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Sarafrazi S, Daugherty SC, Miller N, Boada P, Carpenter TO, Chunn L, Dill K, Econs MJ, Eisenbeis S, Imel EA, Johnson B, Kiel MJ, Krolczyk S, Ramesan P, Truty R, Sabbagh Y. Cover, Volume 43, Issue 2. Hum Mutat 2022. [DOI: 10.1002/humu.24334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Sean C. Daugherty
- Medical Affairs Ultragenyx Pharmaceutical, Inc. Novato California USA
| | - Nicole Miller
- Medical Affairs Ultragenyx Pharmaceutical, Inc. Novato California USA
| | - Patrick Boada
- Medical Affairs Ultragenyx Pharmaceutical, Inc. Novato California USA
| | - Thomas O. Carpenter
- Department of Pediatrics (Endocrinology) Yale University School of Medicine New Haven Connecticut USA
| | - Lauren Chunn
- Data Science Genomenon Inc. Ann Arbor Michigan USA
| | - Kariena Dill
- Medical Affairs Ultragenyx Pharmaceutical, Inc. Novato California USA
| | - Michael J. Econs
- Division of Endocrinology and Metabolism Indiana University School of Medicine Indianapolis Indiana USA
| | - Scott Eisenbeis
- Medical Affairs Ultragenyx Pharmaceutical, Inc. Novato California USA
| | - Erik A. Imel
- Division of Endocrinology and Metabolism Indiana University School of Medicine Indianapolis Indiana USA
| | - Britt Johnson
- Medical Affairs Invitae Corporation San Francisco California USA
| | - Mark J. Kiel
- Data Science Genomenon Inc. Ann Arbor Michigan USA
| | - Stan Krolczyk
- Medical Affairs Ultragenyx Pharmaceutical, Inc. Novato California USA
| | - Prameela Ramesan
- Medical Affairs Ultragenyx Pharmaceutical, Inc. Novato California USA
| | - Rebecca Truty
- External Relations Invitae Corporation San Francisco California USA
| | - Yves Sabbagh
- Research and Development Inozyme Pharma Boston Massachusetts USA
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Sarafrazi S, Daugherty SC, Miller N, Boada P, Carpenter TO, Chunn L, Dill K, Econs MJ, Eisenbeis S, Imel EA, Johnson B, Kiel MJ, Krolczyk S, Ramesan P, Truty R, Sabbagh Y. Novel PHEX gene locus-specific database: Comprehensive characterization of vast number of variants associated with X-linked hypophosphatemia (XLH). Hum Mutat 2021; 43:143-157. [PMID: 34806794 PMCID: PMC9299612 DOI: 10.1002/humu.24296] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 02/01/2023]
Abstract
X‐linked hypophosphatemia (XLH), the most common form of hereditary hypophosphatemia, is caused by disrupting variants in the PHEX gene, located on the X chromosome. XLH is inherited in an X‐linked pattern with complete penetrance observed for both males and females. Patients experience lifelong symptoms resulting from chronic hypophosphatemia, including impaired bone mineralization, skeletal deformities, growth retardation, and diminished quality of life. This chronic condition requires life‐long management with disease‐specific therapies, which can improve patient outcomes especially when initiated early in life. To centralize and disseminate PHEX variant information, we have established a new PHEX gene locus‐specific database, PHEX LSDB. As of April 30, 2021, 870 unique PHEX variants, compiled from an older database of PHEX variants, a comprehensive literature search, a sponsored genetic testing program, and XLH clinical trials, are represented in the PHEX LSDB. This resource is publicly available on an interactive, searchable website (https://www.rarediseasegenes.com/), which includes a table of variants and associated data, graphical/tabular outputs of genotype‐phenotype analyses, and an online submission form for reporting new PHEX variants. The database will be updated regularly with new variants submitted on the website, identified in the published literature, or shared from genetic testing programs.
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Affiliation(s)
- Soodabeh Sarafrazi
- Medical Affairs, Ultragenyx Pharmaceutical, Inc., Novato, California, USA
| | - Sean C Daugherty
- Medical Affairs, Ultragenyx Pharmaceutical, Inc., Novato, California, USA
| | - Nicole Miller
- Medical Affairs, Ultragenyx Pharmaceutical, Inc., Novato, California, USA
| | - Patrick Boada
- Medical Affairs, Ultragenyx Pharmaceutical, Inc., Novato, California, USA
| | - Thomas O Carpenter
- Department of Pediatrics (Endocrinology), Yale University School of Medicine, New Haven, Connecticut, USA
| | - Lauren Chunn
- Data Science, Genomenon Inc., Ann Arbor, Michigan, USA
| | - Kariena Dill
- Medical Affairs, Ultragenyx Pharmaceutical, Inc., Novato, California, USA
| | - Michael J Econs
- Division of Endocrinology and Metabolism, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Scott Eisenbeis
- Medical Affairs, Ultragenyx Pharmaceutical, Inc., Novato, California, USA
| | - Erik A Imel
- Division of Endocrinology and Metabolism, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Britt Johnson
- Medical Affairs, Invitae Corporation, San Francisco, California, USA
| | - Mark J Kiel
- Data Science, Genomenon Inc., Ann Arbor, Michigan, USA
| | - Stan Krolczyk
- Medical Affairs, Ultragenyx Pharmaceutical, Inc., Novato, California, USA
| | - Prameela Ramesan
- Medical Affairs, Ultragenyx Pharmaceutical, Inc., Novato, California, USA
| | - Rebecca Truty
- External Relations, Invitae Corporation, San Francisco, California, USA
| | - Yves Sabbagh
- Research and Development, Inozyme Pharma, Boston, Massachusetts, USA
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Lin M, Xiong Q, Chung M, Daugherty SC, Nagaraj S, Sengamalay N, Ott S, Godinez A, Tallon LJ, Sadzewicz L, Fraser C, Dunning Hotopp JC, Rikihisa Y. Comparative Analysis of Genome of Ehrlichia sp. HF, a Model Bacterium to Study Fatal Human Ehrlichiosis. BMC Genomics 2021; 22:11. [PMID: 33407096 PMCID: PMC7789307 DOI: 10.1186/s12864-020-07309-z] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 12/07/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The genus Ehrlichia consists of tick-borne obligatory intracellular bacteria that can cause deadly diseases of medical and agricultural importance. Ehrlichia sp. HF, isolated from Ixodes ovatus ticks in Japan [also referred to as I. ovatus Ehrlichia (IOE) agent], causes acute fatal infection in laboratory mice that resembles acute fatal human monocytic ehrlichiosis caused by Ehrlichia chaffeensis. As there is no small laboratory animal model to study fatal human ehrlichiosis, Ehrlichia sp. HF provides a needed disease model. However, the inability to culture Ehrlichia sp. HF and the lack of genomic information have been a barrier to advance this animal model. In addition, Ehrlichia sp. HF has several designations in the literature as it lacks a taxonomically recognized name. RESULTS We stably cultured Ehrlichia sp. HF in canine histiocytic leukemia DH82 cells from the HF strain-infected mice, and determined its complete genome sequence. Ehrlichia sp. HF has a single double-stranded circular chromosome of 1,148,904 bp, which encodes 866 proteins with a similar metabolic potential as E. chaffeensis. Ehrlichia sp. HF encodes homologs of all virulence factors identified in E. chaffeensis, including 23 paralogs of P28/OMP-1 family outer membrane proteins, type IV secretion system apparatus and effector proteins, two-component systems, ankyrin-repeat proteins, and tandem repeat proteins. Ehrlichia sp. HF is a novel species in the genus Ehrlichia, as demonstrated through whole genome comparisons with six representative Ehrlichia species, subspecies, and strains, using average nucleotide identity, digital DNA-DNA hybridization, and core genome alignment sequence identity. CONCLUSIONS The genome of Ehrlichia sp. HF encodes all known virulence factors found in E. chaffeensis, substantiating it as a model Ehrlichia species to study fatal human ehrlichiosis. Comparisons between Ehrlichia sp. HF and E. chaffeensis will enable identification of in vivo virulence factors that are related to host specificity, disease severity, and host inflammatory responses. We propose to name Ehrlichia sp. HF as Ehrlichia japonica sp. nov. (type strain HF), to denote the geographic region where this bacterium was initially isolated.
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Affiliation(s)
- Mingqun Lin
- Department of Veterinary Biosciences, The Ohio State University, 1925 Coffey Road, Columbus, OH, 43210, USA.
| | - Qingming Xiong
- Department of Veterinary Biosciences, The Ohio State University, 1925 Coffey Road, Columbus, OH, 43210, USA
| | - Matthew Chung
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD, 21201, USA
| | - Sean C Daugherty
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD, 21201, USA
| | - Sushma Nagaraj
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD, 21201, USA
| | - Naomi Sengamalay
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD, 21201, USA
| | - Sandra Ott
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD, 21201, USA
| | - Al Godinez
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD, 21201, USA
| | - Luke J Tallon
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD, 21201, USA
| | - Lisa Sadzewicz
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD, 21201, USA
| | - Claire Fraser
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD, 21201, USA
- Department of Medicine, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD, 21201, USA
| | - Julie C Dunning Hotopp
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD, 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD, 21201, USA
- Greenebaum Cancer Center, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD, 21201, USA
| | - Yasuko Rikihisa
- Department of Veterinary Biosciences, The Ohio State University, 1925 Coffey Road, Columbus, OH, 43210, USA.
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4
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Korol CB, Shallom SJ, Arora K, Boshoff HI, Freeman AF, King A, Agrawal S, Daugherty SC, Jancel T, Kabat J, Ganesan S, Torrero MN, Sampaio EP, Barry C, Holland SM, Tettelin H, Rosenzweig SD, Zelazny AM. Tissue specific diversification, virulence and immune response to Mycobacterium bovis BCG in a patient with an IFN-γ R1 deficiency. Virulence 2020; 11:1656-1673. [PMID: 33356838 PMCID: PMC7781554 DOI: 10.1080/21505594.2020.1848108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/25/2020] [Accepted: 11/05/2020] [Indexed: 11/16/2022] Open
Abstract
Summary: We characterized Mycobacterium bovis BCG isolates found in lung and brain samples from a previously vaccinated patient with IFNγR1 deficiency. The isolates collected displayed distinct genomic and phenotypic features consistent with host adaptation and associated changes in antibiotic susceptibility and virulence traits. Background: We report a case of a patient with partial recessive IFNγR1 deficiency who developed disseminated BCG infection after neonatal vaccination (BCG-vaccine). Distinct M. bovis BCG-vaccine derived clinical strains were recovered from the patient's lungs and brain. Methods: BCG strains were phenotypically (growth, antibiotic susceptibility, lipid) and genetically (whole genome sequencing) characterized. Mycobacteria cell infection models were used to assess apoptosis, necrosis, cytokine release, autophagy, and JAK-STAT signaling. Results: Clinical isolates BCG-brain and BCG-lung showed distinct Rv0667 rpoB mutations conferring high- and low-level rifampin resistance; the latter displayed clofazimine resistance through Rv0678 gene (MarR-like transcriptional regulator) mutations. BCG-brain and BCG-lung showed mutations in fadA2, fadE5, and mymA operon genes, respectively. Lipid profiles revealed reduced levels of PDIM in BCG-brain and BCG-lung and increased TAGs and Mycolic acid components in BCG-lung, compared to parent BCG-vaccine. In vitro infected cells showed that the BCG-lung induced a higher cytokine release, necrosis, and cell-associated bacterial load effect when compared to BCG-brain; conversely, both strains inhibited apoptosis and altered JAK-STAT signaling. Conclusions: During a chronic-disseminated BCG infection, BCG strains can evolve independently at different sites likely due to particular microenvironment features leading to differential antibiotic resistance, virulence traits resulting in dissimilar responses in different host tissues.
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Affiliation(s)
- Cecilia B. Korol
- Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, USA
| | | | - Kriti Arora
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, USA
| | - Helena I. Boshoff
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, USA
| | - Alexandra F. Freeman
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, USA
| | - Alejandra King
- Department of Pediatric Immunology, Hospital Luis Calvo MacKenna, Universidad De, Chile, Chile
| | - Sonia Agrawal
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA
| | - Sean C. Daugherty
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA
| | - Timothy Jancel
- Department of Pharmacy, Clinical Center, NIH, Bethesda, USA
| | - Juraj Kabat
- Department Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, USA
| | - Sundar Ganesan
- Department Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, USA
| | - Marina N. Torrero
- Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, USA
| | - Elizabeth P. Sampaio
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, USA
| | - Clifton Barry
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, USA
| | - Steve M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, USA
| | - Hervé Tettelin
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA
| | | | - Adrian M. Zelazny
- Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, USA
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5
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Shenoy AT, Brissac T, Gilley RP, Kumar N, Wang Y, Gonzalez-Juarbe N, Hinkle WS, Daugherty SC, Shetty AC, Ott S, Tallon LJ, Deshane J, Tettelin H, Orihuela CJ. Streptococcus pneumoniae in the heart subvert the host response through biofilm-mediated resident macrophage killing. PLoS Pathog 2017; 13:e1006582. [PMID: 28841717 PMCID: PMC5589263 DOI: 10.1371/journal.ppat.1006582] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [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: 04/11/2017] [Revised: 09/07/2017] [Accepted: 08/15/2017] [Indexed: 11/18/2022] Open
Abstract
For over 130 years, invasive pneumococcal disease has been associated with the presence of extracellular planktonic pneumococci, i.e. diplococci or short chains in affected tissues. Herein, we show that Streptococcus pneumoniae that invade the myocardium instead replicate within cellular vesicles and transition into non-purulent biofilms. Pneumococci within mature cardiac microlesions exhibited salient biofilm features including intrinsic resistance to antibiotic killing and the presence of an extracellular matrix. Dual RNA-seq and subsequent principal component analyses of heart- and blood-isolated pneumococci confirmed the biofilm phenotype in vivo and revealed stark anatomical site-specific differences in virulence gene expression; the latter having major implications on future vaccine antigen selection. Our RNA-seq approach also identified three genomic islands as exclusively expressed in vivo. Deletion of one such island, Region of Diversity 12, resulted in a biofilm-deficient and highly inflammogenic phenotype within the heart; indicating a possible link between the biofilm phenotype and a dampened host-response. We subsequently determined that biofilm pneumococci released greater amounts of the toxin pneumolysin than did planktonic or RD12 deficient pneumococci. This allowed heart-invaded wildtype pneumococci to kill resident cardiac macrophages and subsequently subvert cytokine/chemokine production and neutrophil infiltration into the myocardium. This is the first report for pneumococcal biofilm formation in an invasive disease setting. We show that biofilm pneumococci actively suppress the host response through pneumolysin-mediated immune cell killing. As such, our findings contradict the emerging notion that biofilm pneumococci are passively immunoquiescent.
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Affiliation(s)
- Anukul T. Shenoy
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, United States of America
- Department of Microbiology, Immunology, and Molecular Genetics, The University of Texas Health San Antonio, San Antonio, TX, United States of America
| | - Terry Brissac
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Ryan P. Gilley
- Department of Microbiology, Immunology, and Molecular Genetics, The University of Texas Health San Antonio, San Antonio, TX, United States of America
| | - Nikhil Kumar
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Yong Wang
- Division of Pulmonary, Allergy & Critical Care Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Norberto Gonzalez-Juarbe
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Whitney S. Hinkle
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Sean C. Daugherty
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Amol C. Shetty
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Sandra Ott
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Luke J. Tallon
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Jessy Deshane
- Division of Pulmonary, Allergy & Critical Care Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Hervé Tettelin
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Carlos J. Orihuela
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, United States of America
- Department of Microbiology, Immunology, and Molecular Genetics, The University of Texas Health San Antonio, San Antonio, TX, United States of America
- * E-mail:
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6
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Lin M, Bachman K, Cheng Z, Daugherty SC, Nagaraj S, Sengamalay N, Ott S, Godinez A, Tallon LJ, Sadzewicz L, Fraser C, Dunning Hotopp JC, Rikihisa Y. Analysis of complete genome sequence and major surface antigens of Neorickettsia helminthoeca, causative agent of salmon poisoning disease. Microb Biotechnol 2017; 10:933-957. [PMID: 28585301 PMCID: PMC5481527 DOI: 10.1111/1751-7915.12731] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 03/09/2017] [Accepted: 04/25/2017] [Indexed: 12/31/2022] Open
Abstract
Neorickettsia helminthoeca, a type species of the genus Neorickettsia, is an endosymbiont of digenetic trematodes of veterinary importance. Upon ingestion of salmonid fish parasitized with infected trematodes, canids develop salmon poisoning disease (SPD), an acute febrile illness that is particularly severe and often fatal in dogs without adequate treatment. We determined and analysed the complete genome sequence of N. helminthoeca: a single small circular chromosome of 884 232 bp encoding 774 potential proteins. N. helminthoeca is unable to synthesize lipopolysaccharides and most amino acids, but is capable of synthesizing vitamins, cofactors, nucleotides and bacterioferritin. N. helminthoeca is, however, distinct from majority of the family Anaplasmataceae to which it belongs, as it encodes nearly all enzymes required for peptidoglycan biosynthesis, suggesting its structural hardiness and inflammatory potential. Using sera from dogs that were experimentally infected by feeding with parasitized fish or naturally infected in southern California, Western blot analysis revealed that among five predicted N. helminthoeca outer membrane proteins, P51 and strain‐variable surface antigen were uniformly recognized. Our finding will help understanding pathogenesis, prevalence of N. helminthoeca infection among trematodes, canids and potentially other animals in nature to develop effective SPD diagnostic and preventive measures. Recent progresses in large‐scale genome sequencing have been uncovering broad distribution of Neorickettsia spp., the comparative genomics will facilitate understanding of biology and the natural history of these elusive environmental bacteria.
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Affiliation(s)
- Mingqun Lin
- Department of Veterinary Biosciences, The Ohio State University, 1925 Coffey Road, Columbus, OH, 43210, USA
| | - Katherine Bachman
- Department of Veterinary Biosciences, The Ohio State University, 1925 Coffey Road, Columbus, OH, 43210, USA
| | - Zhihui Cheng
- Department of Veterinary Biosciences, The Ohio State University, 1925 Coffey Road, Columbus, OH, 43210, USA
| | - Sean C Daugherty
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD, 21201, USA
| | - Sushma Nagaraj
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD, 21201, USA
| | - Naomi Sengamalay
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD, 21201, USA
| | - Sandra Ott
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD, 21201, USA
| | - Al Godinez
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD, 21201, USA
| | - Luke J Tallon
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD, 21201, USA
| | - Lisa Sadzewicz
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD, 21201, USA
| | - Claire Fraser
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD, 21201, USA.,Department of Medicine, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD, 21201, USA
| | - Julie C Dunning Hotopp
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD, 21201, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, 801 W. Baltimore St, Baltimore, MD, 21201, USA
| | - Yasuko Rikihisa
- Department of Veterinary Biosciences, The Ohio State University, 1925 Coffey Road, Columbus, OH, 43210, USA
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7
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Abstract
We have recently identified small molecule compounds that act as binders of Lipid II, an essential precursor of bacterial cell wall biosynthesis. Lipid II comprised a hydrophilic head group that includes a peptidoglycan subunit composed of N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc) coupled to a short pentapeptide moiety. This headgroup is coupled to a long bactoprenol chain via a pyrophosphate group. Here, we report on the cell wall activity relationship of dimethyl-3-methyl(phenyl)amino-ethenylcyclohexylidene-propenyl-3-ethyl-1,3-benzothiazolium iodide (compound 5107930) obtained by functional and genetic analyses. Our results indicate that compounds bind to Lipid II and cause specific upregulation of the vancomycin-resistance associated gene vraX. vraX is implicated in the cell wall stress stimulon that confers glycopeptide resistance. Our small molecule Lipid II inhibitor retained activity against strains of Staphylococcus aureus mutated in genes encoding the cell wall stress stimulon. This suggests the feasibility of developing this new scaffold as a therapeutic agent in view of increasing glycopeptide resistance.
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Affiliation(s)
- Jakob Malin
- Institute of Human Virology; Department of Biochemistry and Molecular Biology
| | - Amol C Shetty
- Institute for Genome Sciences, University of Maryland Baltimore School of Medicine, Baltimore, MD, USA
| | - Sean C Daugherty
- Institute for Genome Sciences, University of Maryland Baltimore School of Medicine, Baltimore, MD, USA
| | - Erik Ph de Leeuw
- Institute of Human Virology; Department of Biochemistry and Molecular Biology
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8
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Hazen TH, Daugherty SC, Shetty A, Mahurkar AA, White O, Kaper JB, Rasko DA. RNA-Seq analysis of isolate- and growth phase-specific differences in the global transcriptomes of enteropathogenic Escherichia coli prototype isolates. Front Microbiol 2015; 6:569. [PMID: 26124752 PMCID: PMC4464170 DOI: 10.3389/fmicb.2015.00569] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [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: 03/25/2015] [Accepted: 05/24/2015] [Indexed: 11/13/2022] Open
Abstract
Enteropathogenic Escherichia coli (EPEC) are a leading cause of diarrheal illness among infants in developing countries. E. coli isolates classified as typical EPEC are identified by the presence of the locus of enterocyte effacement (LEE) and the bundle-forming pilus (BFP), and absence of the Shiga-toxin genes, while the atypical EPEC also encode LEE but do not encode BFP or Shiga-toxin. Comparative genomic analyses have demonstrated that EPEC isolates belong to diverse evolutionary lineages and possess lineage- and isolate-specific genomic content. To investigate whether this genomic diversity results in significant differences in global gene expression, we used an RNA sequencing (RNA-Seq) approach to characterize the global transcriptomes of the prototype typical EPEC isolates E2348/69, B171, C581-05, and the prototype atypical EPEC isolate E110019. The global transcriptomes were characterized during laboratory growth in two different media and three different growth phases, as well as during adherence of the EPEC isolates to human cells using in vitro tissue culture assays. Comparison of the global transcriptomes during these conditions was used to identify isolate- and growth phase-specific differences in EPEC gene expression. These analyses resulted in the identification of genes that encode proteins involved in survival and metabolism that were coordinately expressed with virulence factors. These findings demonstrate there are isolate- and growth phase-specific differences in the global transcriptomes of EPEC prototype isolates, and highlight the utility of comparative transcriptomics for identifying additional factors that are directly or indirectly involved in EPEC pathogenesis.
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Affiliation(s)
- Tracy H Hazen
- Institute for Genome Sciences, University of Maryland School of Medicine Baltimore, MD, USA ; Department of Microbiology and Immunology, University of Maryland School of Medicine Baltimore, MD, USA
| | - Sean C Daugherty
- Institute for Genome Sciences, University of Maryland School of Medicine Baltimore, MD, USA
| | - Amol Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine Baltimore, MD, USA
| | - Anup A Mahurkar
- Institute for Genome Sciences, University of Maryland School of Medicine Baltimore, MD, USA
| | - Owen White
- Institute for Genome Sciences, University of Maryland School of Medicine Baltimore, MD, USA
| | - James B Kaper
- Department of Microbiology and Immunology, University of Maryland School of Medicine Baltimore, MD, USA
| | - David A Rasko
- Institute for Genome Sciences, University of Maryland School of Medicine Baltimore, MD, USA ; Department of Microbiology and Immunology, University of Maryland School of Medicine Baltimore, MD, USA
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9
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Chancey ST, Bai X, Kumar N, Drabek EF, Daugherty SC, Colon T, Ott S, Sengamalay N, Sadzewicz L, Tallon LJ, Fraser CM, Tettelin H, Stephens DS. Transcriptional attenuation controls macrolide inducible efflux and resistance in Streptococcus pneumoniae and in other Gram-positive bacteria containing mef/mel(msr(D)) elements. PLoS One 2015; 10:e0116254. [PMID: 25695510 PMCID: PMC4335068 DOI: 10.1371/journal.pone.0116254] [Citation(s) in RCA: 31] [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: 08/06/2014] [Accepted: 12/04/2014] [Indexed: 01/30/2023] Open
Abstract
Macrolide resistance, emerging in Streptococcus pneumoniae and other Gram-positive bacteria, is increasingly due to efflux pumps encoded by mef/mel(msr) operons found on discrete mobile genetic elements. The regulation of mef/mel(msr) in these elements is not well understood. We identified the mef(E)/mel transcriptional start, localized the mef(E)/mel promoter, and demonstrated attenuation of transcription as a mechanism of regulation of macrolide-inducible mef-mediated macrolide resistance in S. pneumoniae. The mef(E)/mel transcriptional start site was a guanine 327 bp upstream of mef(E). Consensus pneumococcal promoter -10 (5′-TATACT-3′) and -35 (5′-TTGAAC-3′) boxes separated by 17 bp were identified 7 bp upstream of the start site. Analysis of the predicted secondary structure of the 327 5’ region identified four pairs of inverted repeats R1-R8 predicted to fold into stem-loops, a small leader peptide [MTASMRLR, (Mef(E)L)] required for macrolide induction and a Rho-independent transcription terminator. RNA-seq analyses provided confirmation of transcriptional attenuation. In addition, expression of mef(E)L was also influenced by mef(E)L-dependent mRNA stability. The regulatory region 5’ of mef(E) was highly conserved in other mef/mel(msr)-containing elements including Tn1207.1 and the 5612IQ complex in pneumococci and Tn1207.3 in Group A streptococci, indicating a regulatory mechanism common to a wide variety of Gram-positive bacteria containing mef/mel(msr) elements.
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Affiliation(s)
- Scott T. Chancey
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Laboratories of Microbial Pathogenesis, Department of Veterans Affairs Medical Center, Atlanta, Georgia, United States of America
| | - Xianhe Bai
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Laboratories of Microbial Pathogenesis, Department of Veterans Affairs Medical Center, Atlanta, Georgia, United States of America
| | - Nikhil Kumar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Elliott F. Drabek
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Sean C. Daugherty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Thomas Colon
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Sandra Ott
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Naomi Sengamalay
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Lisa Sadzewicz
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Luke J. Tallon
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Claire M. Fraser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Hervé Tettelin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - David S. Stephens
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Laboratories of Microbial Pathogenesis, Department of Veterans Affairs Medical Center, Atlanta, Georgia, United States of America
- * E-mail:
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10
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Tettelin H, Davidson RM, Agrawal S, Aitken ML, Shallom S, Hasan NA, Strong M, de Moura VCN, De Groote MA, Duarte RS, Hine E, Parankush S, Su Q, Daugherty SC, Fraser CM, Brown-Elliott BA, Wallace RJ, Holland SM, Sampaio EP, Olivier KN, Jackson M, Zelazny AM. High-level relatedness among Mycobacterium abscessus subsp. massiliense strains from widely separated outbreaks. Emerg Infect Dis 2015; 20:364-71. [PMID: 24565502 PMCID: PMC3944860 DOI: 10.3201/eid2003.131106] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Three recently sequenced strains isolated from patients during an outbreak of Mycobacterium abscessus subsp. massiliense infections at a cystic fibrosis center in the United States were compared with 6 strains from an outbreak at a cystic fibrosis center in the United Kingdom and worldwide strains. Strains from the 2 cystic fibrosis outbreaks showed high-level relatedness with each other and major-level relatedness with strains that caused soft tissue infections during an epidemic in Brazil. We identified unique single-nucleotide polymorphisms in cystic fibrosis and soft tissue outbreak strains, separate single-nucleotide polymorphisms only in cystic fibrosis outbreak strains, and unique genomic traits for each subset of isolates. Our findings highlight the necessity of identifying M. abscessus to the subspecies level and screening all cystic fibrosis isolates for relatedness to these outbreak strains. We propose 2 diagnostic strategies that use partial sequencing of rpoB and secA1 genes and a multilocus sequence typing protocol.
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11
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Hiller NL, Eutsey RA, Powell E, Earl JP, Janto B, Martin DP, Dawid S, Ahmed A, Longwell MJ, Dahlgren ME, Ezzo S, Tettelin H, Daugherty SC, Mitchell TJ, Hillman TA, Buchinsky FJ, Tomasz A, de Lencastre H, Sá-Leão R, Post JC, Hu FZ, Ehrlich GD. Differences in genotype and virulence among four multidrug-resistant Streptococcus pneumoniae isolates belonging to the PMEN1 clone. PLoS One 2011; 6:e28850. [PMID: 22205975 PMCID: PMC3242761 DOI: 10.1371/journal.pone.0028850] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [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: 06/07/2011] [Accepted: 11/16/2011] [Indexed: 11/19/2022] Open
Abstract
We report on the comparative genomics and characterization of the virulence phenotypes of four S. pneumoniae strains that belong to the multidrug resistant clone PMEN1 (Spain23F ST81). Strains SV35-T23 and SV36-T3 were recovered in 1996 from the nasopharynx of patients at an AIDS hospice in New York. Strain SV36-T3 expressed capsule type 3 which is unusual for this clone and represents the product of an in vivo capsular switch event. A third PMEN1 isolate – PN4595-T23 – was recovered in 1996 from the nasopharynx of a child attending day care in Portugal, and a fourth strain – ATCC700669 – was originally isolated from a patient with pneumococcal disease in Spain in 1984. We compared the genomes among four PMEN1 strains and 47 previously sequenced pneumococcal isolates for gene possession differences and allelic variations within core genes. In contrast to the 47 strains – representing a variety of clonal types – the four PMEN1 strains grouped closely together, demonstrating high genomic conservation within this lineage relative to the rest of the species. In the four PMEN1 strains allelic and gene possession differences were clustered into 18 genomic regions including the capsule, the blp bacteriocins, erythromycin resistance, the MM1-2008 prophage and multiple cell wall anchored proteins. In spite of their genomic similarity, the high resolution chinchilla model was able to detect variations in virulence properties of the PMEN1 strains highlighting how small genic or allelic variation can lead to significant changes in pathogenicity and making this set of strains ideal for the identification of novel virulence determinants.
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Affiliation(s)
- N Luisa Hiller
- Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences, Pittsburgh, Pennsylvania, United States of America
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12
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Madhusoodanan J, Seo KS, Remortel B, Park JY, Hwang SY, Fox LK, Park YH, Deobald CF, Wang D, Liu S, Daugherty SC, Gill AL, Bohach GA, Gill SR. An Enterotoxin-Bearing Pathogenicity Island in Staphylococcus epidermidis. J Bacteriol 2011; 193:1854-62. [PMID: 21317317 PMCID: PMC3133018 DOI: 10.1128/jb.00162-10] [Citation(s) in RCA: 46] [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] [Received: 02/15/2010] [Accepted: 02/01/2011] [Indexed: 11/20/2022] Open
Abstract
Cocolonization of human mucosal surfaces causes frequent encounters between various staphylococcal species, creating opportunities for the horizontal acquisition of mobile genetic elements. The majority of Staphylococcus aureus toxins and virulence factors are encoded on S. aureus pathogenicity islands (SaPIs). Horizontal movement of SaPIs between S. aureus strains plays a role in the evolution of virulent clinical isolates. Although there have been reports of the production of toxic shock syndrome toxin 1 (TSST-1), enterotoxin, and other superantigens by coagulase-negative staphylococci, no associated pathogenicity islands have been found in the genome of Staphylococcus epidermidis, a generally less virulent relative of S. aureus. We show here the first evidence of a composite S. epidermidis pathogenicity island (SePI), the product of multiple insertions in the genome of a clinical isolate. The taxonomic placement of S. epidermidis strain FRI909 was confirmed by a number of biochemical tests and multilocus sequence typing. The genome sequence of this strain was analyzed for other unique gene clusters and their locations. This pathogenicity island encodes and expresses staphylococcal enterotoxin C3 (SEC3) and staphylococcal enterotoxin-like toxin L (SElL), as confirmed by quantitative reverse transcription-PCR (qRT-PCR) and immunoblotting. We present here an initial characterization of this novel pathogenicity island, and we establish that it is stable, expresses enterotoxins, and is not obviously transmissible by phage transduction. We also describe the genome sequence, excision, replication, and packaging of a novel bacteriophage in S. epidermidis FRI909, as well as attempts to mobilize the SePI element by this phage.
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Affiliation(s)
| | - Keun Seok Seo
- Department of Microbiology, Molecular Biology and Biochemistry, University of Idaho, Moscow, Idaho
| | | | - Joo Youn Park
- Department of Veterinary Medicine, Washington State University, Pullman, Washington
| | - Sun Young Hwang
- Department of Microbiology, Molecular Biology and Biochemistry, University of Idaho, Moscow, Idaho
- Department of Microbiology, College of Veterinary Medicine and School of Agricultural Biotechnology, Seoul National University, Seoul 151-742, South Korea
| | - Lawrence K. Fox
- Department of Veterinary Medicine, Washington State University, Pullman, Washington
| | - Yong Ho Park
- Department of Microbiology, College of Veterinary Medicine and School of Agricultural Biotechnology, Seoul National University, Seoul 151-742, South Korea
| | - Claudia F. Deobald
- Department of Microbiology, Molecular Biology and Biochemistry, University of Idaho, Moscow, Idaho
| | - Dan Wang
- Department of Biostatistics, Roswell Park Cancer Institute, Buffalo, New York
| | - Song Liu
- Department of Biostatistics, Roswell Park Cancer Institute, Buffalo, New York
| | - Sean C. Daugherty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland
| | - Ann Lindley Gill
- Departments of Oral Biology
- Infectious Disease and Genomics, NYS Center of Excellence in Bioinformatics and Life Sciences, The State University of New York
| | - Gregory A. Bohach
- Department of Microbiology, Molecular Biology and Biochemistry, University of Idaho, Moscow, Idaho
| | - Steven R. Gill
- Departments of Oral Biology
- Microbiology and Immunology
- Infectious Disease and Genomics, NYS Center of Excellence in Bioinformatics and Life Sciences, The State University of New York
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13
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Morrison M, Daugherty SC, Nelson WC, Davidsen T, Nelson KE. The FibRumBa database: a resource for biologists with interests in gastrointestinal microbial ecology, plant biomass degradation, and anaerobic microbiology. Microb Ecol 2010; 59:212-213. [PMID: 19609599 DOI: 10.1007/s00248-009-9562-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Accepted: 06/29/2009] [Indexed: 05/28/2023]
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14
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Mongodin EF, Shapir N, Daugherty SC, DeBoy RT, Emerson JB, Shvartzbeyn A, Radune D, Vamathevan J, Riggs F, Grinberg V, Khouri H, Wackett LP, Nelson KE, Sadowsky MJ. Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1. PLoS Genet 2007; 2:e214. [PMID: 17194220 PMCID: PMC1713258 DOI: 10.1371/journal.pgen.0020214] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2006] [Accepted: 11/02/2006] [Indexed: 01/24/2023] Open
Abstract
Arthrobacter sp. strains are among the most frequently isolated, indigenous, aerobic bacterial genera found in soils. Member of the genus are metabolically and ecologically diverse and have the ability to survive in environmentally harsh conditions for extended periods of time. The genome of Arthrobacter aurescens strain TC1, which was originally isolated from soil at an atrazine spill site, is composed of a single 4,597,686 basepair (bp) circular chromosome and two circular plasmids, pTC1 and pTC2, which are 408,237 bp and 300,725 bp, respectively. Over 66% of the 4,702 open reading frames (ORFs) present in the TC1 genome could be assigned a putative function, and 13.2% (623 genes) appear to be unique to this bacterium, suggesting niche specialization. The genome of TC1 is most similar to that of Tropheryma, Leifsonia, Streptomyces, and Corynebacterium glutamicum, and analyses suggest that A. aurescens TC1 has expanded its metabolic abilities by relying on the duplication of catabolic genes and by funneling metabolic intermediates generated by plasmid-borne genes to chromosomally encoded pathways. The data presented here suggest that Arthrobacter's environmental prevalence may be due to its ability to survive under stressful conditions induced by starvation, ionizing radiation, oxygen radicals, and toxic chemicals. Soil systems contain the greatest diversity of microorganisms on earth, with 5,000–10,000 species of microorganism per gram of soil. Arthrobacter sp. strains have a primitive life cycle and are among the most frequently isolated, indigenous soil bacteria, found in common and deep subsurface soils, arctic ice, and environments contaminated with industrial chemicals and radioactive materials. To better understand how these bacteria survive in environmentally harsh conditions, the authors used a structural genomics approach to identify genes involved in soil survival of Arthrobacter aurescens strain TC1, a bacterium originally isolated for its ability to degrade the herbicide atrazine. They found that the genome of this bacterium comprises a single circular chromosome and two plasmids that encode for a large number proteins involved in stress responses due to starvation, desiccation, oxygen radicals, and toxic chemicals. A. aurescens' metabolic versatility is in part due to the presence of duplicated catabolic genes and its ability to funnel plasmid-derived intermediates into chromosomally encoded pathways. Arthrobacter's array of genes that allow for survival in stressful conditions and its ability to produce a temperature-tolerant “cyst”-like resting cell render this soil microorganism able to survive and prosper in a variety of environmental conditions.
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Affiliation(s)
- Emmanuel F Mongodin
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Nir Shapir
- The BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Sean C Daugherty
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Robert T DeBoy
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Joanne B Emerson
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Alla Shvartzbeyn
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Diana Radune
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Jessica Vamathevan
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Florenta Riggs
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Viktoria Grinberg
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Hoda Khouri
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Lawrence P Wackett
- The BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Karen E Nelson
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Michael J Sadowsky
- The BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- * To whom correspondence should be addressed. E-mail:
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15
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Wu D, Daugherty SC, Van Aken SE, Pai GH, Watkins KL, Khouri H, Tallon LJ, Zaborsky JM, Dunbar HE, Tran PL, Moran NA, Eisen JA. Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters. PLoS Biol 2007; 4:e188. [PMID: 16729848 PMCID: PMC1472245 DOI: 10.1371/journal.pbio.0040188] [Citation(s) in RCA: 296] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2005] [Accepted: 04/10/2006] [Indexed: 11/19/2022] Open
Abstract
Mutualistic intracellular symbiosis between bacteria and insects is a widespread phenomenon that has contributed to the global success of insects. The symbionts, by provisioning nutrients lacking from diets, allow various insects to occupy or dominate ecological niches that might otherwise be unavailable. One such insect is the glassy-winged sharpshooter
(Homalodisca coagulata), which feeds on xylem fluid, a diet exceptionally poor in organic nutrients. Phylogenetic studies based on rRNA have shown two types of bacterial symbionts to be coevolving with sharpshooters: the gamma-proteobacterium
Baumannia cicadellinicola and the
Bacteroidetes species
Sulcia muelleri. We report here the sequencing and analysis of the 686,192–base pair genome of
B. cicadellinicola and approximately 150 kilobase pairs of the small genome of
S. muelleri, both isolated from
H. coagulata. Our study, which to our knowledge is the first genomic analysis of an obligate symbiosis involving multiple partners, suggests striking complementarity in the biosynthetic capabilities of the two symbionts:
B. cicadellinicola devotes a substantial portion of its genome to the biosynthesis of vitamins and cofactors required by animals and lacks most amino acid biosynthetic pathways, whereas
S. muelleri apparently produces most or all of the essential amino acids needed by its host. This finding, along with other results of our genome analysis, suggests the existence of metabolic codependency among the two unrelated endosymbionts and their insect host. This dual symbiosis provides a model case for studying correlated genome evolution and genome reduction involving multiple organisms in an intimate, obligate mutualistic relationship. In addition, our analysis provides insight for the first time into the differences in symbionts between insects (e.g., aphids) that feed on phloem versus those like
H. coagulata that feed on xylem. Finally, the genomes of these two symbionts provide potential targets for controlling plant pathogens such as
Xylella fastidiosa, a major agroeconomic problem, for which
H. coagulata and other sharpshooters serve as vectors of transmission.
Sequence data from two obligate bacterial endosymbionts of an insect--the glassy-winged sharpshooter--suggest there is metabolic co-dependency among them and their insect host.
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Affiliation(s)
- Dongying Wu
- 1The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Sean C Daugherty
- 1The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Susan E Van Aken
- 2J. Craig Venter Institute, Joint Technology Center, Rockville, Maryland, United States of America
| | - Grace H Pai
- 2J. Craig Venter Institute, Joint Technology Center, Rockville, Maryland, United States of America
| | - Kisha L Watkins
- 1The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Hoda Khouri
- 1The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Luke J Tallon
- 1The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Jennifer M Zaborsky
- 1The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Helen E Dunbar
- 3Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Phat L Tran
- 3Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Nancy A Moran
- 3Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Jonathan A Eisen
- 1The Institute for Genomic Research, Rockville, Maryland, United States of America
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16
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Shapir N, Mongodin EF, Sadowsky MJ, Daugherty SC, Nelson KE, Wackett LP. Evolution of catabolic pathways: Genomic insights into microbial s-triazine metabolism. J Bacteriol 2006; 189:674-82. [PMID: 17114259 PMCID: PMC1797303 DOI: 10.1128/jb.01257-06] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- N Shapir
- Department of Biochemistry, Molecular Biology, and Biophysics and BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN 55108, USA
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17
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Badger JH, Hoover TR, Brun YV, Weiner RM, Laub MT, Alexandre G, Mrázek J, Ren Q, Paulsen IT, Nelson KE, Khouri HM, Radune D, Sosa J, Dodson RJ, Sullivan SA, Rosovitz MJ, Madupu R, Brinkac LM, Durkin AS, Daugherty SC, Kothari SP, Giglio MG, Zhou L, Haft DH, Selengut JD, Davidsen TM, Yang Q, Zafar N, Ward NL. Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus. J Bacteriol 2006; 188:6841-50. [PMID: 16980487 PMCID: PMC1595504 DOI: 10.1128/jb.00111-06] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The dimorphic prosthecate bacteria (DPB) are alpha-proteobacteria that reproduce in an asymmetric manner rather than by binary fission and are of interest as simple models of development. Prior to this work, the only member of this group for which genome sequence was available was the model freshwater organism Caulobacter crescentus. Here we describe the genome sequence of Hyphomonas neptunium, a marine member of the DPB that differs from C. crescentus in that H. neptunium uses its stalk as a reproductive structure. Genome analysis indicates that this organism shares more genes with C. crescentus than it does with Silicibacter pomeroyi (a closer relative according to 16S rRNA phylogeny), that it relies upon a heterotrophic strategy utilizing a wide range of substrates, that its cell cycle is likely to be regulated in a similar manner to that of C. crescentus, and that the outer membrane complements of H. neptunium and C. crescentus are remarkably similar. H. neptunium swarmer cells are highly motile via a single polar flagellum. With the exception of cheY and cheR, genes required for chemotaxis were absent in the H. neptunium genome. Consistent with this observation, H. neptunium swarmer cells did not respond to any chemotactic stimuli that were tested, which suggests that H. neptunium motility is a random dispersal mechanism for swarmer cells rather than a stimulus-controlled navigation system for locating specific environments. In addition to providing insights into bacterial development, the H. neptunium genome will provide an important resource for the study of other interesting biological processes including chromosome segregation, polar growth, and cell aging.
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Affiliation(s)
- Jonathan H Badger
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
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18
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Palenik B, Ren Q, Dupont CL, Myers GS, Heidelberg JF, Badger JH, Madupu R, Nelson WC, Brinkac LM, Dodson RJ, Durkin AS, Daugherty SC, Sullivan SA, Khouri H, Mohamoud Y, Halpin R, Paulsen IT. Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment. Proc Natl Acad Sci U S A 2006; 103:13555-9. [PMID: 16938853 PMCID: PMC1569201 DOI: 10.1073/pnas.0602963103] [Citation(s) in RCA: 154] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Indexed: 11/18/2022] Open
Abstract
Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have found that the genome of a coastal cyanobacterium, Synechococcus sp. strain CC9311, has significant differences from an open ocean strain, Synechococcus sp. strain WH8102, and these are consistent with the differences between their respective environments. CC9311 has a greater capacity to sense and respond to changes in its (coastal) environment. It has a much larger capacity to transport, store, use, or export metals, especially iron and copper. In contrast, phosphate acquisition seems less important, consistent with the higher concentration of phosphate in coastal environments. CC9311 is predicted to have differences in its outer membrane lipopolysaccharide, and this may be characteristic of the speciation of some cyanobacterial groups. In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments.
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Affiliation(s)
- Brian Palenik
- *Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093; and
| | - Qinghu Ren
- The Institute for Genomic Research, Rockville, MD 20850
| | - Chris L. Dupont
- *Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093; and
| | | | | | | | - Ramana Madupu
- The Institute for Genomic Research, Rockville, MD 20850
| | | | | | | | | | | | | | - Hoda Khouri
- The Institute for Genomic Research, Rockville, MD 20850
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19
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Myers GS, Rasko DA, Cheung JK, Ravel J, Seshadri R, DeBoy RT, Ren Q, Varga J, Awad MM, Brinkac LM, Daugherty SC, Haft DH, Dodson RJ, Madupu R, Nelson WC, Rosovitz M, Sullivan SA, Khouri H, Dimitrov GI, Watkins KL, Mulligan S, Benton J, Radune D, Fisher DJ, Atkins HS, Hiscox T, Jost BH, Billington SJ, Songer JG, McClane BA, Titball RW, Rood JI, Melville SB, Paulsen IT. Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens. Genome Res 2006; 16:1031-40. [PMID: 16825665 PMCID: PMC1524862 DOI: 10.1101/gr.5238106] [Citation(s) in RCA: 240] [Impact Index Per Article: 13.3] [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] [Indexed: 11/25/2022]
Abstract
Clostridium perfringens is a Gram-positive, anaerobic spore-forming bacterium commonly found in soil, sediments, and the human gastrointestinal tract. C. perfringens is responsible for a wide spectrum of disease, including food poisoning, gas gangrene (clostridial myonecrosis), enteritis necroticans, and non-foodborne gastrointestinal infections. The complete genome sequences of Clostridium perfringens strain ATCC 13124, a gas gangrene isolate and the species type strain, and the enterotoxin-producing food poisoning strain SM101, were determined and compared with the published C. perfringens strain 13 genome. Comparison of the three genomes revealed considerable genomic diversity with >300 unique "genomic islands" identified, with the majority of these islands unusually clustered on one replichore. PCR-based analysis indicated that the large genomic islands are widely variable across a large collection of C. perfringens strains. These islands encode genes that correlate to differences in virulence and phenotypic characteristics of these strains. Significant differences between the strains include numerous novel mobile elements and genes encoding metabolic capabilities, strain-specific extracellular polysaccharide capsule, sporulation factors, toxins, and other secreted enzymes, providing substantial insight into this medically important bacterial pathogen.
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Affiliation(s)
- Garry S.A. Myers
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | - David A. Rasko
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | - Jackie K. Cheung
- Australian Bacterial Pathogenesis Program, Department of Microbiology, Monash University, Clayton 3800, Australia
| | - Jacques Ravel
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | - Rekha Seshadri
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | - Robert T. DeBoy
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | - Qinghu Ren
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | - John Varga
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24601, USA
| | - Milena M. Awad
- Australian Bacterial Pathogenesis Program, Department of Microbiology, Monash University, Clayton 3800, Australia
| | | | | | - Daniel H. Haft
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | - Robert J. Dodson
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | - Ramana Madupu
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | | | - M.J. Rosovitz
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | | | - Hoda Khouri
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | | | - Kisha L. Watkins
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | | | - Jonathan Benton
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | - Diana Radune
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | - Derek J. Fisher
- Department of Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
| | - Helen S. Atkins
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, United Kingdom
| | - Tom Hiscox
- Australian Bacterial Pathogenesis Program, Department of Microbiology, Monash University, Clayton 3800, Australia
| | - B. Helen Jost
- Department of Veterinary Science, University of Arizona, Tucson, Arizona 85721, USA
| | | | - J. Glenn Songer
- Department of Veterinary Science, University of Arizona, Tucson, Arizona 85721, USA
| | - Bruce A. McClane
- Department of Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
| | - Richard W. Titball
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, United Kingdom
| | - Julian I. Rood
- Australian Bacterial Pathogenesis Program, Department of Microbiology, Monash University, Clayton 3800, Australia
| | - Stephen B. Melville
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24601, USA
| | - Ian T. Paulsen
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
- Corresponding author.E-mail ; fax (301) 838-0208
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20
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Paulsen IT, Press CM, Ravel J, Kobayashi DY, Myers GSA, Mavrodi DV, DeBoy RT, Seshadri R, Ren Q, Madupu R, Dodson RJ, Durkin AS, Brinkac LM, Daugherty SC, Sullivan SA, Rosovitz MJ, Gwinn ML, Zhou L, Schneider DJ, Cartinhour SW, Nelson WC, Weidman J, Watkins K, Tran K, Khouri H, Pierson EA, Pierson LS, Thomashow LS, Loper JE. Correction: Corrigendum: Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nat Biotechnol 2006. [DOI: 10.1038/nbt0406-466b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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Dunning Hotopp JC, Lin M, Madupu R, Crabtree J, Angiuoli SV, Eisen JA, Eisen J, Seshadri R, Ren Q, Wu M, Utterback TR, Smith S, Lewis M, Khouri H, Zhang C, Niu H, Lin Q, Ohashi N, Zhi N, Nelson W, Brinkac LM, Dodson RJ, Rosovitz MJ, Sundaram J, Daugherty SC, Davidsen T, Durkin AS, Gwinn M, Haft DH, Selengut JD, Sullivan SA, Zafar N, Zhou L, Benahmed F, Forberger H, Halpin R, Mulligan S, Robinson J, White O, Rikihisa Y, Tettelin H. Comparative genomics of emerging human ehrlichiosis agents. PLoS Genet 2006; 2:e21. [PMID: 16482227 PMCID: PMC1366493 DOI: 10.1371/journal.pgen.0020021] [Citation(s) in RCA: 341] [Impact Index Per Article: 18.9] [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: 10/20/2005] [Accepted: 01/09/2006] [Indexed: 11/25/2022] Open
Abstract
Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an emerging infectious disease. We present the complete genome sequences of these organisms along with comparisons to other organisms in the Rickettsiales order. Ehrlichia spp. and Anaplasma spp. display a unique large expansion of immunodominant outer membrane proteins facilitating antigenic variation. All Rickettsiales have a diminished ability to synthesize amino acids compared to their closest free-living relatives. Unlike members of the Rickettsiaceae family, these pathogenic Anaplasmataceae are capable of making all major vitamins, cofactors, and nucleotides, which could confer a beneficial role in the invertebrate vector or the vertebrate host. Further analysis identified proteins potentially involved in vacuole confinement of the Anaplasmataceae, a life cycle involving a hematophagous vector, vertebrate pathogenesis, human pathogenesis, and lack of transovarial transmission. These discoveries provide significant insights into the biology of these obligate intracellular pathogens. Ehrlichiosis is an acute disease that triggers flu-like symptoms in both humans and animals. It is caused by a range of bacteria transmitted by ticks or flukes. Because these bacteria are difficult to culture, however, the organisms are poorly understood. The genomes of three emerging human pathogens causing ehrlichiosis were sequenced. A database was designed to allow the comparison of these three genomes to sixteen other bacteria with similar lifestyles. Analysis from this database reveals new species-specific and disease-specific genes indicating niche adaptations, pathogenic traits, and other features. In particular, one of the organisms contains more than 100 copies of a single gene involved in interactions with the host(s). These comparisons also enabled a reconstruction of the metabolic potential of five representative genomes from these bacteria and their close relatives. With this work, scientists can study these emerging pathogens in earnest.
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22
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Wu M, Ren Q, Durkin AS, Daugherty SC, Brinkac LM, Dodson RJ, Madupu R, Sullivan SA, Kolonay JF, Nelson WC, Tallon LJ, Jones KM, Ulrich LE, Gonzalez JM, Zhulin IB, Robb FT, Eisen JA. Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901. PLoS Genet 2005; 1:e65. [PMID: 16311624 PMCID: PMC1287953 DOI: 10.1371/journal.pgen.0010065] [Citation(s) in RCA: 198] [Impact Index Per Article: 10.4] [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: 08/08/2005] [Accepted: 10/19/2005] [Indexed: 11/20/2022] Open
Abstract
We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO) as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a “minimal” model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously. Carboxydothermus hydrogenoformans, a bacterium isolated from a Russian hotspring, is studied for three major reasons: it grows at very high temperature, it lives almost entirely on a diet of carbon monoxide (CO), and it converts water to hydrogen gas as part of its metabolism. Understanding this organism's unique biology gets a boost from the decoding of its genome, reported in this issue of PLoS Genetics. For example, genome analysis reveals that it encodes five different forms of the protein machine carbon monoxide dehydrogenase (CODH). Most species have no CODH and even species that utilize CO usually have only one or two. The five CODH in C. hydrogenoformans likely allow it to both use CO for diverse cellular processes and out-compete for it when it is limiting. The genome sequence also led the researchers to experimentally document new aspects of this species' biology including the ability to form spores. The researchers then used comparative genomic analysis to identify conserved genes found in all spore-forming species, including Bacillus anthracis, and not in any other species. Finally, the genome sequence and analysis reported here will aid in those trying to develop this and other species into systems to biologically produce hydrogen gas from water.
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Affiliation(s)
- Martin Wu
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Qinghu Ren
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - A. Scott Durkin
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Sean C Daugherty
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Lauren M Brinkac
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Robert J Dodson
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Ramana Madupu
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Steven A Sullivan
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - James F Kolonay
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - William C Nelson
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Luke J Tallon
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Kristine M Jones
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Luke E Ulrich
- Center for Bioinformatics and Computational Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Juan M Gonzalez
- Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, Maryland, United States of America
| | - Igor B Zhulin
- Center for Bioinformatics and Computational Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Frank T Robb
- Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, Maryland, United States of America
| | - Jonathan A Eisen
- The Institute for Genomic Research, Rockville, Maryland, United States of America
- Johns Hopkins University, Baltimore, Maryland, United States of America
- * To whom correspondence should be addressed. E-mail:
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23
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Joardar V, Lindeberg M, Jackson RW, Selengut J, Dodson R, Brinkac LM, Daugherty SC, Deboy R, Durkin AS, Giglio MG, Madupu R, Nelson WC, Rosovitz MJ, Sullivan S, Crabtree J, Creasy T, Davidsen T, Haft DH, Zafar N, Zhou L, Halpin R, Holley T, Khouri H, Feldblyum T, White O, Fraser CM, Chatterjee AK, Cartinhour S, Schneider DJ, Mansfield J, Collmer A, Buell CR. Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition. J Bacteriol 2005; 187:6488-98. [PMID: 16159782 PMCID: PMC1236638 DOI: 10.1128/jb.187.18.6488-6498.2005] [Citation(s) in RCA: 274] [Impact Index Per Article: 14.4] [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: 12/26/2022] Open
Abstract
Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae pv. phaseolicola isolate 1448A, which encodes 5,353 open reading frames (ORFs) on one circular chromosome (5,928,787 bp) and two plasmids (131,950 bp and 51,711 bp). Comparative analyses with a phylogenetically divergent pathovar, P. syringae pv. tomato DC3000, revealed a strong degree of conservation at the gene and genome levels. In total, 4,133 ORFs were identified as putative orthologs in these two pathovars using a reciprocal best-hit method, with 3,941 ORFs present in conserved, syntenic blocks. Although these two pathovars are highly similar at the physiological level, they have distinct host ranges; 1448A causes disease in beans, and DC3000 is pathogenic on tomato and Arabidopsis. Examination of the complement of ORFs encoding virulence, fitness, and survival factors revealed a substantial, but not complete, overlap between these two pathovars. Another distinguishing feature between the two pathovars is their distinctive sets of transposable elements. With access to a fifth complete pseudomonad genome sequence, we were able to identify 3,567 ORFs that likely comprise the core Pseudomonas genome and 365 ORFs that are P. syringae specific.
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Affiliation(s)
- Vinita Joardar
- The Institute for Genomic Research, 9712 Medical Center Dr., Rockville, MD 20850, USA
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24
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Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, Deboy RT, Davidsen TM, Mora M, Scarselli M, Margarit y Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou L, Zafar N, Khouri H, Radune D, Dimitrov G, Watkins K, O'Connor KJB, Smith S, Utterback TR, White O, Rubens CE, Grandi G, Madoff LC, Kasper DL, Telford JL, Wessels MR, Rappuoli R, Fraser CM. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci U S A 2005; 102:13950-5. [PMID: 16172379 PMCID: PMC1216834 DOI: 10.1073/pnas.0506758102] [Citation(s) in RCA: 1526] [Impact Index Per Article: 80.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The development of efficient and inexpensive genome sequencing methods has revolutionized the study of human bacterial pathogens and improved vaccine design. Unfortunately, the sequence of a single genome does not reflect how genetic variability drives pathogenesis within a bacterial species and also limits genome-wide screens for vaccine candidates or for antimicrobial targets. We have generated the genomic sequence of six strains representing the five major disease-causing serotypes of Streptococcus agalactiae, the main cause of neonatal infection in humans. Analysis of these genomes and those available in databases showed that the S. agalactiae species can be described by a pan-genome consisting of a core genome shared by all isolates, accounting for approximately 80% of any single genome, plus a dispensable genome consisting of partially shared and strain-specific genes. Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactiae pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes.
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Affiliation(s)
- Hervé Tettelin
- Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
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25
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Methé BA, Nelson KE, Deming JW, Momen B, Melamud E, Zhang X, Moult J, Madupu R, Nelson WC, Dodson RJ, Brinkac LM, Daugherty SC, Durkin AS, DeBoy RT, Kolonay JF, Sullivan SA, Zhou L, Davidsen TM, Wu M, Huston AL, Lewis M, Weaver B, Weidman JF, Khouri H, Utterback TR, Feldblyum TV, Fraser CM. The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses. Proc Natl Acad Sci U S A 2005; 102:10913-8. [PMID: 16043709 PMCID: PMC1180510 DOI: 10.1073/pnas.0504766102] [Citation(s) in RCA: 431] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The completion of the 5,373,180-bp genome sequence of the marine psychrophilic bacterium Colwellia psychrerythraea 34H, a model for the study of life in permanently cold environments, reveals capabilities important to carbon and nutrient cycling, bioremediation, production of secondary metabolites, and cold-adapted enzymes. From a genomic perspective, cold adaptation is suggested in several broad categories involving changes to the cell membrane fluidity, uptake and synthesis of compounds conferring cryotolerance, and strategies to overcome temperature-dependent barriers to carbon uptake. Modeling of three-dimensional protein homology from bacteria representing a range of optimal growth temperatures suggests changes to proteome composition that may enhance enzyme effectiveness at low temperatures. Comparative genome analyses suggest that the psychrophilic lifestyle is most likely conferred not by a unique set of genes but by a collection of synergistic changes in overall genome content and amino acid composition.
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Affiliation(s)
- Barbara A Methé
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
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26
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Paulsen IT, Press CM, Ravel J, Kobayashi DY, Myers GSA, Mavrodi DV, DeBoy RT, Seshadri R, Ren Q, Madupu R, Dodson RJ, Durkin AS, Brinkac LM, Daugherty SC, Sullivan SA, Rosovitz MJ, Gwinn ML, Zhou L, Schneider DJ, Cartinhour SW, Nelson WC, Weidman J, Watkins K, Tran K, Khouri H, Pierson EA, Pierson LS, Thomashow LS, Loper JE. Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nat Biotechnol 2005; 23:873-8. [PMID: 15980861 PMCID: PMC7416659 DOI: 10.1038/nbt1110] [Citation(s) in RCA: 421] [Impact Index Per Article: 22.2] [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: 03/03/2005] [Accepted: 05/04/2005] [Indexed: 12/11/2022]
Abstract
Pseudomonas fluorescens Pf-5 is a plant commensal bacterium that inhabits the rhizosphere and produces secondary metabolites that suppress soilborne plant pathogens. The complete sequence of the 7.1-Mb Pf-5 genome was determined. We analyzed repeat sequences to identify genomic islands that, together with other approaches, suggested P. fluorescens Pf-5's recent lateral acquisitions include six secondary metabolite gene clusters, seven phage regions and a mobile genomic island. We identified various features that contribute to its commensal lifestyle on plants, including broad catabolic and transport capabilities for utilizing plant-derived compounds, the apparent ability to use a diversity of iron siderophores, detoxification systems to protect from oxidative stress, and the lack of a type III secretion system and toxins found in related pathogens. In addition to six known secondary metabolites produced by P. fluorescens Pf-5, three novel secondary metabolite biosynthesis gene clusters were also identified that may contribute to the biocontrol properties of P. fluorescens Pf-5.
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Affiliation(s)
- Ian T Paulsen
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Caroline M Press
- US Department of Agriculture, Agricultural Research Service, Horticultural Crops Research Laboratory, Corvallis, Oregon USA
| | - Jacques Ravel
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Donald Y Kobayashi
- Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey USA
| | | | - Dmitri V Mavrodi
- Department of Plant Pathology, Washington State University, Pullman, Washington USA
| | - Robert T DeBoy
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Rekha Seshadri
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Qinghu Ren
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Ramana Madupu
- The Institute for Genomic Research, Rockville, Maryland USA
| | | | - A Scott Durkin
- The Institute for Genomic Research, Rockville, Maryland USA
| | | | | | | | | | | | - Liwei Zhou
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Davd J Schneider
- US Department of Agriculture, Agricultural Research Service, Ithaca, New York USA
| | - Samuel W Cartinhour
- US Department of Agriculture, Agricultural Research Service, Ithaca, New York USA
| | | | - Janice Weidman
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Kisha Watkins
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Kevin Tran
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Hoda Khouri
- The Institute for Genomic Research, Rockville, Maryland USA
| | | | - Leland S Pierson
- Department of Plant Sciences, University of Arizona, Tucson, Arizona USA
| | - Linda S Thomashow
- US Department of Agriculture, Agricultural Research Service, Root Disease and Biological Control Research Unit, Pullman, Washington USA
| | - Joyce E Loper
- US Department of Agriculture, Agricultural Research Service, Horticultural Crops Research Laboratory, Corvallis, Oregon USA
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27
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Qi M, Nelson KE, Daugherty SC, Nelson WC, Hance IR, Morrison M, Forsberg CW. Novel molecular features of the fibrolytic intestinal bacterium Fibrobacter intestinalis not shared with Fibrobacter succinogenes as determined by suppressive subtractive hybridization. J Bacteriol 2005; 187:3739-51. [PMID: 15901698 PMCID: PMC1112041 DOI: 10.1128/jb.187.11.3739-3751.2005] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [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] Open
Abstract
Suppressive subtractive hybridization was conducted to identify unique genes coding for plant cell wall hydrolytic enzymes and other properties of the gastrointestinal bacterium Fibrobacter intestinalis DR7 not shared by Fibrobacter succinogenes S85. Subtractive clones from F. intestinalis were sequenced and assembled to form 712 nonredundant contigs with an average length of 525 bp. Of these, 55 sequences were unique to F. intestinalis. The remaining contigs contained 764 genes with BLASTX similarities to other proteins; of these, 80% had the highest similarities to proteins in F. succinogenes, including 30 that coded for carbohydrate active enzymes. The expression of 17 of these genes was verified by Northern dot blot analysis. Of genes not exhibiting BLASTX similarity to F. succinogenes, 30 encoded putative transposases, 6 encoded restriction modification genes, and 45% had highest similarities to proteins in other species of gastrointestinal bacteria, a finding suggestive of either horizontal gene transfer to F. intestinalis or gene loss from F. succinogenes. Analysis of contigs containing segments of two or more adjacent genes revealed that only 35% exhibited BLASTX similarity and were in the same orientation as those of F. succinogenes, indicating extensive chromosomal rearrangement. The expression of eight transposases, and three restriction-modification genes was confirmed by Northern dot blot analysis. These data clearly document the maintenance of carbohydrate active enzymes in F. intestinalis necessitated by the preponderance of polysaccharide substrates available in the ruminal environment. It also documents substantive changes in the genome from that of F. succinogenes, which may be related to the introduction of the array of transposase and restriction-modification genes.
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Affiliation(s)
- Meng Qi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
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28
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Gill SR, Fouts DE, Archer GL, Mongodin EF, Deboy RT, Ravel J, Paulsen IT, Kolonay JF, Brinkac L, Beanan M, Dodson RJ, Daugherty SC, Madupu R, Angiuoli SV, Durkin AS, Haft DH, Vamathevan J, Khouri H, Utterback T, Lee C, Dimitrov G, Jiang L, Qin H, Weidman J, Tran K, Kang K, Hance IR, Nelson KE, Fraser CM. Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain. J Bacteriol 2005; 187:2426-38. [PMID: 15774886 PMCID: PMC1065214 DOI: 10.1128/jb.187.7.2426-2438.2005] [Citation(s) in RCA: 752] [Impact Index Per Article: 39.6] [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: 07/27/2004] [Accepted: 12/13/2004] [Indexed: 01/27/2023] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen and the major causative agent of numerous hospital- and community-acquired infections. Staphylococcus epidermidis has emerged as a causative agent of infections often associated with implanted medical devices. We have sequenced the approximately 2.8-Mb genome of S. aureus COL, an early methicillin-resistant isolate, and the approximately 2.6-Mb genome of S. epidermidis RP62a, a methicillin-resistant biofilm isolate. Comparative analysis of these and other staphylococcal genomes was used to explore the evolution of virulence and resistance between these two species. The S. aureus and S. epidermidis genomes are syntenic throughout their lengths and share a core set of 1,681 open reading frames. Genome islands in nonsyntenic regions are the primary source of variations in pathogenicity and resistance. Gene transfer between staphylococci and low-GC-content gram-positive bacteria appears to have shaped their virulence and resistance profiles. Integrated plasmids in S. epidermidis carry genes encoding resistance to cadmium and species-specific LPXTG surface proteins. A novel genome island encodes multiple phenol-soluble modulins, a potential S. epidermidis virulence factor. S. epidermidis contains the cap operon, encoding the polyglutamate capsule, a major virulence factor in Bacillus anthracis. Additional phenotypic differences are likely the result of single nucleotide polymorphisms, which are most numerous in cell envelope proteins. Overall differences in pathogenicity can be attributed to genome islands in S. aureus which encode enterotoxins, exotoxins, leukocidins, and leukotoxins not found in S. epidermidis.
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Affiliation(s)
- Steven R Gill
- Microbial Genomics, The Institute for Genomic Research, 9712 Medical Center Dr., Rockville, MD 20850, USA.
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29
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Seshadri R, Adrian L, Fouts DE, Eisen JA, Phillippy AM, Methe BA, Ward NL, Nelson WC, Deboy RT, Khouri HM, Kolonay JF, Dodson RJ, Daugherty SC, Brinkac LM, Sullivan SA, Madupu R, Nelson KE, Kang KH, Impraim M, Tran K, Robinson JM, Forberger HA, Fraser CM, Zinder SH, Heidelberg JF. Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science 2005; 307:105-8. [PMID: 15637277 DOI: 10.1126/science.1102226] [Citation(s) in RCA: 317] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Dehalococcoides ethenogenes is the only bacterium known to reductively dechlorinate the groundwater pollutants, tetrachloroethene (PCE) and trichloroethene, to ethene. Its 1,469,720-base pair chromosome contains large dynamic duplicated regions and integrated elements. Genes encoding 17 putative reductive dehalogenases, nearly all of which were adjacent to genes for transcription regulators, and five hydrogenase complexes were identified. These findings, plus a limited repertoire of other metabolic modes, indicate that D. ethenogenes is highly evolved to utilize halogenated organic compounds and H2. Diversification of reductive dehalogenase functions appears to have been mediated by recent genetic exchange and amplification. Genome analysis provides insights into the organism's complex nutrient requirements and suggests that an ancestor was a nitrogen-fixing autotroph.
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Affiliation(s)
- Rekha Seshadri
- Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
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30
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Fouts DE, Mongodin EF, Mandrell RE, Miller WG, Rasko DA, Ravel J, Brinkac LM, DeBoy RT, Parker CT, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Sullivan SA, Shetty JU, Ayodeji MA, Shvartsbeyn A, Schatz MC, Badger JH, Fraser CM, Nelson KE. Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species. PLoS Biol 2005; 3:e15. [PMID: 15660156 PMCID: PMC539331 DOI: 10.1371/journal.pbio.0030015] [Citation(s) in RCA: 398] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2004] [Accepted: 11/11/2004] [Indexed: 12/19/2022] Open
Abstract
Sequencing and comparative genome analysis of four strains of Campylobacter including C. lari RM2100, C. upsaliensis RM3195, and C. coli RM2228 has revealed major structural differences that are associated with the insertion of phage- and plasmid-like genomic islands, as well as major variations in the lipooligosaccharide complex. Poly G tracts are longer, are greater in number, and show greater variability in C. upsaliensis than in the other species. Many genes involved in host colonization, including racR/S, cadF, cdt, ciaB, and flagellin genes, are conserved across the species, but variations that appear to be species specific are evident for a lipooligosaccharide locus, a capsular (extracellular) polysaccharide locus, and a novel Campylobacter putative licABCD virulence locus. The strains also vary in their metabolic profiles, as well as their resistance profiles to a range of antibiotics. It is evident that the newly identified hypothetical and conserved hypothetical proteins, as well as uncharacterized two-component regulatory systems and membrane proteins, may hold additional significant information on the major differences in virulence among the species, as well as the specificity of the strains for particular hosts.
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Affiliation(s)
- Derrick E Fouts
- The Institute for Genomic Research, Rockville, Maryland, United States of America.
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31
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Moran MA, Buchan A, González JM, Heidelberg JF, Whitman WB, Kiene RP, Henriksen JR, King GM, Belas R, Fuqua C, Brinkac L, Lewis M, Johri S, Weaver B, Pai G, Eisen JA, Rahe E, Sheldon WM, Ye W, Miller TR, Carlton J, Rasko DA, Paulsen IT, Ren Q, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Rosovitz MJ, Haft DH, Selengut J, Ward N. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature 2004; 432:910-3. [PMID: 15602564 DOI: 10.1038/nature03170] [Citation(s) in RCA: 316] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2004] [Accepted: 11/01/2004] [Indexed: 11/08/2022]
Abstract
Since the recognition of prokaryotes as essential components of the oceanic food web, bacterioplankton have been acknowledged as catalysts of most major biogeochemical processes in the sea. Studying heterotrophic bacterioplankton has been challenging, however, as most major clades have never been cultured or have only been grown to low densities in sea water. Here we describe the genome sequence of Silicibacter pomeroyi, a member of the marine Roseobacter clade (Fig. 1), the relatives of which comprise approximately 10-20% of coastal and oceanic mixed-layer bacterioplankton. This first genome sequence from any major heterotrophic clade consists of a chromosome (4,109,442 base pairs) and megaplasmid (491,611 base pairs). Genome analysis indicates that this organism relies upon a lithoheterotrophic strategy that uses inorganic compounds (carbon monoxide and sulphide) to supplement heterotrophy. Silicibacter pomeroyi also has genes advantageous for associations with plankton and suspended particles, including genes for uptake of algal-derived compounds, use of metabolites from reducing microzones, rapid growth and cell-density-dependent regulation. This bacterium has a physiology distinct from that of marine oligotrophs, adding a new strategy to the recognized repertoire for coping with a nutrient-poor ocean.
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Affiliation(s)
- Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, Georgia 30602, USA.
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32
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Nierman WC, DeShazer D, Kim HS, Tettelin H, Nelson KE, Feldblyum T, Ulrich RL, Ronning CM, Brinkac LM, Daugherty SC, Davidsen TD, Deboy RT, Dimitrov G, Dodson RJ, Durkin AS, Gwinn ML, Haft DH, Khouri H, Kolonay JF, Madupu R, Mohammoud Y, Nelson WC, Radune D, Romero CM, Sarria S, Selengut J, Shamblin C, Sullivan SA, White O, Yu Y, Zafar N, Zhou L, Fraser CM. Structural flexibility in the Burkholderia mallei genome. Proc Natl Acad Sci U S A 2004; 101:14246-51. [PMID: 15377793 PMCID: PMC521142 DOI: 10.1073/pnas.0403306101] [Citation(s) in RCA: 269] [Impact Index Per Article: 13.5] [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: 11/18/2022] Open
Abstract
The complete genome sequence of Burkholderia mallei ATCC 23344 provides insight into this highly infectious bacterium's pathogenicity and evolutionary history. B. mallei, the etiologic agent of glanders, has come under renewed scientific investigation as a result of recent concerns about its past and potential future use as a biological weapon. Genome analysis identified a number of putative virulence factors whose function was supported by comparative genome hybridization and expression profiling of the bacterium in hamster liver in vivo. The genome contains numerous insertion sequence elements that have mediated extensive deletions and rearrangements of the genome relative to Burkholderia pseudomallei. The genome also contains a vast number (>12,000) of simple sequence repeats. Variation in simple sequence repeats in key genes can provide a mechanism for generating antigenic variation that may account for the mammalian host's inability to mount a durable adaptive immune response to a B. mallei infection.
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Affiliation(s)
- William C Nierman
- Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
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33
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Nelson KE, Fouts DE, Mongodin EF, Ravel J, DeBoy RT, Kolonay JF, Rasko DA, Angiuoli SV, Gill SR, Paulsen IT, Peterson J, White O, Nelson WC, Nierman W, Beanan MJ, Brinkac LM, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Haft DH, Selengut J, Van Aken S, Khouri H, Fedorova N, Forberger H, Tran B, Kathariou S, Wonderling LD, Uhlich GA, Bayles DO, Luchansky JB, Fraser CM. Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species. Nucleic Acids Res 2004; 32:2386-95. [PMID: 15115801 PMCID: PMC419451 DOI: 10.1093/nar/gkh562] [Citation(s) in RCA: 375] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2003] [Revised: 03/21/2004] [Accepted: 04/01/2004] [Indexed: 11/14/2022] Open
Abstract
The genomes of three strains of Listeria monocytogenes that have been associated with food-borne illness in the USA were subjected to whole genome comparative analysis. A total of 51, 97 and 69 strain-specific genes were identified in L.monocytogenes strains F2365 (serotype 4b, cheese isolate), F6854 (serotype 1/2a, frankfurter isolate) and H7858 (serotype 4b, meat isolate), respectively. Eighty-three genes were restricted to serotype 1/2a and 51 to serotype 4b strains. These strain- and serotype-specific genes probably contribute to observed differences in pathogenicity, and the ability of the organisms to survive and grow in their respective environmental niches. The serotype 1/2a-specific genes include an operon that encodes the rhamnose biosynthetic pathway that is associated with teichoic acid biosynthesis, as well as operons for five glycosyl transferases and an adenine-specific DNA methyltransferase. A total of 8603 and 105 050 high quality single nucleotide polymorphisms (SNPs) were found on the draft genome sequences of strain H7858 and strain F6854, respectively, when compared with strain F2365. Whole genome comparative analyses revealed that the L.monocytogenes genomes are essentially syntenic, with the majority of genomic differences consisting of phage insertions, transposable elements and SNPs.
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Affiliation(s)
- Karen E Nelson
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
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34
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Heidelberg JF, Seshadri R, Haveman SA, Hemme CL, Paulsen IT, Kolonay JF, Eisen JA, Ward N, Methe B, Brinkac LM, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Fouts D, Haft DH, Selengut J, Peterson JD, Davidsen TM, Zafar N, Zhou L, Radune D, Dimitrov G, Hance M, Tran K, Khouri H, Gill J, Utterback TR, Feldblyum TV, Wall JD, Voordouw G, Fraser CM. The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nat Biotechnol 2004; 22:554-9. [PMID: 15077118 DOI: 10.1038/nbt959] [Citation(s) in RCA: 407] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2003] [Accepted: 03/03/2004] [Indexed: 11/09/2022]
Abstract
Desulfovibrio vulgaris Hildenborough is a model organism for studying the energy metabolism of sulfate-reducing bacteria (SRB) and for understanding the economic impacts of SRB, including biocorrosion of metal infrastructure and bioremediation of toxic metal ions. The 3,570,858 base pair (bp) genome sequence reveals a network of novel c-type cytochromes, connecting multiple periplasmic hydrogenases and formate dehydrogenases, as a key feature of its energy metabolism. The relative arrangement of genes encoding enzymes for energy transduction, together with inferred cellular location of the enzymes, provides a basis for proposing an expansion to the 'hydrogen-cycling' model for increasing energy efficiency in this bacterium. Plasmid-encoded functions include modification of cell surface components, nitrogen fixation and a type-III protein secretion system. This genome sequence represents a substantial step toward the elucidation of pathways for reduction (and bioremediation) of pollutants such as uranium and chromium and offers a new starting point for defining this organism's complex anaerobic respiration.
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Affiliation(s)
- John F Heidelberg
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA.
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35
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Seshadri R, Myers GSA, Tettelin H, Eisen JA, Heidelberg JF, Dodson RJ, Davidsen TM, DeBoy RT, Fouts DE, Haft DH, Selengut J, Ren Q, Brinkac LM, Madupu R, Kolonay J, Durkin SA, Daugherty SC, Shetty J, Shvartsbeyn A, Gebregeorgis E, Geer K, Tsegaye G, Malek J, Ayodeji B, Shatsman S, McLeod MP, Smajs D, Howell JK, Pal S, Amin A, Vashisth P, McNeill TZ, Xiang Q, Sodergren E, Baca E, Weinstock GM, Norris SJ, Fraser CM, Paulsen IT. Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes. Proc Natl Acad Sci U S A 2004; 101:5646-51. [PMID: 15064399 PMCID: PMC397461 DOI: 10.1073/pnas.0307639101] [Citation(s) in RCA: 211] [Impact Index Per Article: 10.6] [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: 11/18/2022] Open
Abstract
We present the complete 2,843,201-bp genome sequence of Treponema denticola (ATCC 35405) an oral spirochete associated with periodontal disease. Analysis of the T. denticola genome reveals factors mediating coaggregation, cell signaling, stress protection, and other competitive and cooperative measures, consistent with its pathogenic nature and lifestyle within the mixed-species environment of subgingival dental plaque. Comparisons with previously sequenced spirochete genomes revealed specific factors contributing to differences and similarities in spirochete physiology as well as pathogenic potential. The T. denticola genome is considerably larger in size than the genome of the related syphilis-causing spirochete Treponema pallidum. The differences in gene content appear to be attributable to a combination of three phenomena: genome reduction, lineage-specific expansions, and horizontal gene transfer. Genes lost due to reductive evolution appear to be largely involved in metabolism and transport, whereas some of the genes that have arisen due to lineage-specific expansions are implicated in various pathogenic interactions, and genes acquired via horizontal gene transfer are largely phage-related or of unknown function.
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Affiliation(s)
- Rekha Seshadri
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
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36
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Wu M, Sun LV, Vamathevan J, Riegler M, Deboy R, Brownlie JC, McGraw EA, Martin W, Esser C, Ahmadinejad N, Wiegand C, Madupu R, Beanan MJ, Brinkac LM, Daugherty SC, Durkin AS, Kolonay JF, Nelson WC, Mohamoud Y, Lee P, Berry K, Young MB, Utterback T, Weidman J, Nierman WC, Paulsen IT, Nelson KE, Tettelin H, O'Neill SL, Eisen JA. Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol 2004; 2:E69. [PMID: 15024419 PMCID: PMC368164 DOI: 10.1371/journal.pbio.0020069] [Citation(s) in RCA: 587] [Impact Index Per Article: 29.4] [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: 11/19/2003] [Accepted: 01/06/2004] [Indexed: 12/17/2022] Open
Abstract
The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a variety of invertebrate species, are of great interest due to their diverse interactions with different hosts, which range from many forms of reproductive parasitism to mutualistic symbioses. Analysis of the wMel genome, in particular phylogenomic comparisons with other intracellular bacteria, has revealed many insights into the biology and evolution of wMel and Wolbachia in general. For example, the wMel genome is unique among sequenced obligate intracellular species in both being highly streamlined and containing very high levels of repetitive DNA and mobile DNA elements. This observation, coupled with multiple evolutionary reconstructions, suggests that natural selection is somewhat inefficient in wMel, most likely owing to the occurrence of repeated population bottlenecks. Genome analysis predicts many metabolic differences with the closely related Rickettsia species, including the presence of intact glycolysis and purine synthesis, which may compensate for an inability to obtain ATP directly from its host, as Rickettsia can. Other discoveries include the apparent inability of wMel to synthesize lipopolysaccharide and the presence of the most genes encoding proteins with ankyrin repeat domains of any prokaryotic genome yet sequenced. Despite the ability of wMel to infect the germline of its host, we find no evidence for either recent lateral gene transfer between wMel and D. melanogaster or older transfers between Wolbachia and any host. Evolutionary analysis further supports the hypothesis that mitochondria share a common ancestor with the α-Proteobacteria, but shows little support for the grouping of mitochondria with species in the order Rickettsiales. With the availability of the complete genomes of both species and excellent genetic tools for the host, the wMel–D. melanogaster symbiosis is now an ideal system for studying the biology and evolution of Wolbachia infections. The genome sequence of Wolbachia provides insights into the origins of mitochondria, as well as the ecology and evolution of endosymbiosis
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Affiliation(s)
- Martin Wu
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Ling V Sun
- 2Department of Epidemiology and Public Health, Yale University School of MedicineNew Haven, ConnecticutUnited States of America
| | - Jessica Vamathevan
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Markus Riegler
- 3Department of Zoology and Entomology, School of Life SciencesThe University of Queensland, St Lucia, QueenslandAustralia
| | - Robert Deboy
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Jeremy C Brownlie
- 3Department of Zoology and Entomology, School of Life SciencesThe University of Queensland, St Lucia, QueenslandAustralia
| | - Elizabeth A McGraw
- 3Department of Zoology and Entomology, School of Life SciencesThe University of Queensland, St Lucia, QueenslandAustralia
| | - William Martin
- 4Institut für Botanik III, Heinrich-Heine UniversitätDüsseldorfGermany
| | - Christian Esser
- 4Institut für Botanik III, Heinrich-Heine UniversitätDüsseldorfGermany
| | - Nahal Ahmadinejad
- 4Institut für Botanik III, Heinrich-Heine UniversitätDüsseldorfGermany
| | - Christian Wiegand
- 4Institut für Botanik III, Heinrich-Heine UniversitätDüsseldorfGermany
| | - Ramana Madupu
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Maureen J Beanan
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Lauren M Brinkac
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Sean C Daugherty
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - A. Scott Durkin
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - James F Kolonay
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - William C Nelson
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Yasmin Mohamoud
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Perris Lee
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Kristi Berry
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - M. Brook Young
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Teresa Utterback
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Janice Weidman
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - William C Nierman
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Ian T Paulsen
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Karen E Nelson
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Hervé Tettelin
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
| | - Scott L O'Neill
- 2Department of Epidemiology and Public Health, Yale University School of MedicineNew Haven, ConnecticutUnited States of America
- 3Department of Zoology and Entomology, School of Life SciencesThe University of Queensland, St Lucia, QueenslandAustralia
| | - Jonathan A Eisen
- 1The Institute for Genomic Research, RockvilleMarylandUnited States of America
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37
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Methé BA, Nelson KE, Eisen JA, Paulsen IT, Nelson W, Heidelberg JF, Wu D, Wu M, Ward N, Beanan MJ, Dodson RJ, Madupu R, Brinkac LM, Daugherty SC, DeBoy RT, Durkin AS, Gwinn M, Kolonay JF, Sullivan SA, Haft DH, Selengut J, Davidsen TM, Zafar N, White O, Tran B, Romero C, Forberger HA, Weidman J, Khouri H, Feldblyum TV, Utterback TR, Van Aken SE, Lovley DR, Fraser CM. Genome of Geobacter sulfurreducens: metal reduction in subsurface environments. Science 2003; 302:1967-9. [PMID: 14671304 DOI: 10.1126/science.1088727] [Citation(s) in RCA: 480] [Impact Index Per Article: 22.9] [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: 11/02/2022]
Abstract
The complete genome sequence of Geobacter sulfurreducens, a delta-proteobacterium, reveals unsuspected capabilities, including evidence of aerobic metabolism, one-carbon and complex carbon metabolism, motility, and chemotactic behavior. These characteristics, coupled with the possession of many two-component sensors and many c-type cytochromes, reveal an ability to create alternative, redundant, electron transport networks and offer insights into the process of metal ion reduction in subsurface environments. As well as playing roles in the global cycling of metals and carbon, this organism clearly has the potential for use in bioremediation of radioactive metals and in the generation of electricity.
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Affiliation(s)
- B A Methé
- Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
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38
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Nelson KE, Fleischmann RD, DeBoy RT, Paulsen IT, Fouts DE, Eisen JA, Daugherty SC, Dodson RJ, Durkin AS, Gwinn M, Haft DH, Kolonay JF, Nelson WC, Mason T, Tallon L, Gray J, Granger D, Tettelin H, Dong H, Galvin JL, Duncan MJ, Dewhirst FE, Fraser CM. Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83. J Bacteriol 2003; 185:5591-601. [PMID: 12949112 PMCID: PMC193775 DOI: 10.1128/jb.185.18.5591-5601.2003] [Citation(s) in RCA: 330] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The complete 2,343,479-bp genome sequence of the gram-negative, pathogenic oral bacterium Porphyromonas gingivalis strain W83, a major contributor to periodontal disease, was determined. Whole-genome comparative analysis with other available complete genome sequences confirms the close relationship between the Cytophaga-Flavobacteria-Bacteroides (CFB) phylum and the green-sulfur bacteria. Within the CFB phyla, the genomes most similar to that of P. gingivalis are those of Bacteroides thetaiotaomicron and B. fragilis. Outside of the CFB phyla the most similar genome to P. gingivalis is that of Chlorobium tepidum, supporting the previous phylogenetic studies that indicated that the Chlorobia and CFB phyla are related, albeit distantly. Genome analysis of strain W83 reveals a range of pathways and virulence determinants that relate to the novel biology of this oral pathogen. Among these determinants are at least six putative hemagglutinin-like genes and 36 previously unidentified peptidases. Genome analysis also reveals that P. gingivalis can metabolize a range of amino acids and generate a number of metabolic end products that are toxic to the human host or human gingival tissue and contribute to the development of periodontal disease.
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Affiliation(s)
- Karen E Nelson
- The Institute for Genomic Research, Rockville, Maryland 20850, USA.
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Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR, Holtzapple EK, Okstad OA, Helgason E, Rilstone J, Wu M, Kolonay JF, Beanan MJ, Dodson RJ, Brinkac LM, Gwinn M, DeBoy RT, Madpu R, Daugherty SC, Durkin AS, Haft DH, Nelson WC, Peterson JD, Pop M, Khouri HM, Radune D, Benton JL, Mahamoud Y, Jiang L, Hance IR, Weidman JF, Berry KJ, Plaut RD, Wolf AM, Watkins KL, Nierman WC, Hazen A, Cline R, Redmond C, Thwaite JE, White O, Salzberg SL, Thomason B, Friedlander AM, Koehler TM, Hanna PC, Kolstø AB, Fraser CM. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 2003; 423:81-6. [PMID: 12721629 DOI: 10.1038/nature01586] [Citation(s) in RCA: 663] [Impact Index Per Article: 31.6] [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: 08/14/2002] [Accepted: 03/28/2003] [Indexed: 11/09/2022]
Abstract
Bacillus anthracis is an endospore-forming bacterium that causes inhalational anthrax. Key virulence genes are found on plasmids (extra-chromosomal, circular, double-stranded DNA molecules) pXO1 (ref. 2) and pXO2 (ref. 3). To identify additional genes that might contribute to virulence, we analysed the complete sequence of the chromosome of B. anthracis Ames (about 5.23 megabases). We found several chromosomally encoded proteins that may contribute to pathogenicity--including haemolysins, phospholipases and iron acquisition functions--and identified numerous surface proteins that might be important targets for vaccines and drugs. Almost all these putative chromosomal virulence and surface proteins have homologues in Bacillus cereus, highlighting the similarity of B. anthracis to near-neighbours that are not associated with anthrax. By performing a comparative genome hybridization of 19 B. cereus and Bacillus thuringiensis strains against a B. anthracis DNA microarray, we confirmed the general similarity of chromosomal genes among this group of close relatives. However, we found that the gene sequences of pXO1 and pXO2 were more variable between strains, suggesting plasmid mobility in the group. The complete sequence of B. anthracis is a step towards a better understanding of anthrax pathogenesis.
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Affiliation(s)
- Timothy D Read
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA. )
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Seshadri R, Paulsen IT, Eisen JA, Read TD, Nelson KE, Nelson WC, Ward NL, Tettelin H, Davidsen TM, Beanan MJ, Deboy RT, Daugherty SC, Brinkac LM, Madupu R, Dodson RJ, Khouri HM, Lee KH, Carty HA, Scanlan D, Heinzen RA, Thompson HA, Samuel JE, Fraser CM, Heidelberg JF. Complete genome sequence of the Q-fever pathogen Coxiella burnetii. Proc Natl Acad Sci U S A 2003; 100:5455-60. [PMID: 12704232 PMCID: PMC154366 DOI: 10.1073/pnas.0931379100] [Citation(s) in RCA: 383] [Impact Index Per Article: 18.2] [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: 11/25/2002] [Accepted: 02/11/2003] [Indexed: 11/18/2022] Open
Abstract
The 1,995,275-bp genome of Coxiella burnetii, Nine Mile phase I RSA493, a highly virulent zoonotic pathogen and category B bioterrorism agent, was sequenced by the random shotgun method. This bacterium is an obligate intracellular acidophile that is highly adapted for life within the eukaryotic phagolysosome. Genome analysis revealed many genes with potential roles in adhesion, invasion, intracellular trafficking, host-cell modulation, and detoxification. A previously uncharacterized 13-member family of ankyrin repeat-containing proteins is implicated in the pathogenesis of this organism. Although the lifestyle and parasitic strategies of C. burnetii resemble that of Rickettsiae and Chlamydiae, their genome architectures differ considerably in terms of presence of mobile elements, extent of genome reduction, metabolic capabilities, and transporter profiles. The presence of 83 pseudogenes displays an ongoing process of gene degradation. Unlike other obligate intracellular bacteria, 32 insertion sequences are found dispersed in the chromosome, indicating some plasticity in the C. burnetii genome. These analyses suggest that the obligate intracellular lifestyle of C. burnetii may be a relatively recent innovation.
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Affiliation(s)
- Rekha Seshadri
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
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Paulsen IT, Seshadri R, Nelson KE, Eisen JA, Heidelberg JF, Read TD, Dodson RJ, Umayam L, Brinkac LM, Beanan MJ, Daugherty SC, Deboy RT, Durkin AS, Kolonay JF, Madupu R, Nelson WC, Ayodeji B, Kraul M, Shetty J, Malek J, Van Aken SE, Riedmuller S, Tettelin H, Gill SR, White O, Salzberg SL, Hoover DL, Lindler LE, Halling SM, Boyle SM, Fraser CM. The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc Natl Acad Sci U S A 2002; 99:13148-53. [PMID: 12271122 PMCID: PMC130601 DOI: 10.1073/pnas.192319099] [Citation(s) in RCA: 330] [Impact Index Per Article: 15.0] [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: 05/28/2002] [Indexed: 11/18/2022] Open
Abstract
The 3.31-Mb genome sequence of the intracellular pathogen and potential bioterrorism agent, Brucella suis, was determined. Comparison of B. suis with Brucella melitensis has defined a finite set of differences that could be responsible for the differences in virulence and host preference between these organisms, and indicates that phage have played a significant role in their divergence. Analysis of the B. suis genome reveals transport and metabolic capabilities akin to soil/plant-associated bacteria. Extensive gene synteny between B. suis chromosome 1 and the genome of the plant symbiont Mesorhizobium loti emphasizes the similarity between this animal pathogen and plant pathogens and symbionts. A limited repertoire of genes homologous to known bacterial virulence factors were identified.
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Affiliation(s)
- Ian T Paulsen
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
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Tettelin H, Masignani V, Cieslewicz MJ, Eisen JA, Peterson S, Wessels MR, Paulsen IT, Nelson KE, Margarit I, Read TD, Madoff LC, Wolf AM, Beanan MJ, Brinkac LM, Daugherty SC, DeBoy RT, Durkin AS, Kolonay JF, Madupu R, Lewis MR, Radune D, Fedorova NB, Scanlan D, Khouri H, Mulligan S, Carty HA, Cline RT, Van Aken SE, Gill J, Scarselli M, Mora M, Iacobini ET, Brettoni C, Galli G, Mariani M, Vegni F, Maione D, Rinaudo D, Rappuoli R, Telford JL, Kasper DL, Grandi G, Fraser CM. Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae. Proc Natl Acad Sci U S A 2002; 99:12391-6. [PMID: 12200547 PMCID: PMC129455 DOI: 10.1073/pnas.182380799] [Citation(s) in RCA: 395] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2002] [Accepted: 06/26/2002] [Indexed: 11/18/2022] Open
Abstract
The 2,160,267 bp genome sequence of Streptococcus agalactiae, the leading cause of bacterial sepsis, pneumonia, and meningitis in neonates in the U.S. and Europe, is predicted to encode 2,175 genes. Genome comparisons among S. agalactiae, Streptococcus pneumoniae, Streptococcus pyogenes, and the other completely sequenced genomes identified genes specific to the streptococci and to S. agalactiae. These in silico analyses, combined with comparative genome hybridization experiments between the sequenced serotype V strain 2603 V/R and 19 S. agalactiae strains from several serotypes using whole-genome microarrays, revealed the genetic heterogeneity among S. agalactiae strains, even of the same serotype, and provided insights into the evolution of virulence mechanisms.
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Affiliation(s)
- Herve Tettelin
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
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