Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in <named-content content-type="genus-species">Rhodobacter sphaeroides</named-content>

ABSTRACT 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...

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Autores principales:	Brian T. Burger, Saheed Imam, Matthew J. Scarborough, Daniel R. Noguera, Timothy J. Donohue
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	Rhodobacter sphaeroides Tn-seq gene disruption genomics metabolic modeling metabolism Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/2ce40ba3e9124c71b0a22572cb4f5629
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spelling	oai:doaj.org-article:2ce40ba3e9124c71b0a22572cb4f56292021-12-02T18:39:33ZCombining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in <named-content content-type="genus-species">Rhodobacter sphaeroides</named-content>10.1128/mSystems.00015-172379-5077https://doaj.org/article/2ce40ba3e9124c71b0a22572cb4f56292017-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00015-17https://doaj.org/toc/2379-5077ABSTRACT 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. IMPORTANCE Knowledge about the role of genes under a particular growth condition is required for a holistic understanding of a bacterial cell and has implications for health, agriculture, and biotechnology. We developed the Tn-seq analysis software (TSAS) package to provide a flexible and statistically rigorous workflow for the high-throughput analysis of insertion mutant libraries, advanced the knowledge of gene essentiality in R. sphaeroides, and illustrated how Tn-seq data can be used to more accurately identify genes that play important roles in metabolism and other processes that are essential for cellular survival. Author Video: An author video summary of this article is available.Brian T. BurgerSaheed ImamMatthew J. ScarboroughDaniel R. NogueraTimothy J. DonohueAmerican Society for MicrobiologyarticleRhodobacter sphaeroidesTn-seqgene disruptiongenomicsmetabolic modelingmetabolismMicrobiologyQR1-502ENmSystems, Vol 2, Iss 3 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Rhodobacter sphaeroides Tn-seq gene disruption genomics metabolic modeling metabolism Microbiology QR1-502
spellingShingle	Rhodobacter sphaeroides Tn-seq gene disruption genomics metabolic modeling metabolism Microbiology QR1-502 Brian T. Burger Saheed Imam Matthew J. Scarborough Daniel R. Noguera Timothy J. Donohue Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in <named-content content-type="genus-species">Rhodobacter sphaeroides</named-content>
description	ABSTRACT 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. IMPORTANCE Knowledge about the role of genes under a particular growth condition is required for a holistic understanding of a bacterial cell and has implications for health, agriculture, and biotechnology. We developed the Tn-seq analysis software (TSAS) package to provide a flexible and statistically rigorous workflow for the high-throughput analysis of insertion mutant libraries, advanced the knowledge of gene essentiality in R. sphaeroides, and illustrated how Tn-seq data can be used to more accurately identify genes that play important roles in metabolism and other processes that are essential for cellular survival. Author Video: An author video summary of this article is available.
format	article
author	Brian T. Burger Saheed Imam Matthew J. Scarborough Daniel R. Noguera Timothy J. Donohue
author_facet	Brian T. Burger Saheed Imam Matthew J. Scarborough Daniel R. Noguera Timothy J. Donohue
author_sort	Brian T. Burger
title	Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in <named-content content-type="genus-species">Rhodobacter sphaeroides</named-content>
title_short	Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in <named-content content-type="genus-species">Rhodobacter sphaeroides</named-content>
title_full	Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in <named-content content-type="genus-species">Rhodobacter sphaeroides</named-content>
title_fullStr	Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in <named-content content-type="genus-species">Rhodobacter sphaeroides</named-content>
title_full_unstemmed	Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in <named-content content-type="genus-species">Rhodobacter sphaeroides</named-content>
title_sort	combining genome-scale experimental and computational methods to identify essential genes in <named-content content-type="genus-species">rhodobacter sphaeroides</named-content>
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/2ce40ba3e9124c71b0a22572cb4f5629
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Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in <named-content content-type="genus-species">Rhodobacter sphaeroides</named-content>

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