Indirect and suboptimal control of gene expression is widespread in bacteria
Abstract Gene regulation in bacteria is usually described as an adaptive response to an environmental change so that genes are expressed when they are required. We instead propose that most genes are under indirect control: their expression responds to signal(s) that are not directly related to the...
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| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Springer Nature
2013-04-01
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| Series: | Molecular Systems Biology |
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| Online Access: | https://doi.org/10.1038/msb.2013.16 |
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| _version_ | 1849235637214904320 |
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| author | Morgan N Price Adam M Deutschbauer Jeffrey M Skerker Kelly M Wetmore Troy Ruths Jordan S Mar Jennifer V Kuehl Wenjun Shao Adam P Arkin |
| author_facet | Morgan N Price Adam M Deutschbauer Jeffrey M Skerker Kelly M Wetmore Troy Ruths Jordan S Mar Jennifer V Kuehl Wenjun Shao Adam P Arkin |
| author_sort | Morgan N Price |
| collection | DOAJ |
| description | Abstract Gene regulation in bacteria is usually described as an adaptive response to an environmental change so that genes are expressed when they are required. We instead propose that most genes are under indirect control: their expression responds to signal(s) that are not directly related to the genes’ function. Indirect control should perform poorly in artificial conditions, and we show that gene regulation is often maladaptive in the laboratory. In Shewanella oneidensis MR‐1, 24% of genes are detrimental to fitness in some conditions, and detrimental genes tend to be highly expressed instead of being repressed when not needed. In diverse bacteria, there is little correlation between when genes are important for optimal growth or fitness and when those genes are upregulated. Two common types of indirect control are constitutive expression and regulation by growth rate; these occur for genes with diverse functions and often seem to be suboptimal. Because genes that have closely related functions can have dissimilar expression patterns, regulation may be suboptimal in the wild as well as in the laboratory. |
| format | Article |
| id | doaj-art-afea342d8a1148aa8fc4cf19c0fc145a |
| institution | Kabale University |
| issn | 1744-4292 |
| language | English |
| publishDate | 2013-04-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-afea342d8a1148aa8fc4cf19c0fc145a2025-08-20T04:02:44ZengSpringer NatureMolecular Systems Biology1744-42922013-04-019111810.1038/msb.2013.16Indirect and suboptimal control of gene expression is widespread in bacteriaMorgan N Price0Adam M Deutschbauer1Jeffrey M Skerker2Kelly M Wetmore3Troy Ruths4Jordan S Mar5Jennifer V Kuehl6Wenjun Shao7Adam P Arkin8Physical Biosciences Division, Lawrence Berkeley National LabPhysical Biosciences Division, Lawrence Berkeley National LabDepartment of Bioengineering, University of CaliforniaPhysical Biosciences Division, Lawrence Berkeley National LabPhysical Biosciences Division, Lawrence Berkeley National LabDepartment of Bioengineering, University of CaliforniaPhysical Biosciences Division, Lawrence Berkeley National LabDepartment of Molecular and Cell Biology, University of CaliforniaPhysical Biosciences Division, Lawrence Berkeley National LabAbstract Gene regulation in bacteria is usually described as an adaptive response to an environmental change so that genes are expressed when they are required. We instead propose that most genes are under indirect control: their expression responds to signal(s) that are not directly related to the genes’ function. Indirect control should perform poorly in artificial conditions, and we show that gene regulation is often maladaptive in the laboratory. In Shewanella oneidensis MR‐1, 24% of genes are detrimental to fitness in some conditions, and detrimental genes tend to be highly expressed instead of being repressed when not needed. In diverse bacteria, there is little correlation between when genes are important for optimal growth or fitness and when those genes are upregulated. Two common types of indirect control are constitutive expression and regulation by growth rate; these occur for genes with diverse functions and often seem to be suboptimal. Because genes that have closely related functions can have dissimilar expression patterns, regulation may be suboptimal in the wild as well as in the laboratory.https://doi.org/10.1038/msb.2013.16bacterial evolutiongene regulationoptimal regulation |
| spellingShingle | Morgan N Price Adam M Deutschbauer Jeffrey M Skerker Kelly M Wetmore Troy Ruths Jordan S Mar Jennifer V Kuehl Wenjun Shao Adam P Arkin Indirect and suboptimal control of gene expression is widespread in bacteria Molecular Systems Biology bacterial evolution gene regulation optimal regulation |
| title | Indirect and suboptimal control of gene expression is widespread in bacteria |
| title_full | Indirect and suboptimal control of gene expression is widespread in bacteria |
| title_fullStr | Indirect and suboptimal control of gene expression is widespread in bacteria |
| title_full_unstemmed | Indirect and suboptimal control of gene expression is widespread in bacteria |
| title_short | Indirect and suboptimal control of gene expression is widespread in bacteria |
| title_sort | indirect and suboptimal control of gene expression is widespread in bacteria |
| topic | bacterial evolution gene regulation optimal regulation |
| url | https://doi.org/10.1038/msb.2013.16 |
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