scholarly journals Inferring Parameters Shaping Amino Acid Usage in Prokaryotic Genomes via Bayesian MCMC Methods

2005 ◽  
Vol 23 (1) ◽  
pp. 203-211 ◽  
Author(s):  
Hugo Naya ◽  
Daniel Gianola ◽  
Héctor Romero ◽  
Jorge I. Urioste ◽  
Héctor Musto
Keyword(s):  
Amino Acid ◽  
Amino Acid Usage ◽  
Mcmc Methods ◽  
Bayesian Mcmc ◽  
Prokaryotic Genomes

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.

scholarly journals How Does Replication-Associated Mutational Pressure Influence Amino Acid Composition of Proteins?

1999 ◽  
Vol 9 (5) ◽  
pp. 409-416 ◽  
Author(s):  
Pawel Mackiewicz ◽  
Agnieszka Gierlik ◽  
Maria Kowalczuk ◽  
Miroslaw R. Dudek ◽  
Stanislaw Cebrat
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Chromosome Replication ◽  
Amino Acid Substitutions ◽  
Mutational Pressure ◽  
Coding Sequences ◽  
Noncoding Sequences ◽  
Prokaryotic Genomes ◽  
Dna Strands

We have performed detrended DNA walks on whole prokaryotic genomes, on noncoding sequences and, separately, on each position in codons of coding sequences. Our method enables us to distinguish between the mutational pressure associated with replication and the mutational pressure associated with transcription and other mechanisms that introduce asymmetry into prokaryotic chromosomes. In many prokaryotic genomes, each component of mutational pressure affects coding sequences not only in silent positions but also in positions in which changes cause amino acid substitutions in coded proteins. Asymmetry in the silent positions of codons differentiates the rate of translation of mRNA produced from leading and lagging strands. Asymmetry in the amino acid composition of proteins resulting from replication-associated mutational pressure also corresponds to leading and lagging roles of DNA strands, whereas asymmetry connected with transcription and coding function corresponds to the distance of genes from the origin or terminus of chromosome replication.

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 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 Amino Acid Cost and Codon-Usage Biases in 6 Prokaryotic Genomes: A Whole-Genome Analysis

2006 ◽  
Vol 23 (9) ◽  
pp. 1670-1680 ◽  
Author(s):  
Esley M. Heizer ◽  
Douglas W. Raiford ◽  
Michael L. Raymer ◽  
Travis E. Doom ◽  
Robert V. Miller ◽  
...  
Keyword(s):  
Amino Acid ◽  
Codon Usage ◽  
Genome Analysis ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Prokaryotic Genomes

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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