Codon usage bias reveals genomic adaptations to environmental conditions in an acidophilic consortium

Hart, Andrew; Cortés, María Paz; Latorre, Mauricio; Martı́nez, Servet

doi:10.1371/journal.pone.0195869

Cited by 16 publications

(18 citation statements)

References 66 publications

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“…In our current study on ATP6 and ATP8 genes among different species of fishes, birds, and mammals, we observed that the compositional properties and the shape of codon usage differed among these organisms. This is also related with the metabolic rate of an organism . The metabolic rate significantly varied among these organisms and also within each group since habitats were not the same .…”

Section: Discussionmentioning

confidence: 99%

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Similarities and dissimilarities of codon usage in mitochondrial ATP genes among fishes, aves, and mammals

Uddin¹,

Mazumder

Barbhuiya

et al. 2020

IUBMB Life

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In this study, we used bioinformatic approach to analyze the compositional features and codon usage bias (CUB) of ATP6 and ATP8 genes among three groups, namely, fishes, aves, and mammals which thrive in three different habitats as no work was reported yet. The coding sequences of these genes were retrieved from the National Center for Biotechnology Information to explore the similarities and dissimilarities of codon usage of each gene among these groups. Low values of synonymous codon usage order in fishes, aves, and mammals for ATP6 and ATP8 genes suggested that the CUB of ATP6 and ATP8 genes was low. In ATP6 gene, overall GC contents in fishes, aves and mammals were (mean ± SD) 44.09 ± 3.10, 46.65 ± 1.90, and 39.41 ± 2.89%, respectively, whereas in ATP8 gene, the overall GC contents were 42.76 ± 4.38, 44.16 ± 2.43, and 34.19 ± 3.82% in fishes, aves, and mammals, that is, both genes were found to be AT rich. In ATP6 gene, the codon AGC was overrepresented in fishes but under‐represented in aves and mammals, whereas in ATP8 gene, the codon GCC was overrepresented in fishes but underrepresented in aves and mammals. The pattern of codon usage was different in these genes and varied among groups as evident from correspondence analysis. The slope of the regression line in neutrality plot was lower than 0.5, which revealed that the role of natural selection was higher than mutation pressure in shaping the CUB in ATP6 and ATP8 genes.

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Section: Discussionmentioning

confidence: 99%

“…This is also related with the metabolic rate of an organism. 63,64 The metabolic rate significantly varied among these organisms and also within each group since habitats were not the same. 61 Among mammals, most of the species are terrestrial while some are aquatic.…”

Section: Discussionmentioning

confidence: 99%

Similarities and dissimilarities of codon usage in mitochondrial ATP genes among fishes, aves, and mammals

Uddin¹,

Mazumder

Barbhuiya

et al. 2020

IUBMB Life

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“…Fast growing organisms with more abundant tRNA molecules tend to have high CUB for highly expressed genes (Rocha, 2004). Apart from playing a key role in evolution and adaptation biology (Hart, Cortés, Latorre, & Martinez, 2018;Roller, Lucić, Nagy, Perica, & Vlahoviček, 2013;Sharp & Matassi, 1994;Sharp, Emery, & Zeng, 2010), CUB has a prime role in improving the expression level of exogenous genes by the process of codon optimization (Mauro & Chappell, 2014). CUB is species-specific, with many potential environmental and intracellular dynamics affecting the CUB phenomenon (Grantham, Gautier, Gouy, Jacobzone, & Mercier, 1981;Plotkin, Robins, & Levine, 2004).…”

Section: Discussionmentioning

confidence: 99%

Genome‐wide comparison of codon usage dynamics in mitochondrial genes across different species of amphibian genus Bombina

Barbhuiya

Uddin²,

Chakraborty

2019

J Exp Zool Pt B

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The biological phenomenon where some synonymous codons are repeatedly preferred to others in gene transcripts is called codon usage bias (CUB). The analysis of CUB is not only helpful in evolutionary biology but also in improving the expression level of exogenous genes in the host cell by codon optimization. The overall nucleotide composition analysis demonstrated an unequal distribution of four nucleobases and T% was the highest in all seven species. The genes were AT‐rich, evident from overall low GC content. In addition, third codon position analysis indicated that in four Bombina species namely, Bombina fortinuptialis, Bombina lichuanensis, Bombina maxima, Bombina microdeladigitora, nucleobase A3/T3 was the preferred one, whereas A3/C3 was favored in Bombina bombina, Bombina orientalis, and Bombina variegata. Influence of mutation pressure on codon distribution and codon bias was evident from correlation analysis. Correspondence analysis demonstrated that compositional bias driven by mutation pressure along with natural selection acted on CUB of mitochondrial genes. Neutrality plot revealed that natural selection played a major role whereas mutation pressure had a minor but significant role. Our phylogenetic analyses showed that closely linked species belonging to the same genus were noticeably separated in different clades.

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“…Previous work in diverse microbes supports the hypothesis that codon optimization can be used to identify associations between codon usage (either globally or in specific genes) and ecology [12,[39][40][41][42][43]. For example, an analysis of metagenomes collected from mine biofilms shows an enrichment of optimal codons in bacterial and archaeal genes associated with inorganic ion transport [39].…”

Section: Introductionmentioning

confidence: 83%

Signatures of optimal codon usage predict metabolic ecology in budding yeasts

LaBella

Opulente

Steenwyk

et al. 2020

Preprint

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Reverse ecology is the inference of ecological information from patterns of genomic variation. One rich, heretofore underutilized, source of ecologically-relevant genomic information is codon optimality or adaptation. Bias toward codons that match the tRNA pool is robustly associated with high gene expression in diverse organisms, suggesting that codon optimization could be used in a reverse ecology framework to identify highly expressed, ecologically relevant genes. To test this hypothesis, we examined the relationship between optimal codon usage in the classic galactose metabolism (GAL) pathway and known ecological niches for 329 species of budding yeasts, a diverse subphylum of fungi. We find that optimal codon usage in the GAL pathway is positively correlated with quantitative growth on galactose, suggesting that GAL codon optimization reflects increased capacity to grow on galactose. Optimal codon usage in the GAL pathway is also positively correlated with human-associated ecological niches in yeasts of the CUG-Ser1 clade and with dairy-associated ecological niches in the family Saccharomycetaceae. For example, optimal codon usage of GAL genes is greater than 85% of all genes in the major human pathogen Candida albicans (CUG-Ser1 clade) and greater than 75% of genes in the dairy yeast Kluyveromyces lactis (family Saccharomycetaceae). We further find a correlation between optimization in the thiamine biosynthesis and GAL pathways. As a result, optimal codon usage in thiamine biosynthesis genes is also associated with dairy ecological niches in Saccharomycetaceae, which may reflect competition with co-occurring microbes for extracellular thiamine. This work highlights the potential of codon optimization as a tool for gaining insights into the metabolic ecology of microbial eukaryotes. Doing so may be especially illuminating for studying fungal dark matter—species that have yet to be cultured in the lab or have only been identified by genomic material.

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Codon usage bias reveals genomic adaptations to environmental conditions in an acidophilic consortium

Cited by 16 publications

References 66 publications

Similarities and dissimilarities of codon usage in mitochondrial ATP genes among fishes, aves, and mammals

Similarities and dissimilarities of codon usage in mitochondrial ATP genes among fishes, aves, and mammals

Genome‐wide comparison of codon usage dynamics in mitochondrial genes across different species of amphibian genus Bombina

Signatures of optimal codon usage predict metabolic ecology in budding yeasts

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