166 research outputs found
Birth and rapid subcellular adaptation of a hominoid-specific CDC14 protein.
No full textGene duplication was prevalent during hominoid evolution, yet little is known about the functional fate of new ape gene copies. We characterized the CDC14B cell cycle gene and the functional evolution of its hominoid-specific daughter gene, CDC14Bretro. We found that CDC14B encodes four different splice isoforms that show different subcellular localizations (nucleus or microtubule-associated) and functional properties. A microtubular CDC14B variant spawned CDC14Bretro through retroposition in the hominoid ancestor 18-25 million years ago (Mya). CDC14Bretro evolved brain-/testis-specific expression after the duplication event and experienced a short period of intense positive selection in the African ape ancestor 7-12 Mya. Using resurrected ancestral protein variants, we demonstrate that by virtue of amino acid substitutions in distinct protein regions during this time, the subcellular localization of CDC14Bretro progressively shifted from the association with microtubules (stabilizing them) to an association with the endoplasmic reticulum. CDC14Bretro evolution represents a paradigm example of rapid, selectively driven subcellular relocalization, thus revealing a novel mode for the emergence of new gene function.Journal ArticleResearch Support, Non-U.S. Gov'tSCOPUS: ar.jinfo:eu-repo/semantics/publishe
Origins of New Male Germ-line Functions from X-Derived Autosomal Retrogenes in the Mouse
No full textExtensive Structural Renovation of Retrogenes in the Evolution of the Populus Genome
No full textRetroposition, as an important copy mechanism for generating new genes, was believed to play a negligible role in plants. As a representative dicot, the genomic sequences of Populus (poplar; Populus trichocarpa) provide an opportunity to investigate this issue. We identified 106 retrogenes and found the majority (89%) of them are associated with functional signatures in sequence evolution, transcription, and (or) translation. Remarkably, examination of gene structures revealed extensive structural renovation of these retrogenes: we identified 18 (17%) of them undergoing either chimerization to form new chimerical genes and (or) intronization (transformation into intron sequences of previously exonic sequences) to generate new intron-containing genes. Such a change might occur at a high speed, considering eight out of 18 such cases occurred recently after divergence between Arabidopsis (Arabidopsis thaliana) and Populus. This pattern also exists in Arabidopsis, with 15 intronized retrogenes occurring after the divergence between Arabidopsis and papaya (Carica papaya). Thus, the frequency of intronization in dicots revealed its importance as a mechanism in the evolution of exon-intron structure. In addition, we also examined the potential impact of the Populus nascent sex determination system on the chromosomal distribution of retrogenes and did not observe any significant effects of the extremely young sex chromosomes.Plant SciencesSCI(E)PubMed27ARTICLE41943-195115
Establishing a Protocol for the Detection of Gene Duplications in Drosophila melanogaster
No full textvi, 19 p.Duplication is one of the main mechanisms to introduce new genes into a genome. Once duplicated, evolutionary forces will act upon novel genes causing them to either disappear or become fixed in the population. Previous research on duplicate gene pairs in Drosophila melanogaster has focused on duplications that have already become fixed in a given population. However, examining these duplications before they become fixed provides further insight into the evolutionary forces at work on the newly duplicated genes. Microarray hybridizations are one way to locate young genes and changes in copy number, and the efficiency of this technique makes it possible to scan an entire genome. The purpose of this experiment is to determine if the duplicated regions of the D. melanogaster genome can be detected through microarray hybridization.
In this preliminary project, a wild type line was scanned against a line with a known
duplication region. Levels of gene hybridization for both non-duplicated and duplicated regions of the genome were then established. A histogram of the intensity fold differences shows that the duplicated and non-duplicated regions overlap at several intensity folds. Therefore, it is important to specify an intensity fold cutoff that will reduce the amount of genes that need to be verified in a polymorphic gene search. Our research concluded that duplication screens should begin at an intensity fold differences between 1.15 and 1.20, but performing additional replications might allow
this number to become more precise. This protocol and duplication amplification level can be used to scan unknown regions to estimate the number of genes that remain polymorphic in the D. melanogaster genome and eventually examine the selective forces that these genes face during their fixation phase .Department of Ecology and Evolution. University of Chicago. Chicago, Illinois
The rapid generation of chimerical genes expanding protein diversity in zebrafish
No full textBackground: Variation of gene number among species indicates that there is a general process of new gene origination. One of the major mechanism providing raw materials for the origin of new genes is gene duplication. Retroposition, as a special type of gene duplication-the RNA-based duplication, has been found to play an important role in new gene evolution in mammals and plants, but little is known about the process in the teleostei genome. Results: Here we screened the zebrafish genome for identification of retrocopies and new chimerical retrogenes and investigated their origination and evolution. We identified 652 retrocopies, of which 440 are intact retrogenes and 212 are pseudogenes. Retrocopies have long been considered evolutionary dead ends without functional significance due to the presumption that retrocopies lack the regulatory element needed for expression. However, 437 transcribed retrocopies were identified from all of the retrocopies. This discovery combined with the substitution analysis suggested that the majority of all retrocopies are subject to negative selection, indicating that most of the retrocopies may be functional retrogenes. Moreover, we found that 95 chimerical retrogenes had recruited new sequences from neighboring genomic regions that formed de novo splice sites, thus generating new intron-containing chimeric genes. Based on our analysis of 38 pairs of orthologs between Cyprinus carpio and Danio rerio, we found that the synonymous substitution rate of zebrafish genes is 4.13x10(-9) substitution per silent site per year. We also found 10 chimerical retrogenes that were created in the last 10 million years, which is 7.14 times the rate of 0.14 chimerical retrogenes per million years in the primate lineage toward human and 6.25 times the rate of 0.16 chimerical genes per million years in Drosophila. This is among the most rapid rates of generation of chimerical genes, just next to the rice. Conclusion: There is compelling evidence that much of the extensive transcriptional activity of retrogenes does not represent transcriptional "noise" but indicates the functionality of these retrogenes. Our results indicate that retroposition created a large amount of new genes in the zebrafish genome, which has contributed significantly to the evolution of the fish genome
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