TY - JOUR

T1 - The Effect of Codon Reassignment on the Properties and Structure of the Mitochondrial Proteins of the Baikal Amphipods

AU - Yudinceva, A. V.

AU - Romanova, E. V.

AU - Sherbakov, D. Y.

AU - Bukin, Y. S.

PY - 2025

Y1 - 2025

N2 - There are more than ten mitochondrial genetic codes are known in eukaryotes. Genetic code changes also called as codon reassignment may occur through the mechanism including tRNA gene remolding (changing tRNA gene identity through mutations in the anticodon). Our recent study showed that mitochondrial genomes of some amphipod species from Lake Baikal possess tRNA genes copies which underwent remolding along with appropriate canonic tRNA genes. Three cases of tRNA gene remolding were revealed in mitochondrial genome of Acanthogammarus victorii and by one case were shown in mitochondrial genomes of Eulimnogammarus vittatus and Gmelinoides fasciatus. In this work, we performed the analysis of theoretical codon reassignment influence on physicochemical features (molecular weight, average weight of amino-acid residue, isoelectric point, average protein charge) and spatial structure of mitochondrial CYTB protein of aforementioned amphipod species based on amino acid substitutions according to tRNA remolding cases. In silico translation of CYTB gene sequences of three amphipod species was made using standard genetic code, a code with partially reassigned codons, and the completely reassigned genetic code. Physicochemical and spatial features of obtained proteins were compared at species level and between each species. Comparative analysis of proteins obtained both with partially and completely reassigned codons allowed us to conclude that evolutionary distances within proteins estimated at intraspecific level are less than those obtained at the interspecific level, appeared during evolutionary divergence. It was also revealed that codon reassignment leads to changes in both the physicochemical features of the protein and its spatial structure, however these changes were also significantly less than those calculated for proteins in different species of amphipods. Alterations in physicochemical features and spatial structure of CYTB depends on number of reassigned codons as well as on the difference in the properties of the amino acids being replaced. The biggest impact of codon reassignment was shown in A. victorii. Isoelectric point of CYTB protein sets altered from 5.5 to 8.9, and protein charge altered from –3.5 to 9. We suppose that environment conditions in Lake Baikal facilitate appearance of redundant tRNA genes and their remolding in mitochondrial genomes of amphipods.

AB - There are more than ten mitochondrial genetic codes are known in eukaryotes. Genetic code changes also called as codon reassignment may occur through the mechanism including tRNA gene remolding (changing tRNA gene identity through mutations in the anticodon). Our recent study showed that mitochondrial genomes of some amphipod species from Lake Baikal possess tRNA genes copies which underwent remolding along with appropriate canonic tRNA genes. Three cases of tRNA gene remolding were revealed in mitochondrial genome of Acanthogammarus victorii and by one case were shown in mitochondrial genomes of Eulimnogammarus vittatus and Gmelinoides fasciatus. In this work, we performed the analysis of theoretical codon reassignment influence on physicochemical features (molecular weight, average weight of amino-acid residue, isoelectric point, average protein charge) and spatial structure of mitochondrial CYTB protein of aforementioned amphipod species based on amino acid substitutions according to tRNA remolding cases. In silico translation of CYTB gene sequences of three amphipod species was made using standard genetic code, a code with partially reassigned codons, and the completely reassigned genetic code. Physicochemical and spatial features of obtained proteins were compared at species level and between each species. Comparative analysis of proteins obtained both with partially and completely reassigned codons allowed us to conclude that evolutionary distances within proteins estimated at intraspecific level are less than those obtained at the interspecific level, appeared during evolutionary divergence. It was also revealed that codon reassignment leads to changes in both the physicochemical features of the protein and its spatial structure, however these changes were also significantly less than those calculated for proteins in different species of amphipods. Alterations in physicochemical features and spatial structure of CYTB depends on number of reassigned codons as well as on the difference in the properties of the amino acids being replaced. The biggest impact of codon reassignment was shown in A. victorii. Isoelectric point of CYTB protein sets altered from 5.5 to 8.9, and protein charge altered from –3.5 to 9. We suppose that environment conditions in Lake Baikal facilitate appearance of redundant tRNA genes and their remolding in mitochondrial genomes of amphipods.

KW - amino acid substitutions

KW - cytochrome b (CYTB)

KW - evolutionary distances

KW - mitochondrial genome

KW - mitochondrial proteome

UR - https://www.mendeley.com/catalogue/a6e29cfc-2127-34fb-b375-681a69491de3/

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-86000617911&origin=inward&txGid=cdaf01d15a292c9a7a6678c7d52df61c

U2 - 10.17537/2025.20.54

DO - 10.17537/2025.20.54

M3 - Article

VL - 20

SP - 54

EP - 70

JO - Mathematical Biology and Bioinformatics

JF - Mathematical Biology and Bioinformatics

SN - 1994-6538

IS - 1

ER -