scholarly journals Biased Gene Conversion Affects Patterns of Codon Usage and Amino Acid Usage in the Saccharomyces sensu stricto Group of Yeasts

2010 ◽  
Vol 28 (1) ◽  
pp. 117-129 ◽  
Author(s):  
R. J. Harrison ◽  
B. Charlesworth
Keyword(s):  
Amino Acid ◽  
Codon Usage ◽  
Gene Conversion ◽  
Sensu Stricto ◽  
Amino Acid Usage ◽  
Saccharomyces Sensu Stricto ◽  
Biased Gene Conversion

scholarly journals Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia

Microbiology ◽  
2003 ◽  
Vol 149 (9) ◽  
pp. 2585-2596 ◽  
Author(s):  
Joshua T. Herbeck ◽  
Dennis P. Wall ◽  
Jennifer J. Wernegreen
Keyword(s):  
Amino Acid ◽  
Codon Usage ◽  
Genetic Drift ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Tsetse Fly ◽  
High Expression ◽  
Amino Acid Usage ◽  
Mutational Bias ◽  
Low Expression

Wigglesworthia glossinidia brevipalpis, the obligate bacterial endosymbiont of the tsetse fly Glossina brevipalpis, is characterized by extreme genome reduction and AT nucleotide composition bias. Here, multivariate statistical analyses are used to test the hypothesis that mutational bias and genetic drift shape synonymous codon usage and amino acid usage of Wigglesworthia. The results show that synonymous codon usage patterns vary little across the genome and do not distinguish genes of putative high and low expression levels, thus indicating a lack of translational selection. Extreme AT composition bias across the genome also drives relative amino acid usage, but predicted high-expression genes (ribosomal proteins and chaperonins) use GC-rich amino acids more frequently than do low-expression genes. The levels and configuration of amino acid differences between Wigglesworthia and Escherichia coli were compared to test the hypothesis that the relatively GC-rich amino acid profiles of high-expression genes reflect greater amino acid conservation at these loci. This hypothesis is supported by reduced levels of protein divergence at predicted high-expression Wigglesworthia genes and similar configurations of amino acid changes across expression categories. Combined, the results suggest that codon and amino acid usage in the Wigglesworthia genome reflect a strong AT mutational bias and elevated levels of genetic drift, consistent with expected effects of an endosymbiotic lifestyle and repeated population bottlenecks. However, these impacts of mutation and drift are apparently attenuated by selection on amino acid composition at high-expression genes.

scholarly journals Synonymous Codon Usages as an Evolutionary Dynamic for Chlamydiaceae

2018 ◽  
Vol 19 (12) ◽  
pp. 4010
Author(s):  
Zhaocai Li ◽  
Wen Hu ◽  
Xiaoan Cao ◽  
Ping Liu ◽  
Youjun Shang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Codon Usage ◽  
Synonymous Codon ◽  
Family Members ◽  
Synonymous Codon Usage ◽  
Amino Acid Usage ◽  
Codon Usage Pattern ◽  
Evolutionary Trend ◽  
Mutation Pressure ◽  
Wide Range

The family of Chlamydiaceae contains a group of obligate intracellular bacteria that can infect a wide range of hosts. The evolutionary trend of members in this family is a hot topic, which benefits our understanding of the cross-infection of these pathogens. In this study, 14 whole genomes of 12 Chlamydia species were used to investigate the nucleotide, codon, and amino acid usage bias by synonymous codon usage value and information entropy method. The results showed that all the studied Chlamydia spp. had A/T rich genes with over-represented A or T at the third positions and G or C under-represented at these positions, suggesting that nucleotide usages influenced synonymous codon usages. The overall codon usage trend from synonymous codon usage variations divides the Chlamydia spp. into four separate clusters, while amino acid usage divides the Chlamydia spp. into two clusters with some exceptions, which reflected the genetic diversity of the Chlamydiaceae family members. The overall codon usage pattern represented by the effective number of codons (ENC) was significantly positively correlated to gene GC3 content. A negative correlation exists between ENC and the codon adaptation index for some Chlamydia species. These results suggested that mutation pressure caused by nucleotide composition constraint played an important role in shaping synonymous codon usage patterns. Furthermore, codon usage of T3ss and Pmps gene families adapted to that of the corresponding genome. Taken together, analyses help our understanding of evolutionary interactions between nucleotide, synonymous codon, and amino acid usages in genes of Chlamydiaceae family members.

scholarly journals Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion

2018 ◽  
Vol 35 (5) ◽  
pp. 1092-1103 ◽  
Author(s):  
Nicolas Galtier ◽  
Camille Roux ◽  
Marjolaine Rousselle ◽  
Jonathan Romiguier ◽  
Emeric Figuet ◽  
...  
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Population Size ◽  
Gene Conversion ◽  
Effective Population Size ◽  
Codon Usage Bias ◽  
Effective Population ◽  
Biased Gene Conversion

scholarly journals Quantifying codon usage in signal peptides: Gene expression and amino acid usage explain apparent selection for inefficient codons

2018 ◽  
Vol 1860 (12) ◽  
pp. 2479-2485 ◽  
Author(s):  
Alexander L. Cope ◽  
Robert L. Hettich ◽  
Michael A. Gilchrist
Keyword(s):  
Gene Expression ◽  
Amino Acid ◽  
Codon Usage ◽  
Amino Acid Usage ◽  
Signal Peptides ◽  
Selection For

Erratum to “GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates” [Trends in Genetics 25 (2009) 1–5]

2009 ◽  
Vol 25 (7) ◽  
pp. 287 ◽  
Author(s):  
Nicolas Galtier ◽  
Laurent Duret ◽  
Sylvain Glémin ◽  
Vincent Ranwez
Keyword(s):  
Amino Acid ◽  
Gene Conversion ◽  
Biased Gene Conversion

scholarly journals Biased gene conversion drives codon usage in human and precludes selection on translation efficiency

2016 ◽  
Author(s):  
Fanny Pouyet ◽  
Dominique Mouchiroud ◽  
Laurent Duret ◽  
Marie Sémon
Keyword(s):  
Gene Expression ◽  
Codon Usage ◽  
Gene Conversion ◽  
Large Scale ◽  
Synonymous Codon ◽  
Gc Content ◽  
Intragenic Recombination ◽  
Translation Efficiency ◽  
Functional Categories ◽  
Biased Gene Conversion

AbstractIn humans, as in other mammals, synonymous codon usage (SCU) varies widely among genes. In particular, genes involved in cell differentiation or in proliferation display a distinct codon usage, suggesting that SCU is adaptively constrained to optimize translation efficiency in distinct cellular states. However, in mammals, SCU is known to correlate with large-scale fluctuations of GC-content along chromosomes, caused by meiotic recombination, via the non-adaptive process of GC-biased gene conversion (gBGC). To disentangle and to quantify the different factors driving SCU in humans, we analyzed the relationships between functional categories, base composition, recombination, and gene expression. We first demonstrate that SCU is predominantly driven by large-scale variation in GC-content and is not linked to constraints on tRNA abundance, which excludes an effect of translational selection. In agreement with the gBGC model, we show that differences in SCU among functional categories are explained by variation in intragenic recombination rate, which, in turn, is strongly negatively correlated to gene expression levels during meiosis. Our results indicate that variation in SCU among functional categories (including variation associated to differentiation or proliferation) result from differences in levels of meiotic transcription, which interferes with the formation of crossovers and thereby affects gBGC intensity within genes. Overall, the gBGC model explains 70% of the variance in SCU among genes. We argue that the strong heterogeneity of SCU induced by gBGC in mammalian genomes precludes any optimization of the tRNA pool to the demand in codon usage.

scholarly journals Quantifying Codon Usage in Signal Peptides: Gene Expression and Amino Acid Usage Explain Apparent Selection for Inefficient Codons

2018 ◽  
Author(s):  
Alexander L. Cope ◽  
Robert L. Hettich ◽  
Michael A. Gilchrist
Keyword(s):  
Gene Expression ◽  
Population Genetics ◽  
Amino Acid ◽  
Codon Usage ◽  
Amino Acid Usage ◽  
Signal Peptides ◽  
Mutation Bias ◽  
Critical Feature ◽  
Cytoplasmic Proteins ◽  
Adaptation Index

AbstractThe Sec secretion pathway is found across all domains of life. A critical feature of Sec secreted proteins is the signal peptide, a short peptide with distinct physicochemical properties located at the N-terminus of the protein. Previous work indicates signal peptides are biased towards translationally inefficient codons, which is hypothesized to be an adaptation driven by selection to improve the efficacy and efficiency of the protein secretion mechanisms. We investigate codon usage in the signal peptides of E. coli using the Codon Adaptation Index (CAI), the tRNA Adaptation Index (tAI), and the ribosomal overhead cost formulation of the stochastic evolutionary model of protein production rates (ROC-SEMPPR). Comparisons between signal peptides and 5’-end of cytoplasmic proteins using CAI and tAI are consistent with a preference for inefficient codons in signal peptides. Simulations reveal these differences are due to amino acid usage and gene expression - we find these differences disappear when accounting for both factors. In contrast, ROC-SEMPPR, a mechanistic population genetics model capable of separating the effects of selection and mutation bias, shows codon usage bias (CUB) of the signal peptides is indistinguishable from the 5’-ends of cytoplasmic proteins. Additionally, we find CUB at the 5’-ends is weaker than later segments of the gene. Results illustrate the value in using models grounded in population genetics to interpret genetic data. We show failure to account for mutation bias and the effects of gene expression on the efficacy of selection against translation inefficiency can lead to a misinterpretation of codon usage patterns.

scholarly journals Tempo of degeneration across independently evolved non-recombining regions

2021 ◽  
Author(s):  
Fantin Carpentier ◽  
Ricardo Rodriguez De La Vega ◽  
Michael H. Perlin ◽  
Margaret Wallen ◽  
Michael Hood ◽  
...  
Keyword(s):  
Codon Usage ◽  
Gene Conversion ◽  
Mating Type ◽  
Genetic Diseases ◽  
Smut Fungi ◽  
Recombination Suppression ◽  
Optimal Codons ◽  
Optimal Codon ◽  
Biased Gene Conversion

Recombination is beneficial over the long term, allowing more effective selection. Despite long-term advantages of recombination, local recombination suppression is known to evolve and lead to genomic degeneration, in particular on sex and mating-type chromosomes, sometimes linked to severe genetic diseases. Here, we investigated the tempo of degeneration in non-recombining regions, i.e., the function curve for the accumulation of deleterious mutations over time, taking advantage of 17 independent events of large recombination suppression identified on mating-type chromosomes of anther-smut fungi, including five newly identified in the present study. Using high-quality genomes assemblies of alternative mating types of 13 Microbotryum species, we estimated the degeneration levels in terms of accumulation of non-optimal codons and non-synonymous substitutions in non-recombining regions. We found a reduced frequency of optimal codons in the non-recombining regions on mating-type chromosomes compared to autosomes. We showed that the lower frequency of optimal codons in non-recombining regions was not due to less frequent GC-biased gene conversion or lower ancestral expression levels compared to recombining regions. We estimated that the frequency of optimal codon usage decreased linearly at a rate of 0.989 per My. The non-synonymous over synonymous substitution rate (dN/dS) increased rapidly after recombination suppression and then reached a plateau. To our knowledge this is the first study to disentangle effects of reduced selection efficacy from GC-biased gene conversion in the evolution of optimal codon usage to quantify the tempo of degeneration in non-recombining regions, leveraging on multiple independent recombination suppression events. Understanding the tempo of degeneration is important for our knowledge on genomic evolution, on the origin of genetic diseases and on the maintenance of regions without recombination.

scholarly journals Divergent genes in gerbils: prevalence, relation to GC-biased substitution, and phenotypic relevance

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Yichen Dai ◽  
Rodrigo Pracana ◽  
Peter W. H. Holland
Keyword(s):  
Amino Acid ◽  
Gene Conversion ◽  
Gc Content ◽  
Biochemical Properties ◽  
Meriones Unguiculatus ◽  
Metabolic Dysfunction ◽  
Sand Rat ◽  
Metabolic Dysregulation ◽  
Biased Gene Conversion ◽  
Excessive Accumulation

Abstract Background Two gerbil species, sand rat (Psammomys obesus) and Mongolian jird (Meriones unguiculatus), can become obese and show signs of metabolic dysregulation when maintained on standard laboratory diets. The genetic basis of this phenotype is unknown. Recently, genome sequencing has uncovered very unusual regions of high guanine and cytosine (GC) content scattered across the sand rat genome, most likely generated by extreme and localized biased gene conversion. A key pancreatic transcription factor PDX1 is encoded by a gene in the most extreme GC-rich region, is remarkably divergent and exhibits altered biochemical properties. Here, we ask if gerbils have proteins in addition to PDX1 that are aberrantly divergent in amino acid sequence, whether they have also become divergent due to GC-biased nucleotide changes, and whether these proteins could plausibly be connected to metabolic dysfunction exhibited by gerbils. Results We analyzed ~ 10,000 proteins with 1-to-1 orthologues in human and rodents and identified 50 proteins that accumulated unusually high levels of amino acid change in the sand rat and 41 in Mongolian jird. We show that more than half of the aberrantly divergent proteins are associated with GC biased nucleotide change and many are in previously defined high GC regions. We highlight four aberrantly divergent gerbil proteins, PDX1, INSR, MEDAG and SPP1, that may plausibly be associated with dietary metabolism. Conclusions We show that through the course of gerbil evolution, many aberrantly divergent proteins have accumulated in the gerbil lineage, and GC-biased nucleotide substitution rather than positive selection is the likely cause of extreme divergence in more than half of these. Some proteins carry putatively deleterious changes that could be associated with metabolic and physiological phenotypes observed in some gerbil species. We propose that these animals provide a useful model to study the ‘tug-of-war’ between natural selection and the excessive accumulation of deleterious substitutions mutations through biased gene conversion.

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