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

PLOS ONE, Nov 2019

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.

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

April Genome comparison of different Zymomonas mobilis strains provides insights on conservation of the evolution Chen Chen☯ 0 1 Linfeng Wu☯ 0 1 Qinghua Cao 0 1 Huanhuan Shao 0 1 Xuedan Li 0 1 Yizheng Zhang 0 1 Haiyan Wang 0 1 Xuemei Tan 0 1 0 College of Life Sciences, Sichuan University, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology , Chengdu , PR China 1 Editor: Shihui Yang, Hubei University , CHINA 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 B14023 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. - Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Funding: This work is funded by the Nature Science Foundation of China with project No. 30470984. Competing interests: The authors have declared that no competing interests exist. Background Zymomonas mobilis is facultative anaerobic bacterium; it can grow in aerobic or anaerobic conditions [ 1, 2 ]. Z. mobilis has the special Entner-Doudoroff (ED) pathway and demonstrates high ethanol production using glucose, fructose or sucrose as substrates [ 3,4 ]. Z. mobilis has excellent industrial characteristics, including low cell mass formation, high-specific productivity and ethanol yield, notable ethanol tolerance and a wide pH range [5±7]. Z. mobilis has also been used for a variety of other biotechnological purposes, such as the production of levan [ 8, 9 ]. Recently, different genetic techniques were used to improve the industrial biotechnology capacity of Z. mobilis [ 10, 11 ]. Genome sequencing analysis of Z. mobilis provides further opportunities for strain developments and fundamental research [12]. The first genome sequence of the Z. mobilis ZM4 was published in 2005[ 10 ]. This strain is regarded as a model organism in Z. mobilis research and industrial applications [ 12, 13 ]. Thus far, the complete genome sequences of 9 Z. mobilis strains have been reported, including two sequences for Z. mobilis NRRL B-14023 (CP4) [14±19]. In fact, the genomes of Z. mobilis strains NRRL B-12526 and NRRL B-14023 were sequenced in our lab. Draft genome sequences of two Z. mobilis strains (ATCC 31822 and ATCC 31823) have also been reported [ 20,21 ]. Thus, in this article, we chose 8 Z. mobilis strains with complete genome sequences to analyze and compare (Table 1). Currently, three subspecies (subsp.) of Z. mobilis have been found, including ªZ. mobilis subsp. mobilis”, ªZ. mobilis subsp. pomaceae” and ªZ. mobilis subsp. francensis”. [21±23]. ZM4, ATCC 10988, ATCC29191, NRRL B-14023, NRRL B-12526, NCIMB 11163 and NRRL B1960, belonge to Z. mobilis subsp mobilis [21±23]. ATCC 29192 is the type strain of Z. mobilis subsp. pomaceae [ 20 ]. Moreover, different srtains of subspecies have different characteristics. For example, NRRL B-14023 is the most aerotolerant, quickly growing, and ethanol-yielding Z. mobilis strain [ 18 ]. ATCC 29191 is superior to other Z. mobilis strains in levan production [ 15 ]. ATCC 29192 exhibits distinct traits compared to other strains, including low oxygen tolerance, increased nutritional requirements, inability to utilize sucrose, and low DNA hybridization relatedness [ 20 ]. Differences of these strains in physiological and fermentation ability may be related to its genome. Although the complete genome sequences of these strains had been published, the comparative genome analysis has not been reported. Comparative genomics analysis of the genomes of different strains simultaneously could identify similarities and differences among them, which could be helpful for a better understanding o (...truncated)


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Chen Chen, Linfeng Wu, Qinghua Cao, Huanhuan Shao, Xuedan Li, Yizheng Zhang, Haiyan Wang, Xuemei Tan. Genome comparison of different Zymomonas mobilis strains provides insights on conservation of the evolution, PLOS ONE, 2018, Volume 13, Issue 4, DOI: 10.1371/journal.pone.0195994