scholarly journals Features of Recent Codon Evolution: A Comparative Polymorphism-Fixation Study

2010 ◽  
Vol 2010 ◽  
pp. 1-9 ◽  
Author(s):  
Zhongming Zhao ◽  
Cizhong Jiang
Keyword(s):  
Amino Acid ◽  
Protein Evolution ◽  
Purifying Selection ◽  
Nucleotide Polymorphism ◽  
Strong Difference ◽  
Codon Composition ◽  
Mutational Pattern ◽  
Codon Positions ◽  
Polymorphism Level ◽  
Codon Evolution

Features of amino-acid and codon changes can provide us important insights on protein evolution. So far, investigators have often examined mutation patterns at either interspecies fixed substitution or intraspecies nucleotide polymorphism level, but not both. Here, we performed a unique analysis of a combined set of intra-species polymorphisms and inter-species substitutions in human codons. Strong difference in mutational pattern was found at codon positions 1, 2, and 3 between the polymorphism and fixation data. Fixation had strong bias towards increasing the rarest codons but decreasing the most frequently used codons, suggesting that codon equilibrium has not been reached yet. We detected strong CpG effect on CG-containing codons and subsequent suppression by fixation. Finally, we detected the signature of purifying selection against A∣U dinucleotides at synonymous dicodon boundaries. Overall, fixation process could effectively and quickly correct the volatile changes introduced by polymorphisms so that codon changes could be gradual and directional and that codon composition could be kept relatively stable during evolution.

scholarly journals Pervasive Purifying Selection Characterizes the Evolution of I2 Homologs

2006 ◽  
Vol 19 (3) ◽  
pp. 288-303 ◽  
Author(s):  
Brett C. Couch ◽  
Russ Spangler ◽  
Christine Ramos ◽  
Georgiana May
Keyword(s):  
Amino Acid ◽  
Gene Family ◽  
General Pattern ◽  
Purifying Selection ◽  
Gene Family Evolution ◽  
Death Process ◽  
Phylogenetic Distance ◽  
R Gene ◽  
The Family ◽  
Codon Positions

We sampled 384 sequences related to the Solanum pimpinel-lifolium (=Lycopersicon pimpinellifolium) disease resistance (R) gene I2 from six species, potato, S. demissum, tomato, eggplant, pepper, and tobacco. These species represent increasing phylogenetic distance from potato to tobacco, within the family Solanaceae. Using sequence data from the nucleotide binding site (NBS) region of this gene, we tested models of gene family evolution and inferred patterns of selection acting on the NBS gene region and I2 gene family. We find that the I2 family has diversified within the family Solanaceae for at least 14 million years and evolves through a slow birth-and-death process requiring approximately 12 million years to homogenize gene copies within a species. Analyses of selection resolved a general pattern of strong purifying selection acting on individual codon positions within the NBS and on NBS lineages through time. Surprisingly, we find nine codon positions strongly affected by positive selection and six pairs of codon positions demonstrating correlated amino acid substitutions. Evolutionary analyses serve as bioinformatic tools with which to sort through the vast R gene diversity in plants and find candidates for new resistance specificities or to identify specific amino acid positions important for biochemical function. The slow birth-and-death evolution of I2 genes suggests that some NBS-leucine rich repeat-mediated resistances may not be overcome rapidly by virulence evolution and that the natural diversity of R genes is a potentially valuable source for durable resistance.

Assessing the Impact of Secondary Structure and Solvent Accessibility on Protein Evolution

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 445-458 ◽  
Author(s):  
Nick Goldman ◽  
Jeffrey L Thorne ◽  
David T Jones
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Protein Evolution ◽  
Solvent Accessibility ◽  
Strong Association ◽  
Length Distribution ◽  
Parametric Bootstrap ◽  
Amino Acid Replacement ◽  
Physical Constraints ◽  
The Impact

Abstract Empirically derived models of amino acid replacement are employed to study the association between various physical features of proteins and evolution. The strengths of these associations are statistically evaluated by applying the models of protein evolution to 11 diverse sets of protein sequences. Parametric bootstrap tests indicate that the solvent accessibility status of a site has a particularly strong association with the process of amino acid replacement that it experiences. Significant association between secondary structure environment and the amino acid replacement process is also observed. Careful description of the length distribution of secondary structure elements and of the organization of secondary structure and solvent accessibility along a protein did not always significantly improve the fit of the evolutionary models to the data sets that were analyzed. As indicated by the strength of the association of both solvent accessibility and secondary structure with amino acid replacement, the process of protein evolution—both above and below the species level—will not be well understood until the physical constraints that affect protein evolution are identified and characterized.

scholarly journals Ribosome Evolution and Structural Capacitance

2019 ◽  
Author(s):  
Ashley M Buckle ◽  
Malcolm Buckle
Keyword(s):  
Amino Acid ◽  
Genetic Code ◽  
Protein Evolution ◽  
Bioinformatic Analysis ◽  
Amino Acid Usage ◽  
Loss Of Function ◽  
Gain Of Function ◽  
Acceptor Stem ◽  
Ribosome Evolution ◽  
Disordered Regions

In addition to the canonical loss-of-function mutations, mutations in proteins may additionally result in gain-of-function through the binary activation of cryptic ‘structural capacitance elements’. Our previous bioinformatic analysis allowed us to propose a new mechanism of protein evolution - structural capacitance – that arises via the generation of new elements of microstructure upon mutations that cause a disorder-to-order (DO) transition in previously disordered regions of proteins. Here we propose that the DO transition is a necessary follow-on from expected early codon-anticodon and tRNA acceptor stem-amino acid usage, via the accumulation of structural capacitance elements - reservoirs of disorder in proteins. We develop this argument further to posit that structural capacitance is an inherent consequence of the evolution of the genetic code.

scholarly journals Molecular function limits divergent protein evolution on planetary timescales

2017 ◽  
Author(s):  
Mariam M. Konaté ◽  
Germán Plata ◽  
Jimin Park ◽  
Dinara R. Usmanova ◽  
Harris H. Wang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Protein Evolution ◽  
Molecular Function ◽  
Functional Conservation ◽  
Fitness Effects ◽  
Sequence Identity ◽  
The Past ◽  
Independent Evolution

AbstractFunctional conservation is known to constrain protein evolution. Nevertheless, the long-term divergence patterns of proteins maintaining the same molecular function and the possible limits of this divergence have not been explored in detail. We investigate these fundamental questions by characterizing the divergence between ancient protein orthologs with conserved molecular function. Our results demonstrate that the decline of sequence and structural similarities between such orthologs significantly slows down after ~1-2 billion years of independent evolution. As a result, their sequence and structural similarities have not substantially decreased for the past billion years. The effective divergence limit (>25% sequence identity) is not primarily due to protein sites universally conserved in all linages. Instead, less than four amino acid types are accepted, on average, per site in orthologs strictly conserving their molecular function. Our analysis also reveals different divergence patterns for protein sites with experimentally determined small and large fitness effects of mutations.

scholarly journals A Brief Review on Viral Variants of COVID-19 Infection

2021 ◽  
pp. 73-80
Author(s):  
Ishank Panchal ◽  
Sunita Vagha
Keyword(s):  
Respiratory Distress Syndrome ◽  
Distress Syndrome ◽  
Structural Features ◽  
Nucleotide Polymorphism ◽  
Health Crisis ◽  
Global Pandemic ◽  
Mutational Pattern ◽  
Steady Improvement ◽  
Probable Role ◽  
Therapy Strategies

SARS is a type of acute respiratory syndrome. Coronavirus 2 (SARSCoV2), highly contagious, affecting people worldwide. Coronavirus Disease 19 (COVID19) leads to a rapidly spreading respiratory distress syndrome. It has caused a global pandemic and severe health crisis in most countries. Due to its continual evolution, further research into the virus's pathogenicity and virulence mechanisms and the development of efficient therapy techniques are urgently required. The current paper summarises what is known about the virus's evolutionary and structural features to comprehend better its mutational pattern and probable role in the current pandemic. In December 2019, the Coronavirus Disease (SARSCoV2) began a destructive path toward a global pandemic in Wuhan, China. Since then, several SARS CoV2 variants have been discovered. Despite the speedy development of a COVID19 vaccine and ongoing mass vaccination efforts around the globe, the discovery of the latest SARSCoV2 variants could undermine the substantial success till now in stopping the spread of SARSCoV2.This review aims to characterize the different SARS CoV2 mutations and investigate the associated morbidity and death. Due to the virus's steady improvement, with its various unmarried nucleotide polymorphism (SNP) versions and lineages, figuring out SARS-CoV-2 infectivity is extraordinarily hard. but, similarly research into the virus's pathogenicity and virulence mechanisms, as well as the improvement of green therapy strategies, is urgent present-day The present day contribution summarises existing expertise regarding the virus's evolutionary and structural homes to clarify its mutational sample and ability function inside the ongoing pandemic.

Accumulation pattern of amino acid substitutions in protein evolution

1987 ◽  
Vol 24 (4) ◽  
pp. 357-365 ◽  
Author(s):  
Takashi Kunisawa ◽  
Katsuhisa Horimoto ◽  
Jinya Otsuka
Keyword(s):  
Amino Acid ◽  
Protein Evolution ◽  
Amino Acid Substitutions ◽  
Accumulation Pattern

scholarly journals Solution structure of sperm lysin yields novel insights into molecular dynamics of rapid protein evolution

2018 ◽  
Vol 115 (6) ◽  
pp. 1310-1315 ◽  
Author(s):  
Damien B. Wilburn ◽  
Lisa M. Tuttle ◽  
Rachel E. Klevit ◽  
Willie J. Swanson
Keyword(s):  
Protein Evolution ◽  
Solution Structure ◽  
Biochemical Characterization ◽  
Purifying Selection ◽  
Biochemical Properties ◽  
Targeted Mutagenesis ◽  
High Definition ◽  
Binding Interface ◽  
Accelerated Evolution ◽  
Species Specific

Protein evolution is driven by the sum of different physiochemical and genetic processes that usually results in strong purifying selection to maintain biochemical functions. However, proteins that are part of systems under arms race dynamics often evolve at unparalleled rates that can produce atypical biochemical properties. In the marine mollusk abalone, lysin and vitelline envelope receptor for lysin (VERL) are a pair of rapidly coevolving proteins that are essential for species-specific interactions between sperm and egg. Despite extensive biochemical characterization of lysin—including crystal structures of multiple orthologs—it was unclear how sites under positive selection may facilitate recognition of VERL. Using a combination of targeted mutagenesis and multidimensional NMR, we present a high-definition solution structure of sperm lysin from red abalone (Haliotis rufescens). Unapparent from the crystallography data, multiple NMR-based analyses conducted in solution reveal clustering of the N and C termini to form a nexus of 13 positively selected sites that constitute a VERL binding interface. Evolutionary rate was found to be a significant predictor of backbone flexibility, which may be critical for lysin bioactivity and/or accelerated evolution. Flexible, rapidly evolving segments that constitute the VERL binding interface were also the most distorted regions of the crystal structure relative to what was observed in solution. While lysin has been the subject of extensive biochemical and evolutionary analyses for more than 30 years, this study highlights the enhanced insights gained from applying NMR approaches to rapidly evolving proteins.

scholarly journals Codon usage of highly expressed genes affects proteome-wide translation efficiency

2018 ◽  
Vol 115 (21) ◽  
pp. E4940-E4949 ◽  
Author(s):  
Idan Frumkin ◽  
Marc J. Lajoie ◽  
Christopher J. Gregg ◽  
Gil Hornung ◽  
George M. Church ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Protein Translation ◽  
Translation Efficiency ◽  
Synonymous Codons ◽  
Codon Composition ◽  
Theoretical Predictions ◽  
Highly Expressed Genes

Although the genetic code is redundant, synonymous codons for the same amino acid are not used with equal frequencies in genomes, a phenomenon termed “codon usage bias.” Previous studies have demonstrated that synonymous changes in a coding sequence can exert significantciseffects on the gene’s expression level. However, whether the codon composition of a gene can also affect the translation efficiency of other genes has not been thoroughly explored. To study how codon usage bias influences the cellular economy of translation, we massively converted abundant codons to their rare synonymous counterpart in several highly expressed genes inEscherichia coli. This perturbation reduces both the cellular fitness and the translation efficiency of genes that have high initiation rates and are naturally enriched with the manipulated codon, in agreement with theoretical predictions. Interestingly, we could alleviate the observed phenotypes by increasing the supply of the tRNA for the highly demanded codon, thus demonstrating that the codon usage of highly expressed genes was selected in evolution to maintain the efficiency of global protein translation.

Sign in / Sign up

Export Citation Format

Share Document