The Arabidopsis thaliana ABC Protein Superfamily, a Complete Inventory

Rocı́O Sánchez-Fernández,T G Emyr Davies,Julian O.D Coleman,Philip A Rea

doi:10.1074/jbc.m103104200

Rocı́O Sánchez-Fernández, T G Emyr Davies + Show 2 more

Open Access

https://doi.org/10.1074/jbc.m103104200

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Abstract

We describe the first complete inventory of ATP-binding cassette (ABC) proteins from a multicellular organism, the model plant Arabidopsis thaliana. By the application of several search criteria, Arabidopsis 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 Arabidopsis ABC superfamily was the presence of a large yeast-like PDR subfamily, and the absence of genes encoding bona fide cystic fibrosis transmembrane conductance regulator (CFTR), sulfonylurea receptor (SUR), and heavy metal tolerance factor 1 (HMT1) homologs. Arabidopsis was unusual in its large allocation of ORFs (a minimum of 0.5%) to members of the ABC protein superfamily.

Highlights

The ATP-binding cassette (ABC)1 protein superfamily is the largest protein family known (1), and most, but not all, are membrane proteins (“ATPbinding cassette (ABC) transporters”) active in the transport of a broad range of substances across membranes
As a prelude to and resource for future functional genomic investigations of this important group of proteins, we present the first complete inventory and phylogenetic analysis of ABC proteins from a multicellular organism, the model plant Arabidopsis thaliana
Classification of Arabidopsis ABC Proteins—The 129 ABC proteins encoded by the Arabidopsis genome, which range in size from ϳ250 to over 1800 amino acid residues, fell into 12 subfamilies based on their size, orientation, domain organization, and resemblance to ABC proteins from other organisms

Summary

EXPERIMENTAL PROCEDURES

Data Base Searches and Sequence Analyses—The TAIR Arabidopsis data base was first searched using the ABC signature (“C”) motif (4) as query sequence. As an additional fail-safe procedure, the Arabidopsis MIPS data base was repeatedly searched during the course of compiling this inventory with the keyword “ABC” (www.mips.biochem.mpg.de/cgi-bin/ proj/thal/searcher?keyϭabc&contigϩall) to ensure that putative gene products containing ABC signature motifs that had been discovered during the annotation process were not overlooked. Sequence Alignments and Phylogenetic Analyses—The deduced amino acid sequences of the putative ABC proteins identified were aligned using ClustalX (6) and subjected to phylogenetic analysis by both the maximum parsimony and distance with neighbor-joining methods using PAUP4.0b4a (7, 8). Both analyses were subjected to 1000 bootstrap replicates.

RESULTS AND DISCUSSION

A Coherent Phylogeny

Concluding Remarks