Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities
Background Combined metagenomic and metatranscriptomic datasets make it possible to study the molecular evolution of diverse microbial species recovered from their native habitats. The link between gene expression level and sequence conservation was examined using shotgun pyrosequencing of microb...
| Main Authors: | , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
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BioMed Central Ltd.
2011
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| Online Access: | http://hdl.handle.net/1721.1/65635 https://orcid.org/0000-0001-8958-4345 |
| _version_ | 1826195172717756416 |
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| author | Stewart, Frank J. Sharma, Adrian Bryant, Jessica A. Eppley, John Marmaduke DeLong, Edward |
| author2 | Massachusetts Institute of Technology. Department of Civil and Environmental Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Civil and Environmental Engineering Stewart, Frank J. Sharma, Adrian Bryant, Jessica A. Eppley, John Marmaduke DeLong, Edward |
| author_sort | Stewart, Frank J. |
| collection | MIT |
| description | Background
Combined metagenomic and metatranscriptomic datasets make it possible to study the molecular evolution of diverse microbial species recovered from their native habitats. The link between gene expression level and sequence conservation was examined using shotgun pyrosequencing of microbial community DNA and RNA from diverse marine environments, and from forest soil.
Results
Across all samples, expressed genes with transcripts in the RNA sample were significantly more conserved than non-expressed gene sets relative to best matches in reference databases. This discrepancy, observed for many diverse individual genomes and across entire communities, coincided with a shift in amino acid usage between these gene fractions. Expressed genes trended toward GC-enriched amino acids, consistent with a hypothesis of higher levels of functional constraint in this gene pool. Highly expressed genes were significantly more likely to fall within an orthologous gene set shared between closely related taxa (core genes). However, non-core genes, when expressed above the level of detection, were, on average, significantly more highly expressed than core genes based on transcript abundance normalized to gene abundance. Finally, expressed genes showed broad similarities in function across samples, being relatively enriched in genes of energy metabolism and underrepresented by genes of cell growth.
Conclusions
These patterns support the hypothesis, predicated on studies of model organisms, that gene expression level is a primary correlate of evolutionary rate across diverse microbial taxa from natural environments. Despite their complexity, meta-omic datasets can reveal broad evolutionary patterns across taxonomically, functionally, and environmentally diverse communities. |
| first_indexed | 2024-09-23T10:08:19Z |
| format | Article |
| id | mit-1721.1/65635 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T10:08:19Z |
| publishDate | 2011 |
| publisher | BioMed Central Ltd. |
| record_format | dspace |
| spelling | mit-1721.1/656352022-09-30T19:08:07Z Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities Stewart, Frank J. Sharma, Adrian Bryant, Jessica A. Eppley, John Marmaduke DeLong, Edward Massachusetts Institute of Technology. Department of Civil and Environmental Engineering DeLong, Edward Sharma, Adrian Bryant, Jessica A. Eppley, John Marmaduke DeLong, Edward Background Combined metagenomic and metatranscriptomic datasets make it possible to study the molecular evolution of diverse microbial species recovered from their native habitats. The link between gene expression level and sequence conservation was examined using shotgun pyrosequencing of microbial community DNA and RNA from diverse marine environments, and from forest soil. Results Across all samples, expressed genes with transcripts in the RNA sample were significantly more conserved than non-expressed gene sets relative to best matches in reference databases. This discrepancy, observed for many diverse individual genomes and across entire communities, coincided with a shift in amino acid usage between these gene fractions. Expressed genes trended toward GC-enriched amino acids, consistent with a hypothesis of higher levels of functional constraint in this gene pool. Highly expressed genes were significantly more likely to fall within an orthologous gene set shared between closely related taxa (core genes). However, non-core genes, when expressed above the level of detection, were, on average, significantly more highly expressed than core genes based on transcript abundance normalized to gene abundance. Finally, expressed genes showed broad similarities in function across samples, being relatively enriched in genes of energy metabolism and underrepresented by genes of cell growth. Conclusions These patterns support the hypothesis, predicated on studies of model organisms, that gene expression level is a primary correlate of evolutionary rate across diverse microbial taxa from natural environments. Despite their complexity, meta-omic datasets can reveal broad evolutionary patterns across taxonomically, functionally, and environmentally diverse communities. Gordon and Betty Moore Foundation Agouron Institute National Science Foundation (U.S.) Center for Microbial Oceanography: Research and Education 2011-09-09T19:17:15Z 2011-09-09T19:17:15Z 2011-03 2011-02 Article http://purl.org/eprint/type/JournalArticle 1474-760X 1465-6914 1474-7596 http://hdl.handle.net/1721.1/65635 Stewart, Frank J et al. “Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities.” Genome Biology 12 (2011): R26. https://orcid.org/0000-0001-8958-4345 en_US http://dx.doi.org/10.1186/gb-2011-12-3-r26 Genome Biology Creative Commons Attribution http://creativecommons.org/licenses/by/2.0/ application/pdf BioMed Central Ltd. BMC |
| spellingShingle | Stewart, Frank J. Sharma, Adrian Bryant, Jessica A. Eppley, John Marmaduke DeLong, Edward Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities |
| title | Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities |
| title_full | Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities |
| title_fullStr | Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities |
| title_full_unstemmed | Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities |
| title_short | Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities |
| title_sort | community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities |
| url | http://hdl.handle.net/1721.1/65635 https://orcid.org/0000-0001-8958-4345 |
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