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Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers
Published on: June 24, 2019
Environmental shaping of codon usage and functional adaptation across microbial communities
Masa Roller1, Vedran Lucić, István Nagy
1Bioinformatics Group, Department of Molecular Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Temesvári körút 62, H-6726 Szeged, Hungary, MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK and Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316 Oslo, Norway.
Nucleic Acids Research
|August 8, 2013
Summary
Microbial communities exhibit shared codon usage biases, revealing lifestyle-specific genes. This functional metagenomics approach identifies adaptations across entire communities, redefining microbial species concepts.
Area of Science:
- Microbiology
- Genomics
- Bioinformatics
Background:
- Microbial communities are vast reservoirs of Earth's biomass.
- Metagenomics surveys microbial genetic potential but often focuses on species or gene functions.
- Understanding systems-level metabolic complexity requires analysis beyond species boundaries.
Purpose of the Study:
- To investigate if microbes in similar ecological niches share codon usage preferences.
- To explore codon usage bias as a tool for identifying lifestyle-specific genes in microbial communities.
- To establish a 'functional metagenomics' platform for identifying adaptive genes.
Main Methods:
- Analysis of 11 metagenome samples.
- Evaluation of synonymous codon usage patterns.
- Application of translational optimization and codon usage adaptation principles.
Main Results:
- Microbes in the same ecological niche demonstrate common synonymous codon preferences, irrespective of phylogeny.
- Community-wide codon usage bias effectively predicts lifestyle-specific genes.
- A functional metagenomics approach was developed for identifying adaptive genes.
Conclusions:
- Codon usage bias is a reliable indicator of microbial lifestyle and adaptation within communities.
- This study proposes a novel framework for functional metagenomics.
- Findings contribute to defining microbial species based on community interactions.
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