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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

Abstract

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 identifiablemore » 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.« less

Authors:
ORCiD logo [1];  [2];  [2];  [3];  [2];  [4];  [2];  [5];  [3];  [2];  [2];  [2];  [2];  [6];  [7];  [8];  [2];  [3];  [2]
  1. 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
  2. Univ. of Wisconsin-Madison, Madison, WI (United States). Great Lakes Bioenergy Research Center (GLBRC)
  3. Univ. of Athens (NKUA), Athens (Greece). Faculty of Biology and Dept. of Genetics and Biotechnology
  4. 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
  5. Univ. of Wisconsin-Madison, Madison, WI (United States). Great Lakes Bioenergy Research Center (GLBRC); China Three Gorges Univ., Yichang (China)
  6. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioEnergy Science Center (BSC) and Biosciences Division; LanzaTech, Inc., Skokie, IL (United States)
  7. National Renewable Energy Lab. (NREL), Golden, CO (United States). Biosciences Center
  8. National Renewable Energy Lab. (NREL), Golden, CO (United States). National Bioenergy Center
Publication Date:
Research Org.:
National Renewable Energy Lab. (NREL), Golden, CO (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Sponsoring Org.:
USDOE Office of Energy Efficiency and Renewable Energy (EERE), 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 Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
OSTI Identifier:
1439547
Alternate Identifier(s):
OSTI ID: 1459644; OSTI ID: 1476399
Report Number(s):
NREL/JA-2700-71655
Journal ID: ISSN 1754-6834
Grant/Contract Number:  
AC36-08GO28308; SC0018409; FC02-07ER64494; AC05-00OR22725; AC02-05CH11231; 11SYN-7-1579
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Biotechnology for Biofuels
Additional Journal Information:
Journal Volume: 11; Journal Issue: 1; Journal ID: ISSN 1754-6834
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; Zymomonas mobilis; plasmid; genome; genome resequencing; annotation; RNA-Seq; copy number; hydrolysate; fermentation; Zymomonas mobilis, plasmid, genome, genome resequencing, annotation, RNA-Seq, 78 copy number, hydrolysate, fermentation

Citation Formats

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., and Zhang, Yaoping. Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032. United States: N. p., 2018. Web. doi:10.1186/s13068-018-1116-x.
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. Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032. United States. doi:10.1186/s13068-018-1116-x.
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., and Zhang, Yaoping. Wed . "Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032". United States. doi:10.1186/s13068-018-1116-x. https://www.osti.gov/servlets/purl/1439547.
@article{osti_1439547,
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},
author = {Yang, Shihui and Vera, Jessica M. and Grass, Jeff and Savvakis, Giannis and Moskvin, Oleg V. and Yang, Yongfu and McIlwain, Sean J. and Lyu, Yucai and Zinonos, Irene and Hebert, Alexander S. and Coon, Joshua J. and Bates, Donna M. and Sato, Trey K. and Brown, Steven D. and Himmel, Michael E. and Zhang, Min and Landick, Robert and Pappas, Katherine M. and Zhang, Yaoping},
abstractNote = {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.},
doi = {10.1186/s13068-018-1116-x},
journal = {Biotechnology for Biofuels},
issn = {1754-6834},
number = 1,
volume = 11,
place = {United States},
year = {2018},
month = {5}
}

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    Works referencing / citing this record:

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    Establishment and application of a CRISPR–Cas12a assisted genome-editing system in Zymomonas mobilis
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    Prediction and characterization of promoters and ribosomal binding sites of Zymomonas mobilis in system biology era
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