Genome Sequence of Zymomonas mobilis subsp.
            <i>mobilis</i>
            NRRL B-1960

Chacón-Vargas, Katherine; Chirino, Alexandra A.; Davis, Meghan M.; Debler, Sophia A.; Haimer, Wynn Raphael; Wilbur, Justin J.; Mo, Xiaoli; Worthing, Baxter W.; Wainblat, Ethan; Zhao, Shu; Gibbons, John G.

doi:10.1128/genomea.00562-17

Cited by 10 publications

(7 citation statements)

References 18 publications

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“…mobilis NRRL B-1960 plasmid sequence of pZMO1960-1A is identical to the Z . mobilis NCIMB 11163 plasmid pZMO1A, which the complete genome sequences were most closely related between these strains[ 16 ].The sequences of plasmids pZZM401, pZM1252603 pZM1402303,pAZ1001,pZMOB04 and pZMOB05 were relatively similar. However, the plasmid sequences of Z .…”

Section: Resultsmentioning

confidence: 99%

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

Chen

Cao

et al. 2018

PLoS ONE

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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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Section: Resultsmentioning

confidence: 99%

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

Chen

Cao

et al. 2018

PLoS ONE

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“…To facilitate multi-omic data analyses, the genomes of eight Z. mobilis strains have been completely sequenced, including model strain ZM4 [ 17 – 23 ]. In 2009, we improved the genome annotation of Z. mobilis ZM4 (AE008692.2) [ 24 ].…”

Section: Introductionmentioning

confidence: 99%

Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

Yang

Vera

Grass

et al. 2018

Biotechnol Biofuels

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BackgroundZymomonas mobilis is a natural ethanologen being developed and deployed as an industrial biofuel producer. To date, eight Z. mobilis strains have been completely sequenced and found to contain 2–8 native plasmids. However, systematic verification of predicted Z. mobilis plasmid genes and their contribution to cell fitness has not been hitherto addressed. Moreover, the precise number and identities of plasmids in Z. mobilis model strain ZM4 have been unclear. The lack of functional information about plasmid genes in ZM4 impedes ongoing studies for this model biofuel-producing strain.ResultsIn this study, we determined the complete chromosome and plasmid sequences of ZM4 and its engineered xylose-utilizing derivatives 2032 and 8b. Compared to previously published and revised ZM4 chromosome sequences, the ZM4 chromosome sequence reported here contains 65 nucleotide sequence variations as well as a 2400-bp insertion. Four plasmids were identified in all three strains, with 150 plasmid genes predicted in strain ZM4 and 2032, and 153 plasmid genes predicted in strain 8b due to the insertion of heterologous DNA for expanded substrate utilization. Plasmid genes were then annotated using Blast2GO, InterProScan, and systems biology data analyses, and most genes were found to have apparent orthologs in other organisms or identifiable conserved domains. To verify plasmid gene prediction, RNA-Seq was used to map transcripts and also compare relative gene expression under various growth conditions, including anaerobic and aerobic conditions, or growth in different concentrations of biomass hydrolysates. Overall, plasmid genes were more responsive to varying hydrolysate concentrations than to oxygen availability. Additionally, our results indicated that although all plasmids were present in low copy number (about 1–2 per cell), the copy number of some plasmids varied under specific growth conditions or due to heterologous gene insertion.ConclusionsThe complete genome of ZM4 and two xylose-utilizing derivatives is reported in this study, with an emphasis on identifying and characterizing plasmid genes. Plasmid gene annotation, validation, expression levels at growth conditions of interest, and contribution to host fitness are reported for the first time.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1116-x) contains supplementary material, which is available to authorized users.

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“…Cumulative genome assembly size ranged from 2.07 to 2.49 Mb, with GC content ranging from 32 to 36%. Using the PhAME pipeline 39 , we identified 74,825 polymorphic sites between the genomes of the three Z. mobilis strains from pulque and an additional 7 previously sequenced Z. mobilis genomes [40][41][42][43][44][45] . Phylogenetic analysis revealed that the pulque isolates we sequenced were monophyletic with a previously sequenced strain ATCC 10988, which was also isolated from pulque (Fig.…”

Section: Taxonomic Profiling Of Microbial Community During Pulque Fermentioning

confidence: 99%

“…We used the PhaME package 39 to identify single nucleotide polymorphisms between seven publicly available Z. mobilis genomes and the three Z. mobilis genome we isolated from pulque. Strains extracted from the NCBI database included (strain (GenBank accession number)): ATCC31821 (ASM710v1), ATCC10988 (ASM17525v2), ATCC29191 (ASM27775v1), NRRL B-14023 (ASM57616v1), NRRL B-12526 (ASM57612v1), NRRL B-1960 (ASM215884v1), NCIMB 11163 (ASM2424v1) [40][41][42][43][44][45] . We used the ATCC31821 genome as the reference during PHaME analysis.…”

Section: Statistical Analysis and Data Visualizationmentioning

confidence: 99%

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

Chacón-Vargas

Torres

Gilés-Gómez

et al. 2020

Sci Rep

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Pulque is a culturally important 4,000-year-old traditional Mexican fermented drink. Pulque is produced by adding fresh aguamiel (agave sap) to mature pulque, resulting in a mixture of microbial communities and chemical compositions. We performed shotgun metagenomic sequencing of five stages of pulque fermentation to characterize organismal and functional diversity. We identified 6 genera (Acinetobacter, Lactobacillus, Lactococcus, Leuconostoc, Saccharomyces and Zymomonas) and 10 species (Acinetobacter boissieri, Acinetobacter nectaris, Lactobacillus sanfranciscensis, Lactococcus lactis, Lactococcus piscium, Lactococcus plantarum, Leuconostoc citreum, Leuconostoc gelidum, Zymomonas mobilis and Saccharomyces cerevisiae) that were present ≥ 1% in at least one stage of pulque fermentation. The abundance of genera and species changed during fermentation and was associated with a decrease in sucrose and increases in ethanol and lactic acid, suggesting that resource competition shapes organismal diversity. We also predicted functional profiles, based on organismal gene content, for each fermentation stage and identified an abundance of genes associated with the biosynthesis of folate, an essential B-vitamin. Additionally, we investigated the evolutionary relationships of S. cerevisiae and Z. mobilis, two of the major microbial species found in pulque. For S. cerevisiae, we used a metagenomics assembly approach to identify S. cerevisiae scaffolds from pulque, and performed phylogenetic analysis of these sequences along with a collection of 158 S. cerevisiae strains. This analysis suggests that S. cerevisiae from pulque is most closely related to Asian strains isolated from sake and bioethanol. Lastly, we isolated and sequenced the whole-genomes of three strains of Z. mobilis from pulque and compared their relationship to seven previously sequenced isolates. Our results suggest pulque strains may represent a distinct lineage of Z. mobilis.

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Genome Sequence of Zymomonas mobilis subsp. mobilis NRRL B-1960

Cited by 10 publications

References 18 publications

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

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

Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

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

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