title: Identification of MFS proteins in sorghum using semantic similarity.
abstract: The antiporters, uniporters and symporters are the functional classes of MFS that play major role in ions homeostasis, regulation of pumps and channels, membrane structure, transporters activity in tolerance to abiotic stresses. Major facilitator superfamily (MFS) encodes Na(+)/H(+) antiporter that are considered as being sensors of the molecule transports. A large number of MFS proteins have been identified in several plants, rice, maize, Arabidopsis etc. However, the majority of proteins in sorghum are described as putative, uncharacterized till date. This suggested that identified proteins of MFS in sorghum are far from saturation. Hence, we developed gene ontology (GO) terms semantic similarity based method using GOSemSim measure of R package. As a result, total 2,568 high (100 %) semantic similar orthologous proteins from 7 plant species were obtained. These data were used to predict function of 257 putative uncharacterized proteins from 18 families of MFS in Sorghum. Consequently, the identified proteins belonged to the function of regulation of pumps and channels, membrane structure, transporters activity, ions homeostasis, transporter mechanisms and binding process. These identified functions appear to have a distinct mechanism of salt-stress adaptation in plants. The proposed method will help in further identifying new proteins that can help in the development of agronomically and economically important plants.
authors.affiliation: Department of Bioscience and Biotechnology, Banasthali University, P.O. Banasthali Vidyapith, 304022 Vanasthali, Rajasthan, India.
authors.forename: Manoj Kumar
authors.initials: MK
authors.lastname: Sekhwal
authors.forename: Vinay
authors.initials: V
authors.lastname: Sharma
authors.forename: Renu
authors.initials: R
authors.lastname: Sarin
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D030541:Databases, Genetic; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D006706:Homeostasis; D007477:Ions; D008957:Models, Genetic; D010940:Plant Proteins / Q000737:chemistry* / Q000235:genetics; D025941:Protein Interaction Mapping / Q000379:methods*; D040901:Proteomics / Q000379:methods; D012492:Salts / Q000737:chemistry; D016415:Sequence Alignment / Q000379:methods; D017923:Sodium-Hydrogen Exchangers / Q000235:genetics; D012984:Software; D045868:Sorghum / Q000235:genetics* / Q000378:metabolism
chemical_list: D007477:Ions; D010940:Plant Proteins; D012492:Salts; D017923:Sodium-Hydrogen Exchangers