U.S. Department of EnergyOffice of Scientific and Technical Information
The Genetics of Aerotolerant Growth in Zymomonas mobilis
Abstract
Reduced genome bacteria are genetically simplified systems that facilitate biological study and industrial use. The free-living Alphaproteobacterium, Zymomonas mobilis, has a naturally reduced genome containing fewer than 2000 protein coding genes. Despite its small genome, Z. mobilis thrives in diverse conditions including the presence or absence of atmospheric oxygen. However, insufficient characterization of essential and conditionally essential genes has limited broader adoption of Z. mobilis as a model Alphaproteobacterium. Here, we use genome-scale CRISPRi-seq to systematically identify and characterize Z. mobilis genes that are conditionally essential for aerotolerant or anaerobic growth, or are generally essential across both conditions. Comparative genomics revealed that the essentiality of most "generally essential" genes was shared between Z. mobilis and other Alphaproteobacteria, validating Z. mobilis as reduced genome model. Among conditionally essential genes, we found that the DNA repair gene, recJ, was critical only for aerobic growth but reduced the mutation rate under both conditions. Further, we show that genes encoding the F1FO ATP synthase and Rnf respiratory complex are required for anaerobic growth of Z. mobilis. Combining CRISPRi partial knockdowns with metabolomics and membrane potential measurements, we determined that the ATP synthase generates membrane potential that is consumed by Rnf to power downstream processes.more »
- Authors:
-
- GLBRC - University of Wisconsin
- Publication Date:
- DOE Contract Number:
- SC0018409
- Research Org.:
- Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- Subject:
- ATP synthase; Alphaproteobacteria; CRISPR-Cas9; DNA repair; Mismatch-CRISPRi; Mobile-CRISPRi; Rnf complex; Zymomonas mobilis; anaerobic respiration; comparative genomics; essential genes; genome reduction; membrane potential; oxidative stress; metabolomics
- OSTI Identifier:
- 3003523
- DOI:
- https://doi.org/10.82250/3003523
Citation Formats
Peters, Jason M. The Genetics of Aerotolerant Growth in Zymomonas mobilis. United States: N. p., 2023.
Web. doi:10.82250/3003523.
Peters, Jason M. The Genetics of Aerotolerant Growth in Zymomonas mobilis. United States. doi:https://doi.org/10.82250/3003523
Peters, Jason M. 2023.
"The Genetics of Aerotolerant Growth in Zymomonas mobilis". United States. doi:https://doi.org/10.82250/3003523. https://www.osti.gov/servlets/purl/3003523. Pub date:Sun Sep 17 00:00:00 EDT 2023
@article{osti_3003523,
title = {The Genetics of Aerotolerant Growth in Zymomonas mobilis},
author = {Peters, Jason M.},
abstractNote = {Reduced genome bacteria are genetically simplified systems that facilitate biological study and industrial use. The free-living Alphaproteobacterium, Zymomonas mobilis, has a naturally reduced genome containing fewer than 2000 protein coding genes. Despite its small genome, Z. mobilis thrives in diverse conditions including the presence or absence of atmospheric oxygen. However, insufficient characterization of essential and conditionally essential genes has limited broader adoption of Z. mobilis as a model Alphaproteobacterium. Here, we use genome-scale CRISPRi-seq to systematically identify and characterize Z. mobilis genes that are conditionally essential for aerotolerant or anaerobic growth, or are generally essential across both conditions. Comparative genomics revealed that the essentiality of most "generally essential" genes was shared between Z. mobilis and other Alphaproteobacteria, validating Z. mobilis as reduced genome model. Among conditionally essential genes, we found that the DNA repair gene, recJ, was critical only for aerobic growth but reduced the mutation rate under both conditions. Further, we show that genes encoding the F1FO ATP synthase and Rnf respiratory complex are required for anaerobic growth of Z. mobilis. Combining CRISPRi partial knockdowns with metabolomics and membrane potential measurements, we determined that the ATP synthase generates membrane potential that is consumed by Rnf to power downstream processes. Rnf knockdown strains accumulated isoprenoid biosynthesis intermediates, suggesting a key role for Rnf in powering essential biosynthetic reactions. Our work establishes Z. mobilis as a streamlined model for alphaproteobacterial genetics, has broad implications in bacterial energy coupling, and informs Z. mobilis genome manipulation for optimized production of valuable isoprenoid-based bioproducts},
doi = {10.82250/3003523},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Sun Sep 17 00:00:00 EDT 2023},
month = {Sun Sep 17 00:00:00 EDT 2023}
}