Genome comparison of different Zymomonas mobilis strains provides insights on conservation of the evolution

PLoS ONE

Volumn 13, Issue 4, 2018, Pages

  Chen, Chen ^a   Wu, Linfeng ^a   Cao, Qinghua ^a   Shao, Huanhuan ^a   Li, Xuedan ^a   Zhang, Yizheng ^a   Wang, Haiyan ^a   Tan, Xuemei ^a  

^a SICHUAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME; CLINICAL ARTICLE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; COMPARATIVE STUDY; GENOME; HUMAN; IDENTITY; NONHUMAN; PHYLOGENETIC TREE; PLASMID; ZYMOMONAS MOBILIS; BACTERIAL GENOME; CLASSIFICATION; DNA SEQUENCE; GENETICS; GENOME SIZE; METABOLISM; MOLECULAR EVOLUTION; PH; PHYLOGENY; PROCEDURES; ZYMOMONAS;

ALCOHOL;

ETHANOL; EVOLUTION, MOLECULAR; GENOME SIZE; GENOME, BACTERIAL; HYDROGEN-ION CONCENTRATION; PHYLOGENY; SEQUENCE ANALYSIS, DNA; ZYMOMONAS;

EID: 85045904766     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0195994     Document Type: Article

References (47)

1. Yi X, Gu H, Gao Q, Liu ZL, Bao J.Transcriptome analysis of Zymomonas mobilis ZM4 reveals mechanisms of tolerance and detoxification of phenolic aldehyde inhibitors from lignocellulose pretreatment. Biotechnol Biofuels. 2015; 8:153. https://doi.org/10.1186/s13068-015-0333-9 PMID: 26396591
2. He MX, Wu B, Qin H, Ruan ZY, Tan FR, Wang JL,et al. Zymomonas mobilis: a novel platform for future biorefineries.Biotechnol Biofuels.2014; 7:101. https://doi.org/10.1186/1754-6834-7-101 PMID: 25024744
3. Conway T.The Entner-Doudoroff pathway: history, physiology and molecular biology.FEMS Microbiol Rev. 1992; 9:1–27. PMID: 1389313
4. Kalnenieks U, Pentjuss A, Rutkis R, Stalidzans E, Fell DA.Modeling of Zymomonas mobilis central metabolism for novel metabolic engineering strategies. Front Microbiol. 2014; 5:42. https://doi.org/10.3389/fmicb.2014.00042 PMID: 24550906
5. Altintas MM, Eddy CK, Zhang M, McMillan JD, Kompala DS.Kinetic modeling to optimize pentose fermentation in Zymomonas mobilis. Biotechnol Bioeng. 2006; 94:273–295. https://doi.org/10.1002/bit. 20843 PMID: 16570322
6. Lee KY, Park JM, Kim TY, Yun H, Lee SY.The genome-scale metabolic network analysis of Zymomonas mobilis ZM4 explains physiological features and suggests ethanol and succinic acid production strategies. Microb Cell Fact. 2010, 24; 9:94. https://doi.org/10.1186/1475-2859-9-94 PMID: 21092328
7. Yang S, Franden MA, Brown SD, Chou YC, Pienkos PT, Zhang M. Insights into acetate toxicity in Zymomonas mobilis 8b using different substrates. Biotechnol Biofuels, 2014; 7:140. https://doi.org/10.1186/s13068-014-0140-8 PMID: 25298783
8. Silbir S, Dagbagli S, Yegin S, Baysal T, Goksungur Y.Levan production by Zymomonas mobilis in batch and continuous fermentation systems. Carbohydr Polym.2014; 99:454–461. https://doi.org/10.1016/j.carbpol.2013.08.031 PMID: 24274530
9. Senthilkumar V, Rameshkumar N, Busby S, Gunasekaran P.Disruption of the Zymomonas mobilis extracellular sucrase gene (SacC) improves levan production. J Appl Microbiol.2004; 96:671–676. PMID: 15012804
10. Dunn KL, Rao CV. High-throughput sequencing reveals adaptation-induced mutations in pentose-fermenting strains of Zymomonas mobilis. Biotechnol Bioeng. 2015; 112:2228–2240. https://doi.org/10.1002/bit.25631 PMID: 25943255
11. Shui ZX, Qin H, Wu B, Ruan ZY, Wang LS, Tan FR,et al. Adaptive laboratory evolution of ethanologenic Zymomonas mobilis strain tolerant to furfural and acetic acid inhibitors. Appl Microbiol Biotechnol. 2015; 99:5739–5748. https://doi.org/10.1007/s00253-015-6616-z PMID: 25935346
12. Yang S, Pappas KM, Hauser LJ, Land ML, Chen GL, Hurst GB,et al. Improved genome annotation for Zymomonas mobilis. Nat Biotechnol. 2009; 27:893–894. https://doi.org/10.1038/nbt1009-893 PMID: 19816441
13. Seo JS, Chong H, Park HS, Yoon KO, Jung C, Kim GG,et al. The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4. Nat Biotechnol. 2005; 23:63–68. https://doi.org/10.1038/ nbt1045 PMID: 15592456
14. Kouvelis VN, Saunders E, Brettin TS, Bruce D, Detter C,Han C, et al.Complete genome sequence of the ethanol producer Zymomonas mobilis NCIMB 11163. J Bacteriol. 2009; 191:7140–1. https://doi.org/10.1128/JB.01084-09 PMID: 19767433
15. Desiniotis A, Kouvelis VN, Davenport K, Bruce D, Detter C, Tapia R,et al. Complete genome sequence of the ethanol-producing Zymomonas mobilis subsp. mobilis centrotype ATCC 29191. J Bacterio.2012; 194:5966–5967. https://doi.org/10.1128/JB.01398-12 PMID: 23045486
16. Chacon-Vargas K, Chirino AA, Davis MM, Debler SA, Haimer WR, Wilbur JJ,et al. Genome Sequence of Zymomonas mobilis subsp. mobilis NRRL B-1960. Genome Announc.2017; 5(30). https://doi.org/10.1128/genomeA.00562-17 PMID: 28751381
17. Pappas KM, Kouvelis VN, Saunders E, Brettin TS, Bruce D, Detter C,et al. Genome sequence of the ethanol-producing Zymomonas mobilis subsp. mobilis lectotype ATCC 10988. J Bacteriol. 2011; 193:5051–5052. https://doi.org/10.1128/JB.05395-11 PMID: 21725006
18. Kouvelis VN, Teshima H, Bruce D, Detter C, Tapia R,Han C, et al. Finished Genome of Zymomonas mobilis subsp. mobilis Strain CP4, an Applied Ethanol Producer. Genome Announc. 2014 9; 2(1). https://doi.org/10.1128/genomeA.00845-13 PMID: 24407627
19. Zhao N, Bai Y, Zhao X-Q, Yang Z-Y, Bai F-W. Draft genome sequence of the flocculating Zymomonas mobilis Strain ZM401 (ATCC 31822). J Bacteriol. 2012; 194:7008–9. https://doi.org/10.1128/JB.01947-12 PMID: 23209250
20. Kouvelis VN, Davenport KW, Brettin TS, Bruce D, Detter C, Han CS, et al. Genome sequence of the ethanol-producing Zymomonas mobilis subsp.pomaceae lectotype ATCC 29192. J Bacteriol.2011; 193:5049–5050. https://doi.org/10.1128/JB.05273-11 PMID: 21742897
21. Coton M, Laplace JM, Coton E.Zymomonas mobilis subspecies identification by amplified ribosomal DNA restriction analysis. Lett Appl Microbiol. 2005; 40:152–157. https://doi.org/10.1111/j.1472-765X.2004.01652.x PMID: 15644116
22. Coton M, Laplace JM, Auffray Y, Coton E.“Framboisé” spoilage in French ciders: Zymomonas mobilis implication and characterization. LWT-Food Sci Technol. 2006; 39:972–979
23. Coton M, Laplace J-M, Auffray Y, Coton E.Polyphasic study of Zymomonas mobilis strains revealing the existence of a novel subspecies Z. mobilis subsp. francensissubsp. nov., isolated from French cider. Int J Syst Evol Microbiol. 2006; 56:121–125. https://doi.org/10.1099/ijs.0.63732-0 PMID: 16403876
24. Hernandez D, François P, Farinelli L, Osteras M, Schrenzel J.De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome res. 2008; 18:802–809. https://doi.org/10.1101/gr.072033.107 PMID: 18332092
25. Zerbino DR, Birney E.Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008; 18:821–829. https://doi.org/10.1101/gr.074492.107 PMID: 18349386
26. Galardini M, Biondi EG, Bazzicalupo M, Mengoni A.CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes. Source Code Biol Med. 2011; 6:11. https://doi.org/10.1186/ 1751-0473-6-11 PMID: 21693004
27. Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Pakhill J. ACT: the Artemis Comparison Tool.J.Bioinformatics. 2005; 21:3422–3. https://doi.org/10.1093/bioinformatics/bti553 PMID: 15976072
28. Langmead B, Trapnell C, Pop M, Salzberg SL.Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.Genome Biol.2009; 10:R25. https://doi.org/10.1186/gb-2009-10-3-r25 PMID: 19261174
29. Milne I, Bayer M, Cardle L, Shaw P, Stephen G, Wright F,et al. Tablet—next generation sequence assembly visualization. Bioinformatics. 2010; 26:401–402. https://doi.org/10.1093/bioinformatics/ btp666 PMID: 19965881
30. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014; 30:2068–2069. https://doi.org/10.1093/bioinformatics/btu153 PMID: 24642063
31. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010; 11:119. https://doi.org/10.1186/1471-2105-11-119 PMID: 20211023
32. Conesa A, Gotz S, García-Gómez JM, Terol J, Talón M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005; 21:3674–3676. https://doi.org/10.1093/bioinformatics/bti610 PMID: 16081474
33. Darling AC, Mau B, Blattner FR, Perna NT.Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004; 14:1394–403. https://doi.org/10.1101/gr.2289704 PMID: 15231754
34. Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA. BLAST Ring Image Generator (BRIG): simple pro-karyote genome comparisons. BMC Genomics. 2011; 12:402. https://doi.org/10.1186/1471-2164-12-402 PMID: 21824423
35. Tamura K.,Stecher G.,Peterson D.,Filipski A., and Kumar S. MEGA6: molecularevolutionarygeneticsa-nalysisversion6.0. Mol.Biol.Evol. 2013; 30:2725–2729. https://doi.org/10.1093/molbev/mst197 PMID: 24132122
36. Liu G, Zhang W, Lu C.Comparative genomics analysis of Streptococcus agalactiae reveals that isolates from cultured tilapia in China are closely related to the human strain A909. BMC Genomics. 2013; 14:775. https://doi.org/10.1186/1471-2164-14-775 PMID: 24215651
37. Li L, Stoeckert CJ Jr, and Roos DS.OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003; 13:2178–89. https://doi.org/10.1101/gr.1224503 PMID: 12952885
38. Wang R, Li L, Huang Y, Luo F, Liang W, et al. Comparative genome analysis identifies two large deletions in the genome of highly-passaged attenuated Streptococcus agalactiae strain YM001 compared to the parental pathogenic strain HN016.BMC Genomics. 2015; 16:897. https://doi.org/10.1186/ s12864-015-2026-y PMID: 26537657
39. Grissa I, Vergnaud G, Pourcel C.The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics. 2007; 8:172. https://doi.org/10.1186/ 1471-2105-8-172 PMID: 17521438
40. Grissa I, Vergnaud G, Pourcel C.CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.Nucleic Acids Res, 2007; 35:W52–57. https://doi.org/10.1093/nar/gkm360PMID: 17537822
41. Sampson TR, Saroj SD, Llewellyn AC, Tzeng YL, Weiss DS.A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature. 2013; 497:254–257. https://doi.org/10.1038/ nature12048 PMID: 23584588
42. Jore Matthijs M., Brouns Stan J.J., van der Oost John.RNA in Defense: CRISPRs Protect Prokaryotes against Mobile Genetic Elements, Cold Spring Harb Perspect Biol. 2012; 4. https://doi.org/10.1101/cshperspect.a003657 PMID: 21441598
43. Brown SD, Nagaraju S, Utturkar S, De Tissera S, Segovia S, Michell W,et al. Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia. Biotechnol Biofuels.2014; 7:40. https://doi.org/10.1186/1754-6834-7-40 PMID: 24655715
44. Vernikos G, Medini D, Riley DR, Tettelin H. Ten years of pan-genome analyses. Curr Opin Microbiol. 2015; 23:148–154. https://doi.org/10.1016/j.mib.2014.11.016 PMID: 25483351
45. Rouli L, Merhej V, Fournier PE, Raoult D. The bacterial pangenome as a new tool for analysing pathogenic bacteria.New Microbes New Infect. 2015; 7:72–85. https://doi.org/10.1016/j.nmni.2015.06.005PMID: 26442149
46. Meng P, Lu C, Zhang Q, Lin J, Chen F.Exploring the Genomic Diversity and Cariogenic Differences of Streptococcus mutans Strains Through Pan-Genome and Comparative Genome Analysis. Curr Microbiol. 2017; 74:1200–1209. https://doi.org/10.1007/s00284-017-1305-z PMID: 28717847
47. Mongodin EF, Casjens SR, Bruno JF, Xu Y, Drabek EF, Riley B,et al. Inter- and intra-specific pan-genomes of Borrelia burgdorferi sensu lato: genome stability and adaptive radiation. BMC Genomics. 2013; 14:693. https://doi.org/10.1186/1471-2164-14-693 PMID: 24112474