RESUMEN
CRISPR-Cas systems provide adaptive immunity for prokaryotic cells by recognizing and eliminating the recurrent genetic invaders whose sequences had been captured in a prior infection and stored in the CRISPR arrays as spacers. However, the biological/environmental factors determining the efficiency of this immune system have yet to be fully characterized. Recent studies in cultured bacteria showed that slowing the growth rate of bacterial cells could promote their acquisition of novel spacers. This study examined the relationship between the CRISPR-Cas content and the minimal doubling time across the bacteria and the archaea domains. Every completely sequenced genome could be used to predict a minimal doubling time. With a large data set of 4,142 bacterial samples, we found that the predicted minimal doubling times are positively correlated with spacer number and other parameters of the CRISPR-Cas systems, like array number, Cas gene cluster number, and Cas gene number. Different data sets gave different results. Weak results were obtained in analyzing bacterial empirical minimal doubling times and the archaea domain. Still, the conclusion of more spacers in slowly grown prokaryotes was supported. In addition, we found that the minimal doubling times are negatively correlated with the occurrence of prophages, and the spacer numbers per array are negatively associated with the number of prophages. These observations support the existence of an evolutionary trade-off between bacterial growth and adaptive defense against virulent phages. IMPORTANCE Accumulating evidence indicates that slowing the growth of cultured bacteria could stimulate their CRISPR spacer acquisition. We observed a positive correlation between CRISPR-Cas content and cell cycle duration across the bacteria domain. This observation extends the physiological conclusion to an evolutionary one. In addition, the correlation provides evidence supporting the existence of a trade-off between bacterial growth/reproduction and antiviral resistance.
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Bacteriófagos , Sistemas CRISPR-Cas , Bacterias/genética , Archaea/genética , Bacteriófagos/genética , Profagos/genéticaRESUMEN
BACKGROUND: The evolution of spliceosomal introns has been widely studied among various eukaryotic groups. Researchers nearly reached the consensuses on the pattern and the mechanisms of intron losses and gains across eukaryotes. However, according to previous studies that analyzed a few genes or genomes, Nematoda seems to be an eccentric group. RESULTS: Taking advantage of the recent accumulation of sequenced genomes, we extensively analyzed the intron losses and gains using 104 nematode genomes across all the five Clades of the phylum. Nematodes have a wide range of intron density, from less than one to more than nine per kbp coding sequence. The rates of intron losses and gains exhibit significant heterogeneity both across different nematode lineages and across different evolutionary stages of the same lineage. The frequency of intron losses far exceeds that of intron gains. Five pieces of evidence supporting the model of cDNA-mediated intron loss have been observed in ten Caenorhabditis species, the dominance of the precise intron losses, frequent loss of adjacent introns, high-level expression of the intron-lost genes, preferential losses of short introns, and the preferential losses of introns close to 3'-ends of genes. Like studies in most eukaryotic groups, we cannot find the source sequences for the limited number of intron gains detected in the Caenorhabditis genomes. CONCLUSIONS: These results indicate that nematodes are a typical eukaryotic group rather than an outlier in intron evolution.
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Nematodos , Animales , Secuencia de Bases , Eucariontes/genética , Evolución Molecular , Intrones , Nematodos/genética , Filogenia , Empalmosomas/genéticaRESUMEN
Although performing adaptive immunity, CRISPR-Cas systems are present in only 40% of bacterial genomes. We observed an abrupt increase of bacterial CRISPR-Cas abundance at around 45°C. Phylogenetic comparative analyses confirmed that the abundance correlates with growth temperature only at the temperature range around 45°C. From the literature, we noticed that the diversities of cellular predators (like protozoa, nematodes, and myxobacteria) have a steep decline at this temperature range. The grazing risk faced by bacteria reduces substantially at around 45°C and almost disappears above 60°C. We propose that viral lysis would become the dominating factor of bacterial mortality, and antivirus immunity has a higher priority at higher temperatures. In temperature ranges where the abundance of cellular predators does not change with temperature, the growth temperatures of bacteria would not significantly affect their CRISPR-Cas contents. The hypothesis predicts that bacteria should also be rich in CRISPR-Cas systems if they live in other extreme conditions inaccessible to grazing predators.
RESUMEN
BACKGROUND: GC pairs are generally more stable than AT pairs; GC-rich genomes were proposed to be more adapted to high temperatures than AT-rich genomes. Previous studies consistently showed positive correlations between growth temperature and the GC contents of structural RNA genes. However, for the whole genome sequences and the silent sites of the codons in protein-coding genes, the relationship between GC content and growth temperature is in a long-lasting debate. RESULTS: With a dataset much larger than previous studies (681 bacteria and 155 archaea with completely assembled genomes), our phylogenetic comparative analyses showed positive correlations between optimal growth temperature (Topt) and GC content both in bacterial and archaeal structural RNA genes and in bacterial whole genome sequences, chromosomal sequences, plasmid sequences, core genes, and accessory genes. However, in the 155 archaea, we did not observe a significant positive correlation of Topt with whole-genome GC content (GCw) or GC content at four-fold degenerate sites. We randomly drew 155 samples from the 681 bacteria for 1000 rounds. In most cases (> 95%), the positive correlations between Topt and genomic GC contents became statistically nonsignificant (P > 0.05). This result suggested that the small sample sizes might account for the lack of positive correlations between growth temperature and genomic GC content in the 155 archaea and the bacterial samples of previous studies. Comparing the GC content among four categories (psychrophiles/psychrotrophiles, mesophiles, thermophiles, and hyperthermophiles) also revealed a positive correlation between GCw and growth temperature in bacteria. By including the GCw of incompletely assembled genomes, we expanded the sample size of archaea to 303. Positive correlations between GCw and Topt appear especially after excluding the halophilic archaea whose GC contents might be strongly shaped by intense UV radiation. CONCLUSIONS: This study explains the previous contradictory observations and ends a long debate. Prokaryotes growing in high temperatures have higher GC contents. Thermal adaptation is one possible explanation for the positive association. Meanwhile, we propose that the elevated efficiency of DNA repair in response to heat mutagenesis might have the by-product of increasing GC content like that happens in intracellular symbionts and marine bacterioplankton.
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Archaea , Células Procariotas , Archaea/genética , Composición de Base , Filogenia , TemperaturaRESUMEN
BACKGROUND: Although horizontal gene transfer (HGT) is a widely accepted force in the evolution of prokaryotic genomes, its role in the evolution of eukaryotic genomes remains hotly debated. Some bdelloid rotifers that are resistant to extreme desiccation and radiation undergo a very high level of HGT, whereas in another desiccation-resistant invertebrate, the tardigrade, the pattern does not exist. Overall, the DNA double-strand breaks (DSBs) induced by prolonged desiccation have been postulated to open a gateway to the nuclear genome for exogenous DNA integration and thus to facilitate the HGT process, thereby enhancing the rate of endosymbiotic DNA transfer (EDT). RESULTS: We first surveyed the abundance of nuclear mitochondrial DNAs (NUMTs) and nuclear plastid DNAs (NUPTs) in five eukaryotes that are highly resistant to desiccation: the bdelloid rotifers Adineta vaga and Adineta ricciae, the tardigrade Ramazzottius varieornatus, and the resurrection plants Dorcoceras hygrometricum and Selaginella tamariscina. Excessive NUMTs or NUPTs were not detected. Furthermore, we compared 24 groups of desiccation-tolerant organisms with their relatively less desiccation-tolerant relatives but did not find a significant difference in NUMT/NUPT contents. CONCLUSIONS: Desiccation may induce DSBs, but it is unlikely to dramatically increase the frequency of exogenous sequence integration in most eukaryotes. The capture of exogenous DNA sequences is possible only when DSBs are repaired through a subtype of non-homologous end joining, named alternative end joining (alt-EJ). Due to the deleterious effects of the resulting insertion mutations, alt-EJ is less frequently initiated than other mechanisms.
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Núcleo Celular/genética , Desecación , Transferencia de Gen Horizontal , Animales , ADN Mitocondrial , Genoma , Plantas/genética , Plastidios/genética , Rotíferos/genética , Tardigrada/genéticaRESUMEN
Copy number changes in protein-coding genes are detrimental if the consequent changes in protein concentrations disrupt essential cellular functions. The dosage sensitivity of transcription factor (TF) genes is particularly interesting because their products are essential in regulating the expression of genetic information. From four recently curated data sets of dosage-sensitive genes (genes with conserved copy numbers across mammals, ohnologs, and two data sets of haploinsufficient genes), we compiled a data set of the most reliable dosage-sensitive (MRDS) genes and a data set of the most reliable dosage-insensitive (MRDIS) genes. The MRDS genes were those present in all four data sets, while the MRDIS genes were those absent from any one of the four data sets and with the probability of being loss of function-intolerant (pLI) values < 0.5 in both of the haploinsufficient gene data sets. Enrichment analysis of TF genes among the MRDS and MRDIS gene data sets showed that TF genes are more likely to be dosage-sensitive than other genes in the human genome. The nuclear receptor family was the most enriched TF family among the dosage-sensitive genes. TF families with very few members were also deemed more likely to be dosage-sensitive than TF families with more members. In addition, we found a certain number of dosage-insensitive TFs. The most typical were the Krüppel-associated box domain-containing zinc-finger proteins (KZFPs). Gene ontology (GO) enrichment analysis showed that the MRDS TFs were enriched for many more terms than the MRDIS TFs; however, the proteins interacting with these two groups of TFs did not show such sharp differences. Furthermore, we found that the MRDIS KZFPs were not significantly enriched for any GO terms, whereas their interacting proteins were significantly enriched for thousands of GO terms. Further characterizations revealed significant differences between MRDS TFs and MRDIS TFs in the lengths and nucleotide compositions of DNA-binding sites as well as in expression level, protein size, and selective force.
RESUMEN
BACKGROUND: Among the four bases, guanine is the most susceptible to damage from oxidative stress. Replication of DNA containing damaged guanines results in G to T mutations. Therefore, the mutations resulting from oxidative DNA damage are generally expected to predominantly consist of G to T (and C to A when the damaged guanine is not in the reference strand) and result in decreased GC content. However, the opposite pattern was reported 16 years ago in a study of prokaryotic genomes. Although that result has been widely cited and confirmed by nine later studies with similar methods, the omission of the effect of shared ancestry requires a re-examination of the reliability of the results. RESULTS: When aerobic and obligate aerobic prokaryotes were mixed together and anaerobic and obligate anaerobic prokaryotes were mixed together, phylogenetic controlled analyses did not detect significant difference in GC content between aerobic and anaerobic prokaryotes. This result is consistent with two generally neglected studied that had accounted for the phylogenetic relationship. However, when obligate aerobic prokaryotes were compared with aerobic prokaryotes, anaerobic prokaryotes, and obligate anaerobic prokaryotes separately using phylogenetic regression analysis, a significant positive association was observed between aerobiosis and GC content, no matter it was calculated from whole genome sequences or the 4-fold degenerate sites of protein-coding genes. Obligate aerobes have significantly higher GC content than aerobes, anaerobes, and obligate anaerobes. CONCLUSIONS: The positive association between aerobiosis and GC content could be attributed to a mutational force resulting from incorporation of damaged deoxyguanosine during DNA replication rather than oxidation of the guanine nucleotides within DNA sequences. Our results indicate a grade in the aerobiosis-associated mutational force, strong in obligate aerobes, moderate in aerobes, weak in anaerobes and obligate anaerobes.
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Composición de Base/genética , Células Procariotas/metabolismo , Aerobiosis , Anaerobiosis , Humanos , Análisis de los Mínimos Cuadrados , Filogenia , Análisis de Regresión , Reproducibilidad de los ResultadosRESUMEN
Staphylococcus aureus small colony variants (SCVs) can cause persistent infections. However, the genomes and transcriptomes of S. aureus SCVs remain poorly understood. A pair of isogenic wild-type and SCV methicillin-resistant S. aureus (MRSA) strains (IE1 and IE2, respectively) were isolated from a patient with prosthetic valve infectious endocarditis. The SCV strain IE2 grew more slowly than the wild-type strain, and serum killing and mouse lethality assays revealed that the virulence of SCV strain IE2 was decreased. Whole-genome sequencing of the SCV and wild-type strains revealed 15 mutations in nine genes associated with metabolism, virulence and DNA repair, including serine/threonine-protein kinase PrkC (prkC), glycerol-3-phosphate acyltransferase (plsY), 2-deoxyribose-5-phosphate aldolase (deoC), extracellular adherence protein (eap), iron compound ABC uptake transporter substrate-binding protein (sstD), RecU Holliday junction resolvase (recU), excinuclease ABC subunit B (uvrB), type I restriction-modification system, M subunit (hsdM) and smooth muscle caldesmon. Sequencing of RNA transcripts revealed that expression levels of 321 genes were upregulated and 582 genes were downregulated in SCV strain IE2 compared with IE1. Most of the differentially expressed genes were involved in metabolism. Expression levels of several genes involved in the pathways to which plsY, deoC, eap and sstD belonged were changed, associated with the metabolism and virulence of S. aureus. In conclusion, the reduced growth rate and decreased virulence of MRSA SCV strains may be related to mutations in and downregulation of genes associated with metabolism and virulence, especially plsY, deoC, eap and sstD.
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Endocarditis/microbiología , Genoma Bacteriano/genética , Prótesis Valvulares Cardíacas/microbiología , Staphylococcus aureus Resistente a Meticilina , Infecciones Estafilocócicas/tratamiento farmacológico , Transcriptoma/genética , Animales , Antibacterianos/uso terapéutico , Proteínas Bacterianas/genética , Cefoperazona/uso terapéutico , Endocarditis/patología , Femenino , Perfilación de la Expresión Génica , Genotipo , Humanos , Masculino , Staphylococcus aureus Resistente a Meticilina/genética , Staphylococcus aureus Resistente a Meticilina/aislamiento & purificación , Staphylococcus aureus Resistente a Meticilina/patogenicidad , Ratones , Ratones Endogámicos BALB C , Polimorfismo de Nucleótido Simple/genética , Infecciones Estafilocócicas/microbiología , Infecciones Estafilocócicas/patología , Sulbactam/uso terapéutico , Vancomicina/uso terapéutico , Virulencia , Inhibidores de beta-Lactamasas/uso terapéuticoRESUMEN
The origin and subsequent accumulation of spliceosomal introns are prominent events in the evolution of eukaryotic gene structure. However, the mechanisms underlying intron gain remain unclear because there are few proven cases of recently gained introns. In an RNA-dependent RNA polymerase (RdRp) gene, we found that a tandem duplication occurred after the divergence of potato and its wild relatives among other Solanum plants. The duplicated sequence crosses the intron-exon boundary of the first intron and the second exon. A new intron was detected at this duplicated region, and it includes a small previously exonic segment of the upstream copy of the duplicated sequence and the intronic segment of the downstream copy of the duplicated sequence. The donor site of this new intron was directly obtained from the small previously exonic segment. Most of the splicing signals were inherited directly from the parental intron/exon structure, including a putative branch site, the polypyrimidine tract, the 3' splicing site, two putative exonic splicing enhancers, and the GC contents differed between the intron and exon. In the widely cited model of intron gain by tandem genomic duplication, the duplication of an AGGT-containing exonic segment provides the GT and AG splicing sites for the new intron. Our results illustrate that the tandem duplication model of intron gain should be diverse in terms of obtaining the proper splicing signals.
RESUMEN
BACKGROUND: Spliceosomal introns are a common feature of eukaryotic genomes. To approach a comprehensive understanding of intron evolution on Earth, studies should look beyond repeatedly studied groups such as animals, plants, and fungi. The slime mold Dictyostelium belongs to a supergroup of eukaryotes not covered in previous studies. RESULTS: We found 441 precise intron losses in Dictyostelium discoideum and 202 precise intron losses in Dictyostelium purpureum. Consistent with these observations, Dictyostelium discoideum was found to have significantly more copies of reverse transcriptase genes than Dictyostelium purpureum. We also found that the lost introns are significantly further from the 5' end of genes than the conserved introns. Adjacent introns were prone to be lost simultaneously in Dictyostelium discoideum. In both Dictyostelium species, the exonic sequences flanking lost introns were found to have a significantly higher GC content than those flanking conserved introns. Together, these observations support a reverse-transcription model of intron loss in which intron losses were caused by gene conversion between genomic DNA and cDNA reverse transcribed from mature mRNA. We also identified two imprecise intron losses in Dictyostelium discoideum that may have resulted from genomic deletions. Ninety-eight putative intron gains were also observed. Consistent with previous studies of other lineages, the source sequences were found in only a small number of cases, with only two instances of intron gain identified in Dictyostelium discoideum. CONCLUSIONS: Although they diverged very early from animals and fungi, Dictyostelium species have similar mechanisms of intron loss.
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Dictyostelium/clasificación , Dictyostelium/genética , Genoma de Protozoos , Intrones , Composición de Base , Secuencia de Bases , Dictyostelium/enzimología , Dictyostelium/metabolismo , Eucariontes/clasificación , Eucariontes/genética , Exones , Conversión Génica , Datos de Secuencia Molecular , ADN Polimerasa Dirigida por ARN/genética , ADN Polimerasa Dirigida por ARN/metabolismo , Retroelementos , Eliminación de SecuenciaRESUMEN
UNLABELLED: In this study, we identified 19 intron losses, including 11 precise intron losses (PILs), six imprecise intron losses (IILs), one de-exonization, and one exon deletion in tomato and potato, and 17 IILs in Arabidopsis thaliana. Comparative analysis of related genomes confirmed that all of the IILs have been fixed during evolution. Consistent with previous studies, our results indicate that PILs are a major type of intron loss. However, at least in plants, IILs are unlikely to be as rare as previously reported. REVIEWERS: This article was reviewed by Jun Yu and Zhang Zhang. For complete reviews, see the Reviewers' Reports section.
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Arabidopsis/genética , Intrones , Eliminación de Secuencia , Solanum lycopersicum/genética , Solanum tuberosum/genética , Secuencia de Bases , Evolución Molecular , Exones/genética , Genoma de Planta , Mutación INDEL , Alineación de Secuencia , Análisis de Secuencia de ADNRESUMEN
Although intron losses have been widely reported, it is not clear whether they are neutral and therefore random or driven by positive selection. Intron transcription and splicing are time-consuming and can delay the expression of its host gene. For genes that must be activated quickly to respond to physiological or stress signals, intron delay may be deleterious. Promoter proximally paused (PPP) genes are a group of rapidly expressed genes. To respond quickly to activation signals, they generally initiate transcription competently but stall after synthesizing a short RNA. In this study, performed in Drosophila melanogaster, the PPP genes were found to have a significantly higher rate of intron loss than control genes. However, further analysis did not find more significant shrinkage of intron size in PPP genes. Referring to previous studies on the rates of transcription and splicing and to the time saved by deletion of the introns from mouse gene Hes7, it is here suggested that transcription delay is comparable to splicing delay only when the intron is 28.5 kb or larger, which is greater in size than 95% of vertebrate introns, 99.5% of Drosophila introns, and all the annotated introns of Saccharomyces cerevisiae and Arabidopsis thaliana. Delays in intron splicing are probably a selective force, promoting intron loss from quickly expressed genes. In other genes, it may have been an exaptation during the emergency of developmental clocks.
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Drosophila melanogaster/genética , Evolución Molecular , Intrones , Transcripción Genética , AnimalesRESUMEN
The fission yeast, Schizosaccharomyces pombe, is an important model species with a low intron density. Previous studies showed extensive intron losses during its evolution. To test the models of intron loss and gain in fission yeasts, we conducted a comparative genomic analysis in four Schizosaccharomyces species. Both intronization and de-intronization were observed, although both were at a low frequency. A de-intronization event was caused by a degenerative mutation in the branch site. Four cases of imprecise intron losses were identified, indicating that genomic deletion is not a negligible mechanism of intron loss. Most intron losses were precise deletions of introns, and were significantly biased to the 3' sides of genes. Adjacent introns tended to be lost simultaneously. These observations indicated that the main force shaping the exon-intron structures of fission yeasts was precise intron losses mediated by reverse transcriptase. We found two cases of intron gains caused by tandem genomic duplication, but failed to identify the mechanisms for the majority of the intron gain events observed. In addition, we found that intron-lost and intron-gained genes had certain similar features, such as similar Gene Ontology categories and expression levels.
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Intrones/genética , Schizosaccharomyces/genética , Secuencia de Aminoácidos , Secuencia de Bases , Secuencia Conservada/genética , Duplicación de Gen/genética , Genes Fúngicos/genética , Anotación de Secuencia Molecular , Datos de Secuencia Molecular , Mutación/genética , Filogenia , Sitios de Empalme de ARN/genética , Transcripción Reversa/genética , Proteínas de Schizosaccharomyces pombe/química , Proteínas de Schizosaccharomyces pombe/genética , Eliminación de Secuencia/genética , Transcriptoma/genéticaRESUMEN
BACKGROUND: Although intron loss in evolution has been described, the mechanism involved is still unclear. Three models have been proposed, the reverse transcriptase (RT) model, genomic deletion model and double-strand-break repair model. The RT model, also termed mRNA-mediated intron loss, suggests that cDNA molecules reverse transcribed from spliced mRNA recombine with genomic DNA causing intron loss. Many studies have attempted to test this model based on its predictions, such as simultaneous loss of adjacent introns, 3'-side bias of intron loss, and germline expression of intron-lost genes. Evidence either supporting or opposing the model has been reported. The mechanism of intron loss proposed in the RT model shares the process of reverse transcription with the formation of processed pseudogenes. If the RT model is correct, genes that have produced more processed pseudogenes are more likely to undergo intron loss. RESULTS: In the present study, we observed that the frequency of intron loss is correlated with processed pseudogene abundance by analyzing a new dataset of intron loss obtained in mice and rats. Furthermore, we found that mRNA molecules of intron-lost genes are mostly translated on free cytoplasmic ribosomes, a feature shared by mRNA molecules of the parental genes of processed pseudogenes and long interspersed elements. This feature is likely convenient for intron-lost gene mRNA molecules to be reverse transcribed. Analyses of adjacent intron loss, 3'-side bias of intron loss, and germline expression of intron-lost genes also support the RT model. CONCLUSIONS: Compared with previous evidence, the correlation between the abundance of processed pseudogenes and intron loss frequency more directly supports the RT model of intron loss. Exploring such a correlation is a new strategy to test the RT model in organisms with abundant processed pseudogenes.
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Intrones/genética , Modelos Genéticos , Seudogenes/genética , ADN Polimerasa Dirigida por ARN/metabolismo , Animales , Secuencia Conservada , Regulación de la Expresión Génica , Genoma/genética , Elementos de Nucleótido Esparcido Largo/genética , Mamíferos/genética , Ratones , Filogenia , Señales de Clasificación de Proteína/genética , Estructura Terciaria de Proteína , Proteínas/genética , Proteínas/metabolismo , ARN Mensajero/genética , ARN Mensajero/metabolismo , Ratas , Eliminación de Secuencia , SolubilidadRESUMEN
Despite the prevalence of intron losses during eukaryotic evolution, the selective forces acting on them have not been extensively explored. Arabidopsis thaliana lost half of its genome and experienced an elevated rate of intron loss after diverging from A. lyrata. The selective force for genome reduction was suggested to have driven the intron loss. However, the evolutionary mechanism of genome reduction is still a matter of debate. In this study, we found that intron-lost genes have high synonymous substitution rates. Assuming that differences in mutability among different introns are conserved among closely related species, we used the nucleotide substitution rate between orthologous introns in other species as the proxy of the mutation rate of Arabidopsis introns, either lost or extant. The lost introns were found to have higher mutation rates than extant introns. At the genome-wide level, A. thaliana has a higher mutation rate than A. lyrata, which correlates with the higher rate of intron loss and rapid genome reduction of A. thaliana. Our results indicate that selection to minimize mutational hazards might be the selective force for intron loss, and possibly also for genome reduction, in the evolution of A. thaliana. Small genome size and lower genome-wide intron density were widely reported to be correlated with phenotypic features, such as high metabolic rates and rapid growth. We argue that the mutational-hazard hypothesis is compatible with these correlations, by suggesting that selection for rapid growth might indirectly increase mutational hazards.
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Arabidopsis/genética , Evolución Molecular , Tamaño del Genoma , Intrones , Arabidopsis/clasificación , Genoma de Planta , Tasa de Mutación , Filogenia , Eliminación de SecuenciaRESUMEN
One of the large, unsolved problems in human genetics is the proportion of functional sequences in genomes. Recently, the encyclopedia of DNA elements consortium revealed that the majority of the genome is biochemically active, which were described as biochemical functions. This has been used as evidence to pronounce the death of the junk DNA concept. In evolutionary biology, junk DNAs are sequences whose gain or loss does not seriously affect fitness of the host organism. In the human genome, a large amount of biochemical activity should be to repress the sequences so as to avoid their harmful expression. The biochemical activity is very different from functionality in the light of evolution. The single nucleotide polymorphism sites associated with disease and other phenotypes may be functional, but their abundance in the active genome regions is not reliable evidence of functionality. Because of sequence-independent functions, the proportion of functional regions would be underestimated when sequence constraints are used alone. Knockout may be the most effective means of distinguishing functional sequences from junk DNA.
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ADN Intergénico/genética , Enfermedad/genética , Genoma Humano/genética , Enciclopedias como Asunto , Evolución Molecular , Técnicas de Inactivación de Genes , Humanos , Análisis de Secuencia de ADN/métodosRESUMEN
BACKGROUND: The costs and benefits of spliceosomal introns in eukaryotes have not been established. One recognized effect of intron splicing is its known enhancement of gene expression. However, the mechanism regulating such splicing-mediated expression enhancement has not been defined. Previous studies have shown that intron splicing is a time-consuming process, indicating that splicing may not reduce the time required for transcription and processing of spliced pre-mRNA molecules; rather, it might facilitate the later rounds of transcription. Because the densities of active RNA polymerase II on most genes are less than one molecule per gene, direct interactions between the splicing apparatus and transcriptional complexes (from the later rounds of transcription) are infrequent, and thus unlikely to account for splicing-mediated gene expression enhancement. PRESENTATION OF THE HYPOTHESIS: The serine/arginine-rich protein SF2/ASF can inhibit the DNA topoisomerase I activity that removes negative supercoiling of DNA generated by transcription. Consequently, splicing could make genes more receptive to RNA polymerase II during the later rounds of transcription, and thus affect the frequency of gene transcription. Compared with the transcriptional enhancement mediated by strong promoters, intron-containing genes experience a lower frequency of cut-and-paste processes. The cleavage and religation activity of DNA strands by DNA topoisomerase I was recently shown to account for transcription-associated mutagenesis. Therefore, intron-mediated enhancement of gene expression could reduce transcription-associated genome instability. TESTING THE HYPOTHESIS: Experimentally test whether transcription-associated mutagenesis is lower in intron-containing genes than in intronless genes. Use bioinformatic analysis to check whether exons flanking lost introns have higher frequencies of short deletions. IMPLICATIONS OF THE HYPOTHESIS: The mechanism of intron-mediated enhancement proposed here may also explain the positive correlation observed between intron size and gene expression levels in unicellular organisms, and the greater number of intron containing genes in higher organisms. REVIEWERS: This article was reviewed by Dr Arcady Mushegian, Dr Igor B Rogozin (nominated by Dr I King Jordan) and Dr Alexey S Kondrashov. For the full reviews, please go to the Reviewer's Reports section.
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ADN-Topoisomerasas de Tipo I/metabolismo , Eucariontes/metabolismo , Intrones , Mutagénesis , Empalme del ARN , Transcripción Genética , Regulación de la Expresión Génica , Proteínas Nucleares/metabolismo , ARN Polimerasa II/metabolismo , Proteínas de Unión al ARN/metabolismo , Factores de Empalme Serina-ArgininaRESUMEN
Although intron loss and gain have been widely observed, their mechanisms are still to be determined. In four Aspergillus genomes, we found 204 cases of intron loss and 84 cases of intron gain. Using this data, we tested common hypotheses of intron loss or gain. Statistical analysis showed that adjacent introns tend to be lost simultaneously and small introns were preferentially lost, supporting the model of mRNA-mediated intron loss. The lost introns reside in internal regions of genes, which is inconsistent with the traditional version of the model (partial length cDNAs are reverse transcribed from 3' ends of mRNAs), but consistent with an alternate version (partial length cDNAs are produced by self-primed reverse transcription). The latter version was not supported by examination of the abundance of T-rich segments in mRNAs. Preferential loss of internal introns might be explained by highly efficient recombination at internal regions of genes. Among the 84 cases of intron gain, we found a significantly higher frequency of short direct repeats near exon-intron boundary than in conserved introns, supporting the double-strand break repair model. We also found possible source sequences for two cases of intron gain, one by gene conversion and one by insertion of a mitochondrial sequence during double-strand break repair. Source sequences for most gained introns could not be identified and the possible reasons were discussed. In the four Aspergillus genomes studied, we did not find evidence of frequent parallel intron gains.
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Aspergillus/genética , Intrones/genética , Modelos Genéticos , Secuencia de Bases , Secuencia Conservada/genética , ADN Mitocondrial/genética , Conversión Génica/genética , Genes Duplicados/genética , Datos de Secuencia Molecular , Mutagénesis Insercional/genética , Poli A/genética , ARN Mensajero/genéticaRESUMEN
In non-mammalian eukaryotes, an abnormally long 3' untranslated region (UTR) is generally thought to be the definitive signal in the recognition of a premature termination codon (PTC) in nonsense-mediated mRNA decay (NMD). However, because the lengths of 3' UTRs in normal mRNAs are widely distributed, "abnormally long" is hard to define. Distinct peaks of nucleosome deposition and DNA methylation have recently been found at coding region boundaries. We propose that nucleosomes and DNA methylation just upstream of a normal stop codon are ideal indicators for the position of a normal stop codon and may thus serve as signals in PTC recognition.