دورية أكاديمية
Differentially used codons among essential genes in bacteria identified by machine learning-based analysis.
| العنوان: | Differentially used codons among essential genes in bacteria identified by machine learning-based analysis. |
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| المؤلفون: | Kurmi A; Department of Computer Science and Engineering, Tezpur University, Napaam, Assam, 784028, India.; Department of Computer Science and Engineering, The Assam Kaziranga University, Jorhat, Assam, 785006, India., Sen P; Department of Computer Science and Engineering, Tezpur University, Napaam, Assam, 784028, India., Dash M; Department of Electronics and Communication Engineering, NIT, Jote, Arunachal Pradesh, 791113, India., Ray SK; Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Assam, 784028, India., Satapathy SS; Department of Computer Science and Engineering, Tezpur University, Napaam, Assam, 784028, India. ssankar@tezu.ernet.in. |
| المصدر: | Molecular genetics and genomics : MGG [Mol Genet Genomics] 2024 Jul 27; Vol. 299 (1), pp. 72. Date of Electronic Publication: 2024 Jul 27. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Springer-Verlag Country of Publication: Germany NLM ID: 101093320 Publication Model: Electronic Cited Medium: Internet ISSN: 1617-4623 (Electronic) Linking ISSN: 16174623 NLM ISO Abbreviation: Mol Genet Genomics Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: Berlin : Springer-Verlag, c2001- |
| مواضيع طبية MeSH: | Machine Learning* , Genes, Essential*/genetics , Codon Usage* , Escherichia coli*/genetics, Genome, Bacterial/genetics ; Genes, Bacterial ; Codon/genetics ; Bacteria/genetics ; Bacteria/classification |
| مستخلص: | Codon usage bias (CUB), the uneven usage of synonymous codons encoding the same amino acid, differs among genes within and across bacteria genomes. CUB is known to be influenced by gene expression and accordingly, CUB differs between the high-expression and low-expression genes in several bacteria. In this article, we have extended codon usage study considering gene essentiality as a feature. Using machine learning (ML) based approaches, we have analysed Relative Synonymous Codon Usage (RSCU) values between essential and non-essential genes in Escherichia coli and thirty-four other bacterial genomes whose gene essentiality features were available in public databases. We observed significant differences in codon usage patterns between essential and non-essential genes for majority of the bacterial genomes and accordingly, ML based classifiers achieved high area under curve (AUC) scores, with a minimum score of 70.0 across twenty-eight organisms. Further, importance of the codons towards classifying genes found to differ among the codons in each genome. Arg codon CGT and Gly codon GGT were observed to be the most preferred codons among essential genes in Escherichia coli. Interestingly, some of the codons like CGT, ATA, GGT and GGG observed to be contributing consistently towards classifying essential genes across thirty-five bacteria genomes studied. In other hand, codons TGY and CAY encoding amino acids Cys and His respectively were among the least contributing codons towards classification among all these bacteria. This study demonstrates the gene essentiality based differences in synonymous codon usage in bacteria genomes and presents a common codon usage pattern across bacteria. (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.) |
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| فهرسة مساهمة: | Keywords: Bacterial genome; Codon usage bias; Essential genes; Machine learning; Molecular evolution; Selection |
| المشرفين على المادة: | 0 (Codon) |
| تواريخ الأحداث: | Date Created: 20240726 Date Completed: 20240727 Latest Revision: 20240727 |
| رمز التحديث: | 20240729 |
| DOI: | 10.1007/s00438-024-02163-0 |
| PMID: | 39060647 |
| قاعدة البيانات: | MEDLINE |
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| DOI: | 10.1007/s00438-024-02163-0 |