A computational approach to the functional screening of genomes.

Comparative genomics usually involves managing the functional aspects of genomes, by simply comparing gene-by-gene functions. Following this approach, Mushegian and Koonin proposed a hypothetical minimal genome, Minimal Gene Set (MGS), aiming for a possible oldest ancestor genome. They obtained MGS...

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Autores principales:	Davide Chiarugi, Pierpaolo Degano, Roberto Marangoni
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2007
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/de1682b1988f4f97abd819eca51ef48f
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id	oai:doaj.org-article:de1682b1988f4f97abd819eca51ef48f
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spelling	oai:doaj.org-article:de1682b1988f4f97abd819eca51ef48f2021-11-25T05:41:06ZA computational approach to the functional screening of genomes.1553-734X1553-735810.1371/journal.pcbi.0030174https://doaj.org/article/de1682b1988f4f97abd819eca51ef48f2007-09-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.0030174https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Comparative genomics usually involves managing the functional aspects of genomes, by simply comparing gene-by-gene functions. Following this approach, Mushegian and Koonin proposed a hypothetical minimal genome, Minimal Gene Set (MGS), aiming for a possible oldest ancestor genome. They obtained MGS by comparing the genomes of two simple bacteria and eliminating duplicated or functionally identical genes. The authors raised the fundamental question of whether a hypothetical organism possessing MGS is able to live or not. We attacked this viability problem specifying in silico the metabolic pathways of the MGS-based prokaryote. We then performed a dynamic simulation of cellular metabolic activities in order to check whether the MGS-prokaryote reaches some equilibrium state and produces the necessary biomass. We assumed these two conditions to be necessary for a living organism. Our simulations clearly show that the MGS does not express an organism that is able to live. We then iteratively proceeded with functional replacements in order to obtain a genome composition that gives rise to equilibrium. We ruled out 76 of the original 254 genes in the MGS, because they resulted in duplication from a functional point of view. We also added seven genes not present in the MGS. These genes encode for enzymes involved in critical nodes of the metabolic network. These modifications led to a genome composed of 187 elements expressing a virtually living organism, Virtual Cell (ViCe), that exhibits homeostatic capabilities and produces biomass. Moreover, the steady-state distribution of the concentrations of virtual metabolites that resulted was similar to that experimentally measured in bacteria. We conclude then that ViCe is able to "live in silico."Davide ChiarugiPierpaolo DeganoRoberto MarangoniPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 3, Iss 9, Pp 1801-1806 (2007)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Davide Chiarugi Pierpaolo Degano Roberto Marangoni A computational approach to the functional screening of genomes.
description	Comparative genomics usually involves managing the functional aspects of genomes, by simply comparing gene-by-gene functions. Following this approach, Mushegian and Koonin proposed a hypothetical minimal genome, Minimal Gene Set (MGS), aiming for a possible oldest ancestor genome. They obtained MGS by comparing the genomes of two simple bacteria and eliminating duplicated or functionally identical genes. The authors raised the fundamental question of whether a hypothetical organism possessing MGS is able to live or not. We attacked this viability problem specifying in silico the metabolic pathways of the MGS-based prokaryote. We then performed a dynamic simulation of cellular metabolic activities in order to check whether the MGS-prokaryote reaches some equilibrium state and produces the necessary biomass. We assumed these two conditions to be necessary for a living organism. Our simulations clearly show that the MGS does not express an organism that is able to live. We then iteratively proceeded with functional replacements in order to obtain a genome composition that gives rise to equilibrium. We ruled out 76 of the original 254 genes in the MGS, because they resulted in duplication from a functional point of view. We also added seven genes not present in the MGS. These genes encode for enzymes involved in critical nodes of the metabolic network. These modifications led to a genome composed of 187 elements expressing a virtually living organism, Virtual Cell (ViCe), that exhibits homeostatic capabilities and produces biomass. Moreover, the steady-state distribution of the concentrations of virtual metabolites that resulted was similar to that experimentally measured in bacteria. We conclude then that ViCe is able to "live in silico."
format	article
author	Davide Chiarugi Pierpaolo Degano Roberto Marangoni
author_facet	Davide Chiarugi Pierpaolo Degano Roberto Marangoni
author_sort	Davide Chiarugi
title	A computational approach to the functional screening of genomes.
title_short	A computational approach to the functional screening of genomes.
title_full	A computational approach to the functional screening of genomes.
title_fullStr	A computational approach to the functional screening of genomes.
title_full_unstemmed	A computational approach to the functional screening of genomes.
title_sort	computational approach to the functional screening of genomes.
publisher	Public Library of Science (PLoS)
publishDate	2007
url	https://doaj.org/article/de1682b1988f4f97abd819eca51ef48f
work_keys_str_mv	AT davidechiarugi acomputationalapproachtothefunctionalscreeningofgenomes AT pierpaolodegano acomputationalapproachtothefunctionalscreeningofgenomes AT robertomarangoni acomputationalapproachtothefunctionalscreeningofgenomes AT davidechiarugi computationalapproachtothefunctionalscreeningofgenomes AT pierpaolodegano computationalapproachtothefunctionalscreeningofgenomes AT robertomarangoni computationalapproachtothefunctionalscreeningofgenomes
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A computational approach to the functional screening of genomes.

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