title: Differential evolution of members of the rhomboid gene family with conservative and divergent patterns.
abstract: Rhomboid proteins are intramembrane serine proteases that are involved in a plethora of biological functions, but the evolutionary history of the rhomboid gene family is not clear. We performed a comprehensive molecular evolutionary analysis of the rhomboid gene family and also investigated the organization and sequence features of plant rhomboids in different subfamilies. Our results showed that eukaryotic rhomboids could be divided into five subfamilies (RhoA-RhoD and PARL). Most orthology groups appeared to be conserved only as single or low-copy genes in all lineages in RhoB-RhoD and PARL, whereas RhoA genes underwent several duplication events, resulting in multiple gene copies. These duplication events were due to whole genome duplications in plants and animals and the duplicates might have experienced functional divergence. We also identified a novel group of plant rhomboid (RhoB1) that might have lost their enzymatic activity; their existence suggests that they might have evolved new mechanisms. Plant and animal rhomboids have similar evolutionary patterns. In addition, there are mutations affecting key active sites in RBL8, RBL9 and one of the Brassicaceae PARL duplicates. This study delineates a possible evolutionary scheme for intramembrane proteins and illustrates distinct fates and a mechanism of evolution of gene duplicates.
authors.affiliation: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Plant Biology Center for Evolutionary Biology, Fudan University, Shanghai, 200433, China.|Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Sciences, Fudan University, Shanghai, 200433, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Li
authors.affiliation: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Plant Biology Center for Evolutionary Biology, Fudan University, Shanghai, 200433, China.|Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Sciences, Fudan University, Shanghai, 200433, China.
authors.forename: Ning
authors.initials: N
authors.lastname: Zhang
authors.affiliation: Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.|Advanced Institute of Translational Medicine, Tongji University, Shanghai, 200092, China.
authors.forename: Liangsheng
authors.initials: L
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Plant Biology Center for Evolutionary Biology, Fudan University, Shanghai, 200433, China.|Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Sciences, Fudan University, Shanghai, 200433, China.|Institute of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Ma
mesh_terms: D019607:Brassicaceae / Q000235:genetics; D019143:Evolution, Molecular; D020131:Genes, Duplicate; D018745:Genome, Plant / Q000235:genetics*; D008565:Membrane Proteins / Q000235:genetics*; D005810:Multigene Family; D010944:Plants / Q000235:genetics*
chemical_list: D008565:Membrane Proteins
keywords: cell signaling; gene duplication; gene fate; intramembrane proteolysis; meiosis; rhomboid genes