Episodic evolution of pyrin in primates: human mutations recapitulate ancestral amino acid states

10.1038/85893 ◽  
2001 ◽  
Vol 27 (3) ◽  
pp. 318-321 ◽  
Author(s):  
Philip Schaner ◽  
Neil Richards ◽  
Anish Wadhwa ◽  
Ivona Aksentijevich ◽  
Daniel Kastner ◽  
...  
Keyword(s):  
Amino Acid ◽  
Episodic Evolution ◽  
Ancestral Amino Acid

Evidence for an episodic model of protein sequence evolution

2009 ◽  
Vol 37 (4) ◽  
pp. 783-786 ◽  
Author(s):  
Romain A. Studer ◽  
Marc Robinson-Rechavi
Keyword(s):  
Amino Acid ◽  
Protein Sequence ◽  
Protein Function ◽  
Rapid Change ◽  
Sequence Evolution ◽  
Functional Changes ◽  
Codon Models ◽  
Episodic Evolution ◽  
Protein Sequence Evolution ◽  
Amino Acid Conservation

The evolution of protein function appears to involve alternating periods of conservative evolution and of relatively rapid change. Evidence for such episodic evolution, consistent with some theoretical expectations, comes from the application of increasingly sophisticated models of evolution to large sequence datasets. We present here some of the recent methods to detect functional shifts, using amino acid or codon models. Both provide evidence for punctual shifts in patterns of amino acid conservation, including the fixation of key changes by positive selection. Although a link to gene duplication, a presumed source of functional changes, has been difficult to establish, this episodic model appears to apply to a wide variety of proteins and organisms.

scholarly journals Fitness conferred by replaced amino acids declines with time

2012 ◽  
Vol 8 (5) ◽  
pp. 825-828 ◽  
Author(s):  
Sergey A. Naumenko ◽  
Alexey S. Kondrashov ◽  
Georgii A. Bazykin
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
High Probability ◽  
Fitness Landscape ◽  
State Level ◽  
Amino Acid Replacement ◽  
Steady State Level ◽  
Homologous Proteins ◽  
Epistatic Interactions ◽  
Ancestral Amino Acid

The fitness landscape of a locus, the array of fitnesses conferred by its alleles, can be affected by allele replacements at other loci, in the presence of epistatic interactions between loci. In a pair of diverging homologous proteins, the initially high probability that an amino acid replacement in one of them will make it more similar to the other declines with time, implying that the fitness landscapes of homologous sites diverge. Here, we use data on within-population non-synonymous polymorphisms and on amino acid replacements between species to study the dynamics, after an amino acid replacement, of the fitness of the ancestral amino acid, and show that selection against its restoration increases with time. This effect can be owing to increase of fitness conferred by the new amino acid occupying the site, and/or to decline of fitness conferred by the replaced amino acid. We show that the fitness conferred by the replaced amino acid rapidly declines, reaching a new lower steady-state level after approximately 20 per cent of amino acids in the protein get replaced. Therefore, amino acid replacements in evolving proteins are routinely involved in negative epistatic interactions with currently absent amino acids, and chisel off the unused parts of the fitness landscape.

scholarly journals Episodic evolution of coadapted sets of amino acid sites in mitochondrial proteins

PLoS Genetics ◽  
2021 ◽  
Vol 17 (1) ◽  
pp. e1008711
Author(s):  
Alexey D. Neverov ◽  
Anfisa V. Popova ◽  
Gennady G. Fedonin ◽  
Evgeny A. Cheremukhin ◽  
Galya V. Klink ◽  
...  
Keyword(s):  
Amino Acid ◽  
Protein Structures ◽  
Acid Sites ◽  
The Other ◽  
Mitochondrial Proteins ◽  
Amino Acid Substitutions ◽  
Epistatic Interactions ◽  
Rate Of Evolution ◽  
Episodic Evolution ◽  
Selective Forces

The rate of evolution differs between protein sites and changes with time. However, the link between these two phenomena remains poorly understood. Here, we design a phylogenetic approach for distinguishing pairs of amino acid sites that evolve concordantly, i.e., such that substitutions at one site trigger subsequent substitutions at the other; and also pairs of sites that evolve discordantly, so that substitutions at one site impede subsequent substitutions at the other. We distinguish groups of amino acid sites that undergo coordinated evolution and evolve discordantly from other such groups. In mitochondrion-encoded proteins of metazoans and fungi, we show that concordantly evolving sites are clustered in protein structures. By analysing the phylogenetic patterns of substitutions at concordantly and discordantly evolving site pairs, we find that concordant evolution has two distinct causes: epistatic interactions between amino acid substitutions and episodes of selection independently affecting substitutions at different sites. The rate of substitutions at concordantly evolving groups of protein sites changes in the course of evolution, indicating episodes of selection limited to some of the lineages. The phylogenetic positions of these changes are consistent between proteins, suggesting common selective forces underlying them.

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