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Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti

The genome of about 10% of bacterial species is divided among two or more large chromosome-sized replicons. The contribution of each replicon to the microbial life cycle (for example, environmental adaptations and/or niche switching) remains unclear. Here we report a genome-scale metabolic model of...

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Autores principales: diCenzo, George C., Checcucci, Alice, Bazzicalupo, Marco, Mengoni, Alessio, Viti, Carlo, Dziewit, Lukasz, Finan, Turlough M., Galardini, Marco, Fondi, Marco
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4961836/
https://www.ncbi.nlm.nih.gov/pubmed/27447951
http://dx.doi.org/10.1038/ncomms12219
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author diCenzo, George C.
Checcucci, Alice
Bazzicalupo, Marco
Mengoni, Alessio
Viti, Carlo
Dziewit, Lukasz
Finan, Turlough M.
Galardini, Marco
Fondi, Marco
author_facet diCenzo, George C.
Checcucci, Alice
Bazzicalupo, Marco
Mengoni, Alessio
Viti, Carlo
Dziewit, Lukasz
Finan, Turlough M.
Galardini, Marco
Fondi, Marco
author_sort diCenzo, George C.
collection PubMed
description The genome of about 10% of bacterial species is divided among two or more large chromosome-sized replicons. The contribution of each replicon to the microbial life cycle (for example, environmental adaptations and/or niche switching) remains unclear. Here we report a genome-scale metabolic model of the legume symbiont Sinorhizobium meliloti that is integrated with carbon utilization data for 1,500 genes with 192 carbon substrates. Growth of S. meliloti is modelled in three ecological niches (bulk soil, rhizosphere and nodule) with a focus on the role of each of its three replicons. We observe clear metabolic differences during growth in the tested ecological niches and an overall reprogramming following niche switching. In silico examination of the inferred fitness of gene deletion mutants suggests that secondary replicons evolved to fulfil a specialized function, particularly host-associated niche adaptation. Thus, genes on secondary replicons might potentially be manipulated to promote or suppress host interactions for biotechnological purposes.
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spelling pubmed-49618362016-09-06 Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti diCenzo, George C. Checcucci, Alice Bazzicalupo, Marco Mengoni, Alessio Viti, Carlo Dziewit, Lukasz Finan, Turlough M. Galardini, Marco Fondi, Marco Nat Commun Article The genome of about 10% of bacterial species is divided among two or more large chromosome-sized replicons. The contribution of each replicon to the microbial life cycle (for example, environmental adaptations and/or niche switching) remains unclear. Here we report a genome-scale metabolic model of the legume symbiont Sinorhizobium meliloti that is integrated with carbon utilization data for 1,500 genes with 192 carbon substrates. Growth of S. meliloti is modelled in three ecological niches (bulk soil, rhizosphere and nodule) with a focus on the role of each of its three replicons. We observe clear metabolic differences during growth in the tested ecological niches and an overall reprogramming following niche switching. In silico examination of the inferred fitness of gene deletion mutants suggests that secondary replicons evolved to fulfil a specialized function, particularly host-associated niche adaptation. Thus, genes on secondary replicons might potentially be manipulated to promote or suppress host interactions for biotechnological purposes. Nature Publishing Group 2016-07-22 /pmc/articles/PMC4961836/ /pubmed/27447951 http://dx.doi.org/10.1038/ncomms12219 Text en Copyright © 2016, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
diCenzo, George C.
Checcucci, Alice
Bazzicalupo, Marco
Mengoni, Alessio
Viti, Carlo
Dziewit, Lukasz
Finan, Turlough M.
Galardini, Marco
Fondi, Marco
Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti
title Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti
title_full Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti
title_fullStr Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti
title_full_unstemmed Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti
title_short Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti
title_sort metabolic modelling reveals the specialization of secondary replicons for niche adaptation in sinorhizobium meliloti
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4961836/
https://www.ncbi.nlm.nih.gov/pubmed/27447951
http://dx.doi.org/10.1038/ncomms12219
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