scholarly journals Evolution at Two Levels in Fire Ants: The Relationship between Patterns of Gene Expression and Protein Sequence Evolution

2012 ◽  
Vol 30 (2) ◽  
pp. 263-271 ◽  
Author(s):  
B. G. Hunt ◽  
L. Ometto ◽  
L. Keller ◽  
M. A. D. Goodisman
Keyword(s):  
Gene Expression ◽  
Protein Sequence ◽  
Fire Ants ◽  
Sequence Evolution ◽  
In Fire ◽  
The Relationship ◽  
Protein Sequence Evolution

scholarly journals Sex-biased genes expressed in the cricket brain evolve rapidly

2020 ◽  
Author(s):  
Carrie A. Whittle ◽  
Arpita Kulkarni ◽  
Cassandra G. Extavour
Keyword(s):  
Gene Expression ◽  
Sexual Selection ◽  
Positive Selection ◽  
Protein Sequence ◽  
Seminal Fluid ◽  
Sequence Evolution ◽  
Evolutionary Trend ◽  
A Genome ◽  
The Brain ◽  
Protein Sequence Evolution

AbstractBackgroundSex-biased gene expression, particularly male-biased expression in the gonad, has often been linked to rapid protein sequence evolution (dN/dS) in animals. This evolutionary trend may arise from one or both of sexual selection pressures during mating or low pleiotropy. In insects, research on sex-biased transcription and dN/dS remains largely focused on a few holometabolous species, with variable findings on male and female gonadal effects. The brain is central to the mating process, and provides neurological foundation for mating behaviors, such as courtship, intrasex competition and mate choice. However, there is a striking paucity of research on sex-biased expression of genes in the brain and the rate of protein sequence evolution in such genes.ResultsHere, we studied sex-biased gene expression in a hemimetabolous insect, the cricket Gryllus bimaculatus. We generated novel RNA-seq data for two sexual tissue types, the gonad and somatic reproductive system, and for two core components of the nervous system, the brain and ventral nerve cord. From a genome-wide analysis of genes expressed in these tissues, we report the accelerated evolution of testis-biased genes and seminal fluid proteins (SFPs) genes, as compared to ovary-biased and unbiased genes in this cricket model, which includes an elevated frequency of positive selection events. With respect to the brain, while sex-biased brain genes were much less common than for the gonads, they exhibited exceptionally rapid evolution, an effect that was stronger for the female than for the male brain. Certain sex-biased brain genes were predicted to be involved in mating or sex-related functions, which we suggest may cause exposure to sexual selection. Moreover, the sex-biased brain genes exhibited remarkably low cross-tissue expression breadth, or pleiotropy. We speculate that this feature may permit relaxed purifying selection, and allow the freedom for adaptive protein functional changes in these brain-expressed genes.ConclusionsOur results demonstrate that sex-biased expression in the male gonad, and sex-biased gene expression in the brain, especially the female brain, are associated with rapid protein sequence evolution in a cricket model system. We discuss the results with respect to our findings on pleiotropy and positive selection, and consider the potential role of the dynamic mating biology of this cricket model in shaping these patterns.

scholarly journals Roles of Solvent Accessibility and Gene Expression in Modeling Protein Sequence Evolution

2015 ◽  
Vol 11 ◽  
pp. EBO.S22911 ◽  
Author(s):  
Kuangyu Wang ◽  
Shuhui Yu ◽  
Xiang Ji ◽  
Clemens Lakner ◽  
Alexander Griffing ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Sequence ◽  
Solvent Accessibility ◽  
Sequence Evolution ◽  
Protein Sequence Evolution

scholarly journals Biophysical and structural considerations for protein sequence evolution

2011 ◽  
Vol 11 (1) ◽  
pp. 361 ◽  
Author(s):  
Johan A Grahnen ◽  
Priyanka Nandakumar ◽  
Jan Kubelka ◽  
David A Liberles
Keyword(s):  
Protein Sequence ◽  
Sequence Evolution ◽  
Protein Sequence Evolution

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 Reconstructed protein sequence evolution consistent with the evolution of C4 photosynthesis via a C2 ancestor in the Paniceae

2019 ◽  
Author(s):  
Daniel S. Carvalho ◽  
Sunil Kumar Kenchanmane Raju ◽  
Yang Zhang ◽  
James C. Schnable
Keyword(s):  
Protein Sequence ◽  
Evolutionary History ◽  
C4 Photosynthesis ◽  
Sequence Evolution ◽  
Ancestral Branch ◽  
History Of ◽  
Grass Genomes ◽  
Protein Sequence Evolution

AbstractThe grass tribe Paniceae includes a monophyletic subclade of species, the MPC clade, which specialize in each of the three primary C4 sub-pathways NADP-ME, NAD-ME and PCK. The evolutionary history of C4 photosynthesis in this subclade remains ambiguous. Leveraging newly sequenced grass genomes and syntenic orthology data, we estimated rates of protein sequence evolution on ancestral branches for both core enzymes shared across different C4 sub-pathways and enzymes specific to C4 sub-pathways. While core enzymes show elevated rates of protein sequence evolution in ancestral branches consistent with a transition from C3 to C4 photosynthesis in the ancestor for this clade, no subtype specific enzymes showed similar patterns. At least one protein involved in photorespiration also showed elevated rates of protein sequence evolution in the ancestral branch. The set of core C4 enzymes examined here combined with the photorespiratory pathway are necessary for the C2 photosynthetic cycle, a previously proposed intermediate between C3 and C4 photosynthesis. The patterns reported here are consistent with, but not conclusive proof that, C4 photosynthesis in the MPC clade of the Paniceae evolved via a C2 intermediate.

scholarly journals Constrained mutational sampling of amino acids in HIV-1 protease evolution

2018 ◽  
Author(s):  
Jeffrey I. Boucher ◽  
Troy W. Whitfield ◽  
Ann Dauphin ◽  
Gily Nachum ◽  
Carl Hollins ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Code ◽  
Protein Sequence ◽  
Fitness Landscape ◽  
Sequence Evolution ◽  
Single Mutation ◽  
The Impact ◽  
Protein Sequence Evolution ◽  
Hiv 1

AbstractThe evolution of HIV-1 protein sequences should be governed by a combination of factors including nucleotide mutational probabilities, the genetic code, and fitness. The impact of these factors on protein sequence evolution are interdependent, making it challenging to infer the individual contribution of each factor from phylogenetic analyses alone. We investigated the protein sequence evolution of HIV-1 by determining an experimental fitness landscape of all individual amino acid changes in protease. We compared our experimental results to the frequency of protease variants in a publicly available dataset of 32,163 sequenced isolates from drug-naïve individuals. The most common amino acids in sequenced isolates supported robust experimental fitness, indicating that the experimental fitness landscape captured key features of selection acting on protease during viral infections of hosts. Amino acid changes requiring multiple mutations from the likely ancestor were slightly less likely to support robust experimental fitness than single mutations, consistent with the genetic code favoring chemically conservative amino acid changes. Amino acids that were common in sequenced isolates were predominantly accessible by single mutations from the likely protease ancestor. Multiple mutations commonly observed in isolates were accessible by mutational walks with highly fit single mutation intermediates. Our results indicate that the prevalence of multiple base mutations in HIV-1 protease is strongly influenced by mutational sampling.

scholarly journals The constraints between amino acids influence the unequal distribution of codons and protein sequence evolution

2021 ◽  
Vol 8 (6) ◽  
pp. 201852
Author(s):  
Yi Qian ◽  
Rui Zhang ◽  
Xinglu Jiang ◽  
Guoqiu Wu
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Molecular Evolution ◽  
Poisson Distribution ◽  
Protein Sequence ◽  
Sequence Evolution ◽  
Unequal Distribution ◽  
One Stop ◽  
Protein Sequence Evolution

Four nucleotides (A, U, C and G) constitute 64 codons at free combination but 64 codons are unequally assigned to 21 items (20 amino acids plus one stop). About 500 amino acids are known but only 20 are selected to make up the proteins. However, the relationships between amino acid and codon and between 20 amino acids have been unclear. In this paper, we studied the relationships between 20 amino acids in 33 species and found there were three constraints between 20 amino acids, such as the relatively stable mean carbon and hydrogen (C : H) ratios (0.50), similarity interactions between the constituent ratios of amino acids, and the frequency of amino acids according with Poisson distribution under certain conditions. We demonstrated that the unequal distribution of 64 codons and the choice of amino acids in molecular evolution would be constrained to remain stable C : H ratios. The constituent ratios and frequency of 20 amino acids in a species or a protein are two determinants of protein sequence evolution, so this finding showed the constraints between 20 amino acids played an important role in protein sequence evolution.

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