The Arabidopsis thaliana ABC Protein Superfamily, a Complete Inventory

TLDR

The study presents the first complete inventory of ATP‑binding cassette proteins in Arabidopsis thaliana. The inventory was assembled by applying multiple search criteria to the Arabidopsis genome, identifying 129 ORFs encoding ABC proteins. The inventory identified 129 ABC protein ORFs, including 103 putative intrinsic membrane proteins (51 half‑molecule transporters and 52 full‑molecule transporters in five subfamilies), 11 non‑intrinsic proteins in three subfamilies, and 15 orphan ORFs, revealing a large yeast‑like PDR subfamily and the absence of CFTR, SUR, and HMT1 homologs.

Abstract

We describe the first complete inventory of ATP-binding cassette (ABC) proteins from a multicellular organism, the model plant <i>Arabidopsis thaliana</i>. By the application of several search criteria,<i>Arabidopsis</i> was found to contain a total of 129 open reading frames (ORFs) capable of encoding ABC proteins, of which 103 possessed contiguous transmembrane spans and were identified as putative intrinsic membrane proteins. Fifty-two of the putative intrinsic membrane proteins contained at least two transmembrane domains (TMDs) and two nucleotide-binding folds (NBFs) and could be classified as belonging to one of five subfamilies of full-molecule transporters. The other 51 putative membrane proteins, all of which were half-molecule transporters, fell into five subfamilies. Of the remaining ORFs identified, all of which encoded proteins lacking TMDs, 11 could be classified into three subfamilies. There were no obvious homologs in other organisms for 15 of the ORFs which encoded a heterogeneous group of non-intrinsic ABC proteins (NAPs). Unrooted phylogenetic analyses substantiated the subfamily designations. Notable features of the <i>Arabidopsis</i>ABC superfamily was the presence of a large yeast-like PDR subfamily, and the absence of genes encoding <i>bona fide</i>cystic fibrosis transmembrane conductance regulator (CFTR), sulfonylurea receptor (SUR), and heavy metal tolerance factor 1 (HMT1) homologs. <i>Arabidopsis</i>was unusual in its large allocation of ORFs (a minimum of 0.5%) to members of the ABC protein superfamily.