ArticleScientific reports2018
Deciphering the rationale behind specific codon usage pattern in extremophiles.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- AI-Driven Enzyme Engineering: Emerging Models and Next-Generation Biotechnological Applications.Molecules (Basel, Switzerland) · 2025Review
- Life at the extremes: maximally divergent microbes with similar genomic signatures linked to extreme environments.NAR genomics and bioinformatics · 2025Article
- Enhancing stability of enzymes for industrial applications: molecular insights and emerging approaches.World journal of microbiology & biotechnology · 2025Review
- Lessons from Extremophiles: Functional Adaptations and Genomic Innovations across the Eukaryotic Tree of Life.Genome biology and evolution · 2024Article
- Exploring the Roles of Key Mediators IKBKE and HSPA1A in Alzheimer's Disease and Hepatocellular Carcinoma through Bioinformatics Analysis.International journal of molecular sciences · 2024Article
- Hot springs viruses at Yellowstone National Park have ancient origins and are adapted to thermophilic hosts.Communications biology · 2024Article
- BestCRM: An Exhaustive Search for Optimal Cis-Regulatory Modules in Promoters Accelerated by the Multidimensional Hash Function.International journal of molecular sciences · 2024Article
- Codon usage bias in yeasts and its correlation with gene expression, growth temperature, and protein structure.Frontiers in microbiology · 2024Article
- Delving into the lifestyle of Sundarban Wetland resident, biofilm producing, halotolerant Salinicoccus roseus: a comparative genomics-based intervention.BMC genomics · 2023Article
- Environment and taxonomy shape the genomic signature of prokaryotic extremophiles.Scientific reports · 2023Article
- The Mutational Robustness of the Genetic Code and Codon Usage in Environmental Context: A Non-Extremophilic Preference?Life (Basel, Switzerland) · 2021Article
- Phylogenetic analysis of mutational robustness based on codon usage supports that the standard genetic code does not prefer extreme environments.Scientific reports · 2021Article
- Evolutionary History of Mitochondrial Genomes in Discoba, Including the Extreme Halophile Pleurostomum flabellatum (Heterolobosea).Genome biology and evolution · 2021Article
- Combinatorial Fusion Rules to Describe Codon Assignment in the Standard Genetic Code.Life (Basel, Switzerland) · 2020Article
- Evolution of Protein Structure and Stability in Global Warming.International journal of molecular sciences · 2020Review
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2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein stability is affected at different hierarchies - gene, RNA, amino acid sequence and structure. Gene is the first level which contributes via varying codon compositions. Codon selectivity of an organism differs with normal and extremophilic milieu. The present work attempts at detailing the codon usage pattern of six extremophilic classes and their harmony. Homologous gene datasets of thermophile-mesophile, psychrophile-mesophile, thermophile-psychrophile, acidophile-alkaliphile, halophile-nonhalophile and barophile-nonbarophile were analysed for filtering statistically significant attributes. Relative abundance analysis, 1-9 scale ranking, nucleotide compositions, attribute weighting and machine learning algorithms were employed to arrive at findings. AGG in thermophiles and barophiles, CAA in mesophiles and psychrophiles, TGG in acidophiles, GAG in alkaliphiles and GAC in halophiles had highest preference. Preference of GC-rich and G/C-ending codons were observed in halophiles and barophiles whereas, a decreasing trend was reflected in psychrophiles and alkaliphiles. GC-rich codons were found to decrease and G/C-ending codons increased in thermophiles whereas, acidophiles showed equal contents of GC-rich and G/C-ending codons. Codon usage patterns exhibited harmony among different extremophiles and has been detailed. However, the codon attribute preferences and their selectivity of extremophiles varied in comparison to non-extremophiles. The finding can be instrumental in codon optimization application for heterologous expression of extremophilic proteins.
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