scholarly journals The interplay of SARS-CoV-2 evolution and constraints imposed by the structure and functionality of its proteins

2020 ◽  
Author(s):  
Lukasz Jaroszewski ◽  
Mallika Iyer ◽  
Arghavan Alisoltani ◽  
Mayya Sedova ◽  
Adam Godzik
Keyword(s):  
Structural Features ◽  
Protein Coding ◽  
Genetic Changes ◽  
3D Structures ◽  
Evolutionary Selection ◽  
Protein Coding Genes ◽  
Mutation Distribution ◽  
Practical Implications ◽  
Fast Evolution ◽  
Selection Of

AbstractFast evolution of the SARS-CoV-2 virus provides us with unique information about the patterns of genetic changes in a single pathogen in the timescale of months. This data is used extensively to track the phylodynamic of the pandemic’s spread and its split into distinct clades. Here we show that the patterns of SARS-CoV-2 virus mutations along its genome are closely correlated with the structural features of the coded proteins. We show that the foldability of proteins’ 3D structures and conservation of their functions are the universal factors driving evolutionary selection in protein-coding genes. Insights from the analysis of mutation distribution in the context of the SARS-CoV-2 proteins’ structures and functions have practical implications including evaluating potential antigen epitopes or selection of primers for PCR-based COVID-19 tests.

scholarly journals Preliminary assessment of adaptive evolution of mitochondrial protein coding genes in darters (Percidae: Etheostomatinae)

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 464 ◽  
Author(s):  
Leos G. Kral ◽  
Sara Watson
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Gene Evolution ◽  
Mitochondrial Gene ◽  
Mitochondrial Protein ◽  
Preliminary Assessment ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Show Evidence ◽  
Selection Of

Background: Mitochondrial DNA of vertebrates contains genes for 13 proteins involved in oxidative phosphorylation. Some of these genes have been shown to undergo adaptive evolution in a variety of species. This study examines all mitochondrial protein coding genes in 11 darter species to determine if any of these genes show evidence of positive selection. Methods: The mitogenome from four darter was sequenced and annotated. Mitogenome sequences for another seven species were obtained from GenBank. Alignments of each of the protein coding genes were subject to codon-based identification of positive selection by Selecton, MEME and FEL. Results: Evidence of positive selection was obtained for six of the genes by at least one of the methods. CYTB was identified as having evolved under positive selection by all three methods at the same codon location. Conclusions: Given the evidence for positive selection of mitochondrial protein coding genes in darters, a more extensive analysis of mitochondrial gene evolution in all the extant darter species is warranted.

scholarly journals Unbiasing in the Genome Analysis of Iconic Shark Species

2019 ◽  
Author(s):  
Kazuaki Yamaguchi ◽  
Shigehiro Kuraku
Keyword(s):  
Molecular Evolution ◽  
Genome Stability ◽  
White Shark ◽  
Shark Species ◽  
Whole Genome ◽  
Potential Bias ◽  
Short Article ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Selection Of

A previous study involving whole genome sequencing of the white shark suggested unique molecular evolution accounting for gigantism and the enhanced longevity of sharks including positive selection of dozens of protein-coding genes potentially involved in genome stability. We performed a reanalysis on some of the genes and identified serious flaws in their results. In this short article, we scrutinize one of the serious problems we identified, report other concerns, and point out a potential bias in analyzing iconic shark species in general.

scholarly journals Protein-Coding Genes of Helicobacter pylori Predominantly Present Purifying Selection though Many Membrane Proteins Suffer from Selection Pressure: A Proposal to Analyze Bacterial Pangenomes

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 377
Author(s):  
Alejandro Rubio ◽  
Antonio Pérez-Pulido
Keyword(s):  
Helicobacter Pylori ◽  
Membrane Proteins ◽  
Selection Pressure ◽  
Purifying Selection ◽  
Protein Coding ◽  
Evolutionary Selection ◽  
Protein Coding Genes ◽  
The Core ◽  
Genes Encoding ◽  
Selection For

The current availability of complete genome sequences has allowed knowing that bacterial genomes can bear genes not present in the genome of all the strains from a specific species. So, the genes shared by all the strains comprise the core of the species, but the pangenome can be much greater and usually includes genes appearing in one only strain. Once the pangenome of a species is estimated, other studies can be undertaken to generate new knowledge, such as the study of the evolutionary selection for protein-coding genes. Most of the genes of a pangenome are expected to be subject to purifying selection that assures the conservation of function, especially those in the core group. However, some genes can be subject to selection pressure, such as genes involved in virulence that need to escape to the host immune system, which is more common in the accessory group of the pangenome. We analyzed 180 strains of Helicobacter pylori, a bacterium that colonizes the gastric mucosa of half the world population and presents a low number of genes (around 1500 in a strain and 3000 in the pangenome). After the estimation of the pangenome, the evolutionary selection for each gene has been calculated, and we found that 85% of them are subject to purifying selection and the remaining genes present some grade of selection pressure. As expected, the latter group is enriched with genes encoding for membrane proteins putatively involved in interaction to host tissues. In addition, this group also presents a high number of uncharacterized genes and genes encoding for putative spurious proteins. It suggests that they could be false positives from the gene finders used for identifying them. All these results propose that this kind of analyses can be useful to validate gene predictions and functionally characterize proteins in complete genomes.

scholarly journals Measuring evolutionary rates of proteins in a structural context

F1000Research ◽  
2018 ◽  
Vol 6 ◽  
pp. 1845 ◽  
Author(s):  
Dariya K. Sydykova ◽  
Benjamin R. Jack ◽  
Stephanie J. Spielman ◽  
Claus O. Wilke
Keyword(s):  
Solvent Accessibility ◽  
Structural Features ◽  
Relative Solvent Accessibility ◽  
Protein Coding ◽  
Site Specific ◽  
Structural Context ◽  
Protein Coding Genes ◽  
Rates Of Evolution ◽  
Specific Analysis ◽  
Alternative Approaches

We describe how to measure site-specific rates of evolution in protein-coding genes and how to correlate these rates with structural features of the expressed protein, such as relative solvent accessibility, secondary structure, or weighted contact number. We present two alternative approaches to rate calculations: One based on relative amino-acid rates, and the other based on site-specific codon rates measured as dN/dS. We additionally provide a code repository containing scripts to facilitate the specific analysis protocols we recommend.

scholarly journals Measuring evolutionary rates of proteins in a structural context

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 1845 ◽  
Author(s):  
Dariya K. Sydykova ◽  
Benjamin R. Jack ◽  
Stephanie J. Spielman ◽  
Claus O. Wilke
Keyword(s):  
Solvent Accessibility ◽  
Structural Features ◽  
Relative Solvent Accessibility ◽  
Protein Coding ◽  
Site Specific ◽  
Structural Context ◽  
Protein Coding Genes ◽  
Rates Of Evolution ◽  
Specific Analysis ◽  
Alternative Approaches

We describe how to measure site-specific rates of evolution in protein-coding genes and how to correlate these rates with structural features of the expressed protein, such as relative solvent accessibility, secondary structure, or weighted contact number. We present two alternative approaches to rate calculations, one based on relative amino-acid rates and the other based on site-specific codon rates measured as dN/dS. In addition to describing the specific analysis protocols we recommend, we also provide a code repository containing scripts to facilitate these kinds of analyses.

scholarly journals Comparative Complete Chloroplast Genome of Nine Species in Litsea (Lauraceae) and Uncover Evolutionary Dynamic Patterns

2021 ◽  
Author(s):  
Weicai Song ◽  
Zimeng Chen ◽  
Qi Feng ◽  
Chuxuan Ji ◽  
Chengbo Wei ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Trees ◽  
Structural Features ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Protein Coding Genes ◽  
Wide Range ◽  
High Consistency

Abstract Background: Litsea, Lauraceae, is a group of evergreen trees or shrubs that widely distributed in tropical and subtropical countries, such as Asia and America. Species in Litsea are spontaneously distributed at a maximum altitude of 2,700 m from sea level. Pants and its extractions from Litsea species cover a wide range of medicinal and industrial values. The aromatic oil extracted from Litsea is of great value with citral as its main component. At present, studies related to gene resources of Litsea are limited in the morphological analysis, while studies at the genetic level are insufficient. We therefore firstly assembled and annotated the complete chloroplast genome of nine species in Litsea, carried out a serious of comparative analysis, and completed the construction of phylogenetic tree within genus Litsea. Results: The genome length ranged from 152,051 to 152,717 bp. A total of 128 genes were identified, including 84 protein-coding genes, 36 rRNA genes and 8 tRNA genes. High consistency of codon bias, repeats, divergent analysis, single nucleotide polymorphisms (SNP) and insertions and deletions (InDels) revealed highly conserved chloroplast phenotypes in species within the genus Litsea. Changes in gene length and the present of pseudogene ycf1Ψ that caused by IR contraction and expansion were reported. The non-coding regions, especially atpF - atpH and ndhC - trnV-UAC presented high gene divergence. PsbJ - psbE regions showed remarkably high nucleotide diversity (Pi) values. Furthermore, we constructed two phylogenetic trees, demonstrating two dominant clades within genus Litsea. And the differences between trees constructed by full chloroplast (cp) genome and protein-coding genes were revealed. Conclusion: Overall, the evolutionary pattern of Litsea species regarding structural features, repeats sequences and variations presented high consistency. Valuable genomic resources and theoretical basis were also provided for further research of taxonomic discrepancies, molecular marker-assisted breeding and phylogenetic relationships of Litsea and other angiosperm species.

scholarly journals Preliminary assessment of adaptive evolution of mitochondrial protein coding genes in darters (Percidae: Etheostomatinae)

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 464
Author(s):  
Leos G. Kral ◽  
Sara Watson
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Gene Evolution ◽  
Mitochondrial Gene ◽  
Mitochondrial Protein ◽  
Preliminary Assessment ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Show Evidence ◽  
Selection Of

Background: Mitochondrial DNA of vertebrates contains genes for 13 proteins involved in oxidative phosphorylation. Some of these genes have been shown to undergo adaptive evolution in a variety of species. This study examines all mitochondrial protein coding genes in 11 darter species to determine if any of these genes show evidence of positive selection. Methods: The mitogenome from four darter was sequenced and annotated. Mitogenome sequences for another seven species were obtained from GenBank. Alignments of each of the protein coding genes were subject to codon-based identification of positive selection by Selecton, MEME and FEL. Results: Evidence of positive selection was obtained for six of the genes by at least one of the methods. CYTB was identified as having evolved under positive selection by all three methods at the same codon location. Conclusions: Given the evidence for positive selection of mitochondrial protein coding genes in darters, a more extensive analysis of mitochondrial gene evolution in all the extant darter species is warranted.

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