skip to main content

DOE PAGESDOE PAGES

Title: Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides

Rhodobacter sphaeroides is one of the best-studied alphaproteobacteria from biochemical, genetic, and genomic perspectives. To gain a better systems-level understanding of this organism, we generated a large transposon mutant library and used transposon sequencing (Tn-seq) to identify genes that are essential under several growth conditions. Using newly developed Tn-seq analysis software (TSAS), we identified 493 genes as essential for aerobic growth on a rich medium. We then used the mutant library to identify conditionally essential genes under two laboratory growth conditions, identifying 85 additional genes required for aerobic growth in a minimal medium and 31 additional genes required for photosynthetic growth. In all instances, our analyses confirmed essentiality for many known genes and identified genes not previously considered to be essential. We used the resulting Tn-seq data to refine and improve a genome-scale metabolic network model (GEM) for R. sphaeroides. Together, we demonstrate how genetic, genomic, and computational approaches can be combined to obtain a systems-level understanding of the genetic framework underlying metabolic diversity in bacterial species.
Authors:
 [1] ;  [1] ;  [2] ;  [2] ; ORCiD logo [1]
  1. Univ. of Wisconsin, Madison, WI (United States). Great Lakes Bioenergy Research Center, Wisconsin Energy Institute and Department of Bacteriology
  2. Univ. of Wisconsin, Madison, WI (United States). Great Lakes Bioenergy Research Center, Wisconsin Energy Institute and Department of Civil and Environmental Engineering
Publication Date:
Grant/Contract Number:
FC02-07ER64494
Type:
Accepted Manuscript
Journal Name:
mSystems
Additional Journal Information:
Journal Volume: 2; Journal Issue: 3; Journal ID: ISSN 2379-5077
Publisher:
American Society for Microbiology
Research Org:
Univ. of Wisconsin, Madison, WI (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Rhodobacter sphaeroides; Tn-seq; gene disruption; genomics; metabolic modeling; metabolism; photosynthetic bacteria; proteobacteria
OSTI Identifier:
1427587

Burger, Brian T., Imam, Saheed, Scarborough, Matthew J., Noguera, Daniel R., and Donohue, Timothy J.. Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides. United States: N. p., Web. doi:10.1128/mSystems.00015-17.
Burger, Brian T., Imam, Saheed, Scarborough, Matthew J., Noguera, Daniel R., & Donohue, Timothy J.. Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides. United States. doi:10.1128/mSystems.00015-17.
Burger, Brian T., Imam, Saheed, Scarborough, Matthew J., Noguera, Daniel R., and Donohue, Timothy J.. 2017. "Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides". United States. doi:10.1128/mSystems.00015-17. https://www.osti.gov/servlets/purl/1427587.
@article{osti_1427587,
title = {Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides},
author = {Burger, Brian T. and Imam, Saheed and Scarborough, Matthew J. and Noguera, Daniel R. and Donohue, Timothy J.},
abstractNote = {Rhodobacter sphaeroides is one of the best-studied alphaproteobacteria from biochemical, genetic, and genomic perspectives. To gain a better systems-level understanding of this organism, we generated a large transposon mutant library and used transposon sequencing (Tn-seq) to identify genes that are essential under several growth conditions. Using newly developed Tn-seq analysis software (TSAS), we identified 493 genes as essential for aerobic growth on a rich medium. We then used the mutant library to identify conditionally essential genes under two laboratory growth conditions, identifying 85 additional genes required for aerobic growth in a minimal medium and 31 additional genes required for photosynthetic growth. In all instances, our analyses confirmed essentiality for many known genes and identified genes not previously considered to be essential. We used the resulting Tn-seq data to refine and improve a genome-scale metabolic network model (GEM) for R. sphaeroides. Together, we demonstrate how genetic, genomic, and computational approaches can be combined to obtain a systems-level understanding of the genetic framework underlying metabolic diversity in bacterial species.},
doi = {10.1128/mSystems.00015-17},
journal = {mSystems},
number = 3,
volume = 2,
place = {United States},
year = {2017},
month = {6}
}