Genome Comparison of Different Zymomonas Mobilis Strains Provides Insights on Conservation of the Evolution

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2018 Apr 26

PMID 29694430

Citations 5

Authors

Chen Chen

Linfeng Wu

Qinghua Cao

Huanhuan Shao

Xuedan Li

Yizheng Zhang

Haiyan Wang

Xuemei Tan

Affiliations

Soon will be listed here.

Abstract

Zymomonas mobilis has the special Entner-Doudoroff (ED) pathway and it has excellent industrial characteristics, including low cell mass formation, high-specific productivity,ethanol yield, notable ethanol tolerance and wide pH range, a relatively small genome size. In this study, the genome sequences of NRRL B-14023 and NRRL B-12526 were sequenced and compared with other strains to explore their evolutionary relationships and the genetic basis of Z. mobilis. The comparative genomic analyses revealed that the 8 strains share a conserved core chromosomal backbone. ZM4, NRRL B-12526, NRRL B-14023, NCIMB 11163 and NRRL B-1960 share 98% sequence identity across the whole genome sequences. Highly similar plasmids and CRISPR repeats were detected in these strains. A whole-genome phylogenetic tree of the 8 strains indicated that NRRL B-12526, NRRL B-14023 and ATCC 10988 had a close evolutionary relationship with the strain ZM4. Furthermore, strains ATCC29191 and ATCC29192 had distinctive CRISPR with a far distant relationship. The size of the pan-genome was 1945 genes, including 1428 core genes and 517 accessory genes. The genomes of Z. mobilis were highly conserved; particularly strains ZM4, NRRL B-12526, NRRL B-14023, NCIMB 11163 and NRRL B-1960 had a close genomic relationship. This comparative study of Z. mobilis presents a foundation for future functional analyses and applications.

Citing Articles

Improved high-temperature ethanol production from sweet sorghum juice using Zymomonas mobilis overexpressing groESL genes.

Kaewchana A, Techaparin A, Boonchot N, Thanonkeo P, Klanrit P Appl Microbiol Biotechnol. 2021; 105(24):9419-9431.

PMID: 34787692 DOI: 10.1007/s00253-021-11686-0.

Genome Copy Number Quantification Revealed That the Ethanologenic Alpha-Proteobacterium Is Polyploid.

Fuchino K, Wasser D, Soppa J Front Microbiol. 2021; 12:705895.

PMID: 34408736 PMC: 8365228. DOI: 10.3389/fmicb.2021.705895.

Zymomonas diversity and potential for biofuel production.

Felczak M, Bowers R, Woyke T, TerAvest M Biotechnol Biofuels. 2021; 14(1):112.

PMID: 33933155 PMC: 8088579. DOI: 10.1186/s13068-021-01958-2.

Genomic profiling of bacterial and fungal communities and their predictive functionality during pulque fermentation by whole-genome shotgun sequencing.

Chacon-Vargas K, Torres J, Giles-Gomez M, Escalante A, Gibbons J Sci Rep. 2020; 10(1):15115.

PMID: 32934253 PMC: 7493934. DOI: 10.1038/s41598-020-71864-4.

Establishment and application of a CRISPR-Cas12a assisted genome-editing system in Zymomonas mobilis.

Shen W, Zhang J, Geng B, Qiu M, Hu M, Yang Q Microb Cell Fact. 2019; 18(1):162.

PMID: 31581942 PMC: 6777028. DOI: 10.1186/s12934-019-1219-5.

References

Milne I, Bayer M, Cardle L, Shaw P, Stephen G, Wright F . Tablet--next generation sequence assembly visualization. Bioinformatics. 2009; 26(3):401-2. PMC: 2815658. DOI: 10.1093/bioinformatics/btp666. View

Brown S, Nagaraju S, Utturkar S, Tissera S, Segovia S, Mitchell W . 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. PMC: 4022347. DOI: 10.1186/1754-6834-7-40. View

Altintas M, Eddy C, Zhang M, McMillan J, Kompala D . Kinetic modeling to optimize pentose fermentation in Zymomonas mobilis. Biotechnol Bioeng. 2006; 94(2):273-95. DOI: 10.1002/bit.20843. View

Desiniotis A, Kouvelis V, Davenport K, Bruce D, Detter C, Tapia R . Complete genome sequence of the ethanol-producing Zymomonas mobilis subsp. mobilis centrotype ATCC 29191. J Bacteriol. 2012; 194(21):5966-7. PMC: 3486092. DOI: 10.1128/JB.01398-12. View

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. PMC: 3831827. DOI: 10.1186/1471-2164-14-775. View

Yang S, Pappas K, Hauser L, Land M, Chen G, Hurst G . Improved genome annotation for Zymomonas mobilis. Nat Biotechnol. 2009; 27(10):893-4. DOI: 10.1038/nbt1009-893. View

Kalnenieks U, Pentjuss A, Rutkis R, Stalidzans E, Fell D . Modeling of Zymomonas mobilis central metabolism for novel metabolic engineering strategies. Front Microbiol. 2014; 5:42. PMC: 3914154. DOI: 10.3389/fmicb.2014.00042. View

Shui Z, Qin H, Wu B, Ruan Z, Wang L, Tan F . Adaptive laboratory evolution of ethanologenic Zymomonas mobilis strain tolerant to furfural and acetic acid inhibitors. Appl Microbiol Biotechnol. 2015; 99(13):5739-48. DOI: 10.1007/s00253-015-6616-z. View

Rouli L, Merhej V, Fournier P, Raoult D . The bacterial pangenome as a new tool for analysing pathogenic bacteria. New Microbes New Infect. 2015; 7:72-85. PMC: 4552756. DOI: 10.1016/j.nmni.2015.06.005. View

10.

Seemann T . Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014; 30(14):2068-9. DOI: 10.1093/bioinformatics/btu153. View

11.

Sampson T, Saroj S, Llewellyn A, Tzeng Y, Weiss D . A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature. 2013; 497(7448):254-7. PMC: 3651764. DOI: 10.1038/nature12048. View

12.

Seo J, Chong H, Park H, Yoon K, Jung C, Kim J . The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4. Nat Biotechnol. 2004; 23(1):63-8. PMC: 6870993. DOI: 10.1038/nbt1045. View

13.

Pappas K, Kouvelis V, Saunders E, Brettin T, Bruce D, Detter C . Genome sequence of the ethanol-producing Zymomonas mobilis subsp. mobilis lectotype strain ATCC 10988. J Bacteriol. 2011; 193(18):5051-2. PMC: 3165638. DOI: 10.1128/JB.05395-11. View

14.

Jore M, Brouns S, van der Oost J . RNA in defense: CRISPRs protect prokaryotes against mobile genetic elements. Cold Spring Harb Perspect Biol. 2011; 4(6). PMC: 3367551. DOI: 10.1101/cshperspect.a003657. View

15.

Zerbino D, Birney E . Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008; 18(5):821-9. PMC: 2336801. DOI: 10.1101/gr.074492.107. View

16.

Li L, Stoeckert Jr C, Roos D . OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003; 13(9):2178-89. PMC: 403725. DOI: 10.1101/gr.1224503. View

17.

Yi X, Gu H, Gao Q, Liu Z, 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. PMC: 4578398. DOI: 10.1186/s13068-015-0333-9. View

18.

Mongodin E, Casjens S, Bruno J, Xu Y, Drabek E, Riley D . Inter- and intra-specific pan-genomes of Borrelia burgdorferi sensu lato: genome stability and adaptive radiation. BMC Genomics. 2013; 14:693. PMC: 3833655. DOI: 10.1186/1471-2164-14-693. View

19.

Tamura K, Stecher G, Peterson D, Filipski A, Kumar S . MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol. 2013; 30(12):2725-9. PMC: 3840312. DOI: 10.1093/molbev/mst197. View

20.

Vernikos G, Medini D, Riley D, Tettelin H . Ten years of pan-genome analyses. Curr Opin Microbiol. 2014; 23:148-54. DOI: 10.1016/j.mib.2014.11.016. View