Cited by 398Microbial Community Ecology and PhysiologySoil Carbon and Nitrogen DynamicsGenomics and Phylogenetic Studies

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Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed

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Rocca, Jennifer D, Hall, Edward K, Lennon, Jay T, Evans, Sarah E, Waldrop, Mark P, Cotner, James B, Nemergut, Diana R, Graham, Emily B, Wallenstein, Matthew D·2015·The ISME Journal

DOI 10.1038/ismej.2014.252PMC PMC4511926

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Abstract

For any enzyme-catalyzed reaction to occur, the corresponding protein-encoding genes and transcripts are necessary prerequisites. Thus, a positive relationship between the abundance of gene or transcripts and corresponding process rates is often assumed. To test this assumption, we conducted a meta-analysis of the relationships between gene and/or transcript abundances and corresponding process rates. We identified 415 studies that quantified the abundance of genes or transcripts for enzymes involved in carbon or nitrogen cycling. However, in only 59 of these manuscripts did the authors report both gene or transcript abundance and rates of the appropriate process. We found that within studies there was a significant but weak positive relationship between gene abundance and the corresponding process. Correlations were not strengthened by accounting for habitat type, differences among genes or reaction products versus reactants, suggesting that other ecological and methodological factors may affect the strength of this relationship. Our findings highlight the need for fundamental research on the factors that control transcription, translation and enzyme function in natural systems to better link genomic and transcriptomic data to ecosystem processes.

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Authors: Rocca, J. D., Hall, E. K., Lennon, J. T., Evans, S. E., Waldrop, M. P., Cotner, J. B., Nemergut, D. R., Graham, E. B., & Wallenstein, M. D.
Affiliations: Colorado State University (US)
Natural Resource Ecology Laboratory, Colorado State University , Fort Collins, CO, USA
Indiana University Bloomington (US)
Michigan State University (US)
United States Geological Survey (US)
University of Minnesota (US)
Duke University (US)
Corresponding author: Rocca, Jennifer D
ORCID: Rocca, Jennifer D
Lennon, Jay T
Evans, Sarah E
Waldrop, Mark P
Cotner, James B
Graham, Emily B
Wallenstein, Matthew D
Venue: The ISME Journal
Publisher: Oxford University Press (OUP)
Published: 2014-12-23
Volume: 9
Issue: 8
Pages: 1693-1699
ISSN: 1751-7362 (ISSN-L)
1751-7370
DOI: 10.1038/ismej.2014.252
PMC: PMC4511926
OpenAlex: W2024344827
Cited by: 398
References: 45
Citations by year: 2026: 66 · 2025: 32 · 2024: 34 · 2023: 24 · 2022: 48 · 2021: 38 · 2020: 35 · 2019: 30 · 2018: 32 · 2017: 25 · 2016: 28 · 2015: 6
FWCI: 2.13
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: academic.oup.com/pages/standard-publication-reuse-rights (vor)
www.springer.com/tdm (tdm)
Locations: The ISME Journal (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: U.S. Geological Survey
Topics: Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Life Sciences › Agricultural and Biological Sciences › Soil Science › Soil Carbon and Nitrogen Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: gene abundance, mRNA levels, enzyme activity, carbon cycle, nitrogen cycling, transcription and translation, metagenomics, metatranscriptomics, ecosystem processes
MeSH terms: Carbon, Catalysis, Dosage Compensation, Genetic, Nitrogen, Transcription, Genetic, Gene Expression Regulation, Bacterial, Ecosystem, Gene Dosage, Gene Expression Profiling, Biocatalysis

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