Extraordinary expansion of a Sorangium cellulosum genome from an alkaline milieu

Scientific Reports

Volumn 3, Issue , 2013, Pages

  Han, Kui ^a   Li, Zhi Feng ^a   Peng, Ran ^a   Zhu, Li Ping ^a   Zhou, Tao ^b   Wang, Lu Guang ^a   Li, Shu Guang ^a   Zhang, Xiao Bo ^b   Hu, Wei ^a   Wu, Zhi Hong ^a   Qin, Nan ^b   Li, Yue Zhong ^a  

^a SHANDONG UNIVERSITY   (China)

^b BGI SHENZHEN   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALKALI;

BACTERIAL GENOME; GENETICS; MYXOCOCCALES; PH; ARTICLE;

ALKALIES; GENOME, BACTERIAL; HYDROGEN-ION CONCENTRATION; MYXOCOCCALES;

EID: 84880130007     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep02101     Document Type: Article

References (56)

1. McCutcheon, J. P., McDonald, B. R. & Moran, N. A. Origin of an alternative genetic code in the extremely small and GC-rich genome of a bacterial symbiont. PLoS Genet. 5, e1000565 (2009).
2. Schneiker, S. et al. Complete genome sequence of the myxobacterium Sorangium cellulosum. Nat. Biotechnol. 25, 1281-1289 (2007). (Pubitemid 350076516)
3. Stepkowski, T. &Legocki, A. B. Reduction of bacterial genome size and expansion resulting from obligate intracellular lifestyle and adaptation to soil habitat. Acta Biochim. Pol. 48, 367-381 (2001). (Pubitemid 33638621)
4. Konstantinidis, K. T. & Tiedje, J. M. Trends between gene content and genome size in prokaryotic species with larger genomes. Proc. Natl. Acad. Sci. U. S. A. 101, 3160-3165 (2004). (Pubitemid 38327751)
5. Ranea, J.A., Grant, A., Thornton, J.M. &Orengo, C.A.Microeconomic principles explain an optimal genome size in bacteria. Trends Genet. 21, 21-25 (2005). (Pubitemid 40178844)
6. Delaye, L. & Moya, A.Evolution ofreduced prokaryotic genomes and the minimal cell concept: variations on a theme. Bioessays 32, 281-287 (2010).
7. Kobayashi, I., Nobusato, A., Kobayashi-Takahashi, N. & Uchiyama, I. Shaping the genome-restriction-modification systems as mobile genetic elements. Curr. Opin. Genet. Dev. 9, 649-656 (1999).
8. Reichenbach, H. Myxobacteria, producers of novel bioactive substances. J. Ind. Microbiol. Biotechnol. 27, 149-156 (2001). (Pubitemid 34429802)
9. Konovalova, A., Petters, T. & Sogaard-Andersen, L. Extracellular biology of Myxococcus xanthus. FEMS Microbiol. Rev. 34, 89-106 (2010).
10. Reichenbach, H. The ecology of the myxobacteria. Environ. Microbiol. 1, 15-21 (1999). (Pubitemid 129640024)
11. Li, S.-g. et al. The existence and diversity of myxobacteria in lake mud-a previously unexplored myxobacteria habitat. Environ. Microbiol. Rep. 4, 587-595 (2012).
12. Jiang, D. M. et al. Phylogeographic separation of marine and soil myxobacteria at high levels of classification. ISME J. 4, 1520-1530 (2010).
13. Thomas, S. H.etal. The mosaic genomeofAnaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-proteobacteria. PLoS ONE 3, e2103 (2008).
14. Goldman, B. S. et al. Evolution of sensory complexity recorded in a myxobacterial genome. Proc. Natl. Acad. Sci. U. S. A. 103, 15200-15205 (2006). (Pubitemid 44583188)
15. Pérez, J. et al. Eukaryotic-like protein kinases in the prokaryotes and the myxobacterial kinome. Proc. Natl. Acad. Sci. U. S. A. 105, 15950-15955 (2008).
16. Dawid, W. Biology and global distribution of myxobacteria in soils. FEMS Microbiol. Rev. 24, 403-427 (2000).
17. Whitworth, D. E. Myxobacteria: Multicellularity and Differentiation. ASM Press: Washington, DC. (2008).
18. Gong, G. L. et al. Mutation and a high-throughput screening method for improving the production of Epothilones of Sorangium. J. Ind. Microbiol. Biotechnol. 34, 615-623 (2007).
19. Li, Y. et al. Isolation and identification of myxobacteria. Acta Microbiol. Sin. 40, 652 (2000).
20. Li, P.-f. et al. Co-cultivation of Sorangium cellulosum strains affects cellular growth and biosynthesis of secondary metabolite epothilones. FEMS Microbiol. Ecol. In Press (2013).
21. Bollag, D. M. et al. Epothilones, a new class of microtubule-stabilizing agents with a taxol-like mechanism of action. Cancer Res. 55, 2325-2333 (1995).
22. Zhao, L. et al. Glycosylation and production characteristics of epothilones in alkali-tolerant Sorangium cellulosum strain So0157-2. J. Microbiol. 48, 438-444 (2010).
23. Yan, Z. C. et al. Morphologies and phylogenetic classification of cellulolytic myxobacteria. Syst. Appl. Microbiol. 26, 104-109 (2003).
24. Zhao, J. Y. et al. Discovery of the autonomously replicating plasmid pMF1 from Myxococcus fulvus and development of a gene cloning system in Myxococcus xanthus. Appl. Environ. Microbiol. 74, 1980-1987 (2008).
25. Kurland, C. G., Canback, B. & Berg, O. G. Horizontal gene transfer: a critical view. Proc. Natl. Acad. Sci. U. S. A. 100, 9658-9662 (2003). (Pubitemid 37086996)
26. Gevers, D., Vandepoele, K., Simillon, C. & Van de Peer, Y. Gene duplication and biased functional retention of paralogs in bacterial genomes. Trends Microbiol. 12, 148-154 (2004). (Pubitemid 38393733)
27. Wozniak, R. A. & Waldor, M. K. Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nat. Rev. Microbiol. 8, 552-563 (2010).
28. Burrus, V. & Waldor, M. K. Shaping bacterial genomes with integrative and conjugative elements. Res. Microbiol. 155, 376-386 (2004). (Pubitemid 38781181)
29. Muñoz-Dorado, J., Inouye, S. & Inouye, M. A gene encoding a protein serine/threonine kinase is required for normal development of M. xanthus, a gramnegative bacterium. Cell 67, 995-1006 (1991). (Pubitemid 121001513)
30. Zusman, D. R., Scott, A. E., Yang, Z. & Kirby, J. R. Chemosensory pathways, motility and developmentinMyxococcus xanthus. Nat. Rev. Microbiol.5, 862-872 (2007). (Pubitemid 47578387)
31. Horvath, P. & Barrangou, R. CRISPR/Cas, the immune system of bacteria and archaea. Science 327, 167-170 (2010).
32. Makarova, K. S. et al. Evolution and classification of the CRISPR-Cas systems. Nat. Rev. Microbiol. 9, 467-477 (2011).
33. Murray, N. E. 2001 Fred Griffith review lecture. Immigration control of DNA in bacteria: self versus non-self. Microbiology 148, 3-20 (2002). (Pubitemid 34083180)
34. Elhai, J. et al. Reduction of conjugal transfer efficiency by three restriction activities of Anabaena sp. strain PCC 7120. J. Bacteriol. 179, 1998-2005 (1997). (Pubitemid 27123084)
35. Berndt, C., Meier, P. & Wackernagel, W. DNA restriction is a barrier to natural transformation in Pseudomonas stutzeri JM300. Microbiology 149, 895-901 (2003). (Pubitemid 36553359)
36. Cristino, A. S., Tanaka, E. D., Rubio, M., Piulachs, M. D. & Belles, X. Deep sequencing of organ-and stage-specific microRNAs in the evolutionarily basal insect Blattella germanica (L.) (Dictyoptera, Blattellidae). PLoS ONE 6, e19350 (2011).
37. Griffith, M. et al. Alternative expression analysis by RNA sequencing. Nat. Methods 7, 843-847 (2010).
38. Padan, E., Bibi, E., Ito, M. & Krulwich, T. A. Alkaline pH homeostasis in bacteria: new insights. Biochim. Biophys. Acta 1717, 67-88 (2005). (Pubitemid 41682429)
39. Gross, C. A., Lonetto, M. & Losick, R.In McKnight, S. L. &Yamamoto, K. R.(eds), Transcriptional Regulation. Cold Spring Harbor Laboratory Press, Plainview, NY, 129-176 (1992).
40. Merrick, M. J. In a class of its own-the RNA polymerase sigma factor sigma 54 (sigma N). Mol. Microbiol. 10, 903-909 (1993). (Pubitemid 24040867)
41. Kuo, C. H., Moran, N. A. & Ochman, H. The consequences of genetic drift for bacterial genome complexity. Genome Res. 19, 1450-1454 (2009).
42. Li, J. et al. Myxococcus xanthus viability depends on groEL supplied by either of two genes, but the paralogs have different functions during heat shock, predation, and development. J. Bacteriol. 192, 1875-1881 (2010).
43. Wang, Y. et al. Mechanisms involved in the functional divergence of duplicated GroEL chaperonins inMyxococcus xanthus DK1622. PLoS Genet. In Press (2013).
44. Chen, I. & Dubnau, D. DNA uptake during bacterial transformation. Nat. Rev. Microbiol. 2, 241-249 (2004). (Pubitemid 39490085)
45. Nguimbi, E. et al. 16S-23S ribosomal DNA intergenic spacer regions in cellulolytic myxobacteria and differentiation of closely related strains. Syst. Appl. Microbiol. 26, 262-268 (2003). (Pubitemid 36827875)
46. Li, Y. Z. et al. A simple method to isolate salt-tolerant myxobacteria from marine samples. J. Microbiol. Methods 50, 205-209 (2002).
47. Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (1997). (Pubitemid 27359211)
48. Husemann, P. & Stoye, J. r2cat: synteny plots and comparative assembly. Bioinformatics 26, 570-571 (2010).
49. Langmead, B. Aligning short sequencing reads with Bowtie. Curr. Protoc. Bioinformatics. 11.17.11-11.17.14 (2010).
50. Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-595 (2010).
51. Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).
52. Robinson, M. D. & Oshlack, A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 11, R25 (2010).
53. Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010).
54. Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Stat. Methodol. 289-300 (1995).
55. T Method. Methods 25, 402-408 (2001). (Pubitemid 34164012)
56. Xia, Z. J. et al. Improving conjugation efficacy of Sorangium cellulosum by the addition of dual selection antibiotics. J. Ind. Microbiol. Biotechnol. 35, 1157-1163 (2008).