Genomic organization underlying deletional robustness in bacterial metabolic systems.
Details
Serval ID
serval:BIB_69EA3494081A
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Genomic organization underlying deletional robustness in bacterial metabolic systems.
Journal
Proceedings of the National Academy of Sciences of the United States of America
ISSN
1091-6490 (Electronic)
ISSN-L
0027-8424
Publication state
Published
Issued date
03/07/2018
Peer-reviewed
Oui
Volume
115
Number
27
Pages
7075-7080
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Publication Status: ppublish
Abstract
Large-scale DNA deletions and gene loss are pervasive in bacterial genomes. This observation raises the possibility that evolutionary adaptation has altered bacterial genome organization to increase its robustness to large-scale tandem gene deletions. To find out, we systematically analyzed 55 bacterial genome-scale metabolisms and showed that metabolic gene ordering renders an organism's viability in multiple nutrient environments significantly more robust against tandem multigene deletions than expected by chance. This excess robustness is caused by multiple factors, which include the clustering of essential metabolic genes, a greater-than-expected distance of synthetically lethal metabolic gene pairs, and the clustering of nonessential metabolic genes. By computationally creating minimal genomes, we show that a nonadaptive origin of such clustering could in principle arise as a passive byproduct of bacterial genome growth. However, because genome randomization forces such as translocation and inversion would eventually erode such clustering, adaptive processes are necessary to sustain it. We provide evidence suggesting that this organization might result from adaptation to ongoing gene deletions, and from selective advantages associated with coregulating functionally related genes. Horizontal gene transfer in the presence of gene deletions contributes to sustaining the clustering of essential genes. In sum, our observations suggest that the genome organization of bacteria is driven by adaptive processes that provide phenotypic robustness in response to large-scale gene deletions. This robustness may be especially important for bacterial populations that take advantage of gene loss to adapt to new environments.
Keywords
Bacteria/genetics, Bacteria/metabolism, Evolution, Molecular, Gene Deletion, Genome, Bacterial, Multigene Family, deletional robustness, essential genes, genome organization, horizontal gene transfer, metabolic systems
Pubmed
Web of science
Open Access
Yes
Create date
11/09/2018 8:55
Last modification date
21/08/2019 6:17