genomics to gain insight into genetic mechanisms that may contribute to the metabolic versatility and pathogenicity of this important human pathogen. Comparison of the genomes of two A. fumigatus clinical isolates and two closely related, but rarely pathogenic species showed that their genomes contain several large isolate- and species-specific chromosomal islands. The metabolic capabilities encoded by these highly labile regions are likely to contribute to their rapid adaptation to heterogeneous environments such as soil or a living host.
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Affiliation(s)
- Natalie D. Fedorova
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Nora Khaldi
- Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin, Ireland
| | - Vinita S. Joardar
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Rama Maiti
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Paolo Amedeo
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Michael J. Anderson
- School of Medicine and Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Jonathan Crabtree
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Joana C. Silva
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Jonathan H. Badger
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Ahmed Albarraq
- School of Medicine and Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Sam Angiuoli
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Howard Bussey
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Paul Bowyer
- School of Medicine and Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Peter J. Cotty
- Agricultural Research Service, United States Department of Agriculture, Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Paul S. Dyer
- School of Biology, University of Nottingham, Nottingham, United Kingdom
| | - Amy Egan
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Kevin Galens
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | | | - Brian J. Haas
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Jason M. Inman
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Richard Kent
- School of Medicine and Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Sebastien Lemieux
- Institute for Research in Immunology and Cancer, Department of Computer Science and Operations Research, Universite de Montreal, Montreal, Canada
| | - Iran Malavazi
- Departamento de Ciencias Farmaceuticas, Faculdade de Ciencias Farmaceuticas de Ribeirao Preto, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Joshua Orvis
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Terry Roemer
- Merck & Co., Inc., Whitehouse Station, New Jersey, United States of America
| | | | - Jaideep P. Sundaram
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Granger Sutton
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Geoff Turner
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
| | - J. Craig Venter
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Owen R. White
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Brett R. Whitty
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Phil Youngman
- Merck & Co., Inc., Whitehouse Station, New Jersey, United States of America
| | - Kenneth H. Wolfe
- Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin, Ireland
| | - Gustavo H. Goldman
- Departamento de Ciencias Farmaceuticas, Faculdade de Ciencias Farmaceuticas de Ribeirao Preto, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Jennifer R. Wortman
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Bo Jiang
- Merck & Co., Inc., Whitehouse Station, New Jersey, United States of America
| | - David W. Denning
- School of Medicine and Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - William C. Nierman
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
- Department of Biochemistry and Molecular Biology, The George Washington University School of Medicine, Washington DC, United States of America
- * E-mail:
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40
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Myers GSA, Parker D, Al-Hasani K, Kennan RM, Seemann T, Ren Q, Badger JH, Selengut JD, Deboy RT, Tettelin H, Boyce JD, McCarl VP, Han X, Nelson WC, Madupu R, Mohamoud Y, Holley T, Fedorova N, Khouri H, Bottomley SP, Whittington RJ, Adler B, Songer JG, Rood JI, Paulsen IT. Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus. Nat Biotechnol 2007; 25:569-75. [PMID: 17468768 DOI: 10.1038/nbt1302] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Accepted: 04/04/2007] [Indexed: 11/09/2022]
Abstract
Dichelobacter nodosus causes ovine footrot, a disease that leads to severe economic losses in the wool and meat industries. We sequenced its 1.4-Mb genome, the smallest known genome of an anaerobe. It differs markedly from small genomes of intracellular bacteria, retaining greater biosynthetic capabilities and lacking any evidence of extensive ongoing genome reduction. Comparative genomic microarray studies and bioinformatic analysis suggested that, despite its small size, almost 20% of the genome is derived from lateral gene transfer. Most of these regions seem to be associated with virulence. Metabolic reconstruction indicated unsuspected capabilities, including carbohydrate utilization, electron transfer and several aerobic pathways. Global transcriptional profiling and bioinformatic analysis enabled the prediction of virulence factors and cell surface proteins. Screening of these proteins against ovine antisera identified eight immunogenic proteins that are candidate antigens for a cross-protective vaccine.
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Affiliation(s)
- Garry S A Myers
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
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41
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Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol 2007; 4:e286. [PMID: 16933976 PMCID: PMC1557398 DOI: 10.1371/journal.pbio.0040286] [Citation(s) in RCA: 545] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2006] [Accepted: 06/23/2006] [Indexed: 01/05/2023] Open
Abstract
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct nuclei within a single cell. The germline-like micronucleus (MIC) has its genome held in reserve for sexual reproduction. The soma-like macronucleus (MAC), which possesses a genome processed from that of the MIC, is the center of gene expression and does not directly contribute DNA to sexual progeny. We report here the shotgun sequencing, assembly, and analysis of the MAC genome of T. thermophila, which is approximately 104 Mb in length and composed of approximately 225 chromosomes. Overall, the gene set is robust, with more than 27,000 predicted protein-coding genes, 15,000 of which have strong matches to genes in other organisms. The functional diversity encoded by these genes is substantial and reflects the complexity of processes required for a free-living, predatory, single-celled organism. This is highlighted by the abundance of lineage-specific duplications of genes with predicted roles in sensing and responding to environmental conditions (e.g., kinases), using diverse resources (e.g., proteases and transporters), and generating structural complexity (e.g., kinesins and dyneins). In contrast to the other lineages of alveolates (apicomplexans and dinoflagellates), no compelling evidence could be found for plastid-derived genes in the genome. UGA, the only T. thermophila stop codon, is used in some genes to encode selenocysteine, thus making this organism the first known with the potential to translate all 64 codons in nuclear genes into amino acids. We present genomic evidence supporting the hypothesis that the excision of DNA from the MIC to generate the MAC specifically targets foreign DNA as a form of genome self-defense. The combination of the genome sequence, the functional diversity encoded therein, and the presence of some pathways missing from other model organisms makes T. thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance.
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Affiliation(s)
- Jonathan A Eisen
- The Institute for Genomic Research, Rockville, Maryland, United States of America.
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42
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Badger JH, Hoover TR, Brun YV, Weiner RM, Laub MT, Alexandre G, Mrázek J, Ren Q, Paulsen IT, Nelson KE, Khouri HM, Radune D, Sosa J, Dodson RJ, Sullivan SA, Rosovitz MJ, Madupu R, Brinkac LM, Durkin AS, Daugherty SC, Kothari SP, Giglio MG, Zhou L, Haft DH, Selengut JD, Davidsen TM, Yang Q, Zafar N, Ward NL. Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus. J Bacteriol 2006; 188:6841-50. [PMID: 16980487 PMCID: PMC1595504 DOI: 10.1128/jb.00111-06] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The dimorphic prosthecate bacteria (DPB) are alpha-proteobacteria that reproduce in an asymmetric manner rather than by binary fission and are of interest as simple models of development. Prior to this work, the only member of this group for which genome sequence was available was the model freshwater organism Caulobacter crescentus. Here we describe the genome sequence of Hyphomonas neptunium, a marine member of the DPB that differs from C. crescentus in that H. neptunium uses its stalk as a reproductive structure. Genome analysis indicates that this organism shares more genes with C. crescentus than it does with Silicibacter pomeroyi (a closer relative according to 16S rRNA phylogeny), that it relies upon a heterotrophic strategy utilizing a wide range of substrates, that its cell cycle is likely to be regulated in a similar manner to that of C. crescentus, and that the outer membrane complements of H. neptunium and C. crescentus are remarkably similar. H. neptunium swarmer cells are highly motile via a single polar flagellum. With the exception of cheY and cheR, genes required for chemotaxis were absent in the H. neptunium genome. Consistent with this observation, H. neptunium swarmer cells did not respond to any chemotactic stimuli that were tested, which suggests that H. neptunium motility is a random dispersal mechanism for swarmer cells rather than a stimulus-controlled navigation system for locating specific environments. In addition to providing insights into bacterial development, the H. neptunium genome will provide an important resource for the study of other interesting biological processes including chromosome segregation, polar growth, and cell aging.
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Affiliation(s)
- Jonathan H Badger
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
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Palenik B, Ren Q, Dupont CL, Myers GS, Heidelberg JF, Badger JH, Madupu R, Nelson WC, Brinkac LM, Dodson RJ, Durkin AS, Daugherty SC, Sullivan SA, Khouri H, Mohamoud Y, Halpin R, Paulsen IT. Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment. Proc Natl Acad Sci U S A 2006; 103:13555-9. [PMID: 16938853 PMCID: PMC1569201 DOI: 10.1073/pnas.0602963103] [Citation(s) in RCA: 154] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Indexed: 11/18/2022] Open
Abstract
Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have found that the genome of a coastal cyanobacterium, Synechococcus sp. strain CC9311, has significant differences from an open ocean strain, Synechococcus sp. strain WH8102, and these are consistent with the differences between their respective environments. CC9311 has a greater capacity to sense and respond to changes in its (coastal) environment. It has a much larger capacity to transport, store, use, or export metals, especially iron and copper. In contrast, phosphate acquisition seems less important, consistent with the higher concentration of phosphate in coastal environments. CC9311 is predicted to have differences in its outer membrane lipopolysaccharide, and this may be characteristic of the speciation of some cyanobacterial groups. In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments.
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Affiliation(s)
- Brian Palenik
- *Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093; and
| | - Qinghu Ren
- The Institute for Genomic Research, Rockville, MD 20850
| | - Chris L. Dupont
- *Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093; and
| | | | | | | | - Ramana Madupu
- The Institute for Genomic Research, Rockville, MD 20850
| | | | | | | | | | | | | | - Hoda Khouri
- The Institute for Genomic Research, Rockville, MD 20850
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44
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Fedorova ND, Badger JH, Robson GD, Wortman JR, Nierman WC. Comparative analysis of programmed cell death pathways in filamentous fungi. BMC Genomics 2005; 6:177. [PMID: 16336669 PMCID: PMC1325252 DOI: 10.1186/1471-2164-6-177] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2005] [Accepted: 12/08/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fungi can undergo autophagic- or apoptotic-type programmed cell death (PCD) on exposure to antifungal agents, developmental signals, and stress factors. Filamentous fungi can also exhibit a form of cell death called heterokaryon incompatibility (HI) triggered by fusion between two genetically incompatible individuals. With the availability of recently sequenced genomes of Aspergillus fumigatus and several related species, we were able to define putative components of fungi-specific death pathways and the ancestral core apoptotic machinery shared by all fungi and metazoa. RESULTS Phylogenetic profiling of HI-associated proteins from four Aspergilli and seven other fungal species revealed lineage-specific protein families, orphan genes, and core genes conserved across all fungi and metazoa. The Aspergilli-specific domain architectures include NACHT family NTPases, which may function as key integrators of stress and nutrient availability signals. They are often found fused to putative effector domains such as Pfs, SesB/LipA, and a newly identified domain, HET-s/LopB. Many putative HI inducers and mediators are specific to filamentous fungi and not found in unicellular yeasts. In addition to their role in HI, several of them appear to be involved in regulation of cell cycle, development and sexual differentiation. Finally, the Aspergilli possess many putative downstream components of the mammalian apoptotic machinery including several proteins not found in the model yeast, Saccharomyces cerevisiae. CONCLUSION Our analysis identified more than 100 putative PCD associated genes in the Aspergilli, which may help expand the range of currently available treatments for aspergillosis and other invasive fungal diseases. The list includes species-specific protein families as well as conserved core components of the ancestral PCD machinery shared by fungi and metazoa.
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Affiliation(s)
- Natalie D Fedorova
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
| | - Jonathan H Badger
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
| | - Geoff D Robson
- Faculty of Life Sciences, 1.800 Stopford Building, University of Manchester, Manchester M13 9PT, UK
| | - Jennifer R Wortman
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
| | - William C Nierman
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
- The George Washington University School of Medicine, Department of Biochemistry and Molecular Biology, 2300 Eye Street, NW Washington, DC 20837, USA
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45
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Badger JH, Eisen JA, Ward NL. Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders 'Rhodobacterales' and Caulobacterales. Int J Syst Evol Microbiol 2005; 55:1021-1026. [PMID: 15879228 DOI: 10.1099/ijs.0.63510-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hyphomonas neptunium is a marine prosthecate alpha-proteobacterium currently classified as a member of the order 'Rhodobacterales'. Although this classification is supported by 16S rRNA gene sequence phylogeny, 23S rRNA gene sequence analysis, concatenated ribosomal proteins, HSP70 and EF-Tu phylogenies all support classifying Hyphomonas neptunium as a member of the Caulobacterales instead. The possible reasons why the 16S rRNA gene sequence gives conflicting results in this case are also discussed.
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MESH Headings
- Alphaproteobacteria/classification
- Alphaproteobacteria/genetics
- Bacterial Proteins/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Genes, rRNA
- HSP70 Heat-Shock Proteins/genetics
- Peptide Elongation Factor Tu/genetics
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Jonathan H Badger
- The Institute for Genomic Research, 9712 Medical Center Dr., Rockville, MD 20850, USA
| | - Jonathan A Eisen
- The Institute for Genomic Research, 9712 Medical Center Dr., Rockville, MD 20850, USA
| | - Naomi L Ward
- The Institute for Genomic Research, 9712 Medical Center Dr., Rockville, MD 20850, USA
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46
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Fouts DE, Mongodin EF, Mandrell RE, Miller WG, Rasko DA, Ravel J, Brinkac LM, DeBoy RT, Parker CT, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Sullivan SA, Shetty JU, Ayodeji MA, Shvartsbeyn A, Schatz MC, Badger JH, Fraser CM, Nelson KE. Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species. PLoS Biol 2005; 3:e15. [PMID: 15660156 PMCID: PMC539331 DOI: 10.1371/journal.pbio.0030015] [Citation(s) in RCA: 398] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2004] [Accepted: 11/11/2004] [Indexed: 12/19/2022] Open
Abstract
Sequencing and comparative genome analysis of four strains of Campylobacter including C. lari RM2100, C. upsaliensis RM3195, and C. coli RM2228 has revealed major structural differences that are associated with the insertion of phage- and plasmid-like genomic islands, as well as major variations in the lipooligosaccharide complex. Poly G tracts are longer, are greater in number, and show greater variability in C. upsaliensis than in the other species. Many genes involved in host colonization, including racR/S, cadF, cdt, ciaB, and flagellin genes, are conserved across the species, but variations that appear to be species specific are evident for a lipooligosaccharide locus, a capsular (extracellular) polysaccharide locus, and a novel Campylobacter putative licABCD virulence locus. The strains also vary in their metabolic profiles, as well as their resistance profiles to a range of antibiotics. It is evident that the newly identified hypothetical and conserved hypothetical proteins, as well as uncharacterized two-component regulatory systems and membrane proteins, may hold additional significant information on the major differences in virulence among the species, as well as the specificity of the strains for particular hosts.
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Affiliation(s)
- Derrick E Fouts
- The Institute for Genomic Research, Rockville, Maryland, United States of America.
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Li M, Badger JH, Chen X, Kwong S, Kearney P, Zhang H. An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics 2001; 17:149-54. [PMID: 11238070 DOI: 10.1093/bioinformatics/17.2.149] [Citation(s) in RCA: 364] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Traditional sequence distances require an alignment and therefore are not directly applicable to the problem of whole genome phylogeny where events such as rearrangements make full length alignments impossible. We present a sequence distance that works on unaligned sequences using the information theoretical concept of Kolmogorov complexity and a program to estimate this distance. RESULTS We establish the mathematical foundations of our distance and illustrate its use by constructing a phylogeny of the Eutherian orders using complete unaligned mitochondrial genomes. This phylogeny is consistent with the commonly accepted one for the Eutherians. A second, larger mammalian dataset is also analyzed, yielding a phylogeny generally consistent with the commonly accepted one for the mammals. AVAILABILITY The program to estimate our sequence distance, is available at http://www.cs.cityu.edu.hk/~cssamk/gencomp/GenCompress1.htm. The distance matrices used to generate our phylogenies are available at http://www.math.uwaterloo.ca/~mli/distance.html.
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Affiliation(s)
- M Li
- Bioinformatics Laboratory, Computer Science Department, University of Waterloo, N2L 3G1, Canada.
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Abstract
Gene recognition is essential to understanding existing and future DNA sequence data. CRITICA (Coding Region Identification Tool Invoking Comparative Analysis) is a suite of programs for identifying likely protein-coding sequences in DNA by combining comparative analysis of DNA sequences with more common noncomparative methods. In the comparative component of the analysis, regions of DNA are aligned with related sequences from the DNA databases; if the translation of the aligned sequences has greater amino acid identity than expected for the observed percentage nucleotide identity, this is interpreted as evidence for coding. CRITICA also incorporates noncomparative information derived from the relative frequencies of hexanucleotides in coding frames versus other contexts (i.e., dicodon bias). The dicodon usage information is derived by iterative analysis of the data, such that CRITICA is not dependent on the existence or accuracy of coding sequence annotations in the databases. This independence makes the method particularly well suited for the analysis of novel genomes. CRITICA was tested by analyzing the available Salmonella typhimurium DNA sequences. Its predictions were compared with the DNA sequence annotations and with the predictions of GenMark. CRITICA proved to be more accurate than GenMark, and moreover, many of its predictions that would seem to be errors instead reflect problems in the sequence databases. The source code of CRITICA is freely available by anonymous FTP (rdp.life.uiuc.edu in/pub/critica) and on the World Wide Web (http:/(/)rdpwww.life.uiuc.edu).
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Affiliation(s)
- J H Badger
- Department of Microbiology, University of Illinois, Urbana 61801, USA
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Haney PJ, Badger JH, Buldak GL, Reich CI, Woese CR, Olsen GJ. Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. Proc Natl Acad Sci U S A 1999; 96:3578-83. [PMID: 10097079 PMCID: PMC22336 DOI: 10.1073/pnas.96.7.3578] [Citation(s) in RCA: 257] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genome sequence of the extremely thermophilic archaeon Methanococcus jannaschii provides a wealth of data on proteins from a thermophile. In this paper, sequences of 115 proteins from M. jannaschii are compared with their homologs from mesophilic Methanococcus species. Although the growth temperatures of the mesophiles are about 50 degrees C below that of M. jannaschii, their genomic G+C contents are nearly identical. The properties most correlated with the proteins of the thermophile include higher residue volume, higher residue hydrophobicity, more charged amino acids (especially Glu, Arg, and Lys), and fewer uncharged polar residues (Ser, Thr, Asn, and Gln). These are recurring themes, with all trends applying to 83-92% of the proteins for which complete sequences were available. Nearly all of the amino acid replacements most significantly correlated with the temperature change are the same relatively conservative changes observed in all proteins, but in the case of the mesophile/thermophile comparison there is a directional bias. We identify 26 specific pairs of amino acids with a statistically significant (P < 0.01) preferred direction of replacement.
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Affiliation(s)
- P J Haney
- Department of Microbiology, University of Illinois, B103 Chemical and Life Sciences Laboratory, 601 South Goodwin Avenue, Urbana, IL 61801, USA
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Klenk HP, Clayton RA, Tomb JF, White O, Nelson KE, Ketchum KA, Dodson RJ, Gwinn M, Hickey EK, Peterson JD, Richardson DL, Kerlavage AR, Graham DE, Kyrpides NC, Fleischmann RD, Quackenbush J, Lee NH, Sutton GG, Gill S, Kirkness EF, Dougherty BA, McKenney K, Adams MD, Loftus B, Peterson S, Reich CI, McNeil LK, Badger JH, Glodek A, Zhou L, Overbeek R, Gocayne JD, Weidman JF, McDonald L, Utterback T, Cotton MD, Spriggs T, Artiach P, Kaine BP, Sykes SM, Sadow PW, D'Andrea KP, Bowman C, Fujii C, Garland SA, Mason TM, Olsen GJ, Fraser CM, Smith HO, Woese CR, Venter JC. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 1997; 390:364-70. [PMID: 9389475 DOI: 10.1038/37052] [Citation(s) in RCA: 990] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Archaeoglobus fulgidus is the first sulphur-metabolizing organism to have its genome sequence determined. Its genome of 2,178,400 base pairs contains 2,436 open reading frames (ORFs). The information processing systems and the biosynthetic pathways for essential components (nucleotides, amino acids and cofactors) have extensive correlation with their counterparts in the archaeon Methanococcus jannaschii. The genomes of these two Archaea indicate dramatic differences in the way these organisms sense their environment, perform regulatory and transport functions, and gain energy. In contrast to M. jannaschii, A. fulgidus has fewer restriction-modification systems, and none of its genes appears to contain inteins. A quarter (651 ORFs) of the A. fulgidus genome encodes functionally uncharacterized yet conserved proteins, two-thirds of which are shared with M. jannaschii (428 ORFs). Another quarter of the genome encodes new proteins indicating substantial archaeal gene diversity.
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Affiliation(s)
- H P Klenk
- Institute for Genomic Research, Rockville, Maryland 20850, USA
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