Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates

<p>Abstract</p> <p>Background</p> <p>Progressive diversification of paralogs after gene expansion is essential to increase their functional specialization. However, mode and tempo of this divergence remain mostly unclear. Here we report the comparative analysis of PRDM genes, a family of putative transcriptional regulators involved in human tumorigenesis.</p> <p>Results</p> <p>Our analysis assessed that the PRDM genes originated in metazoans, expanded in vertebrates and further duplicated in primates. We experimentally showed that fast-evolving paralogs are poorly expressed, and that the most recent duplicates, such as primate-specific <it>PRDM7</it>, acquire tissue-specificity. <it>PRDM7 </it>underwent major structural rearrangements that decreased the number of encoded Zn-Fingers and modified gene splicing. Through internal duplication and activation of a non-canonical splice site (GC-AG), <it>PRDM7 </it>can acquire a novel intron. We also detected an alternative isoform that can retain the intron in the mature transcript and that is predominantly expressed in human melanocytes.</p> <p>Conclusion</p> <p>Our findings show that (a) molecular evolution of paralogs correlates with their expression pattern; (b) gene diversification is obtained through massive genomic rearrangements; and (c) splicing modification contributes to the functional specialization of novel genes.</p

Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates-1

<p><b>Copyright information:</b></p><p>Taken from "Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates"</p><p>http://www.biomedcentral.com/1471-2148/7/187</p><p>BMC Evolutionary Biology 2007;7():187-187.</p><p>Published online 4 Oct 2007</p><p>PMCID:PMC2082429.</p><p></p>yan. and are represented as grey blocks. The chromosome number in the corresponding genome is provided. Dashed lines correspond to regions of break of synteny. Abbreviations: , Homo sapiens; , Pan troglodytes; , Macaca mulatta; , Mus musculus; , Rattus norvegicus; , Gallus gallus. . Since for chimp and macaque no mRNA sequences are available, the human and were used as templates for gene predictions. In chimp, the intron putatively gained by is composed of eight repeats. In the genomic regions corresponding to chimp , there are four additional Zn-Fingers, which are reported in black because there is no evidence for their transcription. The dashed lines represent regions of gaps in the genome assembly. In rodents, the last intron is longer and not in scale; the corresponding length is reported in brackets. . The grey lines represent the genomic regions of segmental duplication. The corresponding chromosome number, chromosomal coordinates and direction of transcription are given. For , the splicing variants present in the database are shown. For , both the database transcripts and the isoforms detected in this study are reported together with an in-silico gene prediction obtained by using the PRDM9 long isoform as template

Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates-0

<p><b>Copyright information:</b></p><p>Taken from "Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates"</p><p>http://www.biomedcentral.com/1471-2148/7/187</p><p>BMC Evolutionary Biology 2007;7():187-187.</p><p>Published online 4 Oct 2007</p><p>PMCID:PMC2082429.</p><p></p>are shown in grey. On main bifurcations, the corresponding posterior probability from Bayesian inference is reported (see Methods). Different colours associated to tree branches correspond to the main subfamilies. For each subfamily, the gene structure of human PRDM ortholog is depicted. The scale refers to exons only. The tree image was produced using iTOL [44]. . PRDM genes are ordered by increasing evolutionary divergence, calculated as cumulative branch lengths from the tip to the root of the phylogenetic tree. The expression data were measured as the mean values of different assays for each gene (see Methods). The upper limit of the 2values was set to 10. For original values see Additional file

OsWRKY22, a monocot WRKY gene, plays a role in the resistance response to blast

With the aim of identifying novel regulators of host and nonhost resistance to fungi in rice, we carried out a systematic mutant screen of mutagenized lines. Two mutant wrky22 knockout lines revealed clear-cut enhanced susceptibility to both virulent and avirulent Magnaporthe oryzae strains and altered cellular responses to nonhost Magnaporthe grisea and Blumeria graminis fungi. In addition, the analysis of the pathogen responses of 24 overexpressor OsWRKY22 lines revealed enhanced resistance phenotypes on infection with virulent M. oryzae strain, confirming that OsWRKY22 is involved in rice resistance to blast. Bioinformatic analyses determined that the OsWRKY22 gene belongs to a well-defined cluster of monocotspecific WRKYs. The co-regulatory analysis revealed no significant co-regulation of OsWRKY22 with a representative panel of OsWRKYs, supporting its unique role in a series of transcriptional responses. In contrast, inquiring a subset of biotic stress-related Affymetrix data, a large number of resistance and defencerelated genes were found to be putatively co-expressed with OsWRKY22. Taken together, all gathered experimental evidence places the monocot-specific OsWRKY22 gene at the convergence point of signal transduction circuits in response to both host and nonhost fungi encountering rice plants. (Résumé d'auteur