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Deciphering the rationale behind specific codon usage pattern in extremophiles.
Mohd Faheem Khan1, Sanjukta Patra2
1Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
Scientific Reports
|October 21, 2018
Summary
Extremophiles exhibit unique codon usage patterns, differing from non-extremophiles. Understanding these genetic code preferences aids in optimizing protein expression for extreme environments.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Protein stability is influenced by genetic factors, including codon composition.
- Organismal codon selectivity varies between normal and extremophilic environments.
Purpose of the Study:
- To analyze and detail codon usage patterns across six classes of extremophiles.
- To investigate the harmony and variations in codon selectivity among extremophiles.
Main Methods:
- Analysis of homologous gene datasets from various extremophile-non-extremophile pairs.
- Application of relative abundance analysis, nucleotide composition analysis, and machine learning algorithms.
Main Results:
- Identified specific preferred codons for thermophiles (AGG), mesophiles/psychrophiles (CAA), acidophiles (TGG), alkaliphiles (GAG), and halophiles (GAC).
- Observed distinct trends in GC-rich and G/C-ending codon preferences across different extremophile groups.
- Codon usage patterns showed harmony within extremophiles but differed from non-extremophiles.
Conclusions:
- Extremophile codon usage patterns are distinct and exhibit internal harmony.
- These findings are valuable for heterologous expression of extremophilic proteins through codon optimization.
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