Global analysis of the MATE gene family of metabolite transporters in tomato

Abstract

Background

Species 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.

Results

We 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.

Conclusions

Altogether, 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.

Electronic supplementary material

The online version of this article (10.1186/s12870-017-1115-2) contains supplementary material, which is available to authorized users.

Contributors

Vagner Augusto Benedito: [phone] , [e-mail]

Journal

Journal ID (nlm-ta): BMC Plant Biol

Journal ID (iso-abbrev): BMC Plant Biol

Title: BMC Plant Biology

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2229

Publication date (Electronic): 30 October 2017

Publication date PMC-release: 30 October 2017

Publication date Collection: 2017

Volume: 17

Affiliations

[1 ]ISNI 0000 0001 2156 6140, GRID grid.268154.c, Division of Plant and Soil Sciences, , West Virginia University, ; 3425 New Agricultural Sciences Building, Morgantown, WV 26506-6108 USA

[2 ]ISNI 0000 0000 8816 9513, GRID grid.411269.9, Plant Molecular Physiology Laboratory, Biology Department, , Federal University of Lavras (UFLA), ; Lavras, MG Brazil

[3 ]ISNI 0000 0001 0664 9773, GRID grid.59056.3f, Department of Biotechnology, , University of Calcutta, ; Kolkata, India

[4 ]ISNI 0000 0004 1760 4804, GRID grid.411389.6, State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Sciences, , Anhui Agricultural University, ; Hefei, 230036 China

Article

Publisher ID: 1115

DOI: 10.1186/s12870-017-1115-2

PMC ID: 5663081

Copyright statement: © The Author(s). 2017

License:

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100002322, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior;

Categories

Subject: Research Article

Custom metadata

issue-copyright-statement © The Author(s) 2017