Abstract:BackgroundThe timing of the origin of introns is of crucial importance for an understanding of early genome architecture. The Exon theory of genes proposed a role for introns in the formation of multi-exon proteins by exon shuffling and predicts the presence of conserved splice sites in ancient genes. In this study, large-scale analysis of potential conserved splice sites was performed using an intron-exon database (ExInt) derived from GenBank.ResultsA set of conserved intron positions was found by matching id… Show more
“…These results agree with those previously reported showing that introns with phase 0 were normally located in more conserved portions of genes than introns with phases 1 or 2 [36]. Previous studies demonstrated that conserved intron positions were found within a variety of ancient protein modules, suggesting that the initial function of exons did not represent the boundaries of functional protein modules, but that the domain itself was assembled from exons [37]. These results suggest that the phases of introns and the numbers of the VHA-H genes were well-conserved and that some introns (i.e., those located in the middle portion of the N-terminal domain) maintained their specificity.…”
The vacuolar H+-ATPase (V-ATPase) plays many important roles in cell growth and in response to stresses in plants. The V-ATPase subunit H (VHA-H) is required to form a stable and active V-ATPase. Genome-wide analyses of VHA-H genes in crops contribute significantly to a systematic understanding of their functions. A total of 22 VHA-H genes were identified from 11 plants representing major crops including cotton, rice, millet, sorghum, rapeseed, maize, wheat, soybean, barley, potato, and beet. All of these VHA-H genes shared exon-intron structures similar to those of Arabidopsis thaliana. The C-terminal domain of VHA-H was shorter and more conserved than the N-terminal domain. The VHA-H gene was effectively used as a genetic marker to infer the phylogenetic relationships among plants, which were congruent with currently accepted taxonomic groupings. The VHA-H genes from six species of crops (Gossypium raimondii, Brassica napus, Glycine max, Solanum tuberosum, Triticum aestivum, and Zea mays) showed high gene structural diversity. This resulted from the gains and losses of introns. Seven VHA-H genes in six species of crops (Gossypium raimondii, Hordeum vulgare, Solanum tuberosum, Setaria italica, Triticum aestivum, and Zea mays) contained multiple transcript isoforms arising from alternative splicing. The study of cis-acting elements of gene promoters and RNA-seq gene expression patterns confirms the role of VHA-H genes as eco-enzymes. The gene structural diversity and proteomic diversity of VHA-H genes in our crop sampling facilitate understanding of their functional diversity, including stress responses and traits important for crop improvement.
“…These results agree with those previously reported showing that introns with phase 0 were normally located in more conserved portions of genes than introns with phases 1 or 2 [36]. Previous studies demonstrated that conserved intron positions were found within a variety of ancient protein modules, suggesting that the initial function of exons did not represent the boundaries of functional protein modules, but that the domain itself was assembled from exons [37]. These results suggest that the phases of introns and the numbers of the VHA-H genes were well-conserved and that some introns (i.e., those located in the middle portion of the N-terminal domain) maintained their specificity.…”
The vacuolar H+-ATPase (V-ATPase) plays many important roles in cell growth and in response to stresses in plants. The V-ATPase subunit H (VHA-H) is required to form a stable and active V-ATPase. Genome-wide analyses of VHA-H genes in crops contribute significantly to a systematic understanding of their functions. A total of 22 VHA-H genes were identified from 11 plants representing major crops including cotton, rice, millet, sorghum, rapeseed, maize, wheat, soybean, barley, potato, and beet. All of these VHA-H genes shared exon-intron structures similar to those of Arabidopsis thaliana. The C-terminal domain of VHA-H was shorter and more conserved than the N-terminal domain. The VHA-H gene was effectively used as a genetic marker to infer the phylogenetic relationships among plants, which were congruent with currently accepted taxonomic groupings. The VHA-H genes from six species of crops (Gossypium raimondii, Brassica napus, Glycine max, Solanum tuberosum, Triticum aestivum, and Zea mays) showed high gene structural diversity. This resulted from the gains and losses of introns. Seven VHA-H genes in six species of crops (Gossypium raimondii, Hordeum vulgare, Solanum tuberosum, Setaria italica, Triticum aestivum, and Zea mays) contained multiple transcript isoforms arising from alternative splicing. The study of cis-acting elements of gene promoters and RNA-seq gene expression patterns confirms the role of VHA-H genes as eco-enzymes. The gene structural diversity and proteomic diversity of VHA-H genes in our crop sampling facilitate understanding of their functional diversity, including stress responses and traits important for crop improvement.
“…The addition of genetic polymorphism thus serves as a mechanism by which variation was reintroduced and phenotypic robustness restored over subsequent generations. Other work has shown that robustness to mutations in the P450 protein was higher in larger and more polymorphic populations compared to smaller and less polymorphic populations such that genetic polymorphism is likely responsible for higher robustness 46 . It was further revealed that the genetic background in which the HSP90 chaperone is expressed can have a large effect on resultant phenotypes, as is the case in Drosophila 47 .…”
Phenotypic variation is the raw material for selection that is ubiquitous for most traits in natural populations, yet the processes underlying phenotypic evolution or stasis often remain unclear. Here, we report phenotypic evolution in a mutant line of the butterfly Bicyclus anynana after outcrossing with the genetically polymorphic wild type population. The comet mutation modifies two phenotypic traits known to be under sexual selection in this butterfly: the dorsal forewing eyespots and the pheromone-producing structures. The original comet mutant line was inbred and remained phenotypically stable for at least seven years, but when outcrossed to the wild type population the outcrossed comet line surprisingly recovered the wild type phenotype within 8 generations at high (27 °C), but not at low (20 °C), developmental temperatures. Male mating success experiments then revealed that outcrossed comet males with the typical comet phenotype suffered from lower mating success, while mating success of outcrossed comet males resembling wild types was partially restored. We document a fortuitous case where the addition of genetic polymorphism around a spontaneous mutation could have allowed partial restoration of phenotypic robustness. We further argue that sexual selection through mate choice is likely the driving force leading to phenotypic robustness in our system.
“…One can see that the red rectangular boxes that represent the SCP2 domains are found in all 14 protein hits. Additional domains seen in the protein hits are: (1) Band_7 (violet box)—an integral membrane protein involved in regulation of cation conductance; (2) adh_short (brown box)—an NAD or NADP-dependent oxidoreductase domain; (3) MaoC_dehydratas (blue box)—a domain involved in the synthesis of monamine oxidase; (4) Thiolase_N (green box) and (5) Thiolase_C (gray box) domains are both involved in degradative pathways such as fatty acid beta-oxidation. Figure 3.Results of the sample query for the protein domain ‘ SCP2’ in ExDom.…”
Section: Exploring the Utility Of The Database With A Sample Querymentioning
We have developed ExDom, a unique database for the comparative analysis of the exon–intron structures of 96 680 protein domains from seven eukaryotic organisms (Homo sapiens, Mus musculus, Bos taurus, Rattus norvegicus, Danio rerio, Gallus gallus and Arabidopsis thaliana). ExDom provides integrated access to exon-domain data through a sophisticated web interface which has the following analytical capabilities: (i) intergenomic and intragenomic comparative analysis of exon–intron structure of domains; (ii) color-coded graphical display of the domain architecture of proteins correlated with their corresponding exon-intron structures; (iii) graphical analysis of multiple sequence alignments of amino acid and coding nucleotide sequences of homologous protein domains from seven organisms; (iv) comparative graphical display of exon distributions within the tertiary structures of protein domains; and (v) visualization of exon–intron structures of alternative transcripts of a gene correlated to variations in the domain architecture of corresponding protein isoforms. These novel analytical features are highly suited for detailed investigations on the exon–intron structure of domains and make ExDom a powerful tool for exploring several key questions concerning the function, origin and evolution of genes and proteins. ExDom database is freely accessible at: http://66.170.16.154/ExDom/.
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