Purifying selection acting on the sequence of highly expressed proteins in the microevolution
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PROVIDER: PRJNA781148 | ENA |
REPOSITORIES: ENA
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Project description:Constraints on the rate of protein sequence evolution have been a central question in evolutionary biology. Orthology analysis between closely related species has revealed that the evolutionary speed is constrained by the expression level, with highly expressed proteins evolving slowly. This negative correlation between expression levels and evolutionary rates (known as the E-R anticorrelation) has already been widely observed in past macroevolution between species, for example, between Escherichia coli and Salmonella. However, it remains unclear whether this seemingly general law also governs microevolution, including past and de novo, within a species. To explore the ubiquitous impact of expression level on molecular evolution in bacteria, we analysed genome sequences for 99 strains of E. coli for microevolution in nature. We also analysed genomic mutations accumulated under laboratory conditions as a model of de novo microevolution. Here, we show that the E-R anticorrelation is significant in both past microevolution and de novo evolution in E. coli. Our data also indicate that purifying selection acting on highly expressed genes contributes to the ubiquity of the E-R anticorrelation. This study confirmed ongoing purifying selection acting on highly expressed genes, and implied that expression level has a ubiquitous impact on the speed of molecular diversification evolution in bacteria.
2022-09-01 | GSE189008 | GEO
Project description:Plant Y-chromosome degeneration is retarded by haploid purifying selection.
| PRJNA146235 | ENA
Project description:Following antifungal treatment, Candida albicans, and other human pathogenic fungi can undergo microevolution, which leads to the emergence of drug resistance. However, the capacity for microevolutionary adaptation of fungi goes beyond the development of drug resistance. Here we used an experimental microevolution approach to show that one of the central pathogenicity mechanisms of C. albicans, the yeast-to-hyphae transition, can be subject to experimental evolution. The C. albicans cph1Δ/efg1Δ mutant is non-filamentous, as central signalling pathways linking environmental cues to hypha formation are disrupted. We subjected this mutant to constant selection pressure in the hostile environment of the macrophage phagosome. In a comparatively short time-frame, the mutant evolved the ability to escape macrophages by filamentation. To investigate the transcriptional response underlying the yeast-to-filament transition in the evolved strain, we applied RNA-Seq technology. Furthermore, RNA-Seq data were used to identify SNPs, which are specific for the evolved strain.
2015-03-31 | GSE56174 | GEO
Project description:MicroEvolution study of Mycobacterium tuberculosis
| PRJNA52637 | ENA
Project description:Positive selection pressure acting on protein-coding sequences is usually inferred when the rate of nonsynonymous substitution is greater than the synonymous rate. However, purifying selection acting directly on the nucleotide sequence can lower the synonymous substitution rate. This could result in false inference of positive selection because when synonymous changes at some sites are under purifying selection, the average synonymous rate is an underestimate of the neutral rate of evolution. Even though HIV-1 coding sequences contain a number of regions that function at the nucleotide level, and are thus likely to be affected by purifying selection, studies of positive selection assume that synonymous substitutions can be used to estimate the neutral rate of evolution.We modelled site-to-site variation in the synonymous substitution rate across coding regions of the HIV-1 genome. Synonymous substitution rates were found to vary significantly within and between genes. Surprisingly, regions of the genome that encode proteins in more than one frame had significantly higher synonymous substitution rates than regions coding in a single frame. We found evidence of strong purifying selection pressure affecting synonymous mutations in fourteen regions with known functions. These included an exonic splicing enhancer, the rev-responsive element, the poly-purine tract and a transcription factor binding site. A further five highly conserved regions were located within known functional domains. We also found four conserved regions located in env and vpu which have not been characterized previously.We provide the coordinates of genomic regions with markedly lower synonymous substitution rates, which are putatively under the influence of strong purifying selection pressure at the nucleotide level as well as regions encoding proteins in more than one frame. These regions should be excluded from studies of positive selection acting on HIV-1 coding regions.
| S-EPMC2666660 | biostudies-literature
Project description:Genomic analysis of microevolution, reinfection and highly complex diversity in patients with Mycobacterium abscessus sequential isolates
| PRJEB61124 | ENA
Project description:Following antifungal treatment, Candida albicans, and other human pathogenic fungi can undergo microevolution, which leads to the emergence of drug resistance. However, the capacity for microevolutionary adaptation of fungi goes beyond the development of drug resistance. Here we used an experimental microevolution approach to show that one of the central pathogenicity mechanisms of C. albicans, the yeast-to-hyphae transition, can be subject to experimental evolution. The C. albicans cph1?/efg1? mutant is non-filamentous, as central signalling pathways linking environmental cues to hypha formation are disrupted. We subjected this mutant to constant selection pressure in the hostile environment of the macrophage phagosome. In a comparatively short time-frame, the mutant evolved the ability to escape macrophages by filamentation. To investigate the transcriptional response underlying the yeast-to-filament transition in the evolved strain, we applied RNA-Seq technology. Furthermore, RNA-Seq data were used to identify SNPs, which are specific for the evolved strain. For both strains, the cph1?/efg1? mutant and the Evo-strain, two conditions, one promotes yeast growth the other filamentous growth, were investigated. For each condition three biological replicates were analysed.
2015-03-31 | E-GEOD-56174 | biostudies-arrayexpress
Project description:The existence of overlapping genes (OLGs) with significant coding overlaps revolutionises our understanding of genomic complexity. We report two exceptionally long (957 nt and 1536 nt), evolutionarily novel, translated antisense open reading frames (ORFs) embedded within annotated genes in the medically important Gram-negative bacterium Pseudomonas aeruginosa. Both OLG pairs show sequence features consistent with being genes and transcriptional signals in RNA sequencing data. Translation of both OLGs was confirmed by ribosome profiling and mass spectrometry. Quantitative proteomics of samples taken during different phases of growth revealed regulation of protein abundances, implying biological functionality. Both OLGs are taxonomically highly restricted, and likely arose by overprinting within the genus. Evidence for purifying selection further supports functionality. The OLGs reported here, designated olg1 and olg2, are the longest yet proposed in prokaryotes and are among the best attested in terms of translation and evolutionary constraint. These results highlight a potentially large unexplored dimension of prokaryotic genomes.
2022-03-21 | PXD023992 | Pride
Project description:Gene expression levels can be subject to selection. We hypothesized that the age of gene origin is associated with expression constraints, given that it affects the level of gene integration into the functional cellular environment. By studying the genetic variation affecting gene expression levels (cis expression quantitative trait loci [cis-eQTLs]) and protein levels (cis protein QTLs [cis-pQTLs]), we determined that young, primate-specific genes are enriched in cis-eQTLs and cis-pQTLs. Compared to cis-eQTLs of old genes originating before the zebrafish divergence, cis-eQTLs of young genes have a higher effect size, are located closer to the transcription start site, are more significant, and tend to influence genes in multiple tissues and populations. These results suggest that the expression constraint of each gene increases throughout its lifespan. We also detected a positive correlation between expression constraints (approximated by cis-eQTL properties) and coding constraints (approximated by Ka/Ks) and observed that this correlation might be driven by gene age. To uncover factors associated with the increase in gene-age-related expression constraints, we demonstrated that gene connectivity, gene involvement in complex regulatory networks, gene haploinsufficiency, and the strength of posttranscriptional regulation increase with gene age. We also observed an increase in heritability of gene expression levels with age, implying a reduction of the environmental component. In summary, we show that gene age shapes key gene properties during evolution and is therefore an important component of genome function.
| S-EPMC4259975 | biostudies-literature
Project description:The genomic distribution of transposable elements is driven by spatially variable purifying selection
| PRJEB54573 | ENA