Functional divergence in the genus oenococcus as predicted by genome sequencing of the newly-described species, oenococcus kitaharae

PLoS ONE

Volumn 7, Issue 1, 2012, Pages

  Borneman, Anthony R ^a   McCarthy, Jane M ^a   Chambers, Paul J ^a   Bartowsky, Eveline J ^a  

^a AUSTRALIAN WINE RESEARCH INSTITUTE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOCIN; AMINO ACID; LACTIC ACID;

AMINO ACID SYNTHESIS; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL SURVIVAL; BACTERIOPHAGE; CARBOHYDRATE METABOLISM; CONTROLLED STUDY; GENE SEQUENCE; GENETIC VARIABILITY; INTRASPECIFIC COMPETITION; NONHUMAN; NUCLEOTIDE SEQUENCE; OENOCOCCUS; OENOCOCCUS KITAHARAE; PHENOTYPIC VARIATION; SPECIES DIFFERENCE; WINE; BACTERIAL CHROMOSOME; BIOSYNTHESIS; GENETICS; GENOMICS; METABOLISM; PHENOTYPE; PHYSIOLOGY; REPRODUCTION;

BACTERIA (MICROORGANISMS); OENOCOCCUS; OENOCOCCUS OENI;

AMINO ACIDS; CARBOHYDRATE METABOLISM; CHROMOSOMES, BACTERIAL; GENOME, BACTERIAL; GENOMICS; LACTIC ACID; OENOCOCCUS; PHENOTYPE; REPRODUCTION;

EID: 84855312261     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0029626     Document Type: Article

References (39)

1. Endo A, Okada S, (2006) Oenococcus kitaharae sp. nov., a non-acidophilic and non-malolactic-fermenting oenococcus isolated from a composting distilled shochu residue. Int J Syst Evol Microbiol 56: 2345-2348.
2. Dicks LM, Dellaglio F, Collins MD, (1995) Proposal to reclassify Leuconostoc oenos as Oenococcus oeni [corrig.] gen. nov., comb. nov. Int J Syst Bacteriol 45: 395-397.
3. Bartowsky EJ, Borneman AR, (2011) Genomic variations of Oenococcus oeni strains and the potential to impact on malolactic fermentation and aroma compounds in wine. Appl Microbiol Biotechnol 92: 441-447.
4. Mills DA, Rawsthorne H, Parker C, Tamir D, Makarova K, (2005) Genomic analysis of Oenococcus oeni PSU-1 and its relevance to winemaking. FEMS Microbiol Rev 29: 465-475.
5. Makarova K, Slesarev A, Wolf Y, Sorokin A, Mirkin B, et al. (2006) Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci U S A 103: 15611-15616.
6. Borneman AR, Bartowsky EJ, McCarthy J, Chambers PJ, (2010) Genotypic diversity in Oenococcus oeni by high-density microarray comparative genome hybridization and whole genome sequencing. Appl Microbiol Biotechnol 86: 681-691.
7. Delcher AL, Bratke KA, Powers EC, Salzberg SL, (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673-679.
8. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, et al. (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9: 75.
9. Chelo IM, Ze-Ze L, Tenreiro R, (2007) Genome diversity in the genera Fructobacillus, Leuconostoc and Weissella determined by physical and genetic mapping. Microbiology 156: 420-430.
10. De Bruyne K, Camu N, De Vuyst L, Vandamme P, (2010) Weissella fabaria sp. nov., from a Ghanaian cocoa fermentation. Int J Syst Evol Microbiol 60: 1999-2005.
11. Vernikos GS, Parkhill J, (2006) Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics 22: 2196-2203.
12. Sao-Jose C, Santos S, Nascimento J, Brito-Madurro AG, Parreira R, et al. (2004) Diversity in the lysis-integration region of oenophage genomes and evidence for multiple tRNA loci, as targets for prophage integration in Oenococcus oeni. Virology 325: 82-95.
13. Salyers AA, Shoemaker NB, Stevens AM, Li LY, (1995) Conjugative transposons: an unusual and diverse set of integrated gene transfer elements. Microbiol Rev 59: 579-590.
14. van Kranenburg R, Golic N, Bongers R, Leer RJ, de Vos WM, et al. (2005) Functional analysis of three plasmids from Lactobacillus plantarum. Appl Environ Microbiol 71: 1223-1230.
15. Marraffini LA, Sontheimer EJ, (2010) CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat Rev Genet 11: 181-190.
16. Davis CR, Wibowo D, Fleet GH, Lee TH, (1988) Properties of wine lactic-acid bacteria- their potential enological significance. Am J Enol Vitic 39: 137-142.
17. Dicks LM, Holzapfel WH, (2009) Genus II. Oenococcus. In: Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, editors. Bergey's Manual of Systematic Bacteriology second edition New York Springer pp. 635-642.
18. Terrade N, Mira de Orduna R, (2009) Determination of the essential nutrient requirements of wine-related bacteria from the genera Oenococcus and Lactobacillus. Int J Food Microbiol 133: 8-13.
19. Bringel F, Frey L, Boivin S, Hubert JC, (1997) Arginine biosynthesis and regulation in Lactobacillus plantarum: the carA gene and the argCJBDF cluster are divergently transcribed. J Bacteriol 179: 2697-2706.
20. Garvie EI, (1967) Leuconostoc oenos sp.nov. J Gen Microbiol 48: 431-438.
21. Ramos A, Santos H, (1996) Citrate and Sugar Cofermentation in Leuconostoc oenos, a (sup13)C Nuclear Magnetic Resonance Study. Appl Environ Microbiol 62: 2577-2585.
22. Bartowsky EJ, (2005) Oenococcus oeni and malolactic fermentation- moving into the molecular arena. Aust J Grape Wine Res 11: 174-187.
23. Henschke PA, Jiranek V, (1993) Yeasts- metabolism of nitrogen compounds. In: Fleet GH, editors. Wine microbiology and biotechnology Chur, Switzerland Harwood Academic Publishers pp. 77-164.
24. Hernandez-Orte P, Cacho JF, Ferreira V, (2002) Relationship between varietal amino acid profile of grapes and wine aromatic composition. Experiments with model solutions and chemometric study. J Agric Food Chem 50: 2891-2899.
25. Wibowo D, Eschenbruch R, Davis CR, Fleet GH, Lee TH, (1985) Occurrence and growth of lactic-acid bacteria in wine- a Review. Am J Enol Vitic 36: 302-313.
26. Endo A, Okada S, (2005) Monitoring the lactic acid bacterial diversity during shochu fermentation by PCR-denaturing gradient gel electrophoresis. J Biosci Bioeng 99: 216-221.
27. Endo A, Okada S, (2005) Lactobacillus satsumensis sp. nov., isolated from mashes of shochu, a traditional Japanese distilled spirit made from fermented rice and other starchy materials. Int J Syst Evol Microbiol 55: 83-85.
28. Endo A, Okada S, (2007) Lactobacillus composti sp. nov., a lactic acid bacterium isolated from a compost of distilled shochu residue. Int J Syst Evol Microbiol 57: 870-872.
29. Endo A, Okada S, (2007) Lactobacillus farraginis sp. nov. and Lactobacillus parafarraginis sp. nov., heterofermentative Lactobacilli isolated from a compost of distilled shochu residue. Int J Syst Evol Microbiol 57: 708-712.
30. Davis C, Silveira NF, Fleet GH, (1985) Occurrence and properties of bacteriophages of Leuconostoc oenos in Australian wines. Appl Environ Microbiol 50: 872-876.
31. Henick-Kling T, Lee TH, Nicholas DJD, (1986) Inhibition of bacterial growth and malolactic fermentation in wine by bacteriophage. J Appl Bacteriol 61: 287-293.
32. Bartowsky EJ, (2009) Bacterial spoilage of wine and approaches to minimize it. Lett Appl Microbiol 48: 149-156.
33. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
34. Suyama M, Torrents D, Bork P, (2006) PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res 34: W609-612.
35. Carver T, Berriman M, Tivey A, Patel C, Bohme U, et al. (2008) Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics 24: 2672-2676.
36. Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J, (2009) DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 25: 119-120.
37. Chen F, Mackey AJ, Stoeckert CJ, Roos DS, (2006) OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res 34: D363-368.
38. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
39. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, et al. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59: 307-321.