Genome-wide phylogenetic analysis of differences in thermotolerance among closely related Acetobacter pasteurianus strains

Microbiology

Volumn 158, Issue 1, 2012, Pages 229-239

  Matsutani, Minenosuke ^a   Hirakawa, Hideki ^b   Saichana, Natsaran ^a,c   Soemphol, Wichai ^a,d   Yakushi, Toshiharu ^a   Matsushita, Kazunobu ^a  

^a YAMAGUCHI UNIVERSITY   (Japan)

^b KAZUSA DNA RESEARCH INSTITUTE   (Japan)

^c RAMBHAI BARNI RAJABHAT UNIVERSITY   (Thailand)

^d KHON KAEN UNIVERSITY   (Thailand)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ACETOBACTER; ACETOBACTER PASTEURIANUS; ACETOBACTER TROPICALIS; ARTICLE; CONTROLLED STUDY; GENE MUTATION; GENETIC TRANSCRIPTION; HEAT SENSITIVITY; HEAT TOLERANCE; NONHUMAN; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; RNA TRANSLATION; SIGNAL TRANSDUCTION;

ACETIC ACID; ACETOBACTER; BACTERIAL PROTEINS; FERMENTATION; GENOME, BACTERIAL; HOT TEMPERATURE; INDUSTRIAL MICROBIOLOGY; MOLECULAR SEQUENCE DATA; PHYLOGENY;

ACETOBACTER PASTEURIANUS; BACTERIA (MICROORGANISMS); NEGIBACTERIA;

EID: 84855218300     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/mic.0.052134-0     Document Type: Article

References (40)

1. Adékambi, T. & Drancourt, M. (2004). Dissection of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S rRNA, hsp65, sodA, recA and rpoB gene sequencing. Int J Syst Evol Microbiol 54, 2095-2105
2. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402
3. Azuma, Y., Hosoyama, A., Matsutani, M., Furuya, N., Horikawa, H., Harada, T., Hirakawa, H., Kuhara, S., Matsushita, K. & other authors (2009). Whole-genome analyses reveal genetic instability of Acetobacter pasteurianus. Nucleic Acids Res 37, 5768-5783
4. Bertalan, M., Albano, R., de Pádua, V., Rouws, L., Rojas, C., Hemerly, A., Teixeira, K., Schwab, S., Araujo, J. & other authors (2009). Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus Pal5. BMC Genomics 10, 450.
5. Butler, J., MacCallum, I., Kleber, M., Shlyakhter, I. A., Belmonte, M. K., Lander, E. S., Nusbaum, C. & Jaffe, D. B. (2008). ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res 18, 810-820
6. Delcher, A. L., Kasif, S., Fleischmann, R. D., Peterson, J., White, O. & Salzberg, S. L. (1999). Alignment of whole genomes. Nucleic Acids Res 27, 2369-2376
7. Delcher, A. L., Phillippy, A., Carlton, J. & Salzberg, S. L. (2002). Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res 30, 2478-2483
8. Delcher, A. L., Bratke, K. A., Powers, E. C. & Salzberg, S. L. (2007). Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23, 673-679
9. Dohm, J. C., Lottaz, C., Borodina, T. & Himmelbauer, H. (2007). SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Res 17, 1697-1706
10. Farrer, R. A., Kemen, E., Jones, J. D. & Studholme, D. J. (2009). De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads. FEMS Microbiol Lett 291, 103-111
11. Gontcharov, A. A., Marin, B. & Melkonian, M. (2004). Are combined analyses better than single gene phylogenies? A case study using SSU rDNA and rbcL sequence comparisons in the Zygnematophyceae (Streptophyta). Mol Biol Evol 21, 612-624
12. Holt, R. A. & Jones, S. J. (2008). The new paradigm of flow cell sequencing. Genome Res 18, 839-846
13. Kanchanarach, W., Theeragool, G., Inoue, T., Yakushi, T., Adachi, O. & Matsushita, K. (2010a). Acetic acid fermentation of Acetobacter pasteurianus: relationship between acetic acid resistance and pellicle polysaccharide formation. Biosci Biotechnol Biochem 74, 1591-1597
14. Kanchanarach, W., Theeragool, G., Yakushi, T., Toyama, H., Adachi, O. & Matsushita, K. (2010b). Characterization of thermotolerant Acetobacter pasteurianus strains and their quinoprotein alcohol dehydrogenases. Appl Microbiol Biotechnol 85, 741-751
15. Konstantinidis, K. T. & Tiedje, J. M. (2005). Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187, 6258-6264
16. Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C. & Salzberg, S. L. (2004). Versatile and open software for comparing large genomes. Genome Biol 5, R12.
17. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A. & other authors (2007). CLUSTAL W and CLUSTAL_X version 2.0. Bioinformatics 23, 2947-2948
18. MacLean, D., Jones, J. D. & Studholme, D. J. (2009). Application of 'next-generation' sequencing technologies to microbial genetics. Nat Rev Microbiol 7, 287-296
19. Mardis, E. R. (2008). Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9, 387-402
20. Matsutani, M., Hirakawa, H., Yakushi, T. & Matsushita, K. (2011). Genome-wide phylogenetic analysis of Gluconobacter, Acetobacter, and Gluconacetobacter. FEMS Microbiol Lett 315, 122-128
21. Medini, D., Donati, C., Tettelin, H., Masignani, V. & Rappuoli, R. (2005). The microbial pan-genome. Curr Opin Genet Dev 15, 589-594
22. Morse, R., O'Hanlon, K. & Collins, M. D. (2002). Phylogenetic, amino acid content and indel analyses of the β subunit of DNA-dependent RNA polymerase of Gram-positive and Gram-negative bacteria. Int J Syst Evol Microbiol 52, 1477-1484
23. Murata, M., Fujimoto, H., Nishimura, K., Charoensuk, K., Nagamitsu, H., Raina, S., Kosaka, T., Oshima, T., Ogasawara, N. & Yamada, M. (2011). Molecular strategy for survival at a critical high temperature in Escherichia coli. PLoS ONE 6, e20063.
24. Prust, C., Hoffmeister, M., Liesegang, H., Wiezer, A., Fricke, W. F., Ehrenreich, A., Gottschalk, G. & Deppenmeier, U. (2005). Complete genome sequence of the acetic acid bacterium Gluconobacter oxydans. Nat Biotechnol 23, 195-200
25. Rokas, A., Williams, B. L., King, N. & Carroll, S. B. (2003). Genomescale approaches to resolving incongruence in molecular phylogenies. Nature 425, 798-804
26. Saeki, A., Theeragool, G., Matsushita, K., Toyama, H. & Adachi, O. (1997). Development of thermotolerant acetic acid bacteria useful for vinegar fermentation at higher temperatures. Biosci Biotechnol Biochem 61, 138-145
27. Salzberg, S. L., Delcher, A. L., Kasif, S. & White, O. (1998). Microbial gene identification using interpolated Markov models. Nucleic Acids Res 26, 544-548
28. Sievers, M. & Teuber, M. (1995). The microbiology and taxonomy of Acetobacter europaeus in commercial vinegar production. J Appl Bacteriol 79, 84-95
29. Soemphol, W., Deeraksa, A., Matsutani, M., Yakushi, T., Toyama, H., Adachi, O., Yamada, M. & Matsushita, K. (2011). Global analysis of the genes involved in the thermotolerance mechanism of thermotolerant Acetobacter tropicalis SKU1100. Biosci Biotechnol Biochem 75, 1921-1928
30. Stackebrandt, E., Frederiksen, W., Garrity, G. M., Grimont, P. A., Kämpfer, P., Maiden, M. C., Nesme, X., Rosselló-Mora, R., Swings, J. & other authors (2002). Report of the ad hoc committee for the reevaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52, 1043-1047
31. Stothard, P. & Wishart, D. S. (2005). Circular genome visualization and exploration using CGView. Bioinformatics 21, 537-539
32. Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007). MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24, 1596-1599
33. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. & Kumar, S. (2011). MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28, 2731-2739
34. Tatusov, R. L., Koonin, E. V. & Lipman, D. J. (1997). A genomic perspective on protein families. Science 278, 631-637
35. Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B., Koonin, E. V., Krylov, D. M., Mazumder, R., Mekhedov, S. L. & other authors (2003). The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41.
36. Tettelin, H., Masignani, V., Cieslewicz, M. J., Donati, C., Medini, D., Ward, N. L., Angiuoli, S. V., Crabtree, J., Jones, A. L. & other authors (2005). Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci U S A 102, 13950-13955
37. van der Veen, S., Abee, T., de Vos, W. M. & Wells-Bennik, M. H. (2009). Genome-wide screen for Listeria monocytogenes genes important for growth at high temperatures. FEMS Microbiol Lett 295, 195-203
38. Warren, R. L., Sutton, G. G., Jones, S. J. & Holt, R. A. (2007). Assembling millions of short DNA sequences using SSAKE. Bioinformatics 23, 500-501
39. Yamamoto, S. & Harayama, S. (1998). Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16S rRNA genes. Int J Syst Bacteriol 48, 813-819
40. Zerbino, D. R. & Birney, E. (2008). Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18, 821-829.