Evolutionary Constraints on Codon and Amino Acid Usage in Two Strains of Human Pathogenic Actinobacteria Tropheryma whipplei

2006 ◽  
Vol 62 (5) ◽  
pp. 645-658 ◽  
Author(s):  
Sabyasachi Das ◽  
Sandip Paul ◽  
Chitra Dutta
Keyword(s):  
Amino Acid ◽  
Tropheryma Whipplei ◽  
Amino Acid Usage ◽  
Evolutionary Constraints

scholarly journals Translational Selection and Yeast Proteome Evolution

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1291-1303 ◽  
Author(s):  
Hiroshi Akashi
Keyword(s):  
Natural Selection ◽  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Synonymous Codon ◽  
Amino Acid Usage ◽  
Proper Function ◽  
Efficient Synthesis ◽  
Expression Levels ◽  
Speed And Accuracy

AbstractThe primary structures of peptides may be adapted for efficient synthesis as well as proper function. Here, the Saccharomyces cerevisiae genome sequence, DNA microarray expression data, tRNA gene numbers, and functional categorizations of proteins are employed to determine whether the amino acid composition of peptides reflects natural selection to optimize the speed and accuracy of translation. Strong relationships between synonymous codon usage bias and estimates of transcript abundance suggest that DNA array data serve as adequate predictors of translation rates. Amino acid usage also shows striking relationships with expression levels. Stronger correlations between tRNA concentrations and amino acid abundances among highly expressed proteins than among less abundant proteins support adaptation of both tRNA abundances and amino acid usage to enhance the speed and accuracy of protein synthesis. Natural selection for efficient synthesis appears to also favor shorter proteins as a function of their expression levels. Comparisons restricted to proteins within functional classes are employed to control for differences in amino acid composition and protein size that reflect differences in the functional requirements of proteins expressed at different levels.

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.

Quantifying the species-specificity in genomic signatures, synonymous codon choice, amino acid usage and G+C content

Gene ◽  
2003 ◽  
Vol 311 ◽  
pp. 35-42 ◽  
Author(s):  
Rickard Sandberg ◽  
Carl-Ivar Bränden ◽  
Ingemar Ernberg ◽  
Joakim Cöster
Keyword(s):  
Amino Acid ◽  
Synonymous Codon ◽  
Species Specificity ◽  
Amino Acid Usage ◽  
Genomic Signatures

scholarly journals Active Site-Induced Evolutionary Constraints Follow Fold Polarity Principles in Soluble Globular Enzymes

2019 ◽  
Vol 36 (8) ◽  
pp. 1728-1733 ◽  
Author(s):  
Alexander Mayorov ◽  
Matteo Dal Peraro ◽  
Luciano A Abriata
Keyword(s):  
Amino Acid ◽  
Active Sites ◽  
Metabolic Cost ◽  
Evolutionary Rates ◽  
Recent Analysis ◽  
Evolutionary Constraints ◽  
Evolutionary Models ◽  
Data Set ◽  
Soluble Enzymes ◽  
Amino Acid Preference

Abstract A recent analysis of evolutionary rates in >500 globular soluble enzymes revealed pervasive conservation gradients toward catalytic residues. By looking at amino acid preference profiles rather than evolutionary rates in the same data set, we quantified the effects of active sites on site-specific constraints for physicochemical traits. We found that conservation gradients respond to constraints for polarity, hydrophobicity, flexibility, rigidity and structure in ways consistent with fold polarity principles; while sites far from active sites seem to experience no physicochemical constraint, rather being highly variable and favoring amino acids of low metabolic cost. Globally, our results highlight that amino acid variation contains finer information about protein structure than usually regarded in evolutionary models, and that this information is retrievable automatically with simple fits. We propose that analyses of the kind presented here incorporated into models of protein evolution should allow for better description of the physical chemistry that underlies molecular evolution.

scholarly journals Hydrophobicity and Aromaticity Are Primary Factors Shaping Variation in Amino Acid Usage of Chicken Proteome

PLoS ONE ◽  
2014 ◽  
Vol 9 (10) ◽  
pp. e110381 ◽  
Author(s):  
Yousheng Rao ◽  
Zhangfeng Wang ◽  
Xuewen Chai ◽  
Qinghua Nie ◽  
Xiquan Zhang
Keyword(s):  
Amino Acid ◽  
Amino Acid Usage

scholarly journals Levels of tRNAs in bacterial cells as affected by amino acid usage in proteins

1991 ◽  
Vol 19 (22) ◽  
pp. 6119-6122 ◽  
Author(s):  
Fumiaki Yamao ◽  
Yoshiki Andachi ◽  
Akira Muto ◽  
Toshimichi Ikemura ◽  
Syozo Osawa
Keyword(s):  
Amino Acid ◽  
Amino Acid Usage ◽  
Bacterial Cells

scholarly journals The tRNA levels in bacterial cells as affected by amino acid usage in proteins.

1989 ◽  
Vol 65 (4) ◽  
pp. 73-75 ◽  
Author(s):  
Fumiaki YAMAO ◽  
Yoshiki ANDACHI ◽  
Akira MUTO ◽  
Toshimichi IKEMURA ◽  
Syozo OSAWA
Keyword(s):  
Amino Acid ◽  
Amino Acid Usage ◽  
Bacterial Cells
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