Amino acid repeats avert mRNA folding through conservative substitutions and synonymous codons, regardless of codon bias

Barik, Sailen

doi:10.1016/j.heliyon.2017.e00492

Cited by 6 publications

(5 citation statements)

References 27 publications

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“…The smaller amount of CAA triplets encoding for polyQ regions associated to polyQ diseases suggests a role for CAA codons as phenotype modulators. Even though the frequency of codons different to CAA interrupting consecutive CAG stretches is low, is has been previously reported a role of these interruptions evading homologous DNA recombination ( Barik 2017 ), slowing the aggregation rates of polyQ regions, decreasing fiber formation rates, increasing oligomer stability ( Menon et al. 2013 ), and preventing CAG expansion ( Ciesiolka et al.…”

Section: Discussionmentioning

confidence: 99%

Glutamine Codon Usage and polyQ Evolution in Primates Depend on the Q Stretch Length

Mier

Andrade‐Navarro

2018

Genome Biology and Evolution

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Amino acid usage in a proteome depends mostly on its taxonomy, as it does the codon usage in transcriptomes. Here, we explore the level of variation in the codon usage of a specific amino acid, glutamine, in relation to the number of consecutive glutamine residues. We show that CAG triplets are consistently more abundant in short glutamine homorepeats (polyQ, four to eight residues) than in shorter glutamine stretches (one to three residues), leading to the evolutionary growth of the repeat region in a CAG-dependent manner. The length of orthologous polyQ regions is mostly stable in primates, particularly the short ones. Interestingly, given a short polyQ the CAG usage is higher in unstable-in-length orthologous polyQ regions. This indicates that CAG triplets produce the necessary instability for a glutamine stretch to grow. Proteins related to polyQ-associated diseases behave in a more extreme way, with longer glutamine stretches in human and evolutionarily closer nonhuman primates, and an overall higher CAG usage. In the light of our results, we suggest an evolutionary model to explain the glutamine codon usage in polyQ regions.

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Section: Discussionmentioning

confidence: 99%

Glutamine Codon Usage and polyQ Evolution in Primates Depend on the Q Stretch Length

Mier

Andrade‐Navarro

2018

Genome Biology and Evolution

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“…AARs and hotspots are expected to exist in share-ome containing protein sequences, and AARs have been reported to play a key role in protein structure and function [ 49 ], such as molecular recognition and molecular assembly [ 48 ]. Additionally, abundance of repeats may be an indication of selective pressure exerted on the genome, signifying a conserved region among orthologous proteins, as observed in lysine, glutamic acid, proline, serine and alanine rich repeat proteins [ 50 ].…”

Section: Methodsmentioning

confidence: 99%

A systematic bioinformatics approach for large-scale identification and characterization of host-pathogen shared sequences

et al. 2021

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Background Biology has entered the era of big data with the advent of high-throughput omics technologies. Biological databases provide public access to petabytes of data and information facilitating knowledge discovery. Over the years, sequence data of pathogens has seen a large increase in the number of records, given the relatively small genome size and their important role as infectious and symbiotic agents. Humans are host to numerous pathogenic diseases, such as that by viruses, many of which are responsible for high mortality and morbidity. The interaction between pathogens and humans over the evolutionary history has resulted in sharing of sequences, with important biological and evolutionary implications. Results This study describes a large-scale, systematic bioinformatics approach for identification and characterization of shared sequences between the host and pathogen. An application of the approach is demonstrated through identification and characterization of the Flaviviridae-human share-ome. A total of 2430 nonamers represented the Flaviviridae-human share-ome with 100% identity. Although the share-ome represented a small fraction of the repertoire of Flaviviridae (~ 0.12%) and human (~ 0.013%) non-redundant nonamers, the 2430 shared nonamers mapped to 16,946 Flaviviridae and 7506 human non-redundant protein sequences. The shared nonamer sequences mapped to 125 species of Flaviviridae, including several with unclassified genus. The majority (~ 68%) of the shared sequences mapped to Hepacivirus C species; West Nile, dengue and Zika viruses of the Flavivirus genus accounted for ~ 11%, ~ 7%, and ~ 3%, respectively, of the Flaviviridae protein sequences (16,946) mapped by the share-ome. Further characterization of the share-ome provided important structural-functional insights to Flaviviridae-human interactions. Conclusion Mapping of the host-pathogen share-ome has important implications for the design of vaccines and drugs, diagnostics, disease surveillance and the discovery of unknown, potential host-pathogen interactions. The generic workflow presented herein is potentially applicable to a variety of pathogens, such as of viral, bacterial or parasitic origin.

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“…These results suggest the effect of natural selection to enhance metabolic efficiency by increasing the use of more costly amino acids in lowly expressed genes but the use of less costly amino acid in highly expressed genes, respectively. Moreover, a significant number of genes across all living species encodes proteins with amino acid repeats of different length and composition that play important role in overall protein structure and function [61]. In addition to its role as a substrate for protein synthesis, recently it was reviewed that amino acids in concert with hormones modulate various signal transduction pathways, which regulate mRNA translation [62].…”

Section: Amino Acid Compositionmentioning

confidence: 99%

A report on DNA sequence determinants in gene expression

Singh

Sophiarani

2020

Bioinformation

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The authors state that they adhere with COPE guidelines on publishing ethics as described elsewhere at https://publicationethics.org/. The authors also undertake that they are not associated with any other third party (governmental or non-governmental agencies) linking with any form of unethical issues connecting to this publication. The authors also declare that they are not withholding any information that is misleading to the publisher in regard to this article.

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Amino acid repeats avert mRNA folding through conservative substitutions and synonymous codons, regardless of codon bias

Cited by 6 publications

References 27 publications

Glutamine Codon Usage and polyQ Evolution in Primates Depend on the Q Stretch Length

Glutamine Codon Usage and polyQ Evolution in Primates Depend on the Q Stretch Length

A systematic bioinformatics approach for large-scale identification and characterization of host-pathogen shared sequences

A report on DNA sequence determinants in gene expression

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