title: Proteome scale census of major facilitator superfamily transporters in Trichoderma reesei using protein sequence and structure based classification enhanced ranking.
abstract: Trichoderma spp. have been acknowledged as potent bio-control agents against microbial pathogens and also as plant growth promoters. Various secondary metabolites are attributed for these beneficial activities. Major facilitator superfamily (MFS) includes the large proportion of efflux-pumps which are linked with membrane transport of these secondary metabolites. We have carried out a proteome-wide identification of MFS transporters using protein sequence and structure based hierarchical method in Trichoderma reesei. 448 proteins out of 9115 were detected to carry transmembrane helices. MFS specific intragenic gene duplication and its context with transport function have been presented. Finally, using homology based techniques, domains and motifs of MFS families have been identified and utilized to classify them. From query dataset of 448 transmembrane proteins, 148 proteins are identified as potential MFS transporters. Sugar porter, drug: H(+) antiporter-1, monocarboxylate porter and anion: cation symporter emerged as major MFS families with 51, 35, 17 and 11 members respectively. Representative protein tertiary structures of these families are homology modeled for structure-function analysis. This study may help to understand the molecular basis of secretion and transport of agriculturally valuable secondary metabolites produced by these bio-control fungal agents which may be exploited in future for enhancing its biotechnological applications in eco-friendly sustainable development.
authors.affiliation: School of Earth and Environmental Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh 176206, India.
authors.forename: Nitika
authors.initials: N
authors.lastname: Chaudhary
authors.affiliation: School of Earth and Environmental Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh 176206, India.
authors.forename: Indu
authors.initials: I
authors.lastname: Kumari
authors.affiliation: School of Life Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh 176206, India.
authors.forename: Padmani
authors.initials: P
authors.lastname: Sandhu
authors.affiliation: School of Earth and Environmental Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh 176206, India. Electronic address: mushtaq.cuhp@gmail.com.
authors.forename: Mushtaq
authors.initials: M
authors.lastname: Ahmed
authors.affiliation: School of Life Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh 176206, India. Electronic address: yusuf@daad-alumni.de.
authors.forename: Yusuf
authors.initials: Y
authors.lastname: Akhter
mesh_terms: D020816:Amino Acid Motifs / Q000235:genetics; D000595:Amino Acid Sequence; D008565:Membrane Proteins / Q000235:genetics*; D026901:Membrane Transport Proteins / Q000235:genetics*; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D021381:Protein Transport / Q000235:genetics*; D020543:Proteome / Q000235:genetics; D013329:Structure-Activity Relationship; D014242:Trichoderma / Q000235:genetics* / Q000378:metabolism
chemical_list: D008565:Membrane Proteins; D026901:Membrane Transport Proteins; D020543:Proteome
keywords: Bio-control agent; Intragenic duplication; Major facilitator superfamily; Membrane transporters; Transport protein families; Trichoderma spp.