Abstract
BackgroundSpecies in the Solanaceae family are known for producing plethora of specialized metabolites. In addition to biosynthesis pathways, a full comprehension of secondary metabolism must also take into account the transport and subcellular compartmentalization of substances. Here, we examined the MATE (Multidrug and Toxic Compound Extrusion, or Multi-Antimicrobial Extrusion) gene family in the tomato (Solanum lycopersicum) genome with the objective of better understanding the transport of secondary metabolites in this model species. MATE membrane effluxers encompass an ancient gene family of secondary transporters present in all kingdoms of life, but with a remarkable expansion in plants. They mediate the transport of primary and secondary metabolites using the proton motive force through several membrane systems of the cell.ResultsWe identified 67 genes coding for MATE transporters in the tomato genome, 33 of which are expressed constitutively whereas 34 are expressed in specific cell types or environmental conditions. Synteny analyses revealed bona fide paralogs and Arabidopsis orthologs. Co-expression analysis between MATE and regulatory genes revealed 78 positive and 8 negative strong associations (ρ≥|0.8|). We found no evidence of MATE transporters belonging to known metabolic gene clusters in tomato.ConclusionsAltogether, our expression data, phylogenetic analyses, and synteny study provide strong evidence of functional homologies between MATE genes of tomato and Arabidopsis thaliana. Our co-expression study revealed potential transcriptional regulators of MATE genes that warrant further investigation. This work sets the stage for genome-wide functional analyses of MATE transporters in tomato and other Solanaceae species of economic relevance.
Highlights
Species in the Solanaceae family are known for producing plethora of specialized metabolites
* Correspondence: vagner.benedito@mail.wvu.edu †Equal contributors 1Division of Plant and Soil Sciences, West Virginia University, 3425 New Agricultural Sciences Building, Morgantown, WV 26506-6108, USA Full list of author information is available at the end of the article (Solanum lycopersicum) has been chosen as the biological model species for this family, and for the whole Asterid clade, which comprises of numerous agricultural species, including crops from varied families that produce relevant secondary metabolites, such as stimulant alkaloids in coffee (Rubiaceae), tea (Theaceae), and yerba mate (Aquifoliaceae)
Aiming to guide future molecular studies, we identified 67 genes coding for Multidrug and Toxic Compound Extrusion (MATE) transporters in the tomato genome, and produced a genomic inventory of MATE genes in order to provide a close look into the functional roles MATE transporters may play in the tomato’s physiology and cellular metabolism
Summary
Species in the Solanaceae family are known for producing plethora of specialized metabolites. Given the economic significance as a crop as well as its phenotypic and genetic advantages, the tomato (Solanum lycopersicum) has been chosen as the biological model species for this family, and for the whole Asterid clade, which comprises of numerous agricultural species, including crops from varied families that produce relevant secondary metabolites, such as stimulant alkaloids in coffee (Rubiaceae), tea (Theaceae), and yerba mate (Aquifoliaceae) This clade contains important Asteraceae crops (lettuce, sunflower, artichoke, stevia, echinacea, and daisies), and common Lamiaceae herbs (basil, lavender, marjoram, mint, oregano, rosemary, sage, thyme), to name just a few. The choice of the tomato over the wellestablished Rosid model, Arabidopsis thaliana, is justified by the closer relationship of tomato to other Asteridae crops, and because many features of agricultural relevance are not available in Arabidopsis, such as development of a complex leaf pattern, climacteric fleshy fruit
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