Purifying selection against gene conversions between the polyamine transport (TPO) genes of Saccharomyces species.

Saccharomyces species have five TPO genes, TPO1 through TPO5, coding for proteins that are involved in up taking or excreting intracellular spermine, putrescine or spermidine. Here, we investigate the evolutionary fate and functional impacts of gene conversions between these genes. Our results show that gene conversions occurred only between the TPO2 and TPO3 genes of the six Saccharomyces species we studied. They also show that these gene conversions occurred independently in all six species. The facts that they only occur between closely related genes having similar function, and that they are limited to the transmembrane domain of these proteins, suggest that they have little functional impact. These gene conversions therefore likely represent neutral mutations which are not subject to purifying selection.

Purifying selection against gene conversions in the folate receptor genes of primates.

We characterized the gene conversions between the human folate receptor (FOLR) genes and those of five other primate species. We found 26 gene conversions having an average length of 534 nucleotides. The length of these conversions is correlated with sequence similarity, converted regions have a higher GC-content and the average size of converted regions from a functional donor to another functional donor is significantly smaller than the average size from a functional donor to a pseudogene. Furthermore, the few conversions observed in the FOLR1 and FOLR2 genes did not change any amino acids in their coding regions and did not affect their promoter regions. In contrast, the promoter and coding regions of the FOLR3 gene are frequently converted and these conversions changed many amino acids in marmoset. These results suggest that purifying selection is limiting the functional impact that frequent gene conversions have on functional folate receptor genes.

Multiple independent insertions of 5S rRNA genes in the spliced-leader gene family of trypanosome species.

Analyses of the 5S rRNA genes found in the spliced-leader (SL) gene repeat units of numerous trypanosome species suggest that such linkages were not inherited from a common ancestor, but were the result of independent 5S rRNA gene insertions. In trypanosomes, 5S rRNA genes are found either in the tandemly repeated units coding for SL genes or in independent tandemly repeated units. Given that trypanosome species where 5S rRNA genes are within the tandemly repeated units coding for SL genes are phylogenetically related, one might hypothesize that this arrangement is the result of an ancestral insertion of 5S rRNA genes into the tandemly repeated SL gene family of trypanosomes. Here, we use the types of 5S rRNA genes found associated with SL genes, the flanking regions of the inserted 5S rRNA genes and the position of these insertions to show that most of the 5S rRNA genes found within SL gene repeat units of trypanosome species were not acquired from a common ancestor but are the results of independent insertions. These multiple 5S rRNA genes insertion events in trypanosomes are likely the result of frequent founder events in different hosts and/or geographical locations in species having short generation times.

Gene conversions are frequent but not under positive selection in the Siglec gene families of primates.

Siglecs are cell surface proteins that belong to the immunoglobulin superfamily and which bind sialic acids. They are composed of two groups, the conserved Siglecs and the CD33-related Siglecs. Previous studies have reported the occurrence of gene conversions between human CD33-related Siglecs and suggested that these conversions are adaptive because they increase the diversity of these immunoglobulin-related genes. Here, we analyze the Siglec genes of five primate species and show that gene conversions are not observed between conserved Siglec genes but that they are frequent between primate CD33-related Siglecs. The gene conversions between CD33-related Siglec genes only occur between similar genes and equally frequently in sialic acid binding and nonbinding domains. Furthermore, dN/dS ratio tests show that most of the Ig-like V-type 1 and the Ig-like C2-type 1 domains of Siglec genes evolve either neutrally or under purifying selection and that gene conversions were not responsible for the positively selected regions detected in the Ig-like V-type1 domain of the human SIGLEC7 and SIGLEC9 genes. Our results suggest that the frequent gene conversions between CD33-related Siglec genes are simply a consequence of the high degree of sequence similarity of these genes and that they are not adaptive.

[High gene conversion frequency between genes encoding 2-deoxyglucose-6-phosphate phosphatase in 3 Saccharomyces species]. / Haute fréquence de conversions géniques entre les gènes codant pour la phosphatase du 2-déoxyglucose 6-phosphate chez trois espèces du genre Saccharomyces.

Gene conversions are nonreciprocal sequence exchanges between genes. They are relatively common in Saccharomyces cerevisiae, but few studies have investigated the evolutionary fate of gene conversions or their functional impacts. Here, we analyze the evolution and impact of gene conversions between the two genes encoding 2-deoxyglucose-6-phosphate phosphatase in S. cerevisiae, Saccharomyces paradoxus and Saccharomyces mikatae. Our results demonstrate that the last half of these genes are subject to gene conversions among these three species. The greater similarity and the greater percentage of GC nucleotides in the converted regions, as well as the absence of long regions of adjacent common converted sites, suggest that these gene conversions are frequent and occur independently in all three species. The high frequency of these conversions probably result from the fact that they have little impact on the protein sequences encoded by these genes.

Gene conversions are under purifying selection in the carcinoembryonic antigen immunoglobulin gene families of primates.

The carcinoembryonic antigen (CEA) family contains a large number of glycoproteins belonging to the immunoglobulin superfamily. Here, we investigate whether the gene conversions occurring between primate CEA-related genes are adaptive. Our results show that primate CEA-related genes are subject to frequent and repeated gene conversion events. Furthermore, gene conversions occur most frequently between nearby genes sharing similar sequences, are not more frequent in Ig-like V-type 1 domains than in the Ig-like C2-type 1 domains and dN/dS ratio tests shown that both these domains evolve either neutrally or under purifying selection. Our results therefore suggest that CEA-related genes evolve under purifying selection and the frequent gene conversion events we observed likely represent selectively neutral events between genes having similar sequences and functions.

Chromatin diminution in the copepod Mesocyclops edax: elimination of both highly repetitive and nonhighly repetitive DNA.

Chromatin diminution, a developmentally regulated process of DNA elimination, is found in numerous eukaryotic species. In the copepod Mesocyclops edax, some 90% of its genomic DNA is eliminated during the differentiation of embryonic cells into somatic cells. Previous studies have shown that the eliminated DNA contains highly repetitive sequences. Here, we sequenced DNA fragments from pre- and postdiminution cells to determine whether nonhighly repetitive sequences are also eliminated during the process of chromatin diminution. Comparative analyses of these sequences, as well as the sequences eliminated from the genome of the copepod Cyclops kolensis, show that they all share similar abundances of tandem repeats, dispersed repeats, transposable elements, and various coding and noncoding sequences. This suggests that, in the chromatin diminution observed in M. edax, both highly repetitive and nonhighly repetitive sequences are eliminated and that there is no bias in the type of nonhighly repetitive DNA being eliminated.

Strong purifying selection against gene conversions in the trypsin genes of primates.

The trypsin gene families of primate species are composed of members who share a remarkable level of sequence similarity. Here, we investigated the gene conversions occurring within the trypsin gene family in five primate species. A total of 36 conversion events, with an average length (±standard deviation) of 1,526 ± 1,124 nucleotides, were detected using two methods. Such extensive gene conversions are likely both the cause and the consequence of the high sequence similarity between primate trypsin genes. In the trypsins encoded by these genes, both the overall amino acid sequences and critical amino acid residues are conserved. Therefore, the numerous long gene conversions we detected between trypsin genes did not alter any of their functionally important amino acid sites. This suggest that, in the trypsin genes of the five primate species studied here, strong purifying selection against gene conversions is occurring in regions containing functionally important residues.

5S rRNA gene arrangements in protists: a case of nonadaptive evolution.

Given their high copy number and high level of expression, one might expect that both the sequence and organization of eukaryotic ribosomal RNA genes would be conserved during evolution. Although the organization of 18S, 5.8S and 28S ribosomal RNA genes is indeed relatively well conserved, that of 5S rRNA genes is much more variable. Here, we review the different types of 5S rRNA gene arrangements which have been observed in protists. This includes linkages to the other ribosomal RNA genes as well as linkages to ubiquitin, splice-leader, snRNA and tRNA genes. Mapping these linkages to independently derived phylogenies shows that these diverse linkages have repeatedly been gained and lost during evolution. This argues against such linkages being the primitive condition not only in protists but also in other eukaryote species. Because the only characteristic the diverse genes with which 5S rRNA genes are found linked with is that they are tandemly repeated, these arrangements are unlikely to provide any selective advantage. Rather, the observed high variability in 5S rRNA genes arrangements is likely the result of the fact that 5S rRNA genes contain internal promoters, that these genes are often transposed by diverse recombination mechanisms and that these new gene arrangements are rapidly homogenized by unequal crossingovers and/or by gene conversions events in species with short generation times and frequent founder events.

Stronger purifying selection against gene conversions in a pathogenic Saccharomyces cerevisiae strain.

Gene conversions most often have no selective impact, but some are selectively disadvantageous whereas others are selectively advantageous. Although gene conversions have been extensively studied in yeasts, very little is known about their selective impact in pathological yeasts. Here, we used the GENECONV software to compare the characteristics of candidate gene conversions found in a pathogenic strain (YJM789) and a nonpathogenic strain (S288c) of Saccharomyces cerevisiae. Interestingly, the pathogenic strain has fewer gene conversions when compared with the nonpathogenic strain. Of the 123 conversions we identified, 27 were identical or similar between the two strains, 62 were specific to the S288c strain, and 34 were specific to the YJM789 strain. Identical and similar conversions likely represent conversions that are under similar levels of purifying selection in both strains. The lower number of gene conversions in most gene families of the pathogenic strain is likely the result of higher purifying selection in this strain. In contrast, the higher number of conversions found in the YRF1 helicase gene family of the pathogenic strain could represent an example of adaptive gene conversions involved in maintaining its telomeres.

The abundance of processed pseudogenes derived from glycolytic genes is correlated with their expression level.

The abundance of processed pseudogenes in different vertebrate species is known to be proportional to the length of their oogenesis. However, this hypothesis cannot explain why, in a given species, certain genes produce more processed pseudogenes than others. In particular, one would expect that all genes of the glycolytic pathway would generate roughly the same number of processed pseudogenes. However, some glycolitic genes generate more processed pseudogenes than others. Here, we show that there is a positive correlation between the abundance of processed pseudogene generated from glycolytic genes and their level of expression. The variation in expression level of different glycolytic genes likely reflects the fact that some of them, such a GAPDH, have functions other than those they play in glycolysis. Furthermore, the age distribution of GAPDH-processed pseudogenes corresponds to the age distribution of LINE1 elements, which are the source of the reverse transcriptase that generates processed pseudogenes. These results support the hypothesis that gene expression levels affect the level of processed pseudogene production.

Gene conversions in the growth hormone gene family of primates: stronger homogenizing effects in the Hominidae lineage.

In humans, the growth hormone/chorionic somatomammotropin gene family is composed of five highly similar genes. We characterized the gene conversions that occurred between the growth hormone genes of 11 primate species. We detected 48 conversions using GENECONV and others were only detected using phylogenetic analyses. Gene conversions were detected in all species analyzed, their average size (±standard deviation) is 197.8±230.4 nucleotides, the size of the conversions is correlated with sequence similarity and converted regions are significantly more GC-rich than non-converted regions. Gene conversions have a stronger homogenizing effect in Hominidae genes than in other primate species. They are also less frequent in conserved gene regions and towards functionally important genes. This suggests that the high degree of sequence similarity observed between the growth hormone genes of primate species is a consequence of frequent gene conversions in gene regions which are under little selective constraints.

The increase in the number of subunits in eukaryotic RNA polymerase III relative to RNA polymerase II is due to the permanent recruitment of general transcription factors.

The number of subunits of RNA polymerases (RNAPs) increases during evolution from 5 in eubacteria to 12 in archaea. In eukaryotes, which have at least three RNAPs, the number of subunits has expanded from 12 in RNA polymerase II (RNAPII) to 14 in RNA polymerase I (RNAPI) and to 17 in RNA polymerase III (RNAPIII). It was recently demonstrated that the two additional subunits found in RNAPI relative to RNAPII are homologous to TFIIF, a dimeric general transcription factor of RNAPII. Here, we extend this finding by demonstrating that four of the five RNAPIII-specific subunits are also homologous to transcription factors of RNAPII. We use the available evidence to propose an evolutionary history of the eukaryotic RNAPs and argue that the increases in the number of subunits that occurred in RNAPs I and III are due to the permanent recruitment of preexisting transcription factors.

Inactivation dates of the human and guinea pig vitamin C genes.

The capacity to biosynthesize ascorbic acid has been lost in a number of species including primates, guinea pigs, teleost fishes, bats, and birds. This inability results from mutations in the GLO gene coding for L-gulono-γ-lactone oxidase, the enzyme responsible for catalyzing the last step in the vitamin C biosynthetic pathway. We analyzed available primate and rodent GLO gene sequences to determine their evolutionary history. We used a method based on sequence comparisons of lineages with and without functional GLO genes to calculate inactivation dates of 61 and 14 MYA for the primate and guinea pig genes, respectively. These estimates are consistent with previous phylogeny-based estimates. An analysis of transposable element distribution in the primate and rodent GLO sequences did not reveal conclusive evidence that illegitimate recombination between repeats has contributed to the loss of exons in the primate and guinea pig genes.

Patient-partner engagement at the Centre de recherche du CHUS in the Province of Québec, Canada: from an intuitive methodology to outreach after three years of implementation.

BACKGROUND: Medical societies and funding agencies strongly recommend that patients be included as partners in research publications and grant applications. Although this "top-down" approach is certainly efficient at forcing this new and desirable type of collaboration, our past experience demonstrated that it often results in an ambiguous relationship as not yet well integrated into the cultures of either patients' or the researchers'. The question our group raised from this observation was: "How to generate a cultural shift toward a fruitful and long-lasting collaboration between patients and researchers? A "bottom-up" approach was key to our stakeholders. The overall objective was to build a trusting and bidirectional-ecosystem between patients and researchers. The specific objectives were to document: 1) the steps that led to the development of the first patient-partner strategic committee within a research center in the Province of Québec; 2) the committee's achievements after 3 years. METHODS: Eighteen volunteer members, 12 patient-partners and 6 clinician/institutional representatives, were invited to represent the six research themes of the Centre de recherche du CHU de Sherbrooke (CRCHUS) (Quebec, Canada). Information on the services offered by Committee was disseminated internally and to external partners. Committee members satisfaction was evaluated. RESULTS: From May 2017 to April 2020, members attended 29 scheduled and 6 ad hoc meetings and contributed to activities requiring over 1000 h of volunteer time in 2018-2019 and 1907 h in the 2019-2020 period. The Committee's implication spanned governance, expertise, and knowledge transfer in research. Participation in these activities increased annually at local, provincial, national and international levels. The Patient-Partner Committee collaborated with various local (n = 7), provincial (n = 6) and national (n = 4) partners. Member satisfaction with the Committee's mandate and format was 100%. CONCLUSIONS: The CRCHUS co-constructed a Patient-Partner Strategic Committee which resulted in meaningful bilateral, trusting and fruitful collaborations between patients, researchers and partners. The "bottom-up" approach - envisioned and implemented by the Committee, where the expertise and the needs of patients complemented those of researchers, foundations, networks and decision-makers - is key to the success of a cultural shift. The CRCHUS Committee created a hub to develop the relevant intrinsic potential aimed at changing the socio-cultural environment of science.

The evolutionary rates of eukaryotic RNA polymerases and of their transcription factors are affected by the level of concerted evolution of the genes they transcribe.

A defining characteristic of all eukaryotes is the presence of three RNA polymerases, each of which transcribes a particular subset of nuclear genes. RNA polymerase I transcribes rRNA genes; RNA polymerase II transcribes mRNA, miRNA, snRNA, and snoRNA genes; and RNA polymerase III transcribes 5S rRNA and tRNA genes. Here, we use the sequences of up to 25 Ascomycete species to show that the type of genes transcribed by each RNA polymerase affects their evolutionary rates and those of their transcription factors (TFs). The RNA polymerase subunits and TFs of genes whose promoters experience higher levels of concerted evolution evolve significantly faster than those experiencing lower levels of concerted evolution. The rates of evolution of RNA polymerase genes and their TFs are therefore not only the result of diverse selective constraints but are also influenced by the level of concerted evolution of the genes they transcribe.

Structural differentiation of the three eukaryotic RNA polymerases.

All eukaryotes have three different RNA polymerases (RNAPs) which transcribe different types of genes. RNA polymerase I transcribes rRNA genes, RNA polymerase II transcribes mRNA, miRNA, snRNA, and snoRNA genes, and RNA polymerase III transcribes tRNA and 5S rRNA genes. Here, we use an in silico approach to identify putative functional differences between these three RNAPs. Our results show that cleft loops are the most conserved regions of RNAPs, but that these regions have several significant length differences between the three RNAPs. There were also significant shifts in the rates of evolution of some amino acid sites in all three enzymes prior to the diversification of eukaryotes and these amino acids are preferentially located near the catalytic center of the three enzymes. These results suggest that functional differences exist between the three RNAPs and that these differences are all clustered near the active sites.

Ectopic gene conversions in the human genome.

We used the GENCONV method to characterize the gene conversions that occurred amongst the 1434 protein coding human gene families with three or more genes. Conversions occur at a frequency of 0.88% (483 conversion events/55,050 gene pairs compared) and have an average length of 371+/-752 bp (+/-standard deviation). Both the size and the frequency of conversions are positively correlated with the similarity of the sequences involved in these conversions. The frequency of conversions and the local recombination rate are also positively correlated. Intrachromosomal conversions are almost 5 times more frequent than interchromosomal conversions and the frequency of intrachromosomal conversions increases as the distance between genes decreases. However, the higher frequency of conversions between nearby genes with the same transcriptional orientation is due to the fact that most functional duplicated genes are found next to one another and in the same transcriptional orientation. The average length of a conversion spanning only an intron region is significantly smaller than conversions spanning both exons and introns or only exons. This suggests that the smaller degree of sequence similarity of introns limits the size of conversions between duplicated human genes. The significant excess of conversions at the 3'-end of human genes suggests that incomplete cDNA molecules are often involved in conversions with chromosomal gene copies.

"They heard our voice!" patient engagement councils in community-based primary care practices: a participatory action research pilot study.

BACKGROUND: Patient engagement could improve the quality of primary care practices. However, we know little about effective patient engagement strategies. We aimed to assess the acceptability and feasibility of embedding advisory councils of clinicians, managers, patients and caregivers to conduct patient-oriented quality improvement projects in primary care practices. METHODS: Using a participatory action research approach, we conducted our study in two non-academic primary care practices in Quebec City (Canada). Patient-experts (patients trained in research) were involved in study design, council recruitment and meeting facilitation. Advisory councils were each to include patients and/or caregivers, clinicians and managers. Over six meetings, councils would identify quality improvement priorities and plan projects accordingly. We assessed acceptability and feasibility of the councils using non-participant observations, audio-recordings and self-administered questionnaires. We used descriptive analyses, triangulated qualitative data and performed inductive thematic analysis. RESULTS: Between December 2017 and June 2018, two advisory councils were formed, each with 11 patients (36% male, mean age 53.8 years), a nurse and a manager practising as a family physician (25% male, mean age 45 years). The six meetings per practice occurred within the study period with a mean of eight patients per meeting. Councils worked on two projects each: the first council on a new information leaflet about clinic organization and operation, and on communications about local public health programs; the second on methods to further engage patients in the practice, and on improving the appointment scheduling system. Median patient satisfaction was 8/10, and 66.7% perceived councils had an impact on practice operations. They considered involvement of a manager, facilitation by patient-experts, and the fostering of mutual respect as key to this impact. Clinicians and managers liked having patients as facilitators and the respect among members. Limiting factors were difficulty focusing on a single feasible project and time constraints. Managers in both practices were committed to pursuing the councils post-study. CONCLUSION: Our results indicated that embedding advisory councils of clinicians, managers, patients and caregivers to conduct patient-oriented quality improvement projects in primary care practices is both acceptable and feasible. Future research should assess its transferability to other clinical contexts.

Similar ectopic gene conversion frequencies in the backbone genome of pathogenic and nonpathogenic Escherichia coli strains.

We previously showed that gene conversions were more frequent in the genomes of three Escherichia coli pathogenic strains than in the genome of the nonpathogenic K-12 E. coli strain. However, that study did not address whether the more frequent conversions observed in the genes of pathogenic strains occurred between the backbone genes common to these four strains or in the numerous horizontally transferred genes found only in pathogenic strains. Here, we show that ectopic gene conversions are equally frequent in the backbone genes of pathogenic and nonpathogenic strains, that most of these conversions are short, and that the nucleotide changes they generate are probably selectively neutral. Backbone genes are therefore under similar selective constraints in both pathogenic and nonpathogenic E. coli strains. The higher frequency of gene conversions we previously observed in pathogenic strains is therefore due to higher conversion frequencies between the numerous horizontally transferred genes found only in pathogenic strains.