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Sugino KY, Mandala A, Janssen RC, Gurung S, Trammell M, Day MW, Brush RS, Papin JF, Dyer DW, Agbaga MP, Friedman JE, Castillo-Castrejon M, Jonscher KR, Myers DA. Western diet-induced shifts in the maternal microbiome are associated with altered microRNA expression in baboon placenta and fetal liver. Front Clin Diabetes Healthc 2022; 3:945768. [PMID: 36935840 PMCID: PMC10012127 DOI: 10.3389/fcdhc.2022.945768] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Maternal consumption of a high-fat, Western-style diet (WD) disrupts the maternal/infant microbiome and contributes to developmental programming of the immune system and nonalcoholic fatty liver disease (NAFLD) in the offspring. Epigenetic changes, including non-coding miRNAs in the fetus and/or placenta may also underlie this risk. We previously showed that obese nonhuman primates fed a WD during pregnancy results in the loss of beneficial maternal gut microbes and dysregulation of cellular metabolism and mitochondrial dysfunction in the fetal liver, leading to a perturbed postnatal immune response with accelerated NAFLD in juvenile offspring. Here, we investigated associations between WD-induced maternal metabolic and microbiome changes, in the absence of obesity, and miRNA and gene expression changes in the placenta and fetal liver. After ~8-11 months of WD feeding, dams were similar in body weight but exhibited mild, systemic inflammation (elevated CRP and neutrophil count) and dyslipidemia (increased triglycerides and cholesterol) compared with dams fed a control diet. The maternal gut microbiome was mainly comprised of Lactobacillales and Clostridiales, with significantly decreased alpha diversity (P = 0.0163) in WD-fed dams but no community-wide differences (P = 0.26). At 0.9 gestation, mRNA expression of IL6 and TNF in maternal WD (mWD) exposed placentas trended higher, while increased triglycerides, expression of pro-inflammatory CCR2, and histological evidence for fibrosis were found in mWD-exposed fetal livers. In the mWD-exposed fetus, hepatic expression levels of miR-204-5p and miR-145-3p were significantly downregulated, whereas in mWD-exposed placentas, miR-182-5p and miR-183-5p were significantly decreased. Notably, miR-1285-3p expression in the liver and miR-183-5p in the placenta were significantly associated with inflammation and lipid synthesis pathway genes, respectively. Blautia and Ruminococcus were significantly associated with miR-122-5p in liver, while Coriobacteriaceae and Prevotellaceae were strongly associated with miR-1285-3p in the placenta; both miRNAs are implicated in pathways mediating postnatal growth and obesity. Our findings demonstrate that mWD shifts the maternal microbiome, lipid metabolism, and inflammation prior to obesity and are associated with epigenetic changes in the placenta and fetal liver. These changes may underlie inflammation, oxidative stress, and fibrosis patterns that drive NAFLD and metabolic disease risk in the next generation.
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Affiliation(s)
- Kameron Y. Sugino
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Ashok Mandala
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Rachel C. Janssen
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Sunam Gurung
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - MaJoi Trammell
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Michael W. Day
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Richard S. Brush
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - James F. Papin
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Martin-Paul Agbaga
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Jacob E. Friedman
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Marisol Castillo-Castrejon
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Karen R. Jonscher
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- CORRESPONDENCE: Karen R. Jonscher,
| | - Dean A. Myers
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
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2
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Nima G, Harth-Chu E, Hiers RD, Pecorari VGA, Dyer DW, Khajotia SS, Giannini M, Florez FLE. Antibacterial efficacy of non-thermal atmospheric plasma against Streptococcus mutans biofilm grown on the surfaces of restorative resin composites. Sci Rep 2021; 11:23800. [PMID: 34893687 PMCID: PMC8664839 DOI: 10.1038/s41598-021-03192-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/28/2021] [Indexed: 01/11/2023] Open
Abstract
The aim of this study was to evaluate the antimicrobial efficacy of non-thermal atmospheric plasma (NTAP) against Streptococcus mutans biofilms. Resin discs were fabricated, wet-polished, UV sterilized, and immersed in water for monomer extraction (37 °C, 24 h). Biofilms of bioluminescent S. mutans strain JM10 was grown on resin discs in anaerobic conditions for (37 °C, 24 h). Discs were divided into seven groups: control (CON), 2% chlorhexidine (CHX), only argon gas 150 s (ARG) and four NTAP treatments (30 s, 90 s, 120 s, 150 s). NTAP was applied using a plasma jet device. After treatment, biofilms were analyzed through the counting of viable colonies (CFU), bioluminescence assay (BL), scanning electron microscopy (SEM), and polymerase chain reaction (PCR). All NTAP-treated biofilm yielded a significant CFU reduction when compared to ARG and CON. BL values showed that NTAP treatment for 90 s, 120 s or 150 s resulted in statistically significantly lower metabolic activity when compared to the other groups. CHX displayed the lowest means of CFU and BL. SEM showed significant morphological changes in NTAP-treated biofilm. PCR indicated damage to the DNA structure after NTAP treatment. NTAP treatment was effective in lowering the viability and metabolism of S. mutans in a time-dependent manner, suggesting its use as an intraoral surface-decontamination strategy.
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Affiliation(s)
- Gabriel Nima
- Department of Restorative Dentistry, Dental Materials Division, Piracicaba Dental School, State University of Campinas, Piracicaba, SP, Brazil.
| | - Erika Harth-Chu
- Department of Oral Diagnosis, Piracicaba Dental School, State University of Campinas, Piracicaba, SP, Brazil
| | - Rochelle Denise Hiers
- Department of Restorative Sciences, Division of Dental Biomaterials, College of Dentistry, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | | | - David W Dyer
- Department of Microbiology and Immunology, College of Medicine, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Sharukh Soli Khajotia
- Department of Restorative Sciences, Division of Dental Biomaterials, College of Dentistry, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Marcelo Giannini
- Department of Restorative Dentistry, Operative Dentistry Division, Piracicaba Dental School, State University of Campinas, Piracicaba, SP, Brazil
| | - Fernando Luis Esteban Florez
- Department of Restorative Sciences, Division of Dental Biomaterials, College of Dentistry, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
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Kang J, Ismail AM, Dehghan S, Rajaiya J, Allard MW, Lim HC, Dyer DW, Chodosh J, Seto D. Genomics-based re-examination of the taxonomy and phylogeny of human and simian Mastadenoviruses: an evolving whole genomes approach, revealing putative zoonosis, anthroponosis, and amphizoonosis. Cladistics 2020; 36:358-373. [PMID: 34618969 DOI: 10.1111/cla.12422] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2020] [Indexed: 02/06/2023] Open
Abstract
With the advent of high-resolution and cost-effective genomics and bioinformatics tools and methods contributing to a large database of both human (HAdV) and simian (SAdV) adenoviruses, a genomics-based re-evaluation of their taxonomy is warranted. Interest in these particular adenoviruses is growing in part due to the applications of both in gene transfer protocols, including gene therapy and vaccines, as well in oncolytic protocols. In particular, the re-evaluation of SAdVs as appropriate vectors in humans is important as zoonosis precludes the assumption that human immune system may be naïve to these vectors. Additionally, as important pathogens, adenoviruses are a model organism system for understanding viral pathogen emergence through zoonosis and anthroponosis, particularly among the primate species, along with recombination, host adaptation, and selection, as evidenced by one long-standing human respiratory pathogen HAdV-4 and a recent re-evaluation of another, HAdV-76. The latter reflects the insights on amphizoonosis, defined as infections in both directions among host species including "other than human", that are possible with the growing database of nonhuman adenovirus genomes. HAdV-76 is a recombinant that has been isolated from human, chimpanzee, and bonobo hosts. On-going and potential impacts of adenoviruses on public health and translational medicine drive this evaluation of 174 whole genome sequences from HAdVs and SAdVs archived in GenBank. The conclusion is that rather than separate HAdV and SAdV phylogenetic lineages, a single, intertwined tree is observed with all HAdVs and SAdVs forming mixed clades. Therefore, a single designation of "primate adenovirus" (PrAdV) superseding either HAdV and SAdV is proposed, or alternatively, keeping HAdV for human adenovirus but expanding the SAdV nomenclature officially to include host species identification as in ChAdV for chimpanzee adenovirus, GoAdV for gorilla adenovirus, BoAdV for bonobo adenovirus, and ad libitum.
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Affiliation(s)
- June Kang
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, 20110, USA
| | - Ashrafali Mohamed Ismail
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, 02114, USA
| | - Shoaleh Dehghan
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, 20110, USA.,Chemistry Department, American University, Washington, DC, 20016, USA
| | - Jaya Rajaiya
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, 02114, USA
| | - Marc W Allard
- Division of Microbiology (HFS-710), Center for Food Safety & Applied Nutrition, US Food & Drug Administration, College Park, MD, 20740, USA
| | - Haw Chuan Lim
- Department of Biology, George Mason University Manassas, VA, 20110, USA
| | - David W Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - James Chodosh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, 02114, USA
| | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, 20110, USA
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4
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Ismail AM, Zhou X, Dyer DW, Seto D, Rajaiya J, Chodosh J. Genomic foundations of evolution and ocular pathogenesis in human adenovirus species D. FEBS Lett 2019; 593:3583-3608. [PMID: 31769017 PMCID: PMC7185199 DOI: 10.1002/1873-3468.13693] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 10/21/2019] [Revised: 11/16/2019] [Accepted: 11/20/2019] [Indexed: 12/27/2022]
Abstract
Human adenovirus commonly causes infections of respiratory, gastrointestinal, genitourinary, and ocular surface mucosae. Although most adenovirus eye infections are mild and self-limited, specific viruses within human adenovirus species D are associated with epidemic keratoconjunctivitis (EKC), a severe and highly contagious ocular surface infection, which can lead to chronic and/or recurrent, visually disabling keratitis. In this review, we discuss the links between adenovirus ontogeny, genomics, immune responses, and corneal pathogenesis, for those viruses that cause EKC.
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Affiliation(s)
- Ashrafali M. Ismail
- Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Xiaohong Zhou
- Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - Jaya Rajaiya
- Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - James Chodosh
- Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
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5
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Ismail AM, Cui T, Dommaraju K, Singh G, Dehghan S, Seto J, Shrivastava S, Fedorova NB, Gupta N, Stockwell TB, Halpin R, Madupu R, Heim A, Kajon AE, Romanowski EG, Kowalski RP, Malathi J, Therese KL, Madhavan HN, Zhang Q, Ferreyra LJ, Jones MS, Rajaiya J, Dyer DW, Chodosh J, Seto D. Author Correction: Genomic analysis of a large set of currently-and historically-important human adenovirus pathogens. Emerg Microbes Infect 2018; 7:208. [PMID: 30532034 PMCID: PMC6286714 DOI: 10.1038/s41426-018-0200-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ashrafali M Ismail
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, 02114, USA
| | - Tiange Cui
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, 20110, USA
| | - Kalpana Dommaraju
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, 20110, USA
| | - Gurdeep Singh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, 02114, USA
| | - Shoaleh Dehghan
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, 20110, USA.,Chemistry Department, American University, Washington, DC, 20016, USA
| | - Jason Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, 20110, USA
| | | | | | - Neha Gupta
- J. Craig Venter Institute, Rockville, MD, 20850, USA
| | | | | | - Ramana Madupu
- J. Craig Venter Institute, Rockville, MD, 20850, USA
| | - Albert Heim
- Institut für Virologie, Medizinische Hochschule Hannover, Hannover, 30625, Germany
| | - Adriana E Kajon
- Lovelace Respiratory Research Institute, Albuquerque, NM, 87108, USA
| | - Eric G Romanowski
- Charles T. Campbell Ophthalmic Microbiology Laboratory, Ear and Eye Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Regis P Kowalski
- Charles T. Campbell Ophthalmic Microbiology Laboratory, Ear and Eye Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Jambulingam Malathi
- L &, T Microbiology Research Center, Kamalnayan Bajaj Research Center, Sankara Nethralaya, No. 41 College Road, Chennai, Tamil Nadu, 600006, India
| | - Kuzhanthai L Therese
- L &, T Microbiology Research Center, Kamalnayan Bajaj Research Center, Sankara Nethralaya, No. 41 College Road, Chennai, Tamil Nadu, 600006, India
| | - Hajib Narahari Madhavan
- L &, T Microbiology Research Center, Kamalnayan Bajaj Research Center, Sankara Nethralaya, No. 41 College Road, Chennai, Tamil Nadu, 600006, India
| | - Qiwei Zhang
- Biosafety Level-3 Laboratory, School of Public Health, Southern Medical University, 510515, Guangzhou, China
| | - Leonardo J Ferreyra
- Institute of Virology "J. M. Vanella", Enfermera Gordillo Gómez s/n, Agencia 4, Ciudad Universitaria, CP 5016, Córdoba, Argentina
| | - Morris S Jones
- School of Public Health, University of California Berkeley, Berkeley, CA, 94704, USA
| | - Jaya Rajaiya
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, 02114, USA
| | - David W Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - James Chodosh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, 02114, USA.
| | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, 20110, USA.
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Ismail AM, Lee JS, Lee JY, Singh G, Dyer DW, Seto D, Chodosh J, Rajaiya J. Corrigendum: Adenoviromics: Mining the Human Adenovirus Species D Genome. Front Microbiol 2018; 9:3005. [PMID: 30555456 PMCID: PMC6288599 DOI: 10.3389/fmicb.2018.03005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 11/20/2018] [Indexed: 11/15/2022] Open
Affiliation(s)
- Ashrafali M Ismail
- Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States
| | - Ji Sun Lee
- Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States
| | - Jeong Yoon Lee
- Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States.,Molecular Virology Laboratory, Korea Zoonosis Research Institute Jeonbuk National University, Jeonju, South Korea
| | - Gurdeep Singh
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - David W Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VI, United States
| | - James Chodosh
- Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States
| | - Jaya Rajaiya
- Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States
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7
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Ismail AM, Lee JS, Lee JY, Singh G, Dyer DW, Seto D, Chodosh J, Rajaiya J. Adenoviromics: Mining the Human Adenovirus Species D Genome. Front Microbiol 2018; 9:2178. [PMID: 30254627 PMCID: PMC6141750 DOI: 10.3389/fmicb.2018.02178] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [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: 07/20/2018] [Accepted: 08/24/2018] [Indexed: 12/19/2022] Open
Abstract
Human adenovirus (HAdV) infections cause disease world-wide. Whole genome sequencing has now distinguished 90 distinct genotypes in 7 species (A-G). Over half of these 90 HAdVs fall within species D, with essentially all of the HAdV-D whole genome sequences generated in the last decade. Herein, we describe recent new findings made possible by mining of this expanded genome database, and propose future directions to elucidate new functional elements and new functions for previously known viral components.
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Affiliation(s)
- Ashrafali M Ismail
- Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States
| | - Ji Sun Lee
- Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States
| | - Jeong Yoon Lee
- Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States.,Molecular Virology Laboratory, Korea Zoonosis Research Institute, Jeonbuk National University, Jeonju, South Korea
| | - Gurdeep Singh
- Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - David W Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VI, United States
| | - James Chodosh
- Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States
| | - Jaya Rajaiya
- Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States
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Cole BK, Scott E, Ilikj M, Bard D, Akins DR, Dyer DW, Chavez-Bueno S. Route of infection alters virulence of neonatal septicemia Escherichia coli clinical isolates. PLoS One 2017; 12:e0189032. [PMID: 29236742 PMCID: PMC5728477 DOI: 10.1371/journal.pone.0189032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 03/08/2017] [Accepted: 09/05/2017] [Indexed: 12/03/2022] Open
Abstract
Escherichia coli is the leading cause of Gram-negative neonatal septicemia in the United States. Invasion and passage across the neonatal gut after ingestion of maternal E. coli strains produce bacteremia. In this study, we compared the virulence properties of the neonatal E. coli bacteremia clinical isolate SCB34 with the archetypal neonatal E. coli meningitis strain RS218. Whole-genome sequencing data was used to compare the protein coding sequences among these clinical isolates and 33 other representative E. coli strains. Oral inoculation of newborn animals with either strain produced septicemia, whereas intraperitoneal injection caused septicemia only in pups infected with RS218 but not in those injected with SCB34. In addition to being virulent only through the oral route, SCB34 demonstrated significantly greater invasion and transcytosis of polarized intestinal epithelial cells in vitro as compared to RS218. Protein coding sequences comparisons highlighted the presence of known virulence factors that are shared among several of these isolates, and revealed the existence of proteins exclusively encoded in SCB34, many of which remain uncharacterized. Our study demonstrates that oral acquisition is crucial for the virulence properties of the neonatal bacteremia clinical isolate SCB34. This characteristic, along with its enhanced ability to invade and transcytose intestinal epithelium are likely determined by the specific virulence factors that predominate in this strain.
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Affiliation(s)
- Bryan K. Cole
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Edgar Scott
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Marko Ilikj
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - David Bard
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Darrin R. Akins
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Susana Chavez-Bueno
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
- * E-mail:
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9
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Jackson LA, Day M, Allen J, Scott E, Dyer DW. Iron-regulated small RNA expression as Neisseria gonorrhoeae FA 1090 transitions into stationary phase growth. BMC Genomics 2017; 18:317. [PMID: 28431495 PMCID: PMC5399841 DOI: 10.1186/s12864-017-3684-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 04/06/2017] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND For most pathogens, iron (Fe) homeostasis is crucial for maintenance within the host and the ability to cause disease. The primary transcriptional regulator that controls intracellular Fe levels is the Fur (ferric uptake regulator) protein, which exerts its action on transcription by binding to a promoter-proximal sequence termed the Fur box. Fur-regulated transcriptional responses are often fine-tuned at the post-transcriptional level through the action of small regulatory RNAs (sRNAs). Consequently, identifying sRNAs contributing to the control of Fe homeostasis is important for understanding the Fur-controlled bacterial Fe-response network. RESULTS In this study, we sequenced size-selected directional libraries representing sRNA samples from Neisseria gonorrhoeae strain FA 1090, and examined the Fe- and temporal regulation of these sRNAs. RNA-seq data for all time points identified a pool of at least 340 potential sRNAs. Differential analysis demonstrated that expression appeared to be regulated by Fe availability for at least fifteen of these sRNAs. Fourteen sRNAs were induced in high Fe conditions, consisting of both cis and trans sRNAs, some of which are predicted to control expression of a known virulence factor, and one SAM riboswitch. An additional putative cis-acting sRNA was repressed by Fe availability. In the pathogenic Neisseria species, one sRNA that contributes to Fe-regulated post-transcriptional control is the Fur-repressible sRNA NrrF. The expression of five Fe-induced sRNAs appeared to be at least partially controlled by NrrF, while the remainder was expressed independently of NrrF. The expression of the 14 Fe-induced sRNAs also exhibited temporal control, as their expression levels increased dramatically as the bacteria entered stationary phase. CONCLUSIONS Here we report the temporal expression of Fe-regulated sRNAs in N. gonorrhoeae FA 1090 with several appearing to be controlled by the Fe-repressible sRNA NrrF. Temporal regulation of these sRNAs suggests a regulatory role in controlling functions necessary for survival, and may be important for phenotypes often associated with altered growth rates, such as biofilm formation or intracellular survival. Future functional studies will be needed to understand how these regulatory sRNAs contribute to gonococcal biology and pathogenesis.
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Affiliation(s)
- Lydgia A. Jackson
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences, 975 NE 10th Street, Oklahoma City, OK 73104 USA
| | - Michael Day
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences, 975 NE 10th Street, Oklahoma City, OK 73104 USA
| | - Jennie Allen
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences, 975 NE 10th Street, Oklahoma City, OK 73104 USA
| | - Edgar Scott
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences, 975 NE 10th Street, Oklahoma City, OK 73104 USA
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences, 975 NE 10th Street, Oklahoma City, OK 73104 USA
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10
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Ramke M, Lee JY, Dyer DW, Seto D, Rajaiya J, Chodosh J. The 5'UTR in human adenoviruses: leader diversity in late gene expression. Sci Rep 2017; 7:618. [PMID: 28377580 PMCID: PMC5429599 DOI: 10.1038/s41598-017-00747-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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: 06/07/2016] [Accepted: 03/14/2017] [Indexed: 01/05/2023] Open
Abstract
Human adenoviruses (HAdVs) shut down host cellular cap-dependent mRNA translation while initiating the translation of viral late mRNAs in a cap-independent manner. HAdV 5′ untranslated regions (5′UTRs) are crucial for cap-independent initiation, and influence mRNA localization and stability. However, HAdV translational regulation remains relatively uncharacterized. The HAdV tripartite leader (TPL), composed of three introns (TPL 1–3), is critical to the translation of HAdV late mRNA. Herein, we annotated and analyzed 72 HAdV genotypes for the HAdV TPL and another previously described leader, the i-leader. Using HAdV species D, type 37 (HAdV-D37), we show by reverse transcription PCR and Sanger sequencing that mRNAs of the HAdV-D37 E3 transcription unit are spliced to the TPL. We also identified a polycistronic mRNA for RID-α and RID-β. Analysis of the i-leader revealed a potential open reading frame within the leader sequence and the termination of this potential protein in TPL3. A potential new leader embedded within the E3 region was also detected and tentatively named the j-leader. These results suggest an underappreciated complexity of post-transcriptional regulation, and the importance of HAdV 5′UTRs for precisely coordinated viral protein expression along the path from genotype to phenotype.
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Affiliation(s)
- Mirja Ramke
- Howe Laboratory, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, 243 Charles Street, Boston, Massachusetts, USA
| | - Jeong Yoon Lee
- Howe Laboratory, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, 243 Charles Street, Boston, Massachusetts, USA
| | - David W Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - Jaya Rajaiya
- Howe Laboratory, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, 243 Charles Street, Boston, Massachusetts, USA.
| | - James Chodosh
- Howe Laboratory, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, 243 Charles Street, Boston, Massachusetts, USA.
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Abstract
With hybridization probes derived from the fimbrial locus of Porphyromonas gingivalis strain 381, fimA381' restriction fragment length polymorphisms (RFLPs) were examined at the fimbrillin locus in 39 human and animal strains of this species. The 39 strains were subdivided into nine RFLP groups (I-IX) after genomic digests were probed with the internal coding sequence of the fimA381 gene. Thirty-three strains showed one or more AluI fragments of moderate-to-high homology (≥77%) with the internal coding sequence of fimA381. These strains were distributed into the first seven RFLP groups, based solely on the size of the major hybridizing AluI fragment. Five human strains (RFLP Group VIII) had only one Alu I fragment that hybridized very poorly with this probe. One animal strain did not have homology at all (RFLP Group IX). When all AluI fragments that hybridized with fimA381 were analyzed, RFLP groups I-VIII were further differentiated into 25 distinct RFLP patterns. Hybridizations were also performed with the internal coding sequence of fimA381 to probe PstI genomic digests of selected strains that appeared to have lesser homology with fimA381. These hybridizations were performed to determine the level and location of the region of poor homology within the fimA genes of these strains. The results suggested that fimbrial coding sequences are more commonly conserved between these strains in the 5'-region of the fimA locus (≥92% sequence homology). However, the five human strains of RFLP Group VIII had only one PstI fragment that hybridized very poorly with a probe derived from fimA381 coding sequence, and this sequence homology (only > 66%) was located in the central or 3'-end of the fimA gene. The 5'-region of the fimA allele in Group VIII strains did not have any detectable sequence homology. In contrast, the Group VIII strains were highly homologous with the sequences flanking the fimA381 gene. This indicates that these strains do possess a fimA allele at the same chromosomal location as fimA381.
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Affiliation(s)
- B G Loos
- Department of Oral Biology, School of Dental Medicine, State University of New York, Buffalo 14214
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12
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Kenedy MR, Scott EJ, Shrestha B, Anand A, Iqbal H, Radolf JD, Dyer DW, Akins DR. Consensus computational network analysis for identifying candidate outer membrane proteins from Borrelia spirochetes. BMC Microbiol 2016; 16:141. [PMID: 27400788 PMCID: PMC4939628 DOI: 10.1186/s12866-016-0762-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 02/10/2016] [Accepted: 07/02/2016] [Indexed: 01/15/2023] Open
Abstract
Background Similar to Gram-negative organisms, Borrelia spirochetes are dual-membrane organisms with both an inner and outer membrane. Although the outer membrane contains integral membrane proteins, few of the borrelial outer membrane proteins (OMPs) have been identified and characterized to date. Therefore, we utilized a consensus computational network analysis to identify novel borrelial OMPs. Results Using a series of computer-based algorithms, we selected all protein-encoding sequences predicted to be OM-localized and/or to form β-barrels in the borrelial OM. Using this system, we identified 41 potential OMPs from B. burgdorferi and characterized three (BB0838, BB0405, and BB0406) to confirm that our computer-based methodology did, in fact, identify borrelial OMPs. Triton X-114 phase partitioning revealed that BB0838 is found in the detergent phase, which would be expected of a membrane protein. Proteolysis assays indicate that BB0838 is partially sensitive to both proteinase K and trypsin, further indicating that BB0838 is surface-exposed. Consistent with a prior study, we also confirmed that BB0405 is surface-exposed and associates with the borrelial OM. Furthermore, we have shown that BB0406, the product of a co-transcribed downstream gene, also encodes a novel, previously uncharacterized borrelial OMP. Interestingly, while BB0406 has several physicochemical properties consistent with it being an OMP, it was found to be resistant to surface proteolysis. Consistent with BB0405 and BB0406 being OMPs, both were found to be capable of incorporating into liposomes and exhibit pore-forming activity, suggesting that both proteins are porins. Lastly, we expanded our computational analysis to identify OMPs from other borrelial organisms, including both Lyme disease and relapsing fever spirochetes. Conclusions Using a consensus computer algorithm, we generated a list of candidate OMPs for both Lyme disease and relapsing fever spirochetes and determined that three of the predicted B. burgdorferi proteins identified were indeed novel borrelial OMPs. The combined studies have identified putative spirochetal OMPs that can now be examined for their roles in virulence, physiology, and disease pathogenesis. Importantly, the studies described in this report provide a framework by which OMPs from any human pathogen with a diderm ultrastructure could be cataloged to identify novel virulence factors and vaccine candidates. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0762-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Melisha R Kenedy
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA
| | - Edgar J Scott
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA
| | - Binu Shrestha
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA
| | - Arvind Anand
- Department of Medicine, University of Connecticut Health Center, Farmington, Connecticut, 06030, USA
| | - Henna Iqbal
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA
| | - Justin D Radolf
- Department of Medicine, University of Connecticut Health Center, Farmington, Connecticut, 06030, USA.,Department of Pediatrics, University of Connecticut Health Center, Farmington, Connecticut, 06030, USA.,Department of Genetics and Genomic Science, University of Connecticut Health Center, Farmington, Connecticut, 06030, USA.,Department of Immunology, University of Connecticut Health Center, Farmington, Connecticut, 06030, USA.,Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, 06030, USA
| | - David W Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA
| | - Darrin R Akins
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA.
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13
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Singh G, Zhou X, Lee JY, Yousuf MA, Ramke M, Ismail AM, Lee JS, Robinson CM, Seto D, Dyer DW, Jones MS, Rajaiya J, Chodosh J. Recombination of the epsilon determinant and corneal tropism: Human adenovirus species D types 15, 29, 56, and 69. Virology 2015; 485:452-9. [PMID: 26343864 DOI: 10.1016/j.virol.2015.08.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [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: 05/10/2015] [Revised: 07/03/2015] [Accepted: 08/17/2015] [Indexed: 12/13/2022]
Abstract
Viruses within human adenovirus species D (HAdV-D) infect epithelia at essentially every mucosal site. Hypervariable loops 1 and 2 of the hexon capsid protein contain epitopes that together form the epsilon determinant for serum neutralization. We report our analyses comparing HAdV-D15, 29, 56, and the recently identified type 69, each with highly similar hexons and the same serum neutralization profile, but otherwise disparate genomes. Of these, only HAdV-D type 56 is associated with epidemic keratoconjunctivitis (EKC), a severe infection of ocular surface epithelium and underlying corneal stroma. In the mouse adenovirus keratitis model, all four viruses induced inflammation. However, HAdV-D56 entry into human corneal epithelial cells and fibroblasts in vitro dramatically exceeded that of the other three viruses. We conclude that the hexon epsilon determinant is not a prime contributor to corneal tropism.
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Affiliation(s)
- Gurdeep Singh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
| | - Xiaohong Zhou
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
| | - Jeong Yoon Lee
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
| | - Mohammad A Yousuf
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
| | - Mirja Ramke
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
| | - Ashrafali M Ismail
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
| | - Ji Sun Lee
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
| | - Christopher M Robinson
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
| | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, United States
| | - David W Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Morris S Jones
- Division of Infectious Diseases, Naval Medical Center San Diego, San Diego, CA, United States
| | - Jaya Rajaiya
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States.
| | - James Chodosh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States.
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14
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Abstract
BACKGROUND The Bacillus cereus sensu lato group contains ubiquitous facultative anaerobic soil-borne Gram-positive spore-forming bacilli. Molecular phylogeny and comparative genome sequencing have suggested that these organisms should be classified as a single species. While clonal in nature, there do not appear to be species-specific clonal lineages, excepting B. anthracis, in spite of the wide array of phenotypes displayed by these organisms. RESULTS We compared the protein-coding content of 201 B. cereus sensu lato genomes to characterize differences and understand the consequences of these differences on biological function. From this larger group we selected a subset consisting of 25 whole genomes for deeper analysis. Cluster analysis of orthologous proteins grouped these genomes into five distinct clades. Each clade could be characterized by unique genes shared among the group, with consequences for the phenotype of each clade. Surprisingly, this population structure recapitulates our recent observations on the divergence of the generalized stress response (SigB) regulons in these organisms. Divergence of the SigB regulon among these organisms is primarily due to the placement of SigB-dependent promoters that bring genes from a common gene pool into/out of the SigB regulon. CONCLUSIONS Collectively, our observations suggest the hypothesis that the evolution of these closely related bacteria is a consequence of two distinct processes. Horizontal gene transfer, gene duplication/divergence and deletion dictate the underlying coding capacity in these genomes. Regulatory divergence overlays this protein coding reservoir and shapes the expression of both the unique and shared coding capacity of these organisms, resulting in phenotypic divergence. Data from other organisms suggests that this is likely a common pattern in prokaryotic evolution.
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Affiliation(s)
- Inimary T Toby
- University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC-1106, Oklahoma City, OK 73104, USA
| | - Jonah Widmer
- University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC-1106, Oklahoma City, OK 73104, USA
| | - David W Dyer
- University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC-1106, Oklahoma City, OK 73104, USA
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15
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Dehghan S, Seto J, Jones MS, Dyer DW, Chodosh J, Seto D. Simian adenovirus type 35 has a recombinant genome comprising human and simian adenovirus sequences, which predicts its potential emergence as a human respiratory pathogen. Virology 2013; 447:265-73. [PMID: 24210123 DOI: 10.1016/j.virol.2013.09.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [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] [Received: 08/16/2013] [Revised: 09/05/2013] [Accepted: 09/12/2013] [Indexed: 11/19/2022]
Abstract
Emergent human and simian adenoviruses (HAdVs) may arise from genome recombination. Computational analysis of SAdV type 35 reveals a genome comprising a chassis with elements mostly from two simian adenoviruses, SAdV-B21 and -B27, and regions of high sequence similarity shared with HAdV-B21 and HAdV-B16. Although recombination direction cannot be determined, the presence of these regions suggests prior infections of humans by an ancestor of SAdV-B35, and/or vice versa. Absence of this virus in humans may reflect non-optimal conditions for zoonosis or incomplete typing, e.g., limited epitope-based. The presence of both a critical viral replication element found in HAdV genomes and genes that are highly similar to ones in HAdVs suggest the potential to establish in a human host. This allows a prediction that this virus may be a nascent human respiratory pathogen. The recombination potential of human and simian adenovirus genomes should be considered in the use of SAdVs as vectors for gene delivery in humans.
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Affiliation(s)
- Shoaleh Dehghan
- Chemistry Department, American University, Washington, D.C. 20016, USA; Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA 20110, USA
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16
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Seto D, Jones MS, Dyer DW, Chodosh J. Characterizing, typing, and naming human adenovirus type 55 in the era of whole genome data. J Clin Virol 2013; 58:741-2. [PMID: 24161575 DOI: 10.1016/j.jcv.2013.09.025] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/13/2013] [Accepted: 09/24/2013] [Indexed: 10/26/2022]
Affiliation(s)
- Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA 20110, USA.
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17
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Dehghan S, Seto J, Liu EB, Walsh MP, Dyer DW, Chodosh J, Seto D. Computational analysis of four human adenovirus type 4 genomes reveals molecular evolution through two interspecies recombination events. Virology 2013; 443:197-207. [PMID: 23763770 DOI: 10.1016/j.virol.2013.05.014] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [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: 04/12/2013] [Revised: 05/03/2013] [Accepted: 05/09/2013] [Indexed: 11/17/2022]
Abstract
Computational analysis of human adenovirus type 4 (HAdV-E4), a pathogen that is the only HAdV member of species E, provides insights into its zoonotic origin and molecular adaptation. Its genome encodes a domain of the major capsid protein, hexon, from HAdV-B16 recombined into the genome chassis of a simian adenovirus. Genomes of two recent field strains provide a clue to its adaptation to the new host: recombination of a NF-I binding site motif, which is required for efficient viral replication, from another HAdV genome. This motif is absent in the chimpanzee adenoviruses and the HAdV-E4 prototype, but is conserved amongst other HAdVs. This is the first report of an interspecies recombination event for HAdVs, and the first documentation of a lateral partial gene transfer from a chimpanzee AdV. The potential for such recombination events are important when considering chimpanzee adenoviruses as candidate gene delivery vectors for human patients.
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Affiliation(s)
- Shoaleh Dehghan
- Chemistry Department, American University, Washington, D.C. 20016, USA; Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA 20110, USA
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18
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Robinson CM, Zhou X, Rajaiya J, Yousuf MA, Singh G, DeSerres JJ, Walsh MP, Wong S, Seto D, Dyer DW, Chodosh J, Jones MS. Predicting the next eye pathogen: analysis of a novel adenovirus. mBio 2013; 4:e00595-12. [PMID: 23572555 PMCID: PMC3622935 DOI: 10.1128/mbio.00595-12] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [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: 12/12/2012] [Accepted: 03/12/2013] [Indexed: 01/07/2023] Open
Abstract
UNLABELLED For DNA viruses, genetic recombination, addition, and deletion represent important evolutionary mechanisms. Since these genetic alterations can lead to new, possibly severe pathogens, we applied a systems biology approach to study the pathogenicity of a novel human adenovirus with a naturally occurring deletion of the canonical penton base Arg-Gly-Asp (RGD) loop, thought to be critical to cellular entry by adenoviruses. Bioinformatic analysis revealed a new highly recombinant species D human adenovirus (HAdV-D60). A synthesis of in silico and laboratory approaches revealed a potential ocular tropism for the new virus. In vivo, inflammation induced by the virus was dramatically greater than that by adenovirus type 37, a major eye pathogen, possibly due to a novel alternate ligand, Tyr-Gly-Asp (YGD), on the penton base protein. The combination of bioinformatics and laboratory simulation may have important applications in the prediction of tissue tropism for newly discovered and emerging viruses. IMPORTANCE The ongoing dance between a virus and its host distinctly shapes how the virus evolves. While human adenoviruses typically cause mild infections, recent reports have described newly characterized adenoviruses that cause severe, sometimes fatal human infections. Here, we report a systems biology approach to show how evolution has affected the disease potential of a recently identified novel human adenovirus. A comprehensive understanding of viral evolution and pathogenicity is essential to our capacity to foretell the potential impact on human disease for new and emerging viruses.
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MESH Headings
- Adenoviridae Infections/virology
- Adenoviruses, Human/genetics
- Adenoviruses, Human/isolation & purification
- Adenoviruses, Human/pathogenicity
- Amino Acid Sequence
- Animals
- Cell Line
- DNA, Viral/chemistry
- DNA, Viral/genetics
- Disease Models, Animal
- Eye Diseases/virology
- Female
- Humans
- Infant, Newborn
- Male
- Mice
- Mice, Inbred C57BL
- Models, Molecular
- Molecular Sequence Data
- Protein Conformation
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Deletion
- Systems Biology
- Viral Proteins/chemistry
- Viral Proteins/genetics
- Viral Tropism
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Affiliation(s)
- Christopher M. Robinson
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Xiaohong Zhou
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Jaya Rajaiya
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Mohammad A. Yousuf
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Gurdeep Singh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Michael P. Walsh
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - Sallene Wong
- Provincial Laboratory for Public Health, Calgary, Alberta, Canada
| | - Donald Seto
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - James Chodosh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Morris S. Jones
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
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19
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Robinson CM, Singh G, Lee JY, Dehghan S, Rajaiya J, Liu EB, Yousuf MA, Betensky RA, Jones MS, Dyer DW, Seto D, Chodosh J. Molecular evolution of human adenoviruses. Sci Rep 2013; 3:1812. [PMID: 23657240 PMCID: PMC3648800 DOI: 10.1038/srep01812] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [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: 03/18/2013] [Accepted: 04/22/2013] [Indexed: 11/15/2022] Open
Abstract
The recent emergence of highly virulent human adenoviruses (HAdVs) with new tissue tropisms underscores the need to determine their ontogeny. Here we report complete high quality genome sequences and analyses for all the previously unsequenced HAdV serotypes (n = 20) within HAdV species D. Analysis of nucleotide sequence variability for these in conjunction with another 40 HAdV prototypes, comprising all seven HAdV species, confirmed the uniquely hypervariable regions within species. The mutation rate among HAdV-Ds was low when compared to other HAdV species. Homologous recombination was identified in at least two of five examined hypervariable regions for every virus, suggesting the evolution of HAdV-Ds has been highly dependent on homologous recombination. Patterns of alternating GC and AT rich motifs correlated well with hypervariable region recombination sites across the HAdV-D genomes, suggesting foci of DNA instability lead to formulaic patterns of homologous recombination and confer agility to adenovirus evolution.
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Affiliation(s)
- Christopher M. Robinson
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, 02114, USA
| | - Gurdeep Singh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, 02114, USA
| | - Jeong Yoon Lee
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, 02114, USA
| | - Shoaleh Dehghan
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, 20110, USA
- Chemistry Department, American University, Washington, DC 20016 USA
| | - Jaya Rajaiya
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, 02114, USA
| | - Elizabeth B. Liu
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, 20110, USA
| | - Mohammad A. Yousuf
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, 02114, USA
| | - Rebecca A. Betensky
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115 USA
| | - Morris S. Jones
- Division of Infectious Diseases, Naval Medical Center San Diego, San Diego, CA, 92136, USA
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, 20110, USA
| | - James Chodosh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, 02114, USA
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20
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Scott E, Dyer DW. Divergence of the SigB regulon and pathogenesis of the Bacillus cereus sensu lato group. BMC Genomics 2012; 13:564. [PMID: 23088190 PMCID: PMC3485630 DOI: 10.1186/1471-2164-13-564] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [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: 06/25/2012] [Accepted: 10/10/2012] [Indexed: 12/31/2022] Open
Abstract
Background The Bacillus cereus sensu lato group currently includes seven species (B. cereus, B. anthracis, B. mycoides, B. pseudomycoides, B. thuringiensis, B. weihenstephanensis and B. cytotoxicus) that recent phylogenetic and phylogenomic analyses suggest are likely a single species, despite their varied phenotypes. Although horizontal gene transfer and insertion-deletion events are clearly important for promoting divergence among these genomes, recent studies have demonstrated that a major basis for phenotypic diversity in these organisms may be differential regulation of the highly similar gene content shared by these organisms. To explore this hypothesis, we used an in silico approach to evaluate the relationship of pathogenic potential and the divergence of the SigB-dependent general stress response within the B. cereus sensu lato group, since SigB has been demonstrated to support pathogenesis in Bacillus, Listeria and Staphylococcus species. Results During the divergence of these organisms from a common “SigB-less” ancestor, the placement of SigB promoters at varied locations in the B. cereus sensu lato genomes predict alternative structures for the SigB regulon in different organisms. Predicted promoter changes suggesting differential transcriptional control of a common gene pool predominate over evidence of indels or horizontal gene transfer for explaining SigB regulon divergence. Conclusions Four lineages of the SigB regulon have arisen that encompass different gene contents and suggest different strategies for supporting pathogenesis. This is consistent with the hypothesis that divergence within the B. cereus sensu lato group rests in part on alternative strategies for regulation of a common gene pool.
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Affiliation(s)
- Edgar Scott
- Department of Microbiology and Immunology, Oklahoma University Health Sciences Center, Oklahoma City, 73117, USA
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21
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Zhou X, Robinson CM, Rajaiya J, Dehghan S, Seto D, Jones MS, Dyer DW, Chodosh J. Analysis of human adenovirus type 19 associated with epidemic keratoconjunctivitis and its reclassification as adenovirus type 64. Invest Ophthalmol Vis Sci 2012; 53:2804-11. [PMID: 22467570 PMCID: PMC3367469 DOI: 10.1167/iovs.12-9656] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [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: 02/07/2012] [Revised: 03/08/2012] [Accepted: 03/19/2012] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Human adenovirus species D type 19 (HAdV-D19) has been associated with epidemic keratoconjunctivitis (EKC), a highly inflammatory infection of the ocular surface. Confusion exists regarding the origins of HAdV-D19. The prototype virus (HAdV-D19p) does not cause EKC, while a virus identified later with the identical serologic determinant is a significant ocular pathogen. METHODS High throughput genome sequencing and bioinformatics analysis were performed on HAdV-D19p and three HAdV-D19 EKC strains, and compared to the previously sequenced clinical isolate, HAdV-D19 (C) and HAdV-D37. Corneas of C57BL/6J mice were injected with HAdV-D19p, HAdV-D19 (C), or virus-free buffer, and inflammation assessed by clinical examination, flow cytometry, and cytokine ELISA. Confocal microscopy and real-time PCR of infected corneal cell cultures were used to test viral entry. RESULTS HAdV-D19 (C) and the other clinical EKC isolates showed nearly 100% sequence identity. EKC strains diverged from HAdV-D19p in the penton base, E3, and fiber transcription units. Simplot analysis showed recombination between EKC-associated HAdV-D19 with HAdV-D37, HAdV-D22, and HAdV-D19p, the latter contributing only the hexon gene, the principal serum neutralization determinant. HAdV-D19p induced stromal keratitis in the C57BL/6J mouse, but failed to infect productively human corneal epithelial cells. These data led to retyping of the clinical EKC isolates with a HAdV-D19 hexon gene as HAdV-D64. CONCLUSIONS HAdV-D19 associated with EKC (HAdV-D64) originated from a recombination between HAdV-D19p, HAdV-D37, and HAdV-D22, and was mischaracterized because of a shared hexon gene. HAdV-D19p is not infectious for corneal epithelial cells, thus explaining the lack of any association with keratitis.
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Affiliation(s)
- Xiaohong Zhou
- From the
Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts
| | - Christopher M. Robinson
- From the
Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts
| | - Jaya Rajaiya
- From the
Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts
| | - Shoaleh Dehghan
- School of Systems Biology, George Mason University, Manassas, Virginia
| | - Donald Seto
- School of Systems Biology, George Mason University, Manassas, Virginia
| | - Morris S. Jones
- School of Systems Biology, George Mason University, Manassas, Virginia
| | - David W. Dyer
- and the
Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - James Chodosh
- From the
Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts
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22
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Singh G, Robinson CM, Dehghan S, Schmidt T, Seto D, Jones MS, Dyer DW, Chodosh J. Overreliance on the hexon gene, leading to misclassification of human adenoviruses. J Virol 2012; 86:4693-5. [PMID: 22301156 PMCID: PMC3318657 DOI: 10.1128/jvi.06969-11] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [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] [Received: 11/30/2011] [Accepted: 01/25/2012] [Indexed: 02/02/2023] Open
Abstract
The genome of human adenovirus (HAdV) D30 was sequenced in depth. Sequence assembly and analysis revealed two distinct viral sequences with identical hexon genes, which were the same as the one previously reported for HAdV-D30. However, one of the two viruses was found to be a recombinant of HAdV-D29. Exclusive reliance on serum neutralization can lead to mischaracterization of adenoviruses and miss coinfections. Whole-genome sequencing remains the gold standard for proper classification of HAdVs.
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Affiliation(s)
- Gurdeep Singh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Christopher M. Robinson
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Shoaleh Dehghan
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - Timothy Schmidt
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Donald Seto
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - Morris S. Jones
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - James Chodosh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
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23
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Liu EB, Wadford DA, Seto J, Vu M, Hudson NR, Thrasher L, Torres S, Dyer DW, Chodosh J, Seto D, Jones MS. Computational and serologic analysis of novel and known viruses in species human adenovirus D in which serology and genomics do not correlate. PLoS One 2012; 7:e33212. [PMID: 22427992 PMCID: PMC3302849 DOI: 10.1371/journal.pone.0033212] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [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: 07/23/2011] [Accepted: 02/12/2012] [Indexed: 11/19/2022] Open
Abstract
In November of 2007 a human adenovirus (HAdV) was isolated from a bronchoalveolar lavage (BAL) sample recovered from a biopsy of an AIDS patient who presented with fever, cough, tachycardia, and expiratory wheezes. To better understand the isolated virus, the genome was sequenced and analyzed using bioinformatic and phylogenomic analysis. The results suggest that this novel virus, which is provisionally named HAdV-D59, may have been created from multiple recombination events. Specifically, the penton, hexon, and fiber genes have high nucleotide identity to HAdV-D19C, HAdV-D25, and HAdV-D56, respectively. Serological results demonstrated that HAdV-D59 has a neutralization profile that is similar yet not identical to that of HAdV-D25. Furthermore, we observed a two-fold difference between the ability of HAdV-D15 and HAdV-D25 to be neutralized by reciprocal antiserum indicating that the two hexon proteins may be more similar in epitopic conformation than previously assumed. In contrast, hexon loops 1 and 2 of HAdV-D15 and HAdV-D25 share 79.13 and 92.56 percent nucleotide identity, respectively. These data suggest that serology and genomics do not always correlate.
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Affiliation(s)
- Elizabeth B. Liu
- School of Systems Biology, George Mason University, Manassas, Virginia, United States of America
| | - Debra A. Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California, United States of America
| | - Jason Seto
- School of Systems Biology, George Mason University, Manassas, Virginia, United States of America
| | - Maria Vu
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California, United States of America
| | - Nolan Ryan Hudson
- Clinical Investigation Facility, David Grant USAF Medical Center, Travis AFB, Fairfield, California, United States of America
| | - Lisa Thrasher
- Clinical Investigation Facility, David Grant USAF Medical Center, Travis AFB, Fairfield, California, United States of America
| | - Sarah Torres
- Clinical Investigation Facility, David Grant USAF Medical Center, Travis AFB, Fairfield, California, United States of America
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - James Chodosh
- Howe Laboratory, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Donald Seto
- School of Systems Biology, George Mason University, Manassas, Virginia, United States of America
| | - Morris S. Jones
- School of Systems Biology, George Mason University, Manassas, Virginia, United States of America
- * E-mail:
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24
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Abstract
Gene expression profiling using DNA microarrays has become commonplace in current molecular biology practices, and has dramatically enhanced our understanding of the biology of Neisseria spp., and the interaction of these organisms with the host. With the choice of microarray platforms offered for gene expression profiling and commercially available arrays, investigators must ask several central questions to make decisions based on their research focus. Are arrays on hand for their organism and if not then would it be cost-effective to design custom arrays. Other important considerations; what types of specialized equipment for array hybridization and signal detection are required and is the specificity and sensitivity of the array adequate for your application. Here, we describe the use of a custom 12K CombiMatrix ElectraSense™ oligonucleotide microarray format for assessing global gene expression profiles in Neisseria spp.
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Affiliation(s)
- Lydgia A Jackson
- Department of Microbiology and Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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25
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Dehghan S, Liu EB, Seto J, Torres SF, Hudson NR, Kajon AE, Metzgar D, Dyer DW, Chodosh J, Jones MS, Seto D. Five genome sequences of subspecies B1 human adenoviruses associated with acute respiratory disease. J Virol 2012; 86:635-6. [PMID: 22158846 PMCID: PMC3255920 DOI: 10.1128/jvi.06593-11] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [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: 10/17/2011] [Accepted: 10/21/2011] [Indexed: 11/20/2022] Open
Abstract
Five genomes of human subspecies B1 adenoviruses isolated from cases of acute respiratory disease have been sequenced and archived for reference. These include representatives of two prevalent genomic variants of HAdV-7, i.e., HAdV-7h and HAdV-7d2. The other three are HAdV-3/16, HAdV-16 strain E26, and HAdV-3+7 strain Takeuchi. All are recombinant genomes. Genomics and bioinformatics provide detailed views into the genetic makeup of these pathogens and insight into their molecular evolution. Retrospective characterization of particularly problematic older pathogens such as HAdV-7h (1987) and intriguing isolates such as HAdV-3+7 strain Takeuchi (1958) may provide clues to their phenotypes and serology and may suggest protocols for prevention and treatment.
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Affiliation(s)
- Shoaleh Dehghan
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, USA
| | - Elizabeth B. Liu
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, USA
| | - Jason Seto
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, USA
| | - Sarah F. Torres
- Clinical Investigation Facility, David Grant USAF Medical Center, Travis Air Force Base, California 94535, USA
| | - Nolan R. Hudson
- Clinical Investigation Facility, David Grant USAF Medical Center, Travis Air Force Base, California 94535, USA
| | - Adriana E. Kajon
- Lovelace Respiratory Research Institute, Albuquerque, New Mexico 87108, USA
| | - David Metzgar
- Department of Respiratory Diseases Research, Naval Health Research Center, San Diego, California 92106, USA
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA
| | - James Chodosh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Morris S. Jones
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California 94804, USA
| | - Donald Seto
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, USA
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26
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Siddaramappa S, Challacombe JF, Duncan AJ, Gillaspy AF, Carson M, Gipson J, Orvis J, Zaitshik J, Barnes G, Bruce D, Chertkov O, Detter JC, Han CS, Tapia R, Thompson LS, Dyer DW, Inzana TJ. Horizontal gene transfer in Histophilus somni and its role in the evolution of pathogenic strain 2336, as determined by comparative genomic analyses. BMC Genomics 2011; 12:570. [PMID: 22111657 PMCID: PMC3339403 DOI: 10.1186/1471-2164-12-570] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [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: 06/15/2011] [Accepted: 11/23/2011] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Pneumonia and myocarditis are the most commonly reported diseases due to Histophilus somni, an opportunistic pathogen of the reproductive and respiratory tracts of cattle. Thus far only a few genes involved in metabolic and virulence functions have been identified and characterized in H. somni using traditional methods. Analyses of the genome sequences of several Pasteurellaceae species have provided insights into their biology and evolution. In view of the economic and ecological importance of H. somni, the genome sequence of pneumonia strain 2336 has been determined and compared to that of commensal strain 129Pt and other members of the Pasteurellaceae. RESULTS The chromosome of strain 2336 (2,263,857 bp) contained 1,980 protein coding genes, whereas the chromosome of strain 129Pt (2,007,700 bp) contained only 1,792 protein coding genes. Although the chromosomes of the two strains differ in size, their average GC content, gene density (total number of genes predicted on the chromosome), and percentage of sequence (number of genes) that encodes proteins were similar. The chromosomes of these strains also contained a number of discrete prophage regions and genomic islands. One of the genomic islands in strain 2336 contained genes putatively involved in copper, zinc, and tetracycline resistance. Using the genome sequence data and comparative analyses with other members of the Pasteurellaceae, several H. somni genes that may encode proteins involved in virulence (e.g., filamentous haemaggutinins, adhesins, and polysaccharide biosynthesis/modification enzymes) were identified. The two strains contained a total of 17 ORFs that encode putative glycosyltransferases and some of these ORFs had characteristic simple sequence repeats within them. Most of the genes/loci common to both the strains were located in different regions of the two chromosomes and occurred in opposite orientations, indicating genome rearrangement since their divergence from a common ancestor. CONCLUSIONS Since the genome of strain 129Pt was ~256,000 bp smaller than that of strain 2336, these genomes provide yet another paradigm for studying evolutionary gene loss and/or gain in regard to virulence repertoire and pathogenic ability. Analyses of the complete genome sequences revealed that bacteriophage- and transposon-mediated horizontal gene transfer had occurred at several loci in the chromosomes of strains 2336 and 129Pt. It appears that these mobile genetic elements have played a major role in creating genomic diversity and phenotypic variability among the two H. somni strains.
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Affiliation(s)
- Shivakumara Siddaramappa
- Center for Molecular Medicine and Infectious Diseases, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Jean F Challacombe
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Alison J Duncan
- Center for Molecular Medicine and Infectious Diseases, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Allison F Gillaspy
- Laboratory for Genomics and Bioinformatics, and Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 731042, USA
| | - Matthew Carson
- Laboratory for Genomics and Bioinformatics, and Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 731042, USA
| | - Jenny Gipson
- Laboratory for Genomics and Bioinformatics, and Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 731042, USA
| | - Joshua Orvis
- Laboratory for Genomics and Bioinformatics, and Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 731042, USA
| | - Jeremy Zaitshik
- Laboratory for Genomics and Bioinformatics, and Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 731042, USA
| | - Gentry Barnes
- Laboratory for Genomics and Bioinformatics, and Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 731042, USA
| | - David Bruce
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Olga Chertkov
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - J Chris Detter
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Cliff S Han
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Linda S Thompson
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - David W Dyer
- Laboratory for Genomics and Bioinformatics, and Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 731042, USA
| | - Thomas J Inzana
- Center for Molecular Medicine and Infectious Diseases, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
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27
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Abstract
Haemophilus parasuis is a member of the family Pasteurellaceae and is the etiologic agent of Glässer's disease in pigs, a systemic syndrome associated with only a subset of isolates. The genetic basis for virulence and systemic spread of particular H. parasuis isolates is currently unknown. Strain 29755 is an invasive isolate that has long been used in the study of Glässer's disease. Accordingly, the genome sequence of strain 29755 is of considerable importance to investigators endeavoring to understand the molecular pathogenesis of H. parasuis. Here we describe the features of the 2,224,137 bp draft genome sequence of strain 29755 generated from 454-FLX pyrosequencing. These data comprise the first publicly available genome sequence for this bacterium.
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Affiliation(s)
- Michael A. Mullins
- Virus and Prion Research Unit, USDA/Agricultural Research Service/National Animal Disease Center, Ames, IA, USA
| | - Karen B. Register
- Virus and Prion Research Unit, USDA/Agricultural Research Service/National Animal Disease Center, Ames, IA, USA
| | - Darrell O. Bayles
- Bacterial Diseases of Livestock Research Unit, USDA/Agricultural Research Service/National Animal Disease Center, Ames, IA, USA
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center Biomedical Research Center, Oklahoma City, OK, USA
| | - Joanna S. Kuehn
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University College of Veterinary Medicine, Ames, IA, USA
| | - Gregory J. Phillips
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University College of Veterinary Medicine, Ames, IA, USA
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28
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Liu EB, Ferreyra L, Fischer SL, Pavan JV, Nates SV, Hudson NR, Tirado D, Dyer DW, Chodosh J, Seto D, Jones MS. Genetic analysis of a novel human adenovirus with a serologically unique hexon and a recombinant fiber gene. PLoS One 2011; 6:e24491. [PMID: 21915339 PMCID: PMC3168504 DOI: 10.1371/journal.pone.0024491] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [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: 06/22/2011] [Accepted: 08/11/2011] [Indexed: 01/08/2023] Open
Abstract
In February of 1996 a human adenovirus (formerly known as Ad-Cor-96-487) was isolated from the stool of an AIDS patient who presented with severe chronic diarrhea. To characterize this apparently novel pathogen of potential public health significance, the complete genome of this adenovirus was sequenced to elucidate its origin. Bioinformatic and phylogenetic analyses of this genome demonstrate that this virus, heretofore referred to as HAdV-D58, contains a novel hexon gene as well as a recombinant fiber gene. In addition, serological analysis demonstrated that HAdV-D58 has a different neutralization profile than all previously characterized HAdVs. Bootscan analysis of the HAdV-D58 fiber gene strongly suggests one recombination event.
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Affiliation(s)
- Elizabeth B. Liu
- Department of Bioinformatics and Computational Biology and Department of Systems Biology, George Mason University, Manassas, Virginia, United States of America
| | - Leonardo Ferreyra
- Virology Institute, School of Medical Sciences, National University of Cordoba, Cordoba, Argentina
| | - Stephen L. Fischer
- Naval Hospital Camp Pendleton, Camp Pendleton, California, United States of America
| | - Jorge V. Pavan
- Virology Institute, School of Medical Sciences, National University of Cordoba, Cordoba, Argentina
| | - Silvia V. Nates
- Virology Institute, School of Medical Sciences, National University of Cordoba, Cordoba, Argentina
| | - Nolan Ryan Hudson
- Clinical Investigation Facility, David Grant USAF Medical Center, Travis AFB, Fairfield, California, United States of America
| | - Damaris Tirado
- Clinical Investigation Facility, David Grant USAF Medical Center, Travis AFB, Fairfield, California, United States of America
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - James Chodosh
- Howe Laboratory, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Donald Seto
- Department of Bioinformatics and Computational Biology and Department of Systems Biology, George Mason University, Manassas, Virginia, United States of America
| | - Morris S. Jones
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California, United States of America
- * E-mail:
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29
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Kolb AW, Schmidt TR, Dyer DW, Brandt CR. Sequence variation in the herpes simplex virus U(S)1 ocular virulence determinant. Invest Ophthalmol Vis Sci 2011; 52:4630-8. [PMID: 21519032 DOI: 10.1167/iovs.10-7032] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
PURPOSE The herpes simplex virus type 1 (HSV-1) U(S)1 gene encodes host-range and ocular virulence determinants. Mutations in U(S)1 affecting virulence are known in strain OD4, but the genomic variation across several strains is not known. The goal was to determine the degree of sequence variation in the gene from several ocular HSV isolates. METHODS The U(S)1 gene from six ocular HSV-1 isolates, as well as strains KOS and F, were sequenced, and bioinformatics analyses were applied to the data. RESULTS Strains 17, F, CJ394, and CJ311 had identical amino acid sequences. With the other strains, most of the variability was concentrated in the amino-terminal third of the protein. MEME analysis identified a 63-residue core sequence (motif 1) present in all α-herpesvirus U(S)1 homologs that were located in a region identified as structured. Ten amino acids were absolutely conserved in all the α-herpesvirus U(S)1 homologs and were all located in the central core. Consensus-binding motifs for cyclin-dependent kinases and pocket proteins were also identified. CONCLUSIONS These results suggest that significant sequence variation exists in the U(S)1 gene, that the α22 protein contains a conserved central core region with structurally variable regions at the amino- and carboxyl termini, that 10 amino acids are conserved in α-herpes U(S)1 homologs, and that additional host proteins may interact with the HSV-1 U(S)1 and U(S)1.5 proteins. This information will be valuable in designing further studies on structure-function relationships and on the role these play in host-range determination and keratitis.
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Affiliation(s)
- Aaron W Kolb
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
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30
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Robinson CM, Rajaiya J, Zhou X, Singh G, Dyer DW, Chodosh J. The E3 CR1-gamma gene in human adenoviruses associated with epidemic keratoconjunctivitis. Virus Res 2011; 160:120-7. [PMID: 21683743 DOI: 10.1016/j.virusres.2011.05.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 05/31/2011] [Accepted: 05/31/2011] [Indexed: 01/06/2023]
Abstract
Human adenovirus species D type 37 (HAdV-D37) is an important etiologic agent of epidemic keratoconjunctivitis. Annotation of the whole genome revealed an open reading frame (ORF) in the E3 transcription unit predicted to encode a 31.6kDa protein. This ORF, also known as CR1-γ, is predicted to be an integral membrane protein containing N-terminal signal sequence, luminal, transmembrane, and cytoplasmic domains. HAdV-D19 (C), another viral pathogen causing epidemic keratoconjunctivitis, contains an ORF 100% identical to its HAdV-D37 homologue but only 66% identical to other HAdV-D homologues. Kinetics of RNA expression and confirmation of splicing to the adenovirus tripartite leader sequence suggest a role for the protein product of CR1-γ in the late stages of the viral replication cycle. Confocal microscopy is consistent with expression in the cytoplasm. Sequence analysis reveals a hypervariable luminal domain and a conserved cytoplasmic domain. The luminal domain is predicted to contain multiple N-glycosylation sites. The cytoplasmic domain contains a putative protein kinase C phosphorylation site and potential YXXϕ and dileucine (LL) motifs suggesting a potential role in modification of host proteins.
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Affiliation(s)
- Christopher M Robinson
- Howe Laboratory, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, 243 Charles Street, Boston, MA 02114, USA
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31
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Robinson CM, Seto D, Jones MS, Dyer DW, Chodosh J. Molecular evolution of human species D adenoviruses. Infect Genet Evol 2011; 11:1208-17. [PMID: 21570490 DOI: 10.1016/j.meegid.2011.04.031] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 04/26/2011] [Accepted: 04/27/2011] [Indexed: 12/15/2022]
Abstract
Adenoviruses are medium-sized double stranded DNA viruses that infect vertebrates. Human adenoviruses cause an array of diseases. Currently there are 56 human adenovirus types recognized and characterized within seven species (A-G). Of those types, a majority belongs to species D. In this review, the genomic conservation and diversity are examined among human adenoviruses within species D, particularly in contrast to other human adenovirus species. Specifically, homologous recombination is presented as a driving force for the molecular evolution of human adenoviruses and the emergence of new adenovirus pathogens.
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Affiliation(s)
- Christopher M Robinson
- Howe Laboratory, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, 243 Charles Street, Boston, MA 02114, USA. USA
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32
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Robinson CM, Singh G, Henquell C, Walsh MP, Peigue-Lafeuille H, Seto D, Jones MS, Dyer DW, Chodosh J. Computational analysis and identification of an emergent human adenovirus pathogen implicated in a respiratory fatality. Virology 2011; 409:141-7. [PMID: 21056888 PMCID: PMC3006489 DOI: 10.1016/j.virol.2010.10.020] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [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: 08/24/2010] [Revised: 09/29/2010] [Accepted: 10/13/2010] [Indexed: 11/30/2022]
Abstract
Adenoviral infections are typically acute, self-limiting, and not associated with death. However, we present the genomic and bioinformatics analysis of a novel recombinant human adenovirus (HAdV-D56) isolated in France that caused a rare neonatal fatality, and keratoconjunctivitis in three health care workers who cared for the neonate. Whole genome alignments revealed the expected diversity in the penton base, hexon, E3, and fiber coding regions, and provided evidence for extensive recombination. Bootscan analysis confirmed recombination between HAdV-D9, HAdV-D26, HAdV-D15, and HAdV-D29 in the penton base and hexon proteins, centered around hypervariable loops within the putative proteins. Protein structure analysis of the fiber coding region revealed similarity with HAdV-D8, HAdV-D9, and HAdV-D53, possibly accounting for the ocular tropism of the virus. Based on these data, this virus appears to be a new HAdV-D type (HAdV-D56), underscoring the importance of recombination events in human adenovirus evolution and the emergence of new adenovirus pathogens.
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MESH Headings
- Adenoviruses, Human/genetics
- Adenoviruses, Human/isolation & purification
- Adenoviruses, Human/pathogenicity
- Amino Acid Sequence
- Cluster Analysis
- Computational Biology
- DNA, Viral/chemistry
- DNA, Viral/genetics
- Evolution, Molecular
- Fatal Outcome
- France
- Genome, Viral
- Humans
- Infant, Newborn
- Keratoconjunctivitis/virology
- Molecular Sequence Data
- Phylogeny
- Recombination, Genetic
- Respiratory Tract Infections/mortality
- Respiratory Tract Infections/transmission
- Respiratory Tract Infections/virology
- Sequence Alignment
- Sequence Analysis, DNA
- Viral Proteins/genetics
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Affiliation(s)
- Christopher M. Robinson
- Howe Laboratory, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, 243 Charles Street, Boston, Massachusetts, 02114, USA
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 975 N.E. 10, Oklahoma City, Oklahoma, 73104, USA
| | - Gurdeep Singh
- Howe Laboratory, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, 243 Charles Street, Boston, Massachusetts, 02114, USA
| | - Cécile Henquell
- CHU Clermont-Ferrand, Laboratoire de Virologie, Hôpital Gabriel Montpied, France, Université d'Auvergne, EA-3843, France
| | - Michael P. Walsh
- Department of Bioinformatics and Computational Biology, George Mason University, 10900 University Blvd., MSN 5B3, Manassas, VA, 20110, USA
| | - Hélène Peigue-Lafeuille
- CHU Clermont-Ferrand, Laboratoire de Virologie, Hôpital Gabriel Montpied, France, Université d'Auvergne, EA-3843, France
| | - Donald Seto
- Department of Bioinformatics and Computational Biology, George Mason University, 10900 University Blvd., MSN 5B3, Manassas, VA, 20110, USA
| | - Morris S. Jones
- Clinical Investigation Facility, David Grant USAF Medical Center, 101 Bodin Circle Travis AFB, California, 94535, USA
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 975 N.E. 10, Oklahoma City, Oklahoma, 73104, USA
| | - James Chodosh
- Howe Laboratory, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, 243 Charles Street, Boston, Massachusetts, 02114, USA
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Ducey TF, Jackson L, Orvis J, Dyer DW. Transcript analysis of nrrF, a Fur repressed sRNA of Neisseria gonorrhoeae. Microb Pathog 2009; 46:166-70. [PMID: 19162160 PMCID: PMC4890603 DOI: 10.1016/j.micpath.2008.12.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [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: 09/18/2008] [Revised: 12/12/2008] [Accepted: 12/30/2008] [Indexed: 10/21/2022]
Abstract
Like most microorganisms, Neisseria gonorrhoeae alters gene expression in response to iron availability. The ferric uptake regulator Fur has been shown to be involved in controlling this response, but the extent of this involvement remains unknown. It is known that in addition to working directly to repress gene expression, Fur may also work indirectly by controlling additional regulatory elements. Using in silico analysis, we identified a putative small RNA (sRNA) homolog of the meningococcal nrrF locus, and demonstrate that this sRNA is iron-repressible, suggesting that this is the gonococcal analog of the rhyB locus in Escherichia coli. Quantitative real-time RT-PCR analysis indicates that this transcript may also be temporally regulated. Transcript analysis identified the 5' start of the transcript, using a single reaction, fluorescent-based, primer extension assay. This protocol allows for the rapid identification of transcriptional start sites of RNA transcripts, and could be used for high-throughput transcript mapping.
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Affiliation(s)
- Thomas F Ducey
- Laboratory for Genomics and Bioinformatics, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
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Robinson CM, Shariati F, Zaitshik J, Gillaspy AF, Dyer DW, Chodosh J. Human adenovirus type 19: genomic and bioinformatics analysis of a keratoconjunctivitis isolate. Virus Res 2008; 139:122-6. [PMID: 19000724 DOI: 10.1016/j.virusres.2008.10.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Revised: 10/04/2008] [Accepted: 10/04/2008] [Indexed: 11/28/2022]
Abstract
Human adenovirus type 19 (HAdV-19) is a major etiologic agent of epidemic keratoconjunctivitis (EKC), a common and severe eye infection associated with long-term visual morbidity due to persistent corneal inflammation. Ironically, while the prototype strain of HAdV-19 does not cause eye infections, other isolates of the serotype have caused major outbreaks of EKC. Here we have sequenced a clinical isolate of HAdV-19 (HAdV-19 strain C) from a human patient with EKC. Global pairwise alignment of HAdV-19C to other HAdV species D serotypes identified areas of sequence divergence in the penton base (host cell internalization signal), hexon (principal viral capsid structural protein), E3 (site of immunomodulatory genes), and fiber (host cell-binding ligand) regions. Comparison of HAdV-19 strain C to the recently sequenced HAdV-37, another EKC causing serotype, identified sequence diversity in the penton base and hexon, but sequence conservation in the E3 and fiber regions. Elucidation of the HAdV-19C genome will facilitate future studies into the pathogenesis of EKC, and may shed light on the genetic determinants of corneal tropism.
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Affiliation(s)
- Christopher M Robinson
- The Molecular Pathogenesis of Eye Infection Research Center, Dean A. McGee Eye Institute, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
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Robinson CM, Shariati F, Gillaspy AF, Dyer DW, Chodosh J. Genomic and bioinformatics analysis of human adenovirus type 37: new insights into corneal tropism. BMC Genomics 2008; 9:213. [PMID: 18471294 PMCID: PMC2397415 DOI: 10.1186/1471-2164-9-213] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [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: 12/07/2007] [Accepted: 05/09/2008] [Indexed: 01/22/2023] Open
Abstract
Background Human adenovirus type 37 (HAdV-37) is a major etiologic agent of epidemic keratoconjunctivitis, a common and severe eye infection associated with long-term visual morbidity due to persistent corneal inflammation. While HAdV-37 has been known for over 20 years as an important cause, the complete genome sequence of this serotype has yet to be reported. A detailed bioinformatics analysis of the genome sequence of HAdV-37 is extremely important to understanding its unique pathogenicity in the eye. Results We sequenced and annotated the complete genome of HAdV-37, and performed genomic and bioinformatics comparisons with other HAdVs to identify differences that might underlie the unique corneal tropism of HAdV-37. Global pairwise genome alignment with HAdV-9, a human species D adenovirus not associated with corneal infection, revealed areas of non-conserved sequence principally in genes for the virus fiber (site of host cell binding), penton (host cell internalization signal), hexon (principal viral capsid structural protein), and E3 (site of several genes that mediate evasion of the host immune system). Phylogenetic analysis revealed close similarities between predicted proteins from HAdV-37 of species D and HAdVs from species B and E. However, virtual 2D gel analyses of predicted viral proteins uncovered unexpected differences in pI and/or size of specific proteins thought to be highly similar by phylogenetics. Conclusion This genomic and bioinformatics analysis of the HAdV-37 genome provides a valuable tool for understanding the corneal tropism of this clinically important virus. Although disparities between HAdV-37 and other HAdV within species D in genes encoding structural and host receptor-binding proteins were to some extent expected, differences in the E3 region suggest as yet unknown roles for this area of the genome. The whole genome comparisons and virtual 2D gel analyses reported herein suggest potent areas for future studies.
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Affiliation(s)
- Christopher M Robinson
- Molecular Pathogenesis of Eye Infection Research Center, Dean A. McGee Eye Institute, 608 Stanton L, Young Blvd., Oklahoma City, OK 73104, USA.
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Williams ML, Waldbieser GC, Dyer DW, Gillaspy AF, Lawrence ML. Characterization of the rrn operons in the channel catfish pathogen Edwardsiella ictaluri. J Appl Microbiol 2008; 104:1790-6. [PMID: 18217940 DOI: 10.1111/j.1365-2672.2007.03704.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS To advance diagnostics and phylogenetics of Edwardsiella ictaluri by sequencing and characterizing its rrn operons. METHODS AND RESULTS The Edw. ictaluri rrn operons were identified from a 5-7 kbp insert lambda library and from Edw. ictaluri fosmid clones. We present the complete sequences and analysis of all eight Edw. ictaluri rrn operons and unique regions located upstream and downstream. Two rrn operons were located in tandem with 169 bp separating them, which is apparently a conserved feature between Edw. ictaluri and Edwardsiella tarda. I-CeuI enzyme digestion of Edw. ictaluri genomic DNA and analysis by pulsed field gel electrophoresis indicated that rrn operon number and chromosomal locations are conserved within the species Edw. ictaluri. CONCLUSIONS The rrn operons of Edw. ictaluri have similar structure and flanking regions compared with other members of the family Enterobacteriaceae; however, the presence of eight copies of the rrn operon makes Edw. ictaluri unique within the family. SIGNIFICANCE AND IMPACT OF THE STUDY This research clarifies previous phylogenetic analyses of Edw. ictaluri and provides support for the Edw. ictaluri genome sequencing project. In addition, we identified a unique feature of two rrn operons that shows potential for the development of a diagnostic PCR method.
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Affiliation(s)
- M L Williams
- College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA
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Saban MR, Hellmich HL, Turner M, Nguyen NB, Vadigepalli R, Dyer DW, Hurst RE, Centola M, Saban R. The inflammatory and normal transcriptome of mouse bladder detrusor and mucosa. BMC Physiol 2006; 6:1. [PMID: 16420690 PMCID: PMC1382248 DOI: 10.1186/1472-6793-6-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2005] [Accepted: 01/18/2006] [Indexed: 11/22/2022]
Abstract
Background An organ such as the bladder consists of complex, interacting set of tissues and cells. Inflammation has been implicated in every major disease of the bladder, including cancer, interstitial cystitis, and infection. However, scanty is the information about individual detrusor and urothelium transcriptomes in response to inflammation. Here, we used suppression subtractive hybridizations (SSH) to determine bladder tissue- and disease-specific genes and transcriptional regulatory elements (TRE)s. Unique TREs and genes were assembled into putative networks. Results It was found that the control bladder mucosa presented regulatory elements driving genes such as myosin light chain phosphatase and calponin 1 that influence the smooth muscle phenotype. In the control detrusor network the Pax-3 TRE was significantly over-represented. During development, the Pax-3 transcription factor (TF) maintains progenitor cells in an undifferentiated state whereas, during inflammation, Pax-3 was suppressed and genes involved in neuronal development (synapsin I) were up-regulated. Therefore, during inflammation, an increased maturation of neural progenitor cells in the muscle may underlie detrusor instability. NF-κB was specifically over-represented in the inflamed mucosa regulatory network. When the inflamed detrusor was compared to control, two major pathways were found, one encoding synapsin I, a neuron-specific phosphoprotein, and the other an important apoptotic protein, siva. In response to LPS-induced inflammation, the liver X receptor was over-represented in both mucosa and detrusor regulatory networks confirming a role for this nuclear receptor in LPS-induced gene expression. Conclusion A new approach for understanding bladder muscle-urothelium interaction was developed by assembling SSH, real time PCR, and TRE analysis results into regulatory networks. Interestingly, some of the TREs and their downstream transcripts originally involved in organogenesis and oncogenesis were also activated during inflammation. The latter represents an additional link between inflammation and cancer. The regulatory networks represent key targets for development of novel drugs targeting bladder diseases.
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Affiliation(s)
- Marcia R Saban
- Department of Physiology, The University Oklahoma Health Sciences Center, Oklahoma City, USA
| | - Helen L Hellmich
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, USA
| | - Mary Turner
- Oklahoma Medical Research Foundation (OMRF), Arthritis and Immunology Research Program, Microarray Core Facility, Oklahoma City, USA
| | - Ngoc-Bich Nguyen
- Department of Physiology, The University Oklahoma Health Sciences Center, Oklahoma City, USA
- Cellular & Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, USA
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics and Computational Biology. Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, USA
| | - David W Dyer
- Department of Microbiology and Immunology, Laboratory for Genomics and Bioinformatics, Oklahoma University Health Sciences Center, Oklahoma City, USA
| | - Robert E Hurst
- Department of Urology, The University Oklahoma Health Sciences Center, Oklahoma City, USA
| | - Michael Centola
- Oklahoma Medical Research Foundation (OMRF), Arthritis and Immunology Research Program, Microarray Core Facility, Oklahoma City, USA
| | - Ricardo Saban
- Department of Physiology, The University Oklahoma Health Sciences Center, Oklahoma City, USA
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Harrison A, Dyer DW, Gillaspy A, Ray WC, Mungur R, Carson MB, Zhong H, Gipson J, Gipson M, Johnson LS, Lewis L, Bakaletz LO, Munson RS. Genomic sequence of an otitis media isolate of nontypeable Haemophilus influenzae: comparative study with H. influenzae serotype d, strain KW20. J Bacteriol 2005; 187:4627-36. [PMID: 15968074 PMCID: PMC1151754 DOI: 10.1128/jb.187.13.4627-4636.2005] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.9] [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: 12/14/2022] Open
Abstract
In 1995, the Institute for Genomic Research completed the genome sequence of a rough derivative of Haemophilus influenzae serotype d, strain KW20. Although extremely useful in understanding the basic biology of H. influenzae, these data have not provided significant insight into disease caused by nontypeable H. influenzae, as serotype d strains are not pathogens. In contrast, strains of nontypeable H. influenzae are the primary pathogens of chronic and recurrent otitis media in children. In addition, these organisms have an important role in acute otitis media in children as well as other respiratory diseases. Such strains must therefore contain a gene repertoire that differs from that of strain Rd. Elucidation of the differences between these genomes will thus provide insight into the pathogenic mechanisms of nontypeable H. influenzae. The genome of a representative nontypeable H. influenzae strain, 86-028NP, isolated from a patient with chronic otitis media was therefore sequenced and annotated. Despite large regions of synteny with the strain Rd genome, there are large rearrangements in strain 86-028NP's genome architecture relative to the strain Rd genome. A genomic island similar to an island originally identified in H. influenzae type b is present in the strain 86-028NP genome, while the mu-like phage present in the strain Rd genome is absent from the strain 86-028NP genome. Two hundred eighty open reading frames were identified in the strain 86-028NP genome that were absent from the strain Rd genome. These data provide new insight that complements and extends the ongoing analysis of nontypeable H. influenzae virulence determinants.
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Affiliation(s)
- Alistair Harrison
- Center for Microbial Pathogenesis, Columbus Children's Research Institute, Ohio State University College of Medicine and Public Health, Columbus, Ohio 43205, USA
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Ducey TF, Carson MB, Orvis J, Stintzi AP, Dyer DW. Identification of the iron-responsive genes of Neisseria gonorrhoeae by microarray analysis in defined medium. J Bacteriol 2005; 187:4865-74. [PMID: 15995201 PMCID: PMC1169496 DOI: 10.1128/jb.187.14.4865-4874.2005] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [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: 01/24/2005] [Accepted: 04/11/2005] [Indexed: 11/20/2022] Open
Abstract
To ensure survival, most bacteria must acquire iron, a resource that is sequestered by mammalian hosts. Pathogenic bacteria have therefore evolved intricate systems to sense iron limitation and regulate gene expression appropriately. We used a pan-Neisseria microarray to examine genes regulated in Neisseria gonorrhoeae in response to iron availability in defined medium. Overall, 203 genes varied in expression, 109 up-regulated and 94 down-regulated by iron deprivation. In iron-replete medium, genes essential to rapid bacterial growth were preferentially expressed, while iron transport functions, and predominantly genes of unknown function, were expressed in low-iron medium. Of those TonB-dependent proteins encoded in the FA1090 genome with unknown ligand specificity, expression of three was not controlled by iron availability, suggesting that these receptors may not be high-affinity transporters for iron-containing ligands. Approximately 30% of the operons regulated by iron appeared to be directly under control of Fur. Our data suggest a regulatory cascade where Fur indirectly controls gene expression by affecting the transcription of three secondary regulators. Our data also suggest that a second MerR-like regulator may be directly responding to iron availability and controlling transcription independent of the Fur protein. Comparison of our data with those recently published for Neisseria meningitidis revealed that only a small portion of genes were found to be similarly regulated in these closely related pathogens, while a large number of genes derepressed during iron starvation were unique to each organism.
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Affiliation(s)
- Thomas F Ducey
- Laboratory for Genomics and Bioinformatics, Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Biomedical Research Center, Oklahoma City, 73104, USA.
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Abstract
Genomic sequences and expressed sequence tag data for a diverse group of fungi (Saccharomyces cerevisiae, Schizosaccharomyces pombe, Aspergillus nidulans, Neurospora crassa, and Cryptococcus neoformans) provided the opportunity to accurately characterize conserved intronic elements. An examination of large intron data sets revealed that fungal introns in general are short, that 98% or more of them belong to the canonical splice site (ss) class (5'GU...AG3'), and that they have polypyrimidine tracts predominantly in the region between the 5' ss and the branch point. Information content is high in the 5' ss, branch site, and 3' ss regions of the introns but low in the exon regions adjacent to the introns in the fungi examined. The two yeasts have broader intron length ranges and correspondingly higher intron information content than the other fungi. Generally, as intron length increases in the fungi, so does intron information content. Homologs of U2AF spliceosomal proteins were found in all species except for S. cerevisiae, suggesting a nonconventional role for U2AF in the absence of canonical polypyrimidine tracts in the majority of introns. Our observations imply that splicing in fungi may be different from that in vertebrates and may require additional proteins that interact with polypyrimidine tracts upstream of the branch point. Theoretical protein homologs for Nam8p and TIA-1, two proteins that require U-rich regions upstream of the branch point to function, were found. There appear to be sufficient differences between S. cerevisiae and S. pombe introns and the introns of two filamentous members of the Ascomycota and one member of the Basidiomycota to warrant the development of new model organisms for studying the splicing mechanisms of fungi.
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Affiliation(s)
- Doris M Kupfer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, P.O. Box 26901, BMSB 1053, Oklahoma City, OK 73190, USA
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Munson RS, Harrison A, Gillaspy A, Ray WC, Carson M, Armbruster D, Gipson J, Gipson M, Johnson L, Lewis L, Dyer DW, Bakaletz LO. Partial analysis of the genomes of two nontypeable Haemophilus influenzae otitis media isolates. Infect Immun 2004; 72:3002-10. [PMID: 15102813 PMCID: PMC387840 DOI: 10.1128/iai.72.5.3002-3010.2004] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [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
In 1995, The Institute for Genomic Research completed the genomic sequence of a rough derivative of Haemophilus influenzae serotype d, strain KW20. This sequence, though extremely useful in understanding the basic biology of H. influenzae, has yet to provide significant insight into our understanding of disease caused by nontypeable H. influenzae (NTHI), because serotype d strains are not generally pathogens. In contrast, NTHI strains are frequently mucosal pathogens and are the primary pathogens of chronic otitis media as well as a significant cause of acute otitis media in children. Thus, it is of great importance to further understand their biology. We used a DNA-based microarray approach to identify genes present in a clinical isolate of NTHI that were absent from strain Rd. We also sequenced the genome of a second NTHI isolate from a child with chronic otitis media to threefold coverage and then used an array of bioinformatics tools to identify genes present in this NTHI strain but absent from strain Rd. These methods were complementary in approach and results. We identified, in both strains, homologues of H. influenzae lav, an autotransported protein of unknown function; tnaA, which encodes tryptophanase; as well as a homologue of Pasteurella multocida tsaA, which encodes an alkyl peroxidase that may play a role in protection against reactive oxygen species. We also identified a number of putative restriction-modification systems, bacteriophage genes and transposon-related genes. These data provide new insight that complements and extends our ongoing analysis of NTHI virulence determinants.
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Affiliation(s)
- Robert S Munson
- Center for Microbial Pathogenesis, Columbus Children's Research Institute and The Department of Pediatrics, The Ohio State University, Columbus, Ohio 43205, USA.
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Rohde KH, Dyer DW. Analysis of haptoglobin and hemoglobin-haptoglobin interactions with the Neisseria meningitidis TonB-dependent receptor HpuAB by flow cytometry. Infect Immun 2004; 72:2494-506. [PMID: 15102756 PMCID: PMC387877 DOI: 10.1128/iai.72.5.2494-2506.2004] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2003] [Revised: 11/21/2003] [Accepted: 01/22/2004] [Indexed: 11/20/2022] Open
Abstract
Neisseria meningitidis expresses a two-component TonB-dependent receptor, HpuAB, which mediates heme-iron (Hm-Fe) acquisition from hemoglobin and hemoglobin-haptoglobin complexes. Due to genetic polymorphisms in the human haptoglobin gene, haptoglobin (and hemoglobin-haptoglobin) exists as three structurally distinct phenotypes. In this study, we examined the influence of the haptoglobin phenotype on the interactions of HpuAB with apo-haptoglobin and hemoglobin-haptoglobin. Growth assays confirmed that HpuAB utilizes hemoglobin-haptoglobin more efficiently than hemoglobin as an Fe source and revealed a preference for human-specific, polymeric 2-2 or 2-1 hemoglobin-haptoglobin complexes. We developed a flow cytometry-based assay to measure the binding kinetics of fluorescein-labeled ligands to HpuAB on live, intact meningococci. The binding affinity of HpuAB for hemoglobin-haptoglobin phenotypes correlated well with the ability of each ligand to support Neisseria meningitidis growth, with higher affinities exhibited for types 2-2 and 2-1 hemoglobin-haptoglobin. Saturable binding of Hb and apo-haptoglobin suggested that HpuAB-mediated utilization of hemoglobin-haptoglobin involves specific interactions with both components. In contrast to previous studies, we detected binding of HpuB expressed alone to hemoglobin, apo-haptoglobin, and hemoglobin-haptoglobin of all three phenotypes. However, in the absence of HpuA, the binding capacity and/or affinity of the receptor was reduced and the dissociation of hemoglobin was impaired. We did not detect binding of HpuA alone to hemoglobin, apo-haptoglobin, or hemoglobin-haptoglobin; however, the lipoprotein is crucial for optimal recognition and use of ligands by the receptor. Finally, this study confirmed the integral role of TonB and the proton motive force in the binding and dissociation of Hb and hemoglobin-haptoglobin from HpuAB.
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Affiliation(s)
- Kyle H Rohde
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA.
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Drabenstot SD, Kupfer DM, White JD, Dyer DW, Roe BA, Buchanan KL, Murphy JW. FELINES: a utility for extracting and examining EST-defined introns and exons. Nucleic Acids Res 2004; 31:e141. [PMID: 14602934 PMCID: PMC275578 DOI: 10.1093/nar/gng141] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [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: 11/13/2022] Open
Abstract
FELINES (Finding and Examining Lots of Intron 'N' Exon Sequences) is a utility written to automate construction and analysis of high quality intron and exon sequence databases produced from EST (expressed sequence tag) to genomic sequence alignments. We demonstrated the various programs of the FELINES utility by creating intron and exon sequence databases for the fungal organism Schizosaccharomyces pombe from alignments of EST to genomic sequences. In addition, we analyzed our constructed S.pombe sequence databases and the well-established Saccharomyces cerevisiae intron database from Manuel Ares' Laboratory for conserved sequence motifs. FELINES was shown to be useful for characterizing branchsites, polypyrimidine tracts and 5' and 3' splice sites in the intron databases and exonic splicing enhancers (ESEs) in S.pombe exons. FELINES is available at http://www.genome.ou.edu/informatics.html.
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Affiliation(s)
- Scott D Drabenstot
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, PO Box 26901, BMSB 1053, Oklahoma City, OK 73190, USA
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Rohde KH, Dyer DW. Mechanisms of iron acquisition by the human pathogens Neisseria meningitidis and Neisseria gonorrhoeae. Front Biosci 2003; 8:d1186-218. [PMID: 12957813 DOI: 10.2741/1133] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
It is well established that bacterial pathogenesis is dependent on the ability to acquire iron within the host. The success of the highly adapted obligate human pathogens Neisseria meningitidis (NM) and Neisseria gonorrhoeae (NG) can be attributed in part to the efficient utilization of multiple host iron (Fe) sources, allowing replication on mucosal surfaces, in the bloodstream, and intracellularly. Most Gram-negative bacterial strategies for scavenging iron from the human host rely on the TonB protein to energize active iron transport across the outer membrane. Pathogenic Neisseria express multiple high-affinity iron transporters including a family of two-component TonB-dependent receptors as well as multiple single-component TonB-dependent Fe transporters. This review describes our current understanding of the mechanisms Neisseria have evolved to utilize various iron sources encountered during infection of the human host. Recent studies have provided insight into the interaction of neisserial outer membrane receptors with host iron carrier proteins. Emerging structural information on neisserial iron transporters will be compared with the crystal structures and biochemical data available for homologous Escherichia coli TonB-dependent Fe-siderophore receptors. In the process, we will highlight the aspects of the iron transport process that are unique and those that remain to be experimentally demonstrated in Neisseria. These include receptor structure/function, the mechanism of iron removal from protein ligands, the fate of Fe and heme-Fe after traversing the outer membrane, and the role of TonB-associated energy in receptor functions. Finally, we will discuss regulatory mechanisms that control the expression of iron scavenging systems. The investigation of iron metabolism in NM and NG is important for understanding the biochemistry of this virulence factor, the development of vaccines targeted at outer membrane iron receptors, and therapeutic interventions exploiting these transporters as high affinity drug delivery systems.
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Affiliation(s)
- Kyle H Rohde
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 975 NE 10th Street, Oklahoma City, Oklahoma 73104, USA.
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Williams WA, Hendrickson A, Gillaspy AF, Dyer DW, Lewis LA. Oligonucleotide analysis by sequential injection before analysis (SIBA) capillary electrophoresis. Anal Biochem 2003; 313:183-5. [PMID: 12576078 DOI: 10.1016/s0003-2697(02)00513-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- William A Williams
- Ciphergen Biosystems, Inc, 6611 Dumbarton Circle, Fremont, CA 94555, USA
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Rohde KH, Gillaspy AF, Hatfield MD, Lewis LA, Dyer DW. Interactions of haemoglobin with the Neisseria meningitidis receptor HpuAB: the role of TonB and an intact proton motive force. Mol Microbiol 2002; 43:335-54. [PMID: 11985713 DOI: 10.1046/j.1365-2958.2002.02745.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [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: 11/20/2022]
Abstract
We have characterized the interaction of the Neisseria meningitidis TonB-dependent receptor HpuAB with haemoglobin (Hb). Protease accessibility assays indicated that HpuA and HpuB are surface exposed, HpuB interacts physically with HpuA, and TonB energization affects the conformation of HpuAB. Binding assays using [125I]-Hb revealed that the bipartite receptor has a single binding site for Hb (Kd 150 nM). Competitive binding assays using heterologous Hbs revealed that HpuAB Hb recognition was not species specific. The binding kinetics of Hb to HpuAB were dramatically altered in a TonB- mutant and in wild-type meningococci treated with the protonophore carbonylcyanide m-chlorophenylhydrazone (CCCP), indicating that TonB and an intact proton motive force are required for normal Hb binding and release from HpuAB. Our results support a model in which both HpuA and HpuB are required to form a receptor complex in the outer membrane with a single binding site, whose structure and ligand interactions are significantly affected by the TonB-mediated energy state of the receptor.
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Affiliation(s)
- K H Rohde
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City 73104, USA.
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Register KB, Ducey TF, Brockmeier SL, Dyer DW. Reduced virulence of a Bordetella bronchiseptica siderophore mutant in neonatal swine. Infect Immun 2001; 69:2137-43. [PMID: 11254568 PMCID: PMC98140 DOI: 10.1128/iai.69.4.2137-2143.2001] [Citation(s) in RCA: 22] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2000] [Accepted: 01/04/2001] [Indexed: 11/20/2022] Open
Abstract
One means by which Bordetella bronchiseptica scavenges iron is through production of the siderophore alcaligin. A nonrevertible alcaligin mutant derived from the virulent strain 4609, designated DBB25, was constructed by insertion of a kanamycin resistance gene into alcA, one of the genes essential for alcaligin biosynthesis. The virulence of the alcA mutant in colostrum-deprived, caesarean-delivered piglets was compared with that of the parent strain in two experiments. At 1 week of age, piglets were inoculated with phosphate-buffered saline, 4609, or DBB25. Two piglets in each group were euthanatized on day 10 postinfection. The remainder were euthanatized at 21 days postinfection. Clinical signs, including fever, coughing, and sneezing, were present in both groups. Nasal washes performed 7, 14, and 21 days postinoculation demonstrated that strain DBB25 colonized the nasal cavity but did so at levels that were significantly less than those achieved by strain 4609. Analysis of colonization based on the number of CFU per gram of tissue recovered from the turbinate, trachea, and lung also demonstrated significant differences between DBB25 and 4609, at both day 10 and day 21 postinfection. Mild to moderate turbinate atrophy was apparent in pigs inoculated with strain 4609, while turbinates of those infected with strain DBB25 developed no or mild atrophy. We conclude from these results that siderophore production by B. bronchiseptica is not essential for colonization of swine but is required for maximal virulence. B. bronchiseptica mutants with nonrevertible defects in genes required for alcaligin synthesis may be candidates for evaluation as attenuated, live vaccine strains in conventionally reared pigs.
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Affiliation(s)
- K B Register
- Respiratory Diseases of Livestock Research Unit, USDA Agricultural Research Service National Animal Disease Center, Ames, Iowa 50010, USA.
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Lewis LA, Gipson M, Hartman K, Ownbey T, Vaughn J, Dyer DW. Phase variation of HpuAB and HmbR, two distinct haemoglobin receptors of Neisseria meningitidis DNM2. Mol Microbiol 1999; 32:977-89. [PMID: 10361300 DOI: 10.1046/j.1365-2958.1999.01409.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.5] [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]
Abstract
We have previously described HpuAB, a two-component receptor that mediates binding to haemoglobin (Hb), haemoglobin-haptoglobin (Hb-Hp) and apo-haptoglobin (Hp). In this communication, we constructed non-polar mutations in the hpuA and hpuB loci to examine the individual roles of HpuA and HpuB. Our results indicate that both HpuA and HpuB are required for the acquisition of Fe from Hb and Hb-Hp. We isolated Hb utilization-positive (Hb+) variants of our Hb utilization-negative (Hb-) hpu mutants at a frequency of 10(-3) and demonstrated that the Hb+ phenotype resulted from the expression of a second Hb receptor, HmbR. Expression of HmbR in DNM2 was found to be controlled by translational frameshifting involving a polyguanine (G) tract located within the hmbR locus. The hpuA locus also contains a poly(G) tract, which suggested that meningococci could phase vary each Hb receptor independently by slip-strand mispairing in the poly(G) tracts found in hpuA and hmbR. Thus, we isolated a naturally occurring Hb- variant of DNM2, designated DNM2 Hb-, which did not express either HpuAB or HmbR. Hb+ variants of DNM2Hb- were selected and examined for HpuAB and HmbR expression. In each instance, acquisition of HpuAB or HmbR expression was correlated with phase variation in the poly(G) tract of each Hb receptor.
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Affiliation(s)
- L A Lewis
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 1053 BMSB, 940 Stanton L. Young Blvd, Oklahoma City, OK 73190, USA.
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