title: A new and unified nomenclature for male fertility restorer (RF) proteins in higher plants.
abstract: The male fertility restorer (RF) proteins belong to extended protein families associated with the cytoplasmic male sterility in higher plants. Up till now, there is no devised nomenclature for naming the RF proteins. The systematic sequencing of new plant species in recent years has uncovered the existence of several novel RF genes and their encoded proteins. Their naming has been simply arbitrary and could not be adequately handled in the context of comparative functional genomics. We propose in this study a unified nomenclature for the RF extended protein families across all plant species. This new and unified nomenclature relies upon previously developed nomenclature for the first ever characterized RF gene, RF2A/ALDH2B2, a member of ALDH gene superfamily, and adheres to the guidelines issued by the ALDH Genome Nomenclature Committees. The proposed nomenclature reveals that RF gene superfamily encodes currently members of 51 families. This unified nomenclature accommodates functional RF genes and pseudogenes, and offers the flexibility needed to incorporate additional RFs as they become available in future. In addition, we provide a phylogenetic relationship between the RF extended families and use computational protein modeling to demonstrate the high divergence of RF functional specializations through specific structural features of selected members of RF superfamily.
authors.affiliation: Department of Agronomy, Purdue University, Lilly Hall, West Lafayette, Indiana, United States of America. skotchon@purdue.edu
authors.forename: Simeon O
authors.initials: SO
authors.lastname: Kotchoni
authors.forename: Jose C
authors.initials: JC
authors.lastname: Jimenez-Lopez
authors.forename: Emma W
authors.initials: EW
authors.lastname: Gachomo
authors.forename: Manfredo J
authors.initials: MJ
authors.lastname: Seufferheld
mesh_terms: D000080924:Aldehyde Dehydrogenase 1 Family; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D017343:Genes, Plant; D023281:Genomics; D007527:Isoenzymes / Q000235:genetics* / Q000378:metabolism; D008968:Molecular Conformation; D016366:Open Reading Frames; D010802:Phylogeny; D051479:Plant Infertility; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics; D010944:Plants / Q000378:metabolism; D011487:Protein Conformation; D011544:Pseudogenes; D050697:Retinal Dehydrogenase / Q000235:genetics* / Q000378:metabolism; D012984:Software; D003313:Zea mays / Q000235:genetics
chemical_list: D007527:Isoenzymes; D010940:Plant Proteins; D000080924:Aldehyde Dehydrogenase 1 Family; D050697:Retinal Dehydrogenase