Statistical Extremes of Amino Acid Residue Composition of the Proteome Proteins Can Explain the Origin of the Universality of the Genetic Code
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Genshiro Esumi
Department of Pediatric Surgery, Hospital of the University of Occupational and Environmental Health
https://orcid.org/0000-0003-0618-9943
https://researchmap.jp/esumig
DOI:
https://doi.org/10.51094/jxiv.575Keywords:
amino acid composition, transmembrane domain, intrinsically disordered region, genetic code, optimized translation theory, Chargaff’s second parity rule, GC content, TA skew, GC skewAbstract
Organisms have evolved and diverged from a common ancestor, and today there are many different species in many different environments. Because these organisms share a nearly identical genetic code, it is believed that all species have changed little in their genetic code from that of the ancestor over the course of evolution. However, the reasons for this universality, why almost all organisms have never changed their genetic code, are not well understood.
In the present study, principal component analyses of the amino acid residue composition of proteome proteins from different species revealed that proteins with high amounts of transmembrane domains (TMDs) and proteins with high amounts of intrinsically disordered regions (IDRs) almost universally occupy the two extremes of each proteome plot of their first and second principal components. These TMD- and IDR-rich proteins correlated not only with the amino acid composition of the proteins, but also with the nucleic acid composition of their corresponding genes.
In my previous report, I showed that the genetic code itself has a structure that can assist the generation of TMDs and IDRs by exploiting the partial biases of nucleic acid composition in gene sequences. With the current statistical analyses, I also showed that TMD- and IDR-rich proteins always occupy the statistical extremes of amino acid composition in the proteomes of different organisms. If TMDs and IDRs are always the two largest domains/regions with extreme amino acid composition in the proteome, and if the genetic code has a structure that helps synthesize TMDs and IDRs, then I can conclude that the structure of the current genetic code may have been chosen to meet the requirements of the typical amino acid composition of these functional domains. If this assumption is true, it would be reasonable to assume that such a genetic code has become universal.
This is a new explanation for the universality of the genetic code, and I call it "The Optimized Translation Theory". This theory should provide a partial explanation for the origin of the standard genetic code in terms of its functions.
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Submitted: 2023-12-17 20:56:15 UTC
Published: 2023-12-22 04:20:16 UTC
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