Genome-wide identification of MATE, functional analysis and molecular dynamics of DcMATE21 involved in anthocyanin accumulation in Daucus carota.

Anthocyanins are a subclass of flavonoids that are synthesized in the endoplasmic reticulum and then transported
to the vacuole in plants. Multidrug and toxic compound extrusion transporters (MATE) is a family of membrane
transporters that transport ions and secondary metabolites, such as anthocyanins, in plants. Although various
studies on MATE transporters have been carried out on different plant species, this is the first comprehensive
report to mine the Daucus carota genome to identify the MATE gene family. Our study identified 45 DcMATEs
through genome-wide analysis and detected five segmental and six tandem duplications from the genome. The
chromosome distribution, phylogenetic analysis, and cis-regulatory elements revealed the structural diversity
and numerous functions associated with the DcMATEs. In addition, we analyzed RNA-seq data obtained from the
European Nucleotide Archive to screen for the expression of DcMATEs involved in anthocyanin biosynthesis.
Among the identified DcMATEs, DcMATE21 correlated with anthocyanin content in the different D. carota varieties.
In addition, the expression of DcMATE21 and anthocyanin biosynthesis genes was correlated under
abscisic acid, methyl jasmonate, sodium nitroprusside, salicylic acid, and phenylalanine treatments, which were
substantiated by anthocyanin accumulation in the in vitro cultures. Further molecular membrane dynamics of
DcMATE21 with anthocyanin (cyanidin-3-glucoside) identified the binding pocket, showing extensive H-bond
interactions with 10 crucial amino acids present in the transmembrane helix of 7, 8, and 10 of DcMATE21. The
current investigation, using RNA-seq, in vitro cultures, and molecular dynamics studies revealed the involvement
of DcMATE21 in anthocyanin accumulation in vitro cultures of D. carota.