Genotype-Phenotype Associations in a Nonmodel Prokaryote

ABSTRACT To help define the biological functions of nonessential genes of Francisella novicida, we measured the growth of arrayed members of a comprehensive transposon mutant library under a variety of nutrition and stress conditions. Mutant phenotypes were identified for 37% of the genes, correspon...

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Autores principales:	Mark Enstrom, Kiara Held, Beth Ramage, Mitchell Brittnacher, Larry Gallagher, Colin Manoil
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2012
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/ccf55f3555474e7d86cf56ddf7f620ea
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spelling	oai:doaj.org-article:ccf55f3555474e7d86cf56ddf7f620ea2021-11-15T15:39:08ZGenotype-Phenotype Associations in a Nonmodel Prokaryote10.1128/mBio.00001-122150-7511https://doaj.org/article/ccf55f3555474e7d86cf56ddf7f620ea2012-05-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00001-12https://doaj.org/toc/2150-7511ABSTRACT To help define the biological functions of nonessential genes of Francisella novicida, we measured the growth of arrayed members of a comprehensive transposon mutant library under a variety of nutrition and stress conditions. Mutant phenotypes were identified for 37% of the genes, corresponding to ten carbon source utilization pathways, nine amino acid- and nucleotide-biosynthetic pathways, ten intrinsic antibiotic resistance traits, and six other stress resistance traits. The greatest surprise of the analysis was the large number of genotype-phenotype relationships that were not predictable from studies of Escherichia coli and other model species. The study identified candidate genes for a missing glycolysis function (phosphofructokinase), an unusual proline-biosynthetic pathway, parallel outer membrane lipid asymmetry maintenance systems, and novel antibiotic resistance functions. The analysis provides an evaluation of annotation predictions, identifies cases in which fundamental processes differ from those in model species, and helps create an empirical foundation for understanding virulence and other complex processes. IMPORTANCE The value of genome sequences as foundations for analyzing complex traits in nonmodel organisms is limited by the need to rely almost exclusively on sequence similarities to predict gene functions in annotations. Many genes cannot be assigned functions, and some predictions are incorrect or incomplete. Due to these limitations, genome-scale experimental approaches that test and extend bioinformatics-based predictions are sorely needed. In this study, we describe such an approach based on phenotypic analysis of a comprehensive, sequence-defined transposon mutant library.Mark EnstromKiara HeldBeth RamageMitchell BrittnacherLarry GallagherColin ManoilAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 3, Iss 2 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Mark Enstrom Kiara Held Beth Ramage Mitchell Brittnacher Larry Gallagher Colin Manoil Genotype-Phenotype Associations in a Nonmodel Prokaryote
description	ABSTRACT To help define the biological functions of nonessential genes of Francisella novicida, we measured the growth of arrayed members of a comprehensive transposon mutant library under a variety of nutrition and stress conditions. Mutant phenotypes were identified for 37% of the genes, corresponding to ten carbon source utilization pathways, nine amino acid- and nucleotide-biosynthetic pathways, ten intrinsic antibiotic resistance traits, and six other stress resistance traits. The greatest surprise of the analysis was the large number of genotype-phenotype relationships that were not predictable from studies of Escherichia coli and other model species. The study identified candidate genes for a missing glycolysis function (phosphofructokinase), an unusual proline-biosynthetic pathway, parallel outer membrane lipid asymmetry maintenance systems, and novel antibiotic resistance functions. The analysis provides an evaluation of annotation predictions, identifies cases in which fundamental processes differ from those in model species, and helps create an empirical foundation for understanding virulence and other complex processes. IMPORTANCE The value of genome sequences as foundations for analyzing complex traits in nonmodel organisms is limited by the need to rely almost exclusively on sequence similarities to predict gene functions in annotations. Many genes cannot be assigned functions, and some predictions are incorrect or incomplete. Due to these limitations, genome-scale experimental approaches that test and extend bioinformatics-based predictions are sorely needed. In this study, we describe such an approach based on phenotypic analysis of a comprehensive, sequence-defined transposon mutant library.
format	article
author	Mark Enstrom Kiara Held Beth Ramage Mitchell Brittnacher Larry Gallagher Colin Manoil
author_facet	Mark Enstrom Kiara Held Beth Ramage Mitchell Brittnacher Larry Gallagher Colin Manoil
author_sort	Mark Enstrom
title	Genotype-Phenotype Associations in a Nonmodel Prokaryote
title_short	Genotype-Phenotype Associations in a Nonmodel Prokaryote
title_full	Genotype-Phenotype Associations in a Nonmodel Prokaryote
title_fullStr	Genotype-Phenotype Associations in a Nonmodel Prokaryote
title_full_unstemmed	Genotype-Phenotype Associations in a Nonmodel Prokaryote
title_sort	genotype-phenotype associations in a nonmodel prokaryote
publisher	American Society for Microbiology
publishDate	2012
url	https://doaj.org/article/ccf55f3555474e7d86cf56ddf7f620ea
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Genotype-Phenotype Associations in a Nonmodel Prokaryote

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