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Genome sequence of Lactobacillus helveticus, an organism distinguished by selective gene loss and insertion sequence element expansion. J Bacteriol 2007; 190:727-35. [PMID: 17993529 DOI: 10.1128/jb.01295-07] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mobile genetic elements are major contributing factors to the generation of genetic diversity in prokaryotic organisms. For example, insertion sequence (IS) elements have been shown to specifically contribute to niche adaptation by promoting a variety of genetic rearrangements. The complete genome sequence of the cheese culture Lactobacillus helveticus DPC 4571 was determined and revealed significant conservation compared to three nondairy gut lactobacilli. Despite originating from significantly different environments, 65 to 75% of the genes were conserved between the commensal and dairy lactobacilli, which allowed key niche-specific gene sets to be described. However, the primary distinguishing feature was 213 IS elements in the DPC 4571 genome, 10 times more than for the other lactobacilli. Moreover, genome alignments revealed an unprecedented level of genome stability between these four Lactobacillus species, considering the number of IS elements in the L. helveticus genome. Comparative analysis also indicated that the IS elements were not the primary agents of niche adaptation for the L. helveticus genome. A clear bias toward the loss of genes reported to be important for gut colonization was observed for the cheese culture, but there was no clear evidence of IS-associated gene deletion and decay for the majority of genes lost. Furthermore, an extraordinary level of sequence diversity exists between copies of certain IS elements in the DPC 4571 genome, indicating they may represent an ancient component of the L. helveticus genome. These data suggest a special unobtrusive relationship between the DPC 4571 genome and its mobile DNA complement.
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Hain T, Chatterjee SS, Ghai R, Kuenne CT, Billion A, Steinweg C, Domann E, Kärst U, Jänsch L, Wehland J, Eisenreich W, Bacher A, Joseph B, Schär J, Kreft J, Klumpp J, Loessner MJ, Dorscht J, Neuhaus K, Fuchs TM, Scherer S, Doumith M, Jacquet C, Martin P, Cossart P, Rusniock C, Glaser P, Buchrieser C, Goebel W, Chakraborty T. Pathogenomics of Listeria spp. Int J Med Microbiol 2007; 297:541-57. [PMID: 17482873 DOI: 10.1016/j.ijmm.2007.03.016] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2007] [Revised: 03/15/2007] [Accepted: 03/16/2007] [Indexed: 11/20/2022] Open
Abstract
This review provides an overview of recent progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism utilized by the bacteria when growing in diverse and varied environments.
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Affiliation(s)
- Torsten Hain
- Institute for Medical Microbiology, Justus-Liebig-University, Frankfurter Strasse 107, D-35392 Giessen, Germany
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53
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Beres SB, Musser JM. Contribution of exogenous genetic elements to the group A Streptococcus metagenome. PLoS One 2007; 2:e800. [PMID: 17726530 PMCID: PMC1949102 DOI: 10.1371/journal.pone.0000800] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2007] [Accepted: 07/31/2007] [Indexed: 11/29/2022] Open
Abstract
Variation in gene content among strains of a bacterial species contributes to biomedically relevant differences in phenotypes such as virulence and antimicrobial resistance. Group A Streptococcus (GAS) causes a diverse array of human infections and sequelae, and exhibits a complex pathogenic behavior. To enhance our understanding of genotype-phenotype relationships in this important pathogen, we determined the complete genome sequences of four GAS strains expressing M protein serotypes (M2, M4, and 2 M12) that commonly cause noninvasive and invasive infections. These sequences were compared with eight previously determined GAS genomes and regions of variably present gene content were assessed. Consistent with the previously determined genomes, each of the new genomes is ∼1.9 Mb in size, with ∼10% of the gene content of each encoded on variably present exogenous genetic elements. Like the other GAS genomes, these four genomes are polylysogenic and prophage encode the majority of the variably present gene content of each. In contrast to most of the previously determined genomes, multiple exogenous integrated conjugative elements (ICEs) with characteristics of conjugative transposons and plasmids are present in these new genomes. Cumulatively, 242 new GAS metagenome genes were identified that were not present in the previously sequenced genomes. Importantly, ICEs accounted for 41% of the new GAS metagenome gene content identified in these four genomes. Two large ICEs, designated 2096-RD.2 (63 kb) and 10750-RD.2 (49 kb), have multiple genes encoding resistance to antimicrobial agents, including tetracycline and erythromycin, respectively. Also resident on these ICEs are three genes encoding inferred extracellular proteins of unknown function, including a predicted cell surface protein that is only present in the genome of the serotype M12 strain cultured from a patient with acute poststreptococcal glomerulonephritis. The data provide new information about the GAS metagenome and will assist studies of pathogenesis, antimicrobial resistance, and population genomics.
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Affiliation(s)
- Stephen B. Beres
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Houston, Texas, United States of America
| | - James M. Musser
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Houston, Texas, United States of America
- * To whom correspondence should be addressed. E-mail:
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Monchy S, Benotmane MA, Janssen P, Vallaeys T, Taghavi S, van der Lelie D, Mergeay M. Plasmids pMOL28 and pMOL30 of Cupriavidus metallidurans are specialized in the maximal viable response to heavy metals. J Bacteriol 2007; 189:7417-25. [PMID: 17675385 PMCID: PMC2168447 DOI: 10.1128/jb.00375-07] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
We fully annotated two large plasmids, pMOL28 (164 open reading frames [ORFs]; 171,459 bp) and pMOL30 (247 ORFs; 233,720 bp), in the genome of Cupriavidus metallidurans CH34. pMOL28 contains a backbone of maintenance and transfer genes resembling those found in plasmid pSym of C. taiwanensis and plasmid pHG1 of C. eutrophus, suggesting that they belong to a new class of plasmids. Genes involved in resistance to the heavy metals Co(II), Cr(VI), Hg(II), and Ni(II) are concentrated in a 34-kb region on pMOL28, and genes involved in resistance to Ag(I), Cd(II), Co(II), Cu(II), Hg(II), Pb(II), and Zn(II) occur in a 132-kb region on pMOL30. We identified three putative genomic islands containing metal resistance operons flanked by mobile genetic elements, one on pMOL28 and two on pMOL30. Transcriptomic analysis using quantitative PCR and microarrays revealed metal-mediated up-regulation of 83 genes on pMOL28 and 143 genes on pMOL30 that coded for all known heavy metal resistance proteins, some new heavy metal resistance proteins (czcJ, mmrQ, and pbrU), membrane proteins, truncated transposases, conjugative transfer proteins, and many unknown proteins. Five genes on each plasmid were down-regulated; for one of them, chrI localized on pMOL28, the down-regulation occurred in the presence of five cations. We observed multiple cross-responses (induction of specific metal resistance by other metals), suggesting that the cellular defense of C. metallidurans against heavy metal stress involves various regulons and probably has multiple stages, including a more general response and a more metal-specific response.
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Affiliation(s)
- Sébastien Monchy
- Molecular & Cellular Biology, Institute for Health, Environment & Safety, Center of Studies for Nuclear Energy, SCK CEN, B-2400, Mol, Belgium
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55
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Gans JD, Wolinsky M. Genomorama: genome visualization and analysis. BMC Bioinformatics 2007; 8:204. [PMID: 17570856 PMCID: PMC1906841 DOI: 10.1186/1471-2105-8-204] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Accepted: 06/14/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The ability to visualize genomic features and design experimental assays that can target specific regions of a genome is essential for modern biology. To assist in these tasks, we present Genomorama, a software program for interactively displaying multiple genomes and identifying potential DNA hybridization sites for assay design. RESULTS Useful features of Genomorama include genome search by DNA hybridization (probe binding and PCR amplification), efficient multi-scale display and manipulation of multiple genomes, support for many genome file types and the ability to search for and retrieve data from the National Center for Biotechnology Information (NCBI) Entrez server. CONCLUSION Genomorama provides an efficient computational platform for visualizing and analyzing multiple genomes.
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Affiliation(s)
- Jason D Gans
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Murray Wolinsky
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA
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56
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Domann E, Hain T, Ghai R, Billion A, Kuenne C, Zimmermann K, Chakraborty T. Comparative genomic analysis for the presence of potential enterococcal virulence factors in the probiotic Enterococcus faecalis strain Symbioflor 1. Int J Med Microbiol 2007; 297:533-9. [PMID: 17466591 DOI: 10.1016/j.ijmm.2007.02.008] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2006] [Revised: 02/08/2007] [Accepted: 02/08/2007] [Indexed: 11/29/2022] Open
Abstract
Enterococci are members of the natural microbiota of animal and human intestinal tracts and are capable of causing opportunistic infections. They are also used as starter cultures in the food industry as well as in health supplements and probiotics by the pharmaceutical industry. This Janus-faced status requires a careful evaluation on the basis of pathogenic traits to ensure the safety of the strain used to produce food and pharmaceuticals. We performed gapped-genome sequencing of a probiotic strain Enterococcus faecalis Symbioflor 1 and present initial results deriving from comparative genome analysis with that of the previously sequenced pathogenic clinical isolate E. faecalis V583. There was strong overall conservation of synteny between both strains and a detailed analysis revealed the absence of large genomic regions from the chromosome of the probiotic strain, indicating gene loss. Genes absent from the Symbioflor 1 strain included those encoding the enterococcal cytolysin, enterococcal surface protein, and gelatinase (coccolysin) as well as hyaluronidase and the peptide antibiotic AS-48. This data was confirmed using PCR primers specific for the respective genes. However, other enterococcal determinants such as aggregation substance, collagen adhesion protein, the ability to resist oxygen anions as well as capsule formation were detected. The presence of these traits may be advantageous for the strain Symbioflor 1 since they potentially enable colonization and proliferation of the bacterium on mucosal surfaces thereby conferring on it probiotic traits.
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Affiliation(s)
- Eugen Domann
- Institute of Medical Microbiology, University of Giessen, Frankfurter Strasse 107, D-35392 Giessen, Germany.
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57
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Johnson TJ, Kariyawasam S, Wannemuehler Y, Mangiamele P, Johnson SJ, Doetkott C, Skyberg JA, Lynne AM, Johnson JR, Nolan LK. The genome sequence of avian pathogenic Escherichia coli strain O1:K1:H7 shares strong similarities with human extraintestinal pathogenic E. coli genomes. J Bacteriol 2007; 189:3228-36. [PMID: 17293413 PMCID: PMC1855855 DOI: 10.1128/jb.01726-06] [Citation(s) in RCA: 284] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli strains that cause disease outside the intestine are known as extraintestinal pathogenic E. coli (ExPEC) and include human uropathogenic E. coli (UPEC) and avian pathogenic E. coli (APEC). Regardless of host of origin, ExPEC strains share many traits. It has been suggested that these commonalities may enable APEC to cause disease in humans. Here, we begin to test the hypothesis that certain APEC strains possess potential to cause human urinary tract infection through virulence genotyping of 1,000 APEC and UPEC strains, generation of the first complete genomic sequence of an APEC (APEC O1:K1:H7) strain, and comparison of this genome to all available human ExPEC genomic sequences. The genomes of APEC O1 and three human UPEC strains were found to be remarkably similar, with only 4.5% of APEC O1's genome not found in other sequenced ExPEC genomes. Also, use of multilocus sequence typing showed that some of the sequenced human ExPEC strains were more like APEC O1 than other human ExPEC strains. This work provides evidence that at least some human and avian ExPEC strains are highly similar to one another, and it supports the possibility that a food-borne link between some APEC and UPEC strains exists. Future studies are necessary to assess the ability of APEC to overcome the hurdles necessary for such a food-borne transmission, and epidemiological studies are required to confirm that such a phenomenon actually occurs.
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Affiliation(s)
- Timothy J Johnson
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, 1802 Elwood Drive, VMRI #2, Iowa State University, Ames, IA 50011, USA
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58
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Chain PSG, Denef VJ, Konstantinidis KT, Vergez LM, Agulló L, Reyes VL, Hauser L, Córdova M, Gómez L, González M, Land M, Lao V, Larimer F, LiPuma JJ, Mahenthiralingam E, Malfatti SA, Marx CJ, Parnell JJ, Ramette A, Richardson P, Seeger M, Smith D, Spilker T, Sul WJ, Tsoi TV, Ulrich LE, Zhulin IB, Tiedje JM. Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proc Natl Acad Sci U S A 2006; 103:15280-7. [PMID: 17030797 PMCID: PMC1622818 DOI: 10.1073/pnas.0606924103] [Citation(s) in RCA: 252] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Burkholderia xenovorans LB400 (LB400), a well studied, effective polychlorinated biphenyl-degrader, has one of the two largest known bacterial genomes and is the first nonpathogenic Burkholderia isolate sequenced. From an evolutionary perspective, we find significant differences in functional specialization between the three replicons of LB400, as well as a more relaxed selective pressure for genes located on the two smaller vs. the largest replicon. High genomic plasticity, diversity, and specialization within the Burkholderia genus are exemplified by the conservation of only 44% of the genes between LB400 and Burkholderia cepacia complex strain 383. Even among four B. xenovorans strains, genome size varies from 7.4 to 9.73 Mbp. The latter is largely explained by our findings that >20% of the LB400 sequence was recently acquired by means of lateral gene transfer. Although a range of genetic factors associated with in vivo survival and intercellular interactions are present, these genetic factors are likely related to niche breadth rather than determinants of pathogenicity. The presence of at least eleven "central aromatic" and twenty "peripheral aromatic" pathways in LB400, among the highest in any sequenced bacterial genome, supports this hypothesis. Finally, in addition to the experimentally observed redundancy in benzoate degradation and formaldehyde oxidation pathways, the fact that 17.6% of proteins have a better LB400 paralog than an ortholog in a different genome highlights the importance of gene duplication and repeated acquirement, which, coupled with their divergence, raises questions regarding the role of paralogs and potential functional redundancies in large-genome microbes.
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Affiliation(s)
- Patrick S. G. Chain
- Biosciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
- Joint Genome Institute, Walnut Creek, CA 94598
| | - Vincent J. Denef
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824
- Department of Bioscience Engineering, Universiteit Gent, 9000 Gent, Belgium
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720; and
| | - Konstantinos T. Konstantinidis
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824
- Department of Civil and Environmental Engineering, Massachussets Institute of Technology, Boston, MA 02139
| | - Lisa M. Vergez
- Biosciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
- Joint Genome Institute, Walnut Creek, CA 94598
| | - Loreine Agulló
- Nucleus Millennium of Microbial Ecology and Environmental Microbiology and Biotechnology, Universidad Técnica Federico Santa María, Casilla 110-V, Valparaíso, Chile
| | - Valeria Latorre Reyes
- Nucleus Millennium of Microbial Ecology and Environmental Microbiology and Biotechnology, Universidad Técnica Federico Santa María, Casilla 110-V, Valparaíso, Chile
- Departamento de Ciencias y Recursos Naturales, Universidad de Magallanes, Casilla 113-D, Punta Arenas, Chile
| | - Loren Hauser
- Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Macarena Córdova
- Nucleus Millennium of Microbial Ecology and Environmental Microbiology and Biotechnology, Universidad Técnica Federico Santa María, Casilla 110-V, Valparaíso, Chile
| | - Luis Gómez
- Nucleus Millennium of Microbial Ecology and Environmental Microbiology and Biotechnology, Universidad Técnica Federico Santa María, Casilla 110-V, Valparaíso, Chile
| | - Myriam González
- Nucleus Millennium of Microbial Ecology and Environmental Microbiology and Biotechnology, Universidad Técnica Federico Santa María, Casilla 110-V, Valparaíso, Chile
| | - Miriam Land
- Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Victoria Lao
- Biosciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | | | - John J. LiPuma
- Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI 48109
| | | | - Stephanie A. Malfatti
- Biosciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
- Joint Genome Institute, Walnut Creek, CA 94598
| | - Christopher J. Marx
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - J. Jacob Parnell
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824
| | - Alban Ramette
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824
- Max-Planck-Institute for Marine Microbiology, 28359 Bremen, Germany
| | | | - Michael Seeger
- Nucleus Millennium of Microbial Ecology and Environmental Microbiology and Biotechnology, Universidad Técnica Federico Santa María, Casilla 110-V, Valparaíso, Chile
| | - Daryl Smith
- Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Theodore Spilker
- Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI 48109
| | - Woo Jun Sul
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824
| | - Tamara V. Tsoi
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824
| | - Luke E. Ulrich
- Joint Institute for Computational Sciences, University of Tennessee–Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Igor B. Zhulin
- Joint Institute for Computational Sciences, University of Tennessee–Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - James M. Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824
- To whom correspondence should be addressed at:
Center for Microbial Ecology, 540E Plant and Soil Sciences Building, Michigan State University, East Lansing, MI 48824. E-mail:
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59
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Konstantinidis KT, Ramette A, Tiedje JM. Toward a more robust assessment of intraspecies diversity, using fewer genetic markers. Appl Environ Microbiol 2006; 72:7286-93. [PMID: 16980418 PMCID: PMC1636164 DOI: 10.1128/aem.01398-06] [Citation(s) in RCA: 146] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phylogenetic sequence analysis of single or multiple genes has dominated the study and census of the genetic diversity among closely related bacteria. It remains unclear, however, how the results based on a few genes in the genome correlate with whole-genome-based relatedness and what genes (if any) best reflect whole-genome-level relatedness and hence should be preferentially used to economize on cost and to improve accuracy. We show here that phylogenies of closely related organisms based on the average nucleotide identity (ANI) of their shared genes correspond accurately to phylogenies based on state-of-the-art analysis of their whole-genome sequences. We use ANI to evaluate the phylogenetic robustness of every gene in the genome and show that almost all core genes, regardless of their functions and positions in the genome, offer robust phylogenetic reconstruction among strains that show 80 to 95% ANI (16S rRNA identity, >98.5%). Lack of elapsed time and, to a lesser extent, horizontal transfer and recombination make the selection of genes more critical for applications that target the intraspecies level, i.e., strains that show >95% ANI according to current standards. A much more accurate phylogeny for the Escherichia coli group was obtained based on just three best-performing genes according to our analysis compared to the concatenated alignment of eight genes that are commonly employed for phylogenetic purposes in this group. Our results are reproducible within the Salmonella, Burkholderia, and Shewanella groups and therefore are expected to have general applicability for microevolution studies, including metagenomic surveys.
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60
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Pohlmann A, Fricke WF, Reinecke F, Kusian B, Liesegang H, Cramm R, Eitinger T, Ewering C, Pötter M, Schwartz E, Strittmatter A, Voss I, Gottschalk G, Steinbüchel A, Friedrich B, Bowien B. Genome sequence of the bioplastic-producing “Knallgas” bacterium Ralstonia eutropha H16. Nat Biotechnol 2006; 24:1257-62. [PMID: 16964242 DOI: 10.1038/nbt1244] [Citation(s) in RCA: 407] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2006] [Accepted: 08/03/2006] [Indexed: 11/08/2022]
Abstract
The H(2)-oxidizing lithoautotrophic bacterium Ralstonia eutropha H16 is a metabolically versatile organism capable of subsisting, in the absence of organic growth substrates, on H(2) and CO(2) as its sole sources of energy and carbon. R. eutropha H16 first attracted biotechnological interest nearly 50 years ago with the realization that the organism's ability to produce and store large amounts of poly[R-(-)-3-hydroxybutyrate] and other polyesters could be harnessed to make biodegradable plastics. Here we report the complete genome sequence of the two chromosomes of R. eutropha H16. Together, chromosome 1 (4,052,032 base pairs (bp)) and chromosome 2 (2,912,490 bp) encode 6,116 putative genes. Analysis of the genome sequence offers the genetic basis for exploiting the biotechnological potential of this organism and provides insights into its remarkable metabolic versatility.
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Affiliation(s)
- Anne Pohlmann
- Humboldt-Universität zu Berlin, Institut für Biologie/Mikrobiologie, Chausseestrasse 117, 10115 Berlin, Germany
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61
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Hain T, Steinweg C, Kuenne CT, Billion A, Ghai R, Chatterjee SS, Domann E, Kärst U, Goesmann A, Bekel T, Bartels D, Kaiser O, Meyer F, Pühler A, Weisshaar B, Wehland J, Liang C, Dandekar T, Lampidis R, Kreft J, Goebel W, Chakraborty T. Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes. J Bacteriol 2006; 188:7405-15. [PMID: 16936040 PMCID: PMC1636279 DOI: 10.1128/jb.00758-06] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present the complete genome sequence of Listeria welshimeri, a nonpathogenic member of the genus Listeria. Listeria welshimeri harbors a circular chromosome of 2,814,130 bp with 2,780 open reading frames. Comparative genomic analysis of chromosomal regions between L. welshimeri, Listeria innocua, and Listeria monocytogenes shows strong overall conservation of synteny, with the exception of the translocation of an F(o)F(1) ATP synthase. The smaller size of the L. welshimeri genome is the result of deletions in all of the genes involved in virulence and of "fitness" genes required for intracellular survival, transcription factors, and LPXTG- and LRR-containing proteins as well as 55 genes involved in carbohydrate transport and metabolism. In total, 482 genes are absent from L. welshimeri relative to L. monocytogenes. Of these, 249 deletions are commonly absent in both L. welshimeri and L. innocua, suggesting similar genome evolutionary paths from an ancestor. We also identified 311 genes specific to L. welshimeri that are absent in the other two species, indicating gene expansion in L. welshimeri, including horizontal gene transfer. The species L. welshimeri appears to have been derived from early evolutionary events and an ancestor more compact than L. monocytogenes that led to the emergence of nonpathogenic Listeria spp.
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Affiliation(s)
- Torsten Hain
- Institute for Medical Microbiology, Justus-Liebig-University, Frankfurter Strasse 107, D-35392 Giessen, Germany
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62
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Gressmann H, Linz B, Ghai R, Pleissner KP, Schlapbach R, Yamaoka Y, Kraft C, Suerbaum S, Meyer TF, Achtman M. Gain and loss of multiple genes during the evolution of Helicobacter pylori. PLoS Genet 2006; 1:e43. [PMID: 16217547 PMCID: PMC1245399 DOI: 10.1371/journal.pgen.0010043] [Citation(s) in RCA: 172] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2005] [Accepted: 08/26/2005] [Indexed: 12/16/2022] Open
Abstract
Sequence diversity and gene content distinguish most isolates of Helicobacter pylori. Even greater sequence differences differentiate distinct populations of H. pylori from different continents, but it was not clear whether these populations also differ in gene content. To address this question, we tested 56 globally representative strains of H. pylori and four strains of Helicobacter acinonychis with whole genome microarrays. Of the weighted average of 1,531 genes present in the two sequenced genomes, 25% are absent in at least one strain of H. pylori and 21% were absent or variable in H. acinonychis. We extrapolate that the core genome present in all isolates of H. pylori contains 1,111 genes. Variable genes tend to be small and possess unusual GC content; many of them have probably been imported by horizontal gene transfer. Phylogenetic trees based on the microarray data differ from those based on sequences of seven genes from the core genome. These discrepancies are due to homoplasies resulting from independent gene loss by deletion or recombination in multiple strains, which distort phylogenetic patterns. The patterns of these discrepancies versus population structure allow a reconstruction of the timing of the acquisition of variable genes within this species. Variable genes that are located within the cag pathogenicity island were apparently first acquired en bloc after speciation. In contrast, most other variable genes are of unknown function or encode restriction/modification enzymes, transposases, or outer membrane proteins. These seem to have been acquired prior to speciation of H. pylori and were subsequently lost by convergent evolution within individual strains. Thus, the use of microarrays can reveal patterns of gene gain or loss when examined within a phylogenetic context that is based on sequences of core genes.
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Affiliation(s)
- Helga Gressmann
- Department of Molecular Biology, Max-Planck-Institut für Infektionsbiologie, Berlin, Germany
| | - Bodo Linz
- Department of Molecular Biology, Max-Planck-Institut für Infektionsbiologie, Berlin, Germany
| | - Rohit Ghai
- Institut für Medizinische Mikrobiologie, Justus-Liebig-Universität, Giessen, Germany
| | - Klaus-Peter Pleissner
- Core Facility Bioinformatics, Max-Planck-Institut für Infektionsbiologie, Berlin, Germany
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Yoshio Yamaoka
- Department of Medicine, M.E. DeBakey Veterans Affairs Medical Center and Baylor College of Medicine, Houston, Texas, United States of America
| | - Christian Kraft
- Medizinische Hochschule Hannover, Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Hannover, Germany
| | - Sebastian Suerbaum
- Medizinische Hochschule Hannover, Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Hannover, Germany
| | - Thomas F Meyer
- Department of Molecular Biology, Max-Planck-Institut für Infektionsbiologie, Berlin, Germany
| | - Mark Achtman
- Department of Molecular Biology, Max-Planck-Institut für Infektionsbiologie, Berlin, Germany
- * To whom correspondence should be addressed. E-mail:
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63
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Heizer EM, Raiford DW, Raymer ML, Doom TE, Miller RV, Krane DE. Amino Acid Cost and Codon-Usage Biases in 6 Prokaryotic Genomes: A Whole-Genome Analysis. Mol Biol Evol 2006; 23:1670-80. [PMID: 16754641 DOI: 10.1093/molbev/msl029] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
For most prokaryotic organisms, amino acid biosynthesis represents a significant portion of their overall energy budget. The difference in the cost of synthesis between amino acids can be striking, differing by as much as 7-fold. Two prokaryotic organisms, Escherichia coli and Bacillus subtilis, have been shown to preferentially utilize less costly amino acids in highly expressed genes, indicating that parsimony in amino acid selection may confer a selective advantage for prokaryotes. This study confirms those findings and extends them to 4 additional prokaryotic organisms: Chlamydia trachomatis, Chlamydophila pneumoniae AR39, Synechocystis sp. PCC 6803, and Thermus thermophilus HB27. Adherence to codon-usage biases for each of these 6 organisms is inversely correlated with a coding region's average amino acid biosynthetic cost in a fashion that is independent of chemoheterotrophic, photoautotrophic, or thermophilic lifestyle. The obligate parasites C. trachomatis and C. pneumoniae AR39 are incapable of synthesizing many of the 20 common amino acids. Removing auxotrophic amino acids from consideration in these organisms does not alter the overall trend of preferential use of energetically inexpensive amino acids in highly expressed genes.
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Affiliation(s)
- Esley M Heizer
- Department of Biological Sciences, Wright State University, USA
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64
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Abstract
MOTIVATION Establishment of intra-cellular life involved a profound re-configuration of the genetic characteristics of bacteria, including genome reduction and rearrangements. Understanding the mechanisms underlying these phenomena will shed light on the genome rearrangements essential for the development of an intra-cellular lifestyle. Comparison of genomes with differences in their sizes poses statistical as well as computational problems. Little efforts have been made to develop flexible computational tools with which to analyse genome reduction and rearrangements. RESULTS Investigation of genome reduction and rearrangements in endosymbionts using a novel computational tool (GRAST) identified gathering of genes with similar functions. Conserved clusters of functionally related genes (CGSCs) were detected. Heterogeneous gene and gene cluster non-functionalization/loss are identified between genome regions, functional gene categories and during evolution. Results show that gene non-functionalisation has accelerated during the last 50 MY of Buchnera's evolution while CGSCs have been static.
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Affiliation(s)
- Christina Toft
- Molecular Evolution and Bioinformatics Laboratory, Department of Biology, National University of Ireland Maynooth
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65
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Pritchard L, White JA, Birch PRJ, Toth IK. GenomeDiagram: a python package for the visualization of large-scale genomic data. Bioinformatics 2005; 22:616-7. [PMID: 16377612 DOI: 10.1093/bioinformatics/btk021] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
UNLABELLED We present GenomeDiagram, a flexible, open-source Python module for the visualization of large-scale genomic, comparative genomic and other data with reference to a single chromosome or other biological sequence. GenomeDiagram may be used to generate publication-quality vector graphics, rastered images and in-line streamed graphics for webpages. The package integrates with datatypes from the BioPython project, and is available for Windows, Linux and Mac OS X systems. AVAILABILITY GenomeDiagram is freely available as source code (under GNU Public License) at http://bioinf.scri.ac.uk/lp/programs.html, and requires Python 2.3 or higher, and recent versions of the ReportLab and BioPython packages. SUPPLEMENTARY INFORMATION A user manual, example code and images are available at http://bioinf.scri.ac.uk/lp/programs.html.
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Affiliation(s)
- Leighton Pritchard
- Plant Pathogen Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK.
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66
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Pasek S, Bergeron A, Risler JL, Louis A, Ollivier E, Raffinot M. Identification of genomic features using microsyntenies of domains: domain teams. Genome Res 2005; 15:867-74. [PMID: 15899966 PMCID: PMC1142477 DOI: 10.1101/gr.3638405] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The detection, across several genomes, of local conservation of gene content and proximity considerably helps the prediction of features of interest, such as gene fusions or physical and functional interactions. Here, we want to process realistic models of chromosomes, in which genes (or genomic segments of several genes) can be duplicated within a chromosome, or be absent from some other chromosome(s). Our approach adopts the technique of temporarily forgetting genes and working directly with protein "domains" such as those found in Pfam. This allows the detection of strings of domains that are conserved in their content, but not necessarily in their order, which we refer to as domain teams. The prominent feature of the method is that it relaxes the rigidity of the orthology criterion and avoids many of the pitfalls of gene-families identification methods, often hampered by multidomain proteins or low levels of sequence similarity. This approach, that allows both inter- and intrachromosomal comparisons, proves to be more sensitive than the classical methods based on pairwise sequence comparisons, particularly in the simultaneous treatment of many species. The automated and fast detection of domain teams, together with its increased sensitivity at identifying segments of identical (protein-coding) gene contents as well as gene fusions, should prove a useful complement to other existing methods.
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Affiliation(s)
- Sophie Pasek
- Laboratoire Génome et Informatique, CNRS/UEVE, 91034 Evry cedex, France.
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67
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Watson M. ProGenExpress: visualization of quantitative data on prokaryotic genomes. BMC Bioinformatics 2005; 6:98. [PMID: 15829007 PMCID: PMC1087476 DOI: 10.1186/1471-2105-6-98] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2005] [Accepted: 04/13/2005] [Indexed: 11/10/2022] Open
Abstract
Background The integration of genomic information with quantitative experimental data is a key component of systems biology. An increasing number of microbial genomes are being sequenced, leading to an increasing amount of data from post-genomics technologies. The genomes of prokaryotes contain many structures of interest, such as operons, pathogenicity islands and prophage sequences, whose behaviour is of interest during infection and disease. There is a need for simple and novel tools to display and analyse data from these integrated datasets, and we have developed ProGenExpress as a tool for visualising arbitrarily complex numerical data in the context of prokaryotic genomes. Results Here we describe ProGenExpress, an R package that allows researchers to easily and quickly visualize quantitative measurements, such as those produced by microarray experiments, in the context of the genome organization of sequenced prokaryotes. Data from microarrays, proteomics or other whole-genome technologies can be accurately displayed on the genome. ProGenExpress can also search for novel regions of interest that consist of groups of adjacent genes that show similar patterns across the experimental data set. We demonstrate ProGenExpress with microarray data from a time-course experiment involving Salmonella typhimurium. Conclusion ProGenExpress can be used to visualize quantitative data from complex experiments in the context of the genome of sequenced prokaryotes, and to find novel regions of interest.
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Affiliation(s)
- Michael Watson
- Institute for Animal Health, Compton laboratory, High street, Compton, Newbury, RG20 7NN, UK.
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