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, Shihui; Vera, Jessica M.; Grass, Jeff; Savvakis, Giannis; Moskvin, Oleg V.; Yang, Yongfu; McIlwain, Sean J.; Lyu, Yucai; Zinonos, Irene; Hebert, Alexander S.; Coon, Joshua J.; Bates, Donna M.; Sato, Trey K.; Brown, Steven D.; Himmel, Michael E.; Zhang, Min; Landick, Robert; Pappas, Katherine M.; Zhang, Yaoping

doi:10.1186/s13068-018-1116-x

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

Journal Article · Wed May 02 00:00:00 EDT 2018 · Biotechnology for Biofuels

DOI:https://doi.org/10.1186/s13068-018-1116-x· OSTI ID:1439547

^[1]; Vera, Jessica M. ^[2]; Grass, Jeff ^[2]; Savvakis, Giannis ^[3]; Moskvin, Oleg V. ^[2]; Yang, Yongfu ^[4]; McIlwain, Sean J. ^[2]; Lyu, Yucai ^[5]; Zinonos, Irene ^[3]; Hebert, Alexander S. ^[2]; Coon, Joshua J. ^[2]; Bates, Donna M. ^[2]; Sato, Trey K. ^[2]; Brown, Steven D. ^[6]; Himmel, Michael E. ^[7]; Zhang, Min ^[8]; Landick, Robert ^[2]; Pappas, Katherine M. ^[3]; Zhang, Yaoping ^[2]

Hubei Univ., Wuhan (China). College of Life Sciences, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Environmental Microbial Technology Center and Hubei Key Lab. of Industrial Biotechnology; National Renewable Energy Lab. (NREL), Golden, CO (United States). Biosciences Center
Univ. of Wisconsin-Madison, Madison, WI (United States). Great Lakes Bioenergy Research Center (GLBRC)
Univ. of Athens (NKUA), Athens (Greece). Faculty of Biology and Dept. of Genetics and Biotechnology
Hubei Univ., Wuhan (China). College of Life Sciences, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Environmental Microbial Technology Center and Hubei Key Lab. of Industrial Biotechnology
Univ. of Wisconsin-Madison, Madison, WI (United States). Great Lakes Bioenergy Research Center (GLBRC); China Three Gorges Univ., Yichang (China)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioEnergy Science Center (BSC) and Biosciences Division; LanzaTech, Inc., Skokie, IL (United States)
National Renewable Energy Lab. (NREL), Golden, CO (United States). Biosciences Center
National Renewable Energy Lab. (NREL), Golden, CO (United States). National Bioenergy Center

Background: Zymomonas 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. Results: In 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. Conclusions: The 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.

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Research Organization:: National Renewable Energy Laboratory (NREL), Golden, CO (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Sponsoring Organization:: USDOE Office of Energy Efficiency and Renewable Energy (EERE), Sustainable Transportation Office. Bioenergy Technologies Office; USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities Division; European Union (EU); Siemens Foundation-State Scholarships Foundation (IKY) award

Contributing Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Grant/Contract Number:: AC36-08GO28308; SC0018409; FC02-07ER64494; AC05-00OR22725; AC02-05CH11231; 11SYN-7-1579

OSTI ID:: 1439547

Alternate ID(s):: OSTI ID: 1459644; OSTI ID: 1476399

Report Number(s):: NREL/JA-2700-71655

Journal Information:: Biotechnology for Biofuels, Vol. 11, Issue 1; ISSN 1754-6834

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 36 works

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MOESM10 of Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032 Vera, Jessica; Grass, Jeff; Savvakis, Giannis https://doi.org/10.6084/m9.figshare.6208448 The current record is supplemented by this dataset	dataset	May 2018
MOESM10 of 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, Shihui; Vera, Jessica; Grass, Jeff https://doi.org/10.6084/m9.figshare.6208448.v1 The current record is supplemented by this dataset	dataset	May 2018
MOESM1 of Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032 Vera, Jessica; Grass, Jeff; Savvakis, Giannis https://doi.org/10.6084/m9.figshare.6208466 The current record is supplemented by this figure	figure	May 2018
MOESM1 of Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032 Vera, Jessica; Grass, Jeff; Savvakis, Giannis https://doi.org/10.6084/m9.figshare.6208466.v1 The current record is supplemented by this figure	figure	May 2018
MOESM2 of 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, Shihui; Vera, Jessica; Grass, Jeff https://doi.org/10.6084/m9.figshare.6208493 The current record is supplemented by this dataset	dataset	May 2018
MOESM2 of 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, Shihui; Vera, Jessica; Grass, Jeff https://doi.org/10.6084/m9.figshare.6208493.v1 The current record is supplemented by this dataset	dataset	May 2018
MOESM3 of 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, Shihui; Vera, Jessica; Grass, Jeff https://doi.org/10.6084/m9.figshare.6208520 The current record is supplemented by this dataset	dataset	May 2018
MOESM3 of 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, Shihui; Vera, Jessica; Grass, Jeff https://doi.org/10.6084/m9.figshare.6208520.v1 The current record is supplemented by this dataset	dataset	May 2018
MOESM4 of 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, Shihui; Vera, Jessica; Grass, Jeff https://doi.org/10.6084/M9.FIGSHARE.6208532 The current record is supplemented by this dataset	dataset	May 2018
MOESM4 of 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, Shihui; Vera, Jessica; Grass, Jeff https://doi.org/10.6084/m9.figshare.6208532.v1 The current record is supplemented by this dataset	dataset	May 2018
MOESM5 of 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, Shihui; Vera, Jessica; Grass, Jeff https://doi.org/10.6084/M9.FIGSHARE.6208547 The current record is supplemented by this dataset	dataset	May 2018
MOESM5 of Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032 Vera, Jessica; Grass, Jeff; Savvakis, Giannis https://doi.org/10.6084/m9.figshare.6208547.v1 The current record is supplemented by this dataset	dataset	May 2018
MOESM6 of 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, Shihui; Vera, Jessica; Grass, Jeff https://doi.org/10.6084/M9.FIGSHARE.6208565 The current record is supplemented by this dataset	dataset	May 2018
MOESM6 of Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032 Vera, Jessica; Grass, Jeff; Savvakis, Giannis https://doi.org/10.6084/m9.figshare.6208565.v1 The current record is supplemented by this dataset	dataset	May 2018
MOESM7 of 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, Shihui; Vera, Jessica; Grass, Jeff https://doi.org/10.6084/m9.figshare.6208583 The current record is supplemented by this dataset	dataset	May 2018
MOESM7 of 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, Shihui; Vera, Jessica; Grass, Jeff https://doi.org/10.6084/m9.figshare.6208583.v1 The current record is supplemented by this dataset	dataset	May 2018
MOESM8 of 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, Shihui; Vera, Jessica; Grass, Jeff https://doi.org/10.6084/m9.figshare.6208595 The current record is supplemented by this dataset	dataset	May 2018
MOESM8 of 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, Shihui; Vera, Jessica; Grass, Jeff https://doi.org/10.6084/m9.figshare.6208595.v1 The current record is supplemented by this dataset	dataset	May 2018
MOESM9 of 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, Shihui; Vera, Jessica; Grass, Jeff https://doi.org/10.6084/M9.FIGSHARE.6208607 The current record is supplemented by this dataset	dataset	May 2018
MOESM9 of Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032 Vera, Jessica; Grass, Jeff; Savvakis, Giannis https://doi.org/10.6084/m9.figshare.6208607.v1 The current record is supplemented by this dataset	dataset	May 2018
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, Shihui; Vera, Jessica; Grass, Jeff https://doi.org/10.6084/m9.figshare.c.4086767 The current record is supplemented by this dataset	dataset	May 2018
Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032 [Supplementary Data] Yang, Shihui; Vera, Jessica; Grass, Jeff https://doi.org/10.6084/m9.figshare.c.4086767.v1 The current record is supplemented by this collection	collection	May 2018