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Lomholt HB, Scholz CFP, Brüggemann H, Tettelin H, Kilian M. A comparative study of Cutibacterium (Propionibacterium) acnes clones from acne patients and healthy controls. Anaerobe 2017; 47:57-63. [PMID: 28434779 DOI: 10.1016/j.anaerobe.2017.04.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/22/2017] [Accepted: 04/14/2017] [Indexed: 12/31/2022]
Abstract
BACKGROUND Cutibacterium (Propionibacterium) acnes is assumed to play an important role in the pathogenesis of acne. OBJECTIVES To examine if clones with distinct virulence properties are associated with acne. METHODS Multiple C. acnes isolates from follicles and surface skin of patients with moderate to severe acne and healthy controls were characterized by multilocus sequence typing. To determine if CC18 isolates from acne patients differ from those of controls in the possession of virulence genes or lack of genes conducive to a harmonious coexistence the full genomes of dominating CC18 follicular clones from six patients and five controls were sequenced. RESULTS Individuals carried one to ten clones simultaneously. The dominating C. acnes clones in follicles from acne patients were exclusively from the phylogenetic clade I-1a and all belonged to clonal complex CC18 with the exception of one patient dominated by the worldwide-disseminated and often antibiotic resistant clone ST3. The clonal composition of healthy follicles showed a more heterogeneous pattern with follicles dominated by clones representing the phylogenetic clades I-1a, I-1b, I-2 and II. Comparison of follicular CC18 gene contents, allelic versions of putative virulence genes and their promoter regions, and 54 variable-length intragenic and inter-genic homopolymeric tracts showed extensive conservation and no difference associated with the clinical origin of isolates. CONCLUSIONS The study supports that C. acnes strains from clonal complex CC18 and the often antibiotic resistant clone ST3 are associated with acne and suggests that susceptibility of the host rather than differences within these clones may determine the clinical outcome of colonization.
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Affiliation(s)
- H B Lomholt
- Department of Biomedicine, Faculty of Health, Aarhus University, DK-8000 Aarhus, Denmark.
| | - C F P Scholz
- Department of Biomedicine, Faculty of Health, Aarhus University, DK-8000 Aarhus, Denmark
| | - H Brüggemann
- Department of Biomedicine, Faculty of Health, Aarhus University, DK-8000 Aarhus, Denmark
| | - H Tettelin
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - M Kilian
- Department of Biomedicine, Faculty of Health, Aarhus University, DK-8000 Aarhus, Denmark
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2
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Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH. Standardized metadata for human pathogen/vector genomic sequences. PLoS One 2014; 9:e99979. [PMID: 24936976 PMCID: PMC4061050 DOI: 10.1371/journal.pone.0099979] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 05/15/2014] [Indexed: 11/18/2022] Open
Abstract
High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium's minimal information (MIxS) and NCBI's BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a consistent representation of these data in the BRC resources and other repositories that leverage these data, allowing investigators to identify relevant genomic sequences and perform comparative genomics analyses that are both statistically meaningful and biologically relevant.
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Affiliation(s)
- Vivien G. Dugan
- J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America
- National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
| | - Scott J. Emrich
- University of Notre Dame, Notre Dame, Indiana, United States of America
| | | | - Omar S. Harb
- University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ruchi M. Newman
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Brett E. Pickett
- J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America
| | - Lynn M. Schriml
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Timothy B. Stockwell
- J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America
| | | | - Dan E. Sullivan
- Cyberinfrastructure Division, Virginia Bioinformatics Institute, Blacksburg, Virginia, United States of America
| | - Indresh Singh
- J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America
| | - Doyle V. Ward
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Alison Yao
- National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
| | - Jie Zheng
- University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Tanya Barrett
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, United States of America
| | - Bruce Birren
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Lauren Brinkac
- J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America
| | - Vincent M. Bruno
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Elizabet Caler
- J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America
| | - Sinéad Chapman
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Frank H. Collins
- University of Notre Dame, Notre Dame, Indiana, United States of America
| | | | - Valentina Di Francesco
- National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
| | - Scott Durkin
- J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America
| | - Mark Eppinger
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | | | - Claire Fraser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - W. Florian Fricke
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Maria Giovanni
- National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
| | - Matthew R. Henn
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Erin Hine
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Julie Dunning Hotopp
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Ilene Karsch-Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, United States of America
| | | | - Eun Mi Lee
- National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
| | - Punam Mathur
- National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
| | - Emmanuel F. Mongodin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Cheryl I. Murphy
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Garry Myers
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | | | - Karen E. Nelson
- J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America
| | - William C. Nierman
- J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America
| | - Julia Puzak
- Kelly Government Solutions, Rockville, Maryland, United States of America
| | - David Rasko
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - David S. Roos
- University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Lisa Sadzewicz
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Joana C. Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Bruno Sobral
- Cyberinfrastructure Division, Virginia Bioinformatics Institute, Blacksburg, Virginia, United States of America
| | - R. Burke Squires
- National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
| | - Rick L. Stevens
- Argonne National Laboratory, Lemont, Illinois, United States of America
| | - Luke Tallon
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Herve Tettelin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - David Wentworth
- J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America
| | - Owen White
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Rebecca Will
- Cyberinfrastructure Division, Virginia Bioinformatics Institute, Blacksburg, Virginia, United States of America
| | - Jennifer Wortman
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Yun Zhang
- J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America
| | - Richard H. Scheuermann
- J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America
- Department of Pathology, University of California San Diego, San Diego, California, United States of America
- * E-mail:
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3
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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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4
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Abstract
The whole genome sequence of most human bacterial pathogens is available and the advent of next-generation sequencing technologies will result in a large number of sequenced isolates per pathogenic species. The study of multiple genome sequences of a given bacterium provides insights into its evolution, pathogenic potential and diversity. The pathogen's pan-genome, defined as the sum of the core genome shared by all sequenced strains and the dispensable genome present only in a subset of the isolates, can be analyzed to assess the size and diversity of the gene repertoire that the species has access to. This information is then used to better inform the reverse vaccinology approach whereby vaccine candidates are identified and prioritized in silico based on genomic data. Bioinformatics integration of genome sequence data with functional genomics results and clinical meta-data is essential to maximize the use of this large amount of information to answer biologically relevant questions.
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5
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Valdés J, Pedroso I, Quatrini R, Dodson RJ, Tettelin H, Blake R, Eisen JA, Holmes DS. Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. BMC Genomics 2008; 9:597. [PMID: 19077236 PMCID: PMC2621215 DOI: 10.1186/1471-2164-9-597] [Citation(s) in RCA: 315] [Impact Index Per Article: 19.7] [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: 06/26/2008] [Accepted: 12/11/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). It is a chemolithoautrophic, gamma-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. It thrives at extremely low pH (pH 1-2) and fixes both carbon and nitrogen from the atmosphere. It solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemical cycling in acid environments. The lack of a well-developed system for genetic manipulation has prevented thorough exploration of its physiology. Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism. RESULTS The genome of the type strain A. ferrooxidans ATCC 23270 was sequenced and annotated to identify general features and provide a framework for in silico metabolic reconstruction. Earlier models of iron and sulfur oxidation, biofilm formation, quorum sensing, inorganic ion uptake, and amino acid metabolism are confirmed and extended. Initial models are presented for central carbon metabolism, anaerobic metabolism (including sulfur reduction, hydrogen metabolism and nitrogen fixation), stress responses, DNA repair, and metal and toxic compound fluxes. CONCLUSION Bioinformatics analysis provides a valuable platform for gene discovery and functional prediction that helps explain the activity of A. ferrooxidans in industrial bioleaching and its role as a primary producer in acidic environments. An analysis of the genome of the type strain provides a coherent view of its gene content and metabolic potential.
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Affiliation(s)
- Jorge Valdés
- Center for Bioinformatics and Genome Biology, Fundación Ciencia para la Vida, Facultad de Ciencias de la Salud, Universidad Andres Bello, Santiago, Chile.
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6
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Carucci DJ, Gardner MJ, Tettelin H, Cummings LM, Smith HO, Adams MD, Venter JC, Hoffman SL. Sequencing the genome of Plasmodium falciparum. Curr Opin Infect Dis 2007; 11:531-4. [PMID: 17033418 DOI: 10.1097/00001432-199810000-00003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Advances in microbial genomic sequencing have the potential to revolutionize the control of infectious diseases. Recently, a consortium of researchers and funding agencies from the United States and Great Britain have embarked on a project to sequence the genome from Plasmodium falciparum, the most important cause of human malaria. The Malaria Genome Sequencing Project has reached an important milestone with the completion of the entire DNA sequence and annotation of chromosome 2, a 950 kilobase chromosome of Plasmodium falciparum. This review article will provide an overview of the malaria genome sequencing project, highlight progress in the field of microbial sequencing, and suggest new directions for future malaria research.
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Affiliation(s)
- D J Carucci
- Malaria Program, Naval Medical Research Institute, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA.
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7
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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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Abstract
An international consortium of genome centres, advanced development teams and funding agencies has begun the task of sequencing the genome of the parasite Plasmodium falciparum, the most important cause of human malaria. Sequencing is proceeding chromosome by chromosome, and the annotated sequence of chromosome 2 is nearly finished. With the continual release of sequence data as they are generated, malaria researchers have access to a steady stream of genomic sequences and will soon have the complete annotation of all of the estimated 5000-7000 P. falciparum genes. The task will then be how to best apply these data to the development of new anti-malarial drugs, vaccines and diagnostic tests. This review provides a brief overview of the Malaria Genome Sequencing Project and suggests potential directions for future malaria research.
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Affiliation(s)
- D J Carucci
- Malaria Program, Naval Medical Research Institute, 12300 Washington Avenue, Rockville, MD 20852, USA.
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9
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Paulsen IT, Banerjei L, Myers GSA, Nelson KE, Seshadri R, Read TD, Fouts DE, Eisen JA, Gill SR, Heidelberg JF, Tettelin H, Dodson RJ, Umayam L, Brinkac L, Beanan M, Daugherty S, DeBoy RT, Durkin S, Kolonay J, Madupu R, Nelson W, Vamathevan J, Tran B, Upton J, Hansen T, Shetty J, Khouri H, Utterback T, Radune D, Ketchum KA, Dougherty BA, Fraser CM. Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science 2003; 299:2071-4. [PMID: 12663927 DOI: 10.1126/science.1080613] [Citation(s) in RCA: 686] [Impact Index Per Article: 32.7] [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: 11/02/2022]
Abstract
The complete genome sequence of Enterococcus faecalis V583, a vancomycin-resistant clinical isolate, revealed that more than a quarter of the genome consists of probable mobile or foreign DNA. One of the predicted mobile elements is a previously unknown vanB vancomycin-resistance conjugative transposon. Three plasmids were identified, including two pheromone-sensing conjugative plasmids, one encoding a previously undescribed pheromone inhibitor. The apparent propensity for the incorporation of mobile elements probably contributed to the rapid acquisition and dissemination of drug resistance in the enterococci.
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Affiliation(s)
- I T Paulsen
- Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
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10
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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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11
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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] [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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Abstract
In this era of genomic science, knowledge about biological function is integrated increasingly with DNA sequence data. One area that has been significantly impacted by this accumulation of information is the discovery of drugs to treat microbial infections. Genome sequencing and bioinformatics is driving the discovery and development of novel classes of broad-spectrum antimicrobial compounds, and could enable medical science to keep pace with the increasing resistance of bacteria, fungi and parasites to current antimicrobials. This review discusses the use of genomic information in the rapid identification of target genes for antimicrobial drug discovery.
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Affiliation(s)
- T D. Read
- Microbial Genomics Group, The Institute for Genomic Research, 9712 Medical Center 20851, Tel.: +1 301 838 3554, fax: +1 301 838 0208, Drive Rockville, MD, USA
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13
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Tettelin H, Nelson KE, Paulsen IT, Eisen JA, Read TD, Peterson S, Heidelberg J, DeBoy RT, Haft DH, Dodson RJ, Durkin AS, Gwinn M, Kolonay JF, Nelson WC, Peterson JD, Umayam LA, White O, Salzberg SL, Lewis MR, Radune D, Holtzapple E, Khouri H, Wolf AM, Utterback TR, Hansen CL, McDonald LA, Feldblyum TV, Angiuoli S, Dickinson T, Hickey EK, Holt IE, Loftus BJ, Yang F, Smith HO, Venter JC, Dougherty BA, Morrison DA, Hollingshead SK, Fraser CM. Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 2001; 293:498-506. [PMID: 11463916 DOI: 10.1126/science.1061217] [Citation(s) in RCA: 1032] [Impact Index Per Article: 44.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The 2,160,837-base pair genome sequence of an isolate of Streptococcus pneumoniae, a Gram-positive pathogen that causes pneumonia, bacteremia, meningitis, and otitis media, contains 2236 predicted coding regions; of these, 1440 (64%) were assigned a biological role. Approximately 5% of the genome is composed of insertion sequences that may contribute to genome rearrangements through uptake of foreign DNA. Extracellular enzyme systems for the metabolism of polysaccharides and hexosamines provide a substantial source of carbon and nitrogen for S. pneumoniae and also damage host tissues and facilitate colonization. A motif identified within the signal peptide of proteins is potentially involved in targeting these proteins to the cell surface of low-guanine/cytosine (GC) Gram-positive species. Several surface-exposed proteins that may serve as potential vaccine candidates were identified. Comparative genome hybridization with DNA arrays revealed strain differences in S. pneumoniae that could contribute to differences in virulence and antigenicity.
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Affiliation(s)
- H Tettelin
- The Institute for Genomic Research (TIGR), 9712 Medical Center Drive, Rockville, MD 20850, USA
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14
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Masignani V, Giuliani MM, Tettelin H, Comanducci M, Rappuoli R, Scarlato V. Mu-like Prophage in serogroup B Neisseria meningitidis coding for surface-exposed antigens. Infect Immun 2001; 69:2580-8. [PMID: 11254622 PMCID: PMC98194 DOI: 10.1128/iai.69.4.2580-2588.2001] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sequence analysis of the genome of Neisseria meningititdis serogroup B revealed the presence of an approximately 35-kb region inserted within a putative gene coding for an ABC-type transporter. The region contains 46 open reading frames, 29 of which are colinear and homologous to the genes of Escherichia coli Mu phage. Two prophages with similar organizations were also found in serogroup A meningococcus, and one was found in Haemophilus influenzae. Early and late phage functions are well preserved in this family of Mu-like prophages. Several regions of atypical nucleotide content were identified. These likely represent genes acquired by horizontal transfer. Three of the acquired genes are shown to code for surface-associated antigens, and the encoded proteins are able to induce bactericidal antibodies.
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Affiliation(s)
- V Masignani
- Department of Molecular Biology, IRIS, Chiron S.p.A., 53100 Siena, Italy
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15
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Peterson S, Cline RT, Tettelin H, Sharov V, Morrison DA. Gene expression analysis of the Streptococcus pneumoniae competence regulons by use of DNA microarrays. J Bacteriol 2000; 182:6192-202. [PMID: 11029442 PMCID: PMC94756 DOI: 10.1128/jb.182.21.6192-6202.2000] [Citation(s) in RCA: 150] [Impact Index Per Article: 6.3] [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: 01/30/2023] Open
Abstract
Competence for genetic transformation in Streptococcus pneumoniae is coordinated by the competence-stimulating peptide (CSP), which induces a sudden and transient appearance of competence during exponential growth in vitro. Models of this quorum-sensing mechanism have proposed sequential expression of several regulatory genes followed by induction of target genes encoding DNA-processing-pathway proteins. Although many genes required for transformation are known to be expressed only in response to CSP, the relative timing of their expression has not been established. Overlapping expression patterns for the genes cinA and comD (G. Alloing, B. Martin, C. Granadel, and J. P. Claverys, Mol. Microbiol. 29:75-83, 1998) suggest that at least two distinct regulatory mechanisms may underlie the competence cycle. DNA microarrays were used to estimate mRNA levels for all known competence operons during induction of competence by CSP. The known competence regulatory operons, comAB, comCDE, and comX, exhibited a low or zero initial (uninduced) signal, strongly increased expression during the period between 5 and 12 min after CSP addition, and a decrease nearly to original values by 15 min after initiation of exposure to CSP. The remaining competence genes displayed a similar expression pattern, but with an additional delay of approximately 5 min. In a mutant defective in ComX, which may act as an alternate sigma factor to allow expression of the target competence genes, the same regulatory genes were induced, but the other competence genes were not. Finally, examination of the expression of 60 candidate sites not previously associated with competence identified eight additional loci that could be induced by CSP.
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Affiliation(s)
- S Peterson
- Department of Functional Genomics, The Institute for Genomic Research, Rockville, Maryland 20850, USA
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16
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Saunders NJ, Jeffries AC, Peden JF, Hood DW, Tettelin H, Rappuoli R, Moxon ER. Repeat-associated phase variable genes in the complete genome sequence of Neisseria meningitidis strain MC58. Mol Microbiol 2000; 37:207-15. [PMID: 10931317 DOI: 10.1046/j.1365-2958.2000.02000.x] [Citation(s) in RCA: 185] [Impact Index Per Article: 7.7] [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: 11/20/2022]
Abstract
Phase variation, mediated through variation in the length of simple sequence repeats, is recognized as an important mechanism for controlling the expression of factors involved in bacterial virulence. Phase variation is associated with most of the currently recognized virulence determinants of Neisseria meningitidis. Based upon the complete genome sequence of the N. meningitidis serogroup B strain MC58, we have identified tracts of potentially unstable simple sequence repeats and their potential functional significance determined on the basis of sequence context. Of the 65 potentially phase variable genes identified, only 13 were previously recognized. Comparison with the sequences from the other two pathogenic Neisseria sequencing projects shows differences in the length of the repeats in 36 of the 65 genes identified, including 25 of those not previously known to be phase variable. Six genes that did not have differences in the length of the repeat instead had polymorphisms such that the gene would not be expected to be phase variable in at least one of the other strains. A further 12 candidates did not have homologues in either of the other two genome sequences. The large proportion of these genes that are associated with frameshifts and with differences in repeat length between the neisserial genome sequences is further corroborative evidence that they are phase variable. The number of potentially phase variable genes is substantially greater than for any other species studied to date, and would allow N. meningitidis to generate a very large repertoire of phenotypes through expression of these genes in different combinations. Novel phase variable candidates identified in the strain MC58 genome sequence include a spectrum of genes encoding glycosyltransferases, toxin related products, and metabolic activities as well as several restriction/modification and bacteriocin-related genes and a number of open reading frames (ORFs) for which the function is currently unknown. This suggests that the potential role of phase variation in mediating bacterium-host interactions is much greater than has been appreciated to date. Analysis of the distribution of homopolymeric tract lengths indicates that this species has sequence-specific mutational biases that favour the instability of sequences associated with phase variation.
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Affiliation(s)
- N J Saunders
- The Molecular Infectious Disease Group, Institute of Molecular Medicine, University of Oxford, Headington, Oxford, OX3 9DS, UK.
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17
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Pizza M, Scarlato V, Masignani V, Giuliani MM, Aricò B, Comanducci M, Jennings GT, Baldi L, Bartolini E, Capecchi B, Galeotti CL, Luzzi E, Manetti R, Marchetti E, Mora M, Nuti S, Ratti G, Santini L, Savino S, Scarselli M, Storni E, Zuo P, Broeker M, Hundt E, Knapp B, Blair E, Mason T, Tettelin H, Hood DW, Jeffries AC, Saunders NJ, Granoff DM, Venter JC, Moxon ER, Grandi G, Rappuoli R. Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Science 2000; 287:1816-20. [PMID: 10710308 DOI: 10.1126/science.287.5459.1816] [Citation(s) in RCA: 914] [Impact Index Per Article: 38.1] [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: 11/03/2022]
Abstract
Neisseria meningitidis is a major cause of bacterial septicemia and meningitis. Sequence variation of surface-exposed proteins and cross-reactivity of the serogroup B capsular polysaccharide with human tissues have hampered efforts to develop a successful vaccine. To overcome these obstacles, the entire genome sequence of a virulent serogroup B strain (MC58) was used to identify vaccine candidates. A total of 350 candidate antigens were expressed in Escherichia coli, purified, and used to immunize mice. The sera allowed the identification of proteins that are surface exposed, that are conserved in sequence across a range of strains, and that induce a bactericidal antibody response, a property known to correlate with vaccine efficacy in humans.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Bacterial/biosynthesis
- Antibodies, Bacterial/blood
- Antigens, Bacterial/chemistry
- Antigens, Bacterial/genetics
- Antigens, Bacterial/immunology
- Antigens, Surface/chemistry
- Antigens, Surface/genetics
- Antigens, Surface/immunology
- Bacterial Capsules
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/immunology
- Bacterial Vaccines/genetics
- Bacterial Vaccines/immunology
- Conserved Sequence
- Escherichia coli/genetics
- Genome, Bacterial
- Humans
- Immune Sera/immunology
- Mice
- Neisseria meningitidis/classification
- Neisseria meningitidis/genetics
- Neisseria meningitidis/immunology
- Neisseria meningitidis/pathogenicity
- Open Reading Frames
- Recombinant Fusion Proteins/chemistry
- Recombinant Fusion Proteins/immunology
- Recombinant Fusion Proteins/isolation & purification
- Recombination, Genetic
- Sequence Analysis, DNA
- Serotyping
- Vaccination
- Virulence
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Affiliation(s)
- M Pizza
- IRIS, Chiron S.p.A., Via Fiorentina 1, 53100 Siena, Italy
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18
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Tettelin H, Saunders NJ, Heidelberg J, Jeffries AC, Nelson KE, Eisen JA, Ketchum KA, Hood DW, Peden JF, Dodson RJ, Nelson WC, Gwinn ML, DeBoy R, Peterson JD, Hickey EK, Haft DH, Salzberg SL, White O, Fleischmann RD, Dougherty BA, Mason T, Ciecko A, Parksey DS, Blair E, Cittone H, Clark EB, Cotton MD, Utterback TR, Khouri H, Qin H, Vamathevan J, Gill J, Scarlato V, Masignani V, Pizza M, Grandi G, Sun L, Smith HO, Fraser CM, Moxon ER, Rappuoli R, Venter JC. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science 2000; 287:1809-15. [PMID: 10710307 DOI: 10.1126/science.287.5459.1809] [Citation(s) in RCA: 814] [Impact Index Per Article: 33.9] [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 2,272,351-base pair genome of Neisseria meningitidis strain MC58 (serogroup B), a causative agent of meningitis and septicemia, contains 2158 predicted coding regions, 1158 (53.7%) of which were assigned a biological role. Three major islands of horizontal DNA transfer were identified; two of these contain genes encoding proteins involved in pathogenicity, and the third island contains coding sequences only for hypothetical proteins. Insights into the commensal and virulence behavior of N. meningitidis can be gleaned from the genome, in which sequences for structural proteins of the pilus are clustered and several coding regions unique to serogroup B capsular polysaccharide synthesis can be identified. Finally, N. meningitidis contains more genes that undergo phase variation than any pathogen studied to date, a mechanism that controls their expression and contributes to the evasion of the host immune system.
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Affiliation(s)
- H Tettelin
- The Institute for Genomic Research (TIGR), 9712 Medical Center Drive, Rockville, MD 20850, USA
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19
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Abstract
A new method has been developed for rapidly closing a large number of gaps in a whole-genome shotgun sequencing project. The method employs multiplex PCR and a novel pooling strategy to minimize the number of laboratory procedures required to sequence the unknown DNA that falls in between contiguous sequences. Multiplex sequencing, a novel procedure in which multiple PCR primers are used in a single sequencing reaction, is used to interpret the multiplex PCR results. Two protocols are presented, one that minimizes pipetting and another that minimizes the number of reactions. The pipette optimized multiplex PCR method has been employed in the final phases of closing the Streptococcus pneumoniae genome sequence, with excellent results.
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Affiliation(s)
- H Tettelin
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA.
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20
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Gardner MJ, Tettelin H, Carucci DJ, Cummings LM, Smith HO, Fraser CM, Venter JC, Hoffman SL. The malaria genome sequencing project: complete sequence of Plasmodium falciparum chromosome 2. Parassitologia 1999; 41:69-75. [PMID: 10697835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
An international consortium has been formed to sequence the entire genome of the human malaria parasite Plasmodium falciparum. We sequenced chromosome 2 of clone 3D7 using a shotgun sequencing strategy. Chromosome 2 is 947 kb in length, has a base composition of 80.2% A + T, and contains 210 predicted genes. In comparison to the Saccharomyces cerevisiae genome, chromosome 2 has a lower gene density, a greater proportion of genes containing introns, and nearly twice as many proteins containing predicted non-globular domains. A group of putative surface proteins was identified, rifins, which are encoded by a gene family comprising up to 7% of the protein-encoding gene in the genome. The rifins exhibit considerable sequence diversity and may play an important role in antigenic variation. Sixteen genes encoded on chromosome 2 showed signs of a plastid or mitochondrial origin, including several genes involved in fatty acid biosynthesis. Completion of the chromosome 2 sequence demonstrated that the A + T-rich genome of P. falciparum can be sequenced by the shotgun approach. Within 2-3 years, the sequence of almost all P. falciparum genes will have been determined, paving the way for genetic, biochemical, and immunological research aimed at developing new drugs and vaccines against malaria.
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Affiliation(s)
- M J Gardner
- Institute of Genomic Research, Naval Medical Research Center, Rockville, MD, USA.
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21
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Abstract
Computational gene finding research has emphasized the development of gene finders for bacterial and human DNA. This has left genome projects for some small eukaryotes without a system that addresses their needs. This paper reports on a new system, GlimmerM, that was developed to find genes in the malaria parasite Plasmodium falciparum. Because the gene density in P. falciparum is relatively high, the system design was based on a successful bacterial gene finder, Glimmer. The system was augmented with specially trained modules to find splice sites and was trained on all available data from the P. falciparum genome. Although a precise evaluation of its accuracy is impossible at this time, laboratory tests (using RT-PCR) on a small selection of predicted genes confirmed all of those predictions. With the rapid progress in sequencing the genome of P. falciparum, the availability of this new gene finder will greatly facilitate the annotation process.
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Affiliation(s)
- S L Salzberg
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA.
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22
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Jing J, Lai Z, Aston C, Lin J, Carucci DJ, Gardner MJ, Mishra B, Anantharaman TS, Tettelin H, Cummings LM, Hoffman SL, Venter JC, Schwartz DC. Optical mapping of Plasmodium falciparum chromosome 2. Genome Res 1999; 9:175-81. [PMID: 10022982 PMCID: PMC310721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/1998] [Accepted: 12/15/1998] [Indexed: 02/10/2023]
Abstract
Detailed restriction maps of microbial genomes are a valuable resource in genome sequencing studies but are toilsome to construct by contig construction of maps derived from cloned DNA. Analysis of genomic DNA enables large stretches of the genome to be mapped and circumvents library construction and associated cloning artifacts. We used pulsed-field gel electrophoresis purified Plasmodium falciparum chromosome 2 DNA as the starting material for optical mapping, a system for making ordered restriction maps from ensembles of individual DNA molecules. DNA molecules were bound to derivatized glass surfaces, cleaved with NheI or BamHI, and imaged by digital fluorescence microscopy. Large pieces of the chromosome containing ordered DNA restriction fragments were mapped. Maps were assembled from 50 molecules producing an average contig depth of 15 molecules and high-resolution restriction maps covering the entire chromosome. Chromosome 2 was found to be 976 kb by optical mapping with NheI, and 946 kb with BamHI, which compares closely to the published size of 947 kb from large-scale sequencing. The maps were used to further verify assemblies from the plasmid library used for sequencing. Maps generated in silico from the sequence data were compared to the optical mapping data, and good correspondence was found. Such high-resolution restriction maps may become an indispensable resource for large-scale genome sequencing projects.
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Affiliation(s)
- J Jing
- W.M. Keck Laboratory for Biomolecular Imaging, New York University, Department of Chemistry, New York, New York 10003 USA
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23
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Gardner MJ, Tettelin H, Carucci DJ, Cummings LM, Aravind L, Koonin EV, Shallom S, Mason T, Yu K, Fujii C, Pederson J, Shen K, Jing J, Aston C, Lai Z, Schwartz DC, Pertea M, Salzberg S, Zhou L, Sutton GG, Clayton R, White O, Smith HO, Fraser CM, Adams MD, Venter JC, Hoffman SL. Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science 1998; 282:1126-32. [PMID: 9804551 DOI: 10.1126/science.282.5391.1126] [Citation(s) in RCA: 370] [Impact Index Per Article: 14.2] [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] [Indexed: 11/02/2022]
Abstract
Chromosome 2 of Plasmodium falciparum was sequenced; this sequence contains 947,103 base pairs and encodes 210 predicted genes. In comparison with the Saccharomyces cerevisiae genome, chromosome 2 has a lower gene density, introns are more frequent, and proteins are markedly enriched in nonglobular domains. A family of surface proteins, rifins, that may play a role in antigenic variation was identified. The complete sequencing of chromosome 2 has shown that sequencing of the A+T-rich P. falciparum genome is technically feasible.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antigens, Protozoan/chemistry
- Antigens, Protozoan/genetics
- Base Composition
- Chromosomes/genetics
- Evolution, Molecular
- Genes, Protozoan
- Genome, Protozoan
- Introns
- Membrane Proteins/chemistry
- Membrane Proteins/genetics
- Molecular Sequence Data
- Multigene Family
- Physical Chromosome Mapping
- Plasmodium falciparum/genetics
- Protozoan Proteins/chemistry
- Protozoan Proteins/genetics
- RNA, Protozoan/genetics
- RNA, Transfer, Glu/genetics
- Repetitive Sequences, Nucleic Acid
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Alignment
- Sequence Analysis, DNA
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Affiliation(s)
- M J Gardner
- Institute for Genomic Research, Rockville, MD 20850, USA
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24
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Abstract
The high resolution complete physical maps of chromosomes VII and XV were constructed to form the basis for sequencing these chromosomes as part of the European systematic sequencing programme of the yeast genome, using a unique cosmid library from strain FY1679, and an original top-down mapping strategy involving I-Sce I chromosome fragmentation. A total of 138 and 196 cosmid clones were used to construct the maps for VII and XV, respectively, forming two unique contigs that cover the entirety of chromosomes (1091 kb each), except the telomeric repeats. Colinearity of the cosmid inserts with yeast DNA was verified, and the physical maps were eventually compared with the independently generated genetic maps.
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Affiliation(s)
- H Tettelin
- Département des Biotechnologies (URA 1300 du CNRS and UFR927 Université P.M. Curie), Institut Pasteur, Paris, France
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25
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Caro LH, Tettelin H, Vossen JH, Ram AF, van den Ende H, Klis FM. In silicio identification of glycosyl-phosphatidylinositol-anchored plasma-membrane and cell wall proteins of Saccharomyces cerevisiae. Yeast 1997; 13:1477-89. [PMID: 9434352 DOI: 10.1002/(sici)1097-0061(199712)13:15<1477::aid-yea184>3.0.co;2-l] [Citation(s) in RCA: 239] [Impact Index Per Article: 8.9] [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: 02/05/2023] Open
Abstract
Use of the Von Heijne algorithm allowed the identification of 686 open reading frames (ORFs) in the genome of Saccharomyces cerevisiae that encode proteins with a potential N-terminal signal sequence for entering the secretory pathway. On further analysis, 51 of these proteins contain a potential glycosyl-phosphatidylinositol (GPI)-attachment signal. Seven additional ORFs were found to belong to this group. Upon examination of the possible GPI-attachment sites, it was found that in yeast the most probable amino acids for GPI-attachment as asparagine and glycine. In yeast, GPI-proteins are found at the cell surface, either attached to the plasma-membrane or as an intrinsic part of the cell wall. It was noted that plasma-membrane GPI-proteins possess a dibasic residue motif just before their predicted GPI-attachment site. Based on this, and on homologies between proteins, families of plasma-membrane and cell wall proteins were assigned, revealing 20 potential plasma-membrane and 38 potential cell wall proteins. For members of three plasma-membrane protein families, a function has been described. On the other hand, most of the cell wall proteins seem to be structural components of the wall, responsive to different growth conditions. The GPI-attachment site of yeast slightly differs from mammalian cells. This might be of use in the development of anti-fungal drugs.
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Affiliation(s)
- L H Caro
- Fungal Cell Wall Group Amsterdam, BioCentrum Amsterdam, University of Amsterdam, The Netherlands
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26
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Tettelin H, Agostoni Carbone ML, Albermann K, Albers M, Arroyo J, Backes U, Barreiros T, Bertani I, Bjourson AJ, Brückner M, Bruschi CV, Carignani G, Castagnoli L, Cerdan E, Clemente ML, Coblenz A, Coglievina M, Coissac E, Defoor E, Del Bino S, Delius H, Delneri D, de Wergifosse P, Dujon B, Kleine K. The nucleotide sequence of Saccharomyces cerevisiae chromosome VII. Nature 1997; 387:81-4. [PMID: 9169869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The complete nucleotide sequence of Saccharomyces cerevisiae chromosome VII has 572 predicted open reading frames (ORFs), of which 341 are new. No correlation was found between G+C content and gene density along the chromosome, and their variations are random. Of the ORFs, 17% show high similarity to human proteins. Almost half of the ORFs could be classified in functional categories, and there is a slight increase in the number of transcription (7.0%) and translation (5.2%) factors when compared with the complete S. cerevisiae genome. Accurate verification procedures demonstrate that there are less than two errors per 10,000 base pairs in the published sequence.
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Affiliation(s)
- H Tettelin
- Unité de Biochimie Physiologique, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
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27
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Dujon B, Albermann K, Aldea M, Alexandraki D, Ansorge W, Arino J, Benes V, Bohn C, Bolotin-Fukuhara M, Bordonné R, Boyer J, Camasses A, Casamayor A, Casas C, Chéret G, Cziepluch C, Daignan-Fornier B, Dang DV, de Haan M, Delius H, Durand P, Fairhead C, Feldmann H, Gaillon L, Galisson F, Gamo FJ, Gancedo C, Goffeau A, Goulding SE, Grivell LA, Habbig B, Hand NJ, Hani J, Hattenhorst U, Hebling U, Hernando Y, Herrero E, Heumann K, Hiesel R, Hilger F, Hofmann B, Hollenberg CP, Hughes B, Jauniaux JC, Kalogeropoulos A, Katsoulou C, Kordes E, Lafuente MJ, Landt O, Louis EJ, Maarse AC, Madania A, Mannhaupt G, Marck C, Martin RP, Mewes HW, Michaux G, Paces V, Parle-McDermott AG, Pearson BM, Perrin A, Pettersson B, Poch O, Pohl TM, Poirey R, Portetelle D, Pujol A, Purnelle B, Ramezani Rad M, Rechmann S, Schwager C, Schweizer M, Sor F, Sterky F, Tarassov IA, Teodoru C, Tettelin H, Thierry A, Tobiasch E, Tzermia M, Uhlen M, Unseld M, Valens M, Vandenbol M, Vetter I, Vlcek C, Voet M, Volckaert G, Voss H, Wambutt R, Wedler H, Wiemann S, Winsor B, Wolfe KH, Zollner A, Zumstein E, Kleine K. The nucleotide sequence of Saccharomyces cerevisiae chromosome XV. Nature 1997. [DOI: 10.1038/387s098] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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28
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Van Dyck L, Tettelin H, Purnelle B, Goffeau A. An 18.3 kb DNA fragment from yeast chromosome VII carries four unknown open reading frames, the gene for an Asn synthase, remnants of Ty and three tRNA genes. Yeast 1997; 13:171-6. [PMID: 9046098 DOI: 10.1002/(sici)1097-0061(199702)13:2<171::aid-yea57>3.0.co;2-v] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
An 18.3 kb DNA segment from yeast Saccharomyces cerevisiae VII encompasses the previously characterized MEP1, NUP57 and PPT1 genes as well as seven new open reading frames (ORFs) of at least 100 residues. G6358 is an ubiquitous glutamine-dependent asparagine synthase. G6362 is membrane protein highly homologous to a protein of unknown function in the yeast Schizosaccharomyces pombe. Three ORFs (G6324, G6335 and G6365) have no significant homology with previously reported proteins of characteristic motifs. G6321 and G6359, enclosed in longer ORFs, are not likely to be coding. The segment also contains tRNA genes for Asn, Arg and Ile as well as sigma element and two solo deltas. ORFs and genetic elements are named according to a preliminary working nomenclature.
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Affiliation(s)
- L Van Dyck
- Unité de Biochimie Physiologique, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
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Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG. Life with 6000 genes. Science 1996; 274:546, 563-7. [PMID: 8849441 DOI: 10.1126/science.274.5287.546] [Citation(s) in RCA: 2487] [Impact Index Per Article: 88.8] [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: 02/02/2023]
Abstract
The genome of the yeast Saccharomyces cerevisiae has been completely sequenced through a worldwide collaboration. The sequence of 12,068 kilobases defines 5885 potential protein-encoding genes, approximately 140 genes specifying ribosomal RNA, 40 genes for small nuclear RNA molecules, and 275 transfer RNA genes. In addition, the complete sequence provides information about the higher order organization of yeast's 16 chromosomes and allows some insight into their evolutionary history. The genome shows a considerable amount of apparent genetic redundancy, and one of the major problems to be tackled during the next stage of the yeast genome project is to elucidate the biological functions of all of these genes.
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Affiliation(s)
- A Goffeau
- Université Catholique de Louvain, Unité de Biochimie Physiologique, Place Croix du Sud, 2/20, 1348 Louvain-la-Neuve, Belgium
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Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG. Life with 6000 genes. Science 1996; 274:546-567. [PMID: 8849441 DOI: 10.1126/science.274.5287.54] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The genome of the yeast Saccharomyces cerevisiae has been completely sequenced through a worldwide collaboration. The sequence of 12,068 kilobases defines 5885 potential protein-encoding genes, approximately 140 genes specifying ribosomal RNA, 40 genes for small nuclear RNA molecules, and 275 transfer RNA genes. In addition, the complete sequence provides information about the higher order organization of yeast's 16 chromosomes and allows some insight into their evolutionary history. The genome shows a considerable amount of apparent genetic redundancy, and one of the major problems to be tackled during the next stage of the yeast genome project is to elucidate the biological functions of all of these genes.
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Affiliation(s)
- A Goffeau
- Université Catholique de Louvain, Unité de Biochimie Physiologique, Place Croix du Sud, 2/20, 1348 Louvain-la-Neuve, Belgium
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Dujon B, Alexandraki D, André B, Ansorge W, Baladron V, Ballesta JP, Banrevi A, Bolle PA, Bolotin-Fukuhara M, Bossier P, Bou G, Boyer J, Bultrago MJ, Cheret G, Colleaux L, Dalgnan-Fornler B, del Rey F, Dlon C, Domdey H, Düsterhoft A, Düsterhus S, Entlan KD, Erfle H, Esteban PF, Feldmann H, Fernandes L, Robo GM, Fritz C, Fukuhara H, Gabel C, Gaillon L, Carcia-Cantalejo JM, Garcia-Ramirez JJ, Gent NE, Ghazvini M, Goffeau A, Gonzaléz A, Grothues D, Guerreiro P, Hegemann J, Hewitt N, Hilger F, Hollenberg CP, Horaitis O, Indge KJ, Jacquier A, James CM, Jauniaux C, Jimenez A, Keuchel H, Kirchrath L, Kleine K, Kötter P, Legrain P, Liebl S, Louis EJ, Maia e Silva A, Marck C, Monnier AL, Möstl D, Müller S, Obermaier B, Oliver SG, Pallier C, Pascolo S, Pfeiffer F, Philippsen P, Planta RJ, Pohl FM, Pohl TM, Pöhlmann R, Portetelle D, Purnelle B, Puzos V, Ramezani Rad M, Rasmussen SW, Remacha M, Revuelta JL, Richard GF, Rieger M, Rodrigues-Pousada C, Rose M, Rupp T, Santos MA, Schwager C, Sensen C, Skala J, Soares H, Sor F, Stegemann J, Tettelin H, Thierry A, Tzermia M, Urrestarazu LA, van Dyck L, Van Vliet-Reedijk JC, Valens M, Vandenbo M, Vilela C, Vissers S, von Wettstein D, Voss H, Wiemann S, Xu G, Zimmermann J, Haasemann M, Becker I, Mewes HW. Complete DNA sequence of yeast chromosome XI. Nature 1994; 369:371-8. [PMID: 8196765 DOI: 10.1038/369371a0] [Citation(s) in RCA: 308] [Impact Index Per Article: 10.3] [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: 01/29/2023]
Abstract
The complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome XI has been determined. In addition to a compact arrangement of potential protein coding sequences, the 666,448-base-pair sequence has revealed general chromosome patterns; in particular, alternating regional variations in average base composition correlate with variations in local gene density along the chromosome. Significant discrepancies with the previously published genetic map demonstrate the need for using independent physical mapping criteria.
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Affiliation(s)
- B Dujon
- Unité de Génétique Moléculaire des Levures (URA 1149 du CNRS and UFR927 University P.M. Curie), Départment de Biologie Moléculaire, Insitut Pasteur, Paris, France
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Purnelle B, Tettelin H, Van Dyck L, Skala J, Goffeau A. The sequence of a 17.5 kb DNA fragment on the left arm of yeast chromosome XI identifies the protein kinase gene ELM1, the DNA primase gene PRI2, a new gene encoding a putative histone and seven new open reading frames. Yeast 1993; 9:1379-84. [PMID: 8154189 DOI: 10.1002/yea.320091212] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [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: 01/29/2023] Open
Abstract
A 17.5 kb DNA fragment of chromosome XI, located between the genetic loci mif2 and mak11 was sequenced and analysed. Ten open reading frames were identified. Two of them are the previously sequenced genes ELM1 and PRI2, two (YKL253 and YKL256) show homologies to proteins from other organisms and one (YKL262) to yeast and mouse histone.
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Affiliation(s)
- B Purnelle
- Unité de Biochimie Physiologique, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
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