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Makarova K, Slesarev A, Wolf Y, Sorokin A, Mirkin B, Koonin E, Pavlov A, Pavlova N, Karamychev V, Polouchine N, Shakhova V, Grigoriev I, Lou Y, Rohksar D, Lucas S, Huang K, Goodstein DM, Hawkins T, Plengvidhya V, Welker D, Hughes J, Goh Y, Benson A, Baldwin K, Lee JH, Díaz-Muñiz I, Dosti B, Smeianov V, Wechter W, Barabote R, Lorca G, Altermann E, Barrangou R, Ganesan B, Xie Y, Rawsthorne H, Tamir D, Parker C, Breidt F, Broadbent J, Hutkins R, O'Sullivan D, Steele J, Unlu G, Saier M, Klaenhammer T, Richardson P, Kozyavkin S, Weimer B, Mills D. Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci U S A 2006; 103:15611-6. [PMID: 17030793 PMCID: PMC1622870 DOI: 10.1073/pnas.0607117103] [Citation(s) in RCA: 944] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lactic acid-producing bacteria are associated with various plant and animal niches and play a key role in the production of fermented foods and beverages. We report nine genome sequences representing the phylogenetic and functional diversity of these bacteria. The small genomes of lactic acid bacteria encode a broad repertoire of transporters for efficient carbon and nitrogen acquisition from the nutritionally rich environments they inhabit and reflect a limited range of biosynthetic capabilities that indicate both prototrophic and auxotrophic strains. Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.
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Affiliation(s)
- K. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - A. Slesarev
- Fidelity Systems Inc., 7961 Cessna Avenue, Gaithersburg, MD 20879
| | - Y. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - A. Sorokin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - B. Mirkin
- School of Information Systems and Computer Science, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom
| | - E. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
- To whom correspondence may be addressed. E-mail:
, , , or
| | - A. Pavlov
- Fidelity Systems Inc., 7961 Cessna Avenue, Gaithersburg, MD 20879
| | - N. Pavlova
- Fidelity Systems Inc., 7961 Cessna Avenue, Gaithersburg, MD 20879
| | - V. Karamychev
- Fidelity Systems Inc., 7961 Cessna Avenue, Gaithersburg, MD 20879
| | - N. Polouchine
- Fidelity Systems Inc., 7961 Cessna Avenue, Gaithersburg, MD 20879
| | - V. Shakhova
- Fidelity Systems Inc., 7961 Cessna Avenue, Gaithersburg, MD 20879
| | - I. Grigoriev
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598
| | - Y. Lou
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598
| | - D. Rohksar
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598
| | - S. Lucas
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598
| | - K. Huang
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598
| | - D. M. Goodstein
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598
| | - T. Hawkins
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598
| | - V. Plengvidhya
- Department of Food Science, North Carolina State University, Raleigh, NC 27695
- North Carolina Agricultural Research Service, U.S. Department of Agriculture, Raleigh, NC 27695; Departments of
| | | | | | - Y. Goh
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583
| | - A. Benson
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583
| | - K. Baldwin
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN 55108
| | - J.-H. Lee
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN 55108
| | - I. Díaz-Muñiz
- Department of Food Science, University of Wisconsin, Madison, WI 53706
| | - B. Dosti
- Department of Food Science, University of Wisconsin, Madison, WI 53706
| | - V. Smeianov
- Department of Food Science, University of Wisconsin, Madison, WI 53706
| | - W. Wechter
- Department of Food Science, University of Wisconsin, Madison, WI 53706
| | - R. Barabote
- Department of Biology, University of California at San Diego, La Jolla, CA 92093
| | - G. Lorca
- Department of Biology, University of California at San Diego, La Jolla, CA 92093
| | - E. Altermann
- Department of Food Science, North Carolina State University, Raleigh, NC 27695
| | - R. Barrangou
- Department of Food Science, North Carolina State University, Raleigh, NC 27695
| | - B. Ganesan
- Center for Integrated BioSystems, Utah State University, Logan, UT 84322
| | - Y. Xie
- Nutrition and Food Science and
- Center for Integrated BioSystems, Utah State University, Logan, UT 84322
| | - H. Rawsthorne
- Department of Viticulture and Enology, University of California, Davis, CA 95616; and
| | | | | | - F. Breidt
- Department of Food Science, North Carolina State University, Raleigh, NC 27695
- North Carolina Agricultural Research Service, U.S. Department of Agriculture, Raleigh, NC 27695; Departments of
| | | | - R. Hutkins
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583
| | - D. O'Sullivan
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN 55108
| | - J. Steele
- Department of Food Science, University of Wisconsin, Madison, WI 53706
| | - G. Unlu
- Department of Food Science and Toxicology, University of Idaho, Moscow, ID 83844
| | - M. Saier
- Department of Biology, University of California at San Diego, La Jolla, CA 92093
| | - T. Klaenhammer
- Department of Food Science, North Carolina State University, Raleigh, NC 27695
- To whom correspondence may be addressed. E-mail:
, , , or
| | - P. Richardson
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598
| | - S. Kozyavkin
- Fidelity Systems Inc., 7961 Cessna Avenue, Gaithersburg, MD 20879
| | - B. Weimer
- Nutrition and Food Science and
- Center for Integrated BioSystems, Utah State University, Logan, UT 84322
- To whom correspondence may be addressed. E-mail:
, , , or
| | - D. Mills
- Department of Viticulture and Enology, University of California, Davis, CA 95616; and
- To whom correspondence may be addressed. E-mail:
, , , or
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105
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Billington SJ, Jost BH. Multiple genetic elements carry the tetracycline resistance gene tet(W) in the animal pathogen Arcanobacterium pyogenes. Antimicrob Agents Chemother 2006; 50:3580-7. [PMID: 16966401 PMCID: PMC1635169 DOI: 10.1128/aac.00562-06] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The tet(W) gene is associated with tetracycline resistance in a wide range of bacterial species, including obligately anaerobic rumen bacteria and isolates from the human gut and oral mucosa. However, little is known about how this gene is disseminated and the types of genetic elements it is carried on. We examined tetracycline-resistant isolates of the animal commensal and opportunistic pathogen Arcanobacterium pyogenes, all of which carried tet(W), and identified three genetic elements designated ATE-1, ATE-2, and ATE-3. These elements were found in 25%, 35%, and 60% of tetracycline-resistant isolates, respectively, with some strains carrying both ATE-2 and ATE-3. ATE-1 shows characteristics of a mobilizable transposon, and the tet(W) genes from strains carrying this element can be transferred at low frequencies between A. pyogenes strains. ATE-2 has characteristics of a simple transposon, carrying only the resistance gene and a transposase, while in ATE-3, the tet(W) gene is associated with a streptomycin resistance gene that is 100% identical at the DNA level with the aadE gene from the Campylobacter jejuni plasmid pCG8245. Both ATE-2 and ATE-3 show evidence of being carried on larger genetic elements, but conjugation to other strains was not observed under the conditions tested. ATE-1 was preferentially associated with A. pyogenes strains of bovine origin, while ATE-2 and ATE-3 elements were primarily found in porcine isolates, suggesting that these elements may circulate in different environments. In addition, four alleles of the tet(W) gene, primarily associated with different elements, were detected among A. pyogenes isolates.
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Affiliation(s)
- Stephen J Billington
- Department of Veterinary Science and Microbiology, The University of Arizona, 1117 East Lowell Street, Tucson, AZ 85721, USA.
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106
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Siezen R, Boekhorst J, Muscariello L, Molenaar D, Renckens B, Kleerebezem M. Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria. BMC Genomics 2006; 7:126. [PMID: 16723015 PMCID: PMC1534035 DOI: 10.1186/1471-2164-7-126] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2006] [Accepted: 05/24/2006] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Genomes of gram-positive bacteria encode many putative cell-surface proteins, of which the majority has no known function. From the rapidly increasing number of available genome sequences it has become apparent that many cell-surface proteins are conserved, and frequently encoded in gene clusters or operons, suggesting common functions, and interactions of multiple components. RESULTS A novel gene cluster encoding exclusively cell-surface proteins was identified, which is conserved in a subgroup of gram-positive bacteria. Each gene cluster generally has one copy of four new gene families called cscA, cscB, cscC and cscD. Clusters encoding these cell-surface proteins were found only in complete genomes of Lactobacillus plantarum, Lactobacillus sakei, Enterococcus faecalis, Listeria innocua, Listeria monocytogenes, Lactococcus lactis ssp lactis and Bacillus cereus and in incomplete genomes of L. lactis ssp cremoris, Lactobacillus casei, Enterococcus faecium, Pediococcus pentosaceus, Lactobacillius brevis, Oenococcus oeni, Leuconostoc mesenteroides, and Bacillus thuringiensis. These genes are neither present in the genomes of streptococci, staphylococci and clostridia, nor in the Lactobacillus acidophilus group, suggesting a niche-specific distribution, possibly relating to association with plants. All encoded proteins have a signal peptide for secretion by the Sec-dependent pathway, while some have cell-surface anchors, novel WxL domains, and putative domains for sugar binding and degradation. Transcriptome analysis in L. plantarum shows that the cscA-D genes are co-expressed, supporting their operon organization. Many gene clusters are significantly up-regulated in a glucose-grown, ccpA-mutant derivative of L. plantarum, suggesting catabolite control. This is supported by the presence of predicted CRE-sites upstream or inside the up-regulated cscA-D gene clusters. CONCLUSION We propose that the CscA, CscB, CscC and CscD proteins form cell-surface protein complexes and play a role in carbon source acquisition. Primary occurrence in plant-associated gram-positive bacteria suggests a possible role in degradation and utilization of plant oligo- or poly-saccharides.
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Affiliation(s)
- Roland Siezen
- Wageningen Centre for Food Sciences (WCFS), Wageningen, The Netherlands
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Nijmegen, The Netherlands
- NIZO food research, Ede, The Netherlands
| | - Jos Boekhorst
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Nijmegen, The Netherlands
| | - Lidia Muscariello
- Wageningen Centre for Food Sciences (WCFS), Wageningen, The Netherlands
- NIZO food research, Ede, The Netherlands
| | - Douwe Molenaar
- Wageningen Centre for Food Sciences (WCFS), Wageningen, The Netherlands
- NIZO food research, Ede, The Netherlands
| | - Bernadet Renckens
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Nijmegen, The Netherlands
- NIZO food research, Ede, The Netherlands
| | - Michiel Kleerebezem
- Wageningen Centre for Food Sciences (WCFS), Wageningen, The Netherlands
- NIZO food research, Ede, The Netherlands
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