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Nettere D, Unnithan S, Rodgers N, Nohara J, Cray P, Berry M, Jones C, Armand L, Li SH, Berendam SJ, Fouda GG, Cain DW, Spence TN, Granek JA, Davenport CA, Edwards RJ, Wiehe K, Van Rompay KKA, Moody MA, Permar SR, Pollara J. Conjugation of HIV-1 envelope to hepatitis B surface antigen alters vaccine responses in rhesus macaques. NPJ Vaccines 2023; 8:183. [PMID: 38001122 PMCID: PMC10673864 DOI: 10.1038/s41541-023-00775-y] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
An effective HIV-1 vaccine remains a critical unmet need for ending the AIDS epidemic. Vaccine trials conducted to date have suggested the need to increase the durability and functionality of vaccine-elicited antibodies to improve efficacy. We hypothesized that a conjugate vaccine based on the learned response to immunization with hepatitis B virus could be utilized to expand T cell help and improve antibody production against HIV-1. To test this, we developed an innovative conjugate vaccine regimen that used a modified vaccinia virus Ankara (MVA) co-expressing HIV-1 envelope (Env) and the hepatitis B virus surface antigen (HBsAg) as a prime, followed by two Env-HBsAg conjugate protein boosts. We compared the immunogenicity of this conjugate regimen to matched HIV-1 Env-only vaccines in two groups of 5 juvenile rhesus macaques previously immunized with hepatitis B vaccines in infancy. We found expansion of both HIV-1 and HBsAg-specific circulating T follicular helper cells and elevated serum levels of CXCL13, a marker for germinal center activity, after boosting with HBsAg-Env conjugate antigens in comparison to Env alone. The conjugate vaccine elicited higher levels of antibodies binding to select HIV Env antigens, but we did not observe significant improvement in antibody functionality, durability, maturation, or B cell clonal expansion. These data suggests that conjugate vaccination can engage both HIV-1 Env and HBsAg specific T cell help and modify antibody responses at early time points, but more research is needed to understand how to leverage this strategy to improve the durability and efficacy of next-generation HIV vaccines.
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Affiliation(s)
- Danielle Nettere
- Duke University School of Medicine, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Shakthi Unnithan
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Nicole Rodgers
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Junsuke Nohara
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Paul Cray
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Madison Berry
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Caroline Jones
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Lawrence Armand
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Shuk Hang Li
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Stella J Berendam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
- GSK Rockville Center for Vaccines Research, Rockville, MD, USA
| | - Genevieve G Fouda
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | - Derek W Cain
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Taylor N Spence
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Joshua A Granek
- Quantitative Sciences Core, Duke University Center for AIDS Research, Duke University School of Medicine, Durham, NC, USA
| | - Clemontina A Davenport
- Quantitative Sciences Core, Duke University Center for AIDS Research, Duke University School of Medicine, Durham, NC, USA
| | - Robert J Edwards
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Koen K A Van Rompay
- California National Primate Research Center, University of California, Davis, CA, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Sallie R Permar
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | - Justin Pollara
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA.
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.
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Telzrow CL, Esher Righi S, Cathey JM, Granek JA, Alspaugh JA. Cryptococcus neoformans Mar1 function links mitochondrial metabolism, oxidative stress, and antifungal tolerance. Front Physiol 2023; 14:1150272. [PMID: 36969606 PMCID: PMC10033685 DOI: 10.3389/fphys.2023.1150272] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/27/2023] [Indexed: 03/11/2023] Open
Abstract
Introduction: Microbial pathogens undergo significant physiological changes during interactions with the infected host, including alterations in metabolism and cell architecture. The Cryptococcus neoformans Mar1 protein is required for the proper ordering of the fungal cell wall in response to host-relevant stresses. However, the precise mechanism by which this Cryptococcus-specific protein regulates cell wall homeostasis was not defined. Methods: Here, we use comparative transcriptomics, protein localization, and phenotypic analysis of a mar1D loss-of-function mutant strain to further define the role of C. neoformans Mar1 in stress response and antifungal resistance. Results: We demonstrate that C. neoformans Mar1 is highly enriched in mitochondria. Furthermore, a mar1Δ mutant strain is impaired in growth in the presence of select electron transport chain inhibitors, has altered ATP homeostasis, and promotes proper mitochondrial morphogenesis. Pharmacological inhibition of complex IV of the electron transport chain in wild-type cells promotes similar cell wall changes as the mar1Δ mutant strain, supporting prior associations between mitochondrial function and cell wall homeostasis. Although Mar1 is not required for general susceptibility to the azole antifungals, the mar1Δ mutant strain displays increased tolerance to fluconazole that correlates with repressed mitochondrial metabolic activity. Discussion: Together, these studies support an emerging model in which the metabolic activity of microbial cells directs cell physiological changes to allow persistence in the face of antimicrobial and host stress.
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Affiliation(s)
- Calla L. Telzrow
- Department of Medicine, Duke University School of Medicine, Durham, NC, United States
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
| | - Shannon Esher Righi
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Jackson M. Cathey
- Department of Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Joshua A. Granek
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, United States
| | - J. Andrew Alspaugh
- Department of Medicine, Duke University School of Medicine, Durham, NC, United States
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
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3
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Telzrow CL, Zwack PJ, Esher Righi S, Dietrich FS, Chan C, Owzar K, Alspaugh JA, Granek JA. Comparative analysis of RNA enrichment methods for preparation of Cryptococcus neoformans RNA sequencing libraries. G3 (Bethesda) 2021; 11:jkab301. [PMID: 34518880 PMCID: PMC8527493 DOI: 10.1093/g3journal/jkab301] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 08/19/2021] [Indexed: 11/13/2022]
Abstract
RNA sequencing (RNA-Seq) experiments focused on gene expression involve removal of ribosomal RNA (rRNA) because it is the major RNA constituent of cells. This process, called RNA enrichment, is done primarily to reduce cost: without rRNA removal, deeper sequencing must be performed to compensate for the sequencing reads wasted on rRNA. The ideal RNA enrichment method removes all rRNA without affecting other RNA in the sample. We tested the performance of three RNA enrichment methods on RNA isolated from Cryptococcus neoformans, a fungal pathogen of humans. We find that the RNase H depletion method is more efficient in depleting rRNA and more specific in recapitulating non-rRNA levels present in unenriched controls than the commonly-used Poly(A) isolation method. The RNase H depletion method is also more effective than the Ribo-Zero depletion method as measured by rRNA depletion efficiency and recapitulation of protein-coding RNA levels present in unenriched controls, while the Ribo-Zero depletion method more closely recapitulates annotated non-coding RNA (ncRNA) levels. Finally, we leverage these data to accurately map the C. neoformans mitochondrial rRNA genes, and also demonstrate that RNA-Seq data generated with the RNase H and Ribo-Zero depletion methods can be used to explore novel C. neoformans long non-coding RNA genes.
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Affiliation(s)
- Calla L Telzrow
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Paul J Zwack
- Department of Biology, Duke University, Durham, NC 27710, USA
| | - Shannon Esher Righi
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Fred S Dietrich
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cliburn Chan
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
| | - Kouros Owzar
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
- Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - J Andrew Alspaugh
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Joshua A Granek
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
- Duke Cancer Institute, Duke University, Durham, NC 27710, USA
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McCann JR, Bihlmeyer NA, Roche K, Catherine C, Jawahar J, Kwee LC, Younge NE, Silverman J, Ilkayeva O, Sarria C, Zizzi A, Wootton J, Poppe L, Anderson P, Arlotto M, Wei Z, Granek JA, Valdivia RH, David LA, Dressman HK, Newgard CB, Shah SH, Seed PC, Rawls JF, Armstrong SC. The Pediatric Obesity Microbiome and Metabolism Study (POMMS): Methods, Baseline Data, and Early Insights. Obesity (Silver Spring) 2021; 29:569-578. [PMID: 33624438 PMCID: PMC7927749 DOI: 10.1002/oby.23081] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/17/2022]
Abstract
OBJECTIVE The purpose of this study was to establish a biorepository of clinical, metabolomic, and microbiome samples from adolescents with obesity as they undergo lifestyle modification. METHODS A total of 223 adolescents aged 10 to 18 years with BMI ≥95th percentile were enrolled, along with 71 healthy weight participants. Clinical data, fasting serum, and fecal samples were collected at repeated intervals over 6 months. Herein, the study design, data collection methods, and interim analysis-including targeted serum metabolite measurements and fecal 16S ribosomal RNA gene amplicon sequencing among adolescents with obesity (n = 27) and healthy weight controls (n = 27)-are presented. RESULTS Adolescents with obesity have higher serum alanine aminotransferase, C-reactive protein, and glycated hemoglobin, and they have lower high-density lipoprotein cholesterol when compared with healthy weight controls. Metabolomics revealed differences in branched-chain amino acid-related metabolites. Also observed was a differential abundance of specific microbial taxa and lower species diversity among adolescents with obesity when compared with the healthy weight group. CONCLUSIONS The Pediatric Metabolism and Microbiome Study (POMMS) biorepository is available as a shared resource. Early findings suggest evidence of a metabolic signature of obesity unique to adolescents, along with confirmation of previously reported findings that describe metabolic and microbiome markers of obesity.
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Affiliation(s)
- Jessica R. McCann
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708
| | - Nathan A. Bihlmeyer
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University, Durham, NC, USA 27710
| | - Kimberly Roche
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708
| | | | - Jayanth Jawahar
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708
| | - Lydia Coulter Kwee
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University, Durham, NC, USA 27710
| | - Noelle E. Younge
- Department of Pediatrics, Duke University, Durham, NC, USA 27710
| | | | - Olga Ilkayeva
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University, Durham, NC, USA 27710
| | - Charles Sarria
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708
| | - Alexandra Zizzi
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708
| | - Janet Wootton
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708
| | - Lisa Poppe
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University, Durham, NC, USA 27710
| | - Paul Anderson
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University, Durham, NC, USA 27710
| | - Michelle Arlotto
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University, Durham, NC, USA 27710
| | - Zhengzheng Wei
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708
| | - Joshua A. Granek
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708
- Duke Microbiome Center, Duke University Durham, NC, USA 27710
| | - Raphael H. Valdivia
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708
- Duke Microbiome Center, Duke University Durham, NC, USA 27710
| | - Lawrence A. David
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708
- Duke Microbiome Center, Duke University Durham, NC, USA 27710
| | - Holly K. Dressman
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708
- Duke Microbiome Center, Duke University Durham, NC, USA 27710
| | - Christopher B. Newgard
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University, Durham, NC, USA 27710
| | - Svati H. Shah
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University, Durham, NC, USA 27710
- Duke Clinical Research Institute, Duke University, Durham, NC, USA 27710
| | - Patrick C. Seed
- Ann & Robert H. Lurie Children’s Hospital of Chicago, Northwestern University Feinberg School of Medicine, Stanley Manne Children’s Research Institute, Northwestern University Medical Center, Chicago, IL, USA 60611
| | - John F. Rawls
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708
- Duke Microbiome Center, Duke University Durham, NC, USA 27710
| | - Sarah C. Armstrong
- Department of Pediatrics, Duke University, Durham, NC, USA 27710
- Duke Clinical Research Institute, Duke University, Durham, NC, USA 27710
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5
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Finn SMB, Scheuermann U, Holzknecht ZE, Gao Q, Ibrahim MM, Parker W, Granek JA, Lin SS, McKenney EA, Barbas AS. The effect of levofloxacin on the lung microbiota of laboratory rats. Exp Lung Res 2019; 45:200-208. [PMID: 31298956 DOI: 10.1080/01902148.2019.1639225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Aim: The aim of this study was to investigate the short-term effect of levofloxacin on the microbiota of healthy lungs. Material and methods: Male F344 rats received either no levofloxacin (n = 9), intravenous levofloxacin (n = 12), oral levofloxacin (n = 12), or subcutaneous levofloxacin (n = 14). Rats received a clinically applicable dose (5.56 mg/kg) of levofloxacin via the assigned delivery route once daily for three days. On day four, lung tissue was collected and the lung microbiota composition was investigated using 16S ribosomal RNA gene sequencing. Results: Untreated lungs showed a microbiota dominated by bacteria of the genera Serratia. After treatment with levofloxacin, bacteria of the genus Pantoea dominated the lung microbiota. This was observed for all routes of antibiotic administration, with a significant difference compared to no-antibiotic control group (PERMANOVA: P < 0.001; homogeneity of dispersions: P = 0.656). Conclusion: Our study is the first to demonstrate the effects of levofloxacin therapy on lung microbiota in laboratory rats. Levofloxacin treatment by any route of administration leads to profound changes in the rat lung microbiota, resulting in the predominance of bacteria belonging to the genus Pantoea. Further studies regarding the role of long-term application of broad spectrum antibiotics on induction of lung, allergic and autoimmune diseases are indicated.
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Affiliation(s)
- Sade M B Finn
- a Department of Surgery, Duke University Medical Center , Durham , North Carolina , United States
| | - Uwe Scheuermann
- a Department of Surgery, Duke University Medical Center , Durham , North Carolina , United States
| | - Zoie E Holzknecht
- a Department of Surgery, Duke University Medical Center , Durham , North Carolina , United States
| | - Qimeng Gao
- a Department of Surgery, Duke University Medical Center , Durham , North Carolina , United States
| | - Mohamed M Ibrahim
- a Department of Surgery, Duke University Medical Center , Durham , North Carolina , United States
| | - William Parker
- a Department of Surgery, Duke University Medical Center , Durham , North Carolina , United States
| | - Joshua A Granek
- b Department of Bioinformatics and Biostatistics, Duke University School of Medicine , Durham , North Carolina , United States
| | - Shu S Lin
- a Department of Surgery, Duke University Medical Center , Durham , North Carolina , United States.,c Department of Pathology, Duke University Medical Center , Durham , North Carolina , United States.,d Department of Immunology, Duke University Medical Center , Durham , North Carolina , United States
| | - Erin A McKenney
- e Department of Applied Ecology, NC State University , Raleigh , North Carolina , United States
| | - Andrew S Barbas
- a Department of Surgery, Duke University Medical Center , Durham , North Carolina , United States
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6
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Finn SMB, Scheuermann U, Holzknecht ZE, Parker W, Granek JA, Lin SS, McKenney EA, Barbas AS. Effect of gastric fluid aspiration on the lung microbiota of laboratory rats. Exp Lung Res 2018; 44:201-210. [PMID: 30465452 DOI: 10.1080/01902148.2018.1482976] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
AIM OF THE STUDY The pulmonary microbiota is important for both normal homeostasis and the progression of disease, and may be affected by aspiration of gastric fluid. The aim of this study was to investigate changes in the lung microbiota induced by aspiration of gastric fluid in a laboratory rat model. MATERIAL AND METHODS Using the intratracheal application method, male rats received aspiration with 0.9% normal saline (n = 11); gastric fluid (n = 24) or sterilized (gamma-irradiated) gastric fluid (n = 12) once-weekly for four weeks. On the fifth week, the animals were sacrificed, and the microbiota of the lung was assessed by 16S ribosomal RNA gene sequencing. RESULTS Lungs without aspiration and lungs after aspiration with normal saline had similar microbial compositions, dominated by bacteria of the genera Serratia, Ralstonia and Brucella. Evaluation of the microbiota following aspiration of gastric fluid revealed a much different profile that was dominated by bacteria from the genera Romboutsia and Turicibacter and largely independent of sterilization of the gastric fluid. CONCLUSION In a laboratory rat model, aspiration with gastric fluid caused a substantial shift of the lung microbiota that could be characterized as a shift from Proteobacteria towards Firmicutes, possibly of enteric origin. Bacteria contained in the gastric fluid are not apparently responsible for this change.
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Affiliation(s)
- Sade M B Finn
- a Department of Surgery , Duke University Medical Center , Durham , North Carolina , USA
| | - Uwe Scheuermann
- a Department of Surgery , Duke University Medical Center , Durham , North Carolina , USA
| | - Zoie E Holzknecht
- a Department of Surgery , Duke University Medical Center , Durham , North Carolina , USA
| | - William Parker
- a Department of Surgery , Duke University Medical Center , Durham , North Carolina , USA
| | - Joshua A Granek
- b Department of Bioinformatics and Biostatistics , Duke University School of Medicine , Durham , North Carolina , USA
| | - Shu S Lin
- a Department of Surgery , Duke University Medical Center , Durham , North Carolina , USA.,c Department of Pathology , Duke University Medical Center , Durham , North Carolina , USA.,d Department of Immunology , Duke University Medical Center , Durham , North Carolina , USA
| | - Erin A McKenney
- e Department of Applied Ecology , NC State University , Raleigh , North Carolina , USA
| | - Andrew S Barbas
- a Department of Surgery , Duke University Medical Center , Durham , North Carolina , USA
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7
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Finn S, Scheuermann U, Parker W, Lin SS, McKenney EA, Granek JA. Effect of Gastric Fluid Aspiration on the Lung Microbiota of Laboratory Rats. J Am Coll Surg 2018. [DOI: 10.1016/j.jamcollsurg.2018.08.239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Chow EWL, Clancey SA, Billmyre RB, Averette AF, Granek JA, Mieczkowski P, Cardenas ME, Heitman J. Elucidation of the calcineurin-Crz1 stress response transcriptional network in the human fungal pathogen Cryptococcus neoformans. PLoS Genet 2017; 13:e1006667. [PMID: 28376087 PMCID: PMC5380312 DOI: 10.1371/journal.pgen.1006667] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 03/01/2017] [Indexed: 12/02/2022] Open
Abstract
Calcineurin is a highly conserved Ca2+/calmodulin-dependent serine/threonine-specific protein phosphatase that orchestrates cellular Ca2+ signaling responses. In Cryptococcus neoformans, calcineurin is activated by multiple stresses including high temperature, and is essential for stress adaptation and virulence. The transcription factor Crz1 is a major calcineurin effector in Saccharomyces cerevisiae and other fungi. Calcineurin dephosphorylates Crz1, thereby enabling Crz1 nuclear translocation and transcription of target genes. Here we show that loss of Crz1 confers phenotypes intermediate between wild-type and calcineurin mutants, and demonstrate that deletion of the calcineurin docking domain results in the inability of Crz1 to translocate into the nucleus under thermal stress. RNA-sequencing revealed 102 genes that are regulated in a calcineurin-Crz1-dependent manner at 37°C. The majority of genes were down-regulated in cna1Δ and crz1Δ mutants, indicating these genes are normally activated by the calcineurin-Crz1 pathway at high temperature. About 58% of calcineurin-Crz1 target genes have unknown functions, while genes with known or predicted functions are involved in cell wall remodeling, calcium transport, and pheromone production. We identified three calcineurin-dependent response element motifs within the promoter regions of calcineurin-Crz1 target genes, and show that Crz1 binding to target gene promoters is increased upon thermal stress in a calcineurin-dependent fashion. Additionally, we found a large set of genes independently regulated by calcineurin, and Crz1 regulates 59 genes independently of calcineurin. Given the intermediate crz1Δ mutant phenotype, and our recent evidence for a calcineurin regulatory network impacting mRNA in P-bodies and stress granules independently of Crz1, calcineurin likely acts on factors beyond Crz1 that govern mRNA expression/stability to operate a branched transcriptional/post-transcriptional stress response network necessary for fungal virulence. Taken together, our findings reveal the core calcineurin-Crz1 stress response cascade is maintained from ascomycetes to a pathogenic basidiomycete fungus, but its output in C. neoformans appears to be adapted to promote fungal virulence. The ubquitiously conserved serine/threonine-specific protein phosphatase calcineurin is crucial for virulence of several opportunistic human fungal pathogens including Candida albicans, Aspergillus fumigatus, and Cryptococcus neoformans. We show that Crz1 acts downstream of calcineurin, to 1) govern expression of genes involved in cell wall integrity, and calcium and small molecule transport, and 2) contribute to stress survival and virulence of C. neoformans. Our studies reveal that calcineurin also controls mRNA expression levels of other genes independently of Crz1. We propose that calcineurin operates in a branched signal transduction cascade controlling targets at both the transcriptional and post-transcriptional levels.
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Affiliation(s)
- Eve W. L. Chow
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Shelly A. Clancey
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - R. Blake Billmyre
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Anna Floyd Averette
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Joshua A. Granek
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina, United States of America
- Duke Center for the Genomics of Microbial Systems, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Piotr Mieczkowski
- High-Throughput Sequencing Facility, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Maria E. Cardenas
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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9
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Granek JA, Sergio LE. Evidence for distinct brain networks in the control of rule-based motor behavior. J Neurophysiol 2015; 114:1298-309. [PMID: 26133796 DOI: 10.1152/jn.00233.2014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 06/30/2015] [Indexed: 11/22/2022] Open
Abstract
Reach guidance when the spatial location of the viewed target and hand movement are incongruent (i.e., decoupled) necessitates use of explicit cognitive rules (strategic control) or implicit recalibration of gaze and limb position (sensorimotor recalibration). In a patient with optic ataxia (OA) and bilateral superior parietal lobule damage, we recently demonstrated an increased reliance on strategic control when the patient performed a decoupled reach (Granek JA, Pisella L, Stemberger J, Vighetto A, Rossetti Y, Sergio LE. PLoS One 8: e86138, 2013). To more generally understand the fundamental mechanisms of decoupled visuomotor control and to more specifically test whether we could distinguish these two modes of movement control, we tested healthy participants in a cognitively demanding dual task. Participants continuously counted backward while simultaneously reaching toward horizontal (left or right) or diagonal (equivalent to top-left or top-right) targets with either veridical or rotated (90°) cursor feedback. By increasing the overall neural load and selectively compromising potentially overlapping neural circuits responsible for strategic control, the complex dual task served as a noninvasive means to disrupt the integration of a cognitive rule into a motor action. Complementary to our previous results observed in patients with optic ataxia, here our dual task led to greater performance deficits during movements that required an explicit rule, implying a selective disruption of strategic control in decoupled reaching. Our results suggest that distinct neural processing is required to control these different types of reaching because in considering the current results and previous patient results together, the two classes of movement could be differentiated depending on the type of interference.
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Affiliation(s)
- Joshua A Granek
- School of Kinesiology and Health Science, Centre for Vision Research, York University, Toronto, Ontario, Canada
| | - Lauren E Sergio
- School of Kinesiology and Health Science, Centre for Vision Research, York University, Toronto, Ontario, Canada
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Esher SK, Granek JA, Alspaugh JA. Rapid mapping of insertional mutations to probe cell wall regulation in Cryptococcus neoformans. Fungal Genet Biol 2015; 82:9-21. [PMID: 26112692 DOI: 10.1016/j.fgb.2015.06.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [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: 01/14/2015] [Revised: 06/13/2015] [Accepted: 06/16/2015] [Indexed: 11/16/2022]
Abstract
Random insertional mutagenesis screens are important tools in microbial genetics studies. Investigators in fungal systems have used the plant pathogen Agrobacterium tumefaciens to create tagged, random mutations for genetic screens in their fungal species of interest through a unique process of trans-kingdom cellular transconjugation. However, identifying the locations of insertion has traditionally required tedious PCR-based methods, limiting the effective throughput of this system. We have developed an efficient genomic sequencing and analysis method (AIM-Seq) to facilitate identification of randomly generated genomic insertions in microorganisms. AIM-Seq combines batch sampling, whole genome sequencing, and a novel bioinformatics pipeline, AIM-HII, to rapidly identify sites of genomic insertion. We have specifically applied this technique to Agrobacterium-mediated transconjugation in the human fungal pathogen Cryptococcus neoformans. With this approach, we have screened a library of C. neoformans cell wall mutants, selecting twenty-seven mutants of interest for analysis by AIM-Seq. We identified thirty-five putative genomic insertions in known and previously unknown regulators of cell wall processes in this pathogenic fungus. We confirmed the relevance of a subset of these by creating independent mutant strains and analyzing resulting cell wall phenotypes. Through our sequence-based analysis of these mutations, we observed "typical" insertions of the Agrobacterium transfer DNA as well as atypical insertion events, including large deletions and chromosomal rearrangements. Initially applied to C. neoformans, this mutant analysis tool can be applied to a wide range of experimental systems and methods of mutagenesis, facilitating future microbial genetic screens.
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Affiliation(s)
- Shannon K Esher
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Joshua A Granek
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Bioinformatics and Biostatistics, Duke University School of Medicine, Durham, NC 27710, USA; Duke Center for the Genomics of Microbial Systems, Duke University School of Medicine, Durham, NC 27710, USA.
| | - J Andrew Alspaugh
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.
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Kokes M, Dunn JD, Granek JA, Nguyen BD, Barker JR, Valdivia RH, Bastidas RJ. Integrating chemical mutagenesis and whole-genome sequencing as a platform for forward and reverse genetic analysis of Chlamydia. Cell Host Microbe 2015; 17:716-25. [PMID: 25920978 DOI: 10.1016/j.chom.2015.03.014] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 02/11/2015] [Accepted: 03/17/2015] [Indexed: 11/18/2022]
Abstract
Gene inactivation by transposon insertion or allelic exchange is a powerful approach to probe gene function. Unfortunately, many microbes, including Chlamydia, are not amenable to routine molecular genetic manipulations. Here we describe an arrayed library of chemically induced mutants of the genetically intransigent pathogen Chlamydia trachomatis, in which all mutations have been identified by whole-genome sequencing, providing a platform for reverse genetic applications. An analysis of possible loss-of-function mutations in the collection uncovered plasticity in the central metabolic properties of this obligate intracellular pathogen. We also describe the use of the library in a forward genetic screen that identified InaC as a bacterial factor that binds host ARF and 14-3-3 proteins and modulates F-actin assembly and Golgi redistribution around the pathogenic vacuole. This work provides a robust platform for reverse and forward genetic approaches in Chlamydia and should serve as a valuable resource to the community.
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Affiliation(s)
- Marcela Kokes
- Department of Molecular Genetics and Microbiology and Center for the Genomics of Microbial Systems, Duke University Medical Center, 268 CARL Building, Box 3054, Durham, NC 27710, USA
| | - Joe Dan Dunn
- Department of Molecular Genetics and Microbiology and Center for the Genomics of Microbial Systems, Duke University Medical Center, 268 CARL Building, Box 3054, Durham, NC 27710, USA
| | - Joshua A Granek
- Department of Molecular Genetics and Microbiology and Center for the Genomics of Microbial Systems, Duke University Medical Center, 268 CARL Building, Box 3054, Durham, NC 27710, USA; Department of Biostatistics and Bioinformatics, Duke University Medical Center, 2424 Erwin Road, Suite 1102 Hock Plaza, Box 2721, Durham, NC 27710, USA
| | - Bidong D Nguyen
- Department of Molecular Genetics and Microbiology and Center for the Genomics of Microbial Systems, Duke University Medical Center, 268 CARL Building, Box 3054, Durham, NC 27710, USA
| | - Jeffrey R Barker
- Department of Molecular Genetics and Microbiology and Center for the Genomics of Microbial Systems, Duke University Medical Center, 268 CARL Building, Box 3054, Durham, NC 27710, USA
| | - Raphael H Valdivia
- Department of Molecular Genetics and Microbiology and Center for the Genomics of Microbial Systems, Duke University Medical Center, 268 CARL Building, Box 3054, Durham, NC 27710, USA.
| | - Robert J Bastidas
- Department of Molecular Genetics and Microbiology and Center for the Genomics of Microbial Systems, Duke University Medical Center, 268 CARL Building, Box 3054, Durham, NC 27710, USA.
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12
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Calo S, Shertz-Wall C, Lee SC, Bastidas RJ, Nicolás FE, Granek JA, Mieczkowski P, Torres-Martínez S, Ruiz-Vázquez RM, Cardenas ME, Heitman J. Antifungal drug resistance evoked via RNAi-dependent epimutations. Nature 2014; 513:555-8. [PMID: 25079329 PMCID: PMC4177005 DOI: 10.1038/nature13575] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [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: 09/19/2013] [Accepted: 06/12/2014] [Indexed: 12/16/2022]
Abstract
Microorganisms evolve via a range of mechanisms that may include or involve sexual/parasexual reproduction, mutators, aneuploidy, Hsp90 and even prions. Mechanisms that may seem detrimental can be repurposed to generate diversity. Here we show that the human fungal pathogen Mucor circinelloides develops spontaneous resistance to the antifungal drug FK506 (tacrolimus) via two distinct mechanisms. One involves Mendelian mutations that confer stable drug resistance; the other occurs via an epigenetic RNA interference (RNAi)-mediated pathway resulting in unstable drug resistance. The peptidylprolyl isomerase FKBP12 interacts with FK506 forming a complex that inhibits the protein phosphatase calcineurin. Calcineurin inhibition by FK506 blocks M. circinelloides transition to hyphae and enforces yeast growth. Mutations in the fkbA gene encoding FKBP12 or the calcineurin cnbR or cnaA genes confer FK506 resistance and restore hyphal growth. In parallel, RNAi is spontaneously triggered to silence the fkbA gene, giving rise to drug-resistant epimutants. FK506-resistant epimutants readily reverted to the drug-sensitive wild-type phenotype when grown without exposure to the drug. The establishment of these epimutants is accompanied by generation of abundant fkbA small RNAs and requires the RNAi pathway as well as other factors that constrain or reverse the epimutant state. Silencing involves the generation of a double-stranded RNA trigger intermediate using the fkbA mature mRNA as a template to produce antisense fkbA RNA. This study uncovers a novel epigenetic RNAi-based epimutation mechanism controlling phenotypic plasticity, with possible implications for antimicrobial drug resistance and RNAi-regulatory mechanisms in fungi and other eukaryotes.
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Affiliation(s)
- Silvia Calo
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Cecelia Shertz-Wall
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Soo Chan Lee
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Robert J Bastidas
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Francisco E Nicolás
- 1] Regional Campus of International Excellence "Campus Mare Nostrum", Murcia 30100, Spain [2] Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Murcia 30100, Spain
| | - Joshua A Granek
- 1] Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA [2] Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina 27710, USA [3] Duke Center for the Genomics of Microbial Systems, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Piotr Mieczkowski
- High-Throughput Sequencing Facility, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Santiago Torres-Martínez
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Murcia 30100, Spain
| | - Rosa M Ruiz-Vázquez
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Murcia 30100, Spain
| | - Maria E Cardenas
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
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Granek JA, Murray D, Kayrkçi Ö, Magwene PM. The genetic architecture of biofilm formation in a clinical isolate of Saccharomyces cerevisiae. Genetics 2013; 193:587-600. [PMID: 23172850 PMCID: PMC3567746 DOI: 10.1534/genetics.112.142067] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 11/01/2012] [Indexed: 01/19/2023] Open
Abstract
Biofilms are microbial communities that form on surfaces. They are the primary form of microbial growth in nature and can have detrimental impacts on human health. Some strains of the budding yeast Saccharomyces cerevisiae form colony biofilms, and there is substantial variation in colony architecture between biofilm-forming strains. To identify the genetic basis of biofilm variation, we developed a novel version of quantitative trait locus mapping, which leverages cryptic variation in a clinical isolate of S. cerevisiae. We mapped 13 loci linked to heterogeneity in biofilm architecture and identified the gene most closely associated with each locus. Of these candidate genes, six are members of the cyclic AMP-protein kinase A pathway, an evolutionarily conserved cell signaling network. Principal among these is CYR1, which encodes the enzyme that catalyzes production of cAMP. Through a combination of gene expression measurements, cell signaling assays, and gene overexpression, we determined the functional effects of allelic variation at CYR1. We found that increased pathway activity resulting from protein coding and expression variation of CYR1 enhances the formation of colony biofilms. Four other candidate genes encode kinases and transcription factors that are targets of this pathway. The protein products of several of these genes together regulate expression of the sixth candidate, FLO11, which encodes a cell adhesion protein. Our results indicate that epistatic interactions between alleles with both positive and negative effects on cyclic AMP-protein kinase A signaling underlie much of the architectural variation we observe in colony biofilms. They are also among the first to demonstrate genetic variation acting at multiple levels of an integrated signaling and regulatory network. Based on these results, we propose a mechanistic model that relates genetic variation to gene network function and phenotypic outcomes.
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Affiliation(s)
- Joshua A. Granek
- Department of Biology and Center for Systems Biology, Duke University, Durham, North Carolina 27708
| | - Debra Murray
- Department of Biology and Center for Systems Biology, Duke University, Durham, North Carolina 27708
| | - Ömür Kayrkçi
- Department of Biology and Center for Systems Biology, Duke University, Durham, North Carolina 27708
| | - Paul M. Magwene
- Department of Biology and Center for Systems Biology, Duke University, Durham, North Carolina 27708
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Granek JA, Kayıkçı Ö, Magwene PM. Pleiotropic signaling pathways orchestrate yeast development. Curr Opin Microbiol 2011; 14:676-81. [PMID: 21962291 DOI: 10.1016/j.mib.2011.09.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Revised: 08/31/2011] [Accepted: 09/07/2011] [Indexed: 12/15/2022]
Abstract
Developmental phenotypes in Saccharomyces cerevisiae and related yeasts include responses such as filamentous growth, sporulation, and the formation of biofilms and complex colonies. These developmental phenotypes are regulated by evolutionarily conserved, nutrient-responsive signaling networks. The signaling mechanisms that control development in yeast are highly pleiotropic--all the known pathways contribute to the regulation of multiple developmental outcomes. This degree of pleiotropy implies that perturbations of these signaling pathways, whether genetic, biochemical, or environmentally induced, can manifest in multiple (and sometimes unexpected) ways. We summarize the current state of knowledge of developmental pleiotropy in yeast and discuss its implications for understanding functional relationships.
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Affiliation(s)
- Joshua A Granek
- Department of Biology and IGSP Center for Systems Biology, Duke University, Box 90338, Durham, NC 27708, USA
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15
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Abstract
Nutrient stresses trigger a variety of developmental switches in the budding yeast Saccharomyces cerevisiae. One of the least understood of such responses is the development of complex colony morphology, characterized by intricate, organized, and strain-specific patterns of colony growth and architecture. The genetic bases of this phenotype and the key environmental signals involved in its induction have heretofore remained poorly understood. By surveying multiple strain backgrounds and a large number of growth conditions, we show that limitation for fermentable carbon sources coupled with a rich nitrogen source is the primary trigger for the colony morphology response in budding yeast. Using knockout mutants and transposon-mediated mutagenesis, we demonstrate that two key signaling networks regulating this response are the filamentous growth MAP kinase cascade and the Ras-cAMP-PKA pathway. We further show synergistic epistasis between Rim15, a kinase involved in integration of nutrient signals, and other genes in these pathways. Ploidy, mating-type, and genotype-by-environment interactions also appear to play a role in the controlling colony morphology. Our study highlights the high degree of network reuse in this model eukaryote; yeast use the same core signaling pathways in multiple contexts to integrate information about environmental and physiological states and generate diverse developmental outputs.
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Affiliation(s)
- Joshua A. Granek
- Department of Biology and Center for Systems Biology, Duke University, Durham, North Carolina, United States of America
| | - Paul M. Magwene
- Department of Biology and Center for Systems Biology, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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16
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Granek JA, Gorbet DJ, Sergio LE. Extensive video-game experience alters cortical networks for complex visuomotor transformations. Cortex 2009; 46:1165-77. [PMID: 20060111 DOI: 10.1016/j.cortex.2009.10.009] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [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: 04/28/2009] [Revised: 09/24/2009] [Accepted: 10/23/2009] [Indexed: 11/18/2022]
Abstract
Using event-related functional magnetic resonance imaging (fMRI), we examined the effect of video-game experience on the neural control of increasingly complex visuomotor tasks. Previously, skilled individuals have demonstrated the use of a more efficient movement control brain network, including the prefrontal, premotor, primary sensorimotor and parietal cortices. Our results extend and generalize this finding by documenting additional prefrontal cortex activity in experienced video gamers planning for complex eye-hand coordination tasks that are distinct from actual video-game play. These changes in activation between non-gamers and extensive gamers are putatively related to the increased online control and spatial attention required for complex visually guided reaching. These data suggest that the basic cortical network for processing complex visually guided reaching is altered by extensive video-game play.
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Affiliation(s)
- Joshua A Granek
- School of Kinesiology and Health Science, York University, Toronto, ON, Canada
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17
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Liu X, Lee CK, Granek JA, Clarke ND, Lieb JD. Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. Genome Res 2006; 16:1517-28. [PMID: 17053089 PMCID: PMC1665635 DOI: 10.1101/gr.5655606] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [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: 01/27/2023]
Abstract
Sequence motifs that are potentially recognized by DNA-binding proteins occur far more often in genomic DNA than do observed in vivo protein-DNA interactions. To determine how chromatin influences the utilization of particular DNA-binding sites, we compared the in vivo genome-wide binding location of the yeast transcription factor Leu3 to the binding location observed on the same genomic DNA in the absence of any protein cofactors. We found that the DNA-sequence motif recognized by Leu3 in vitro and in vivo was functionally indistinguishable, but Leu3 bound different genomic locations under the two conditions. Accounting for nucleosome occupancy in addition to DNA-sequence motifs significantly improved the prediction of protein-DNA interactions in vivo, but not the prediction of sites bound by purified Leu3 in vitro. Use of histone modification data does not further improve binding predictions, presumably because their effect is already manifest in the global histone distribution. Measurements of nucleosome occupancy in strains that differ in Leu3 genotype show that low nucleosome occupancy at loci bound by Leu3 is not a consequence of Leu3 binding. These results permit quantitation of the epigenetic influence that chromatin exerts on DNA binding-site selection, and provide evidence for an instructive, functionally important role for nucleosome occupancy in determining patterns of regulatory factor targeting genome-wide.
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Affiliation(s)
- Xiao Liu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Cheol-Koo Lee
- Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Joshua A. Granek
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Neil D. Clarke
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
- Genome Institute of Singapore, #02-01 Genome, Singapore 138672
| | - Jason D. Lieb
- Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Corresponding author.E-mail ; fax (919) 962-1625
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18
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Granek JA, Clarke ND. Explicit equilibrium modeling of transcription-factor binding and gene regulation. Genome Biol 2005; 6:R87. [PMID: 16207358 PMCID: PMC1257470 DOI: 10.1186/gb-2005-6-10-r87] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2005] [Revised: 06/17/2005] [Accepted: 08/30/2005] [Indexed: 12/02/2022] Open
Abstract
A computational model, GOMER, is presented that predicts transcription-factor binding and incorporates effects of cooperativity and competition. We have developed a computational model that predicts the probability of transcription factor binding to any site in the genome. GOMER (generalizable occupancy model of expression regulation) calculates binding probabilities on the basis of position weight matrices, and incorporates the effects of cooperativity and competition by explicit calculation of coupled binding equilibria. GOMER can be used to test hypotheses regarding gene regulation that build upon this physically principled prediction of protein-DNA binding.
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Affiliation(s)
- Joshua A Granek
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, North Wolfe Street, Baltimore, MD 21205, USA
- National Evolutionary Synthesis Center, Broad Street, Durham, NC 27705, USA
| | - Neil D Clarke
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, North Wolfe Street, Baltimore, MD 21205, USA
- Genome Institute of Singapore, Biopolis Street, Singapore 138672, Republic of Singapore
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Abstract
MOTIVATION Genome sequences and transcriptome analyses allow the correlation between gene regulation and DNA sequence features to be studied at the whole-genome level. To quantify these correlations, metrics are needed that can be applied to any sequence feature, regardless of its statistical distribution. It is also desirable for the metric values to be determined objectively, that is, without the use of subjective threshold values. RESULTS We compare two metrics for quantifying the correlation of DNA sequence features with gene regulation. Each of the metrics is calculated from a rank-ordering of genes based on the value of the sequence feature of interest. The first metric is the area under the curve for a receiver operator characteristic plot (ROC AUC), a common way of summarizing the tradeoff between sensitivity and specificity for different values of a prediction criterion. We call the second metric the mean normalized conditional probability (MNCP). The MNCP can be thought of as the predictive value of the sequence feature averaged over all regulated genes. The statistical significance (P-value) of each metric can be estimated from simulations. Importantly, the P-value of the MNCP metric is less dramatically affected by the presence of false positives among the set of co-regulated genes than is the ROC AUC. This is especially useful in analyzing gene sets identified by DNA microarray analysis because such data cannot distinguish direct regulation by transcription factor binding from indirect regulation. We demonstrate that these two metrics, taken together, are useful tools for defining the binding site representation and regulatory control regions that best explain the difference between genes that are regulated by a given transcription factor and those that are not. Applications to other gene features are also described. AVAILABILITY A Python program for calculating the ROC AUC and MNCP metric values given input rank orders is available from ftp://ftp.bs.jhmi.edu/users/nclarke/MNCP/
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Affiliation(s)
- Neil D Clarke
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
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Senkevich TG, White CL, Weisberg A, Granek JA, Wolffe EJ, Koonin EV, Moss B. Expression of the vaccinia virus A2.5L redox protein is required for virion morphogenesis. Virology 2002; 300:296-303. [PMID: 12350360 DOI: 10.1006/viro.2002.1608] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [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: 11/22/2022]
Abstract
In this article we report the initial biochemical, genetic, and electron microscopic analysis of a previously uncharacterized, 8.9-kDa, predicted thiol-redox protein. The name A2.5L was assigned to the corresponding vaccinia virus gene, which is conserved in all sequenced poxviruses. Multiple alignment analysis and secondary structure prediction indicated that the A2.5L gene product is an all-alpha-helical protein with a conserved Cxx(x)C motif in the N-terminal alpha-helix. The DNA replication requirement and kinetics of A2.5L protein accumulation in virus-infected cells were typical of a late gene product, in agreement with the predicted promoter sequence. The A2.5L protein was a monomer under reducing conditions, but was mostly associated with the vaccinia virus E10R redox protein as a heterodimer under nonreducing conditions. The A2.5L protein was detected in virus particles at various stages of assembly, suggesting that it is an integral component of intracellular virions. An inducer-dependent A2.5L null mutant was constructed: in the absence of inducer, infectious virus formation was abolished and electron microscopy revealed an assembly block with an accumulation of crescent membranes and immature virions. This stage of assembly block was similar to that occurring when the E10R and G4L redox proteins were repressed, which is compatible with the involvement of E10R, A2.5L, and G4L in the same redox pathway.
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Affiliation(s)
- Tatiana G Senkevich
- Laboratory of viral Deseases, National Institute of Allergy and Infectious Desseases, Bethesda, Maryland 20892, USA
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21
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Noll DM, Gogos A, Granek JA, Clarke ND. The C-terminal domain of the adenine-DNA glycosylase MutY confers specificity for 8-oxoguanine.adenine mispairs and may have evolved from MutT, an 8-oxo-dGTPase. Biochemistry 1999; 38:6374-9. [PMID: 10350454 DOI: 10.1021/bi990335x] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.4] [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: 11/29/2022]
Abstract
MutY is an adenine-DNA glycosylase with specificity for mismatches involving 8-oxoguanine (oG.A) or guanine (G.A). In addition to a 25 kDa catalytic domain common to all members of its DNA glycosylase superfamily, MutY has a 14 kDa C-terminal domain. Sequence analyses suggest that this C-terminal domain is distantly related to MutT, a pyrophosphohydrolase specific for 2'-deoxy-8-oxoguanosine triphosphate (doGTP). Here we present biochemical evidence that the MutT-like domain of MutY is the principal determinant of oG specificity. First, MutY dissociates approximately 1500-fold more slowly from oG-containing product DNA than from G-containing product, but a truncated protein lacking the C-terminal domain dissociates as rapidly from oG-DNA as the full-length protein dissociates from G-DNA. Second, MutY removes adenine from oG.A mismatches almost 30-fold faster than from G.A mismatches in a pre-steady-state assay, but deletion of the C-terminal domain reduces this specificity for oG.A to less than 4-fold. The kinetic data are consistent with a model in which binding of oG to the C-terminal domain of MutY accelerates the pre-steady-state glycosylase reaction by facilitating adenine base flipping. The observation that oG specificity derives almost exclusively from the C-terminal domain of MutY adds credence to the sequence analyses and suggests that specificity for oG.A mismatches was acquired by fusion of a MutT-like protein onto the core catalytic domain of an adenine-DNA glycosylase.
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Affiliation(s)
- D M Noll
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
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