Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology

Abstract

Background: The ATP-binding cassette (ABC) transporter gene superfamily is ubiquitous among extant organisms and prominently represented in plants. ABC transporters act to transport compounds across cellular membranes and are involved in a diverse range of biological processes. Thus, the applicability to biotechnology is vast, including cancer resistance in humans, drug resistance among vertebrates, and herbicide and other xenobiotic resistance in plants. In addition, plants appear to harbor the highest diversity of ABC transporter genes compared with any other group of organisms. This study applied transcriptome analysis to survey the kingdom-wide ABC transporter diversity in plants and suggest biotechnology applications of this diversity.

Results: We utilized sequence similarity-based informatics techniques to infer the identity of ABC transporter gene candidates from 1295 phylogenetically-diverse plant transcriptomes. A total of 97,149 putative (approximately 25 % were full-length) ABC transporter gene members were identified; each RNA-Seq library (plant sample) had 88 ± 30 gene members. As expected, simpler organisms, such as algae, had fewer unique members than vascular land plants. Differences were also noted in the richness of certain ABC transporter subfamilies. Land plants had more unique ABCB, ABCC, and ABCG transporter gene members on average (p < 0.005), and green algae, red algae, and bryophytes had significantly more ABCF transporter gene members (p < 0.005). Ferns had significantly fewer ABCA transporter gene members than all other plant groups (p < 0.005).

Conclusions: We present a transcriptomic overview of ABC transporter gene members across all major plant groups. An increase in the number of gene family members present in the ABCB, ABCC, and ABCD transporter subfamilies may indicate an expansion of the ABC transporter superfamily among green land plants, which include all crop species. The striking difference between the number of ABCA subfamily transporter gene members between ferns and other plant taxa is surprising and merits further investigation. Discussed is the potential exploitation of ABC transporters in plant biotechnology, with an emphasis on crops.

Keywords: ABC transporter; Computational biology; Taxonomic diversity; Transcriptomics.

Fig. 1

Flax and castor bean ABC transporter unique gene distribution inferred from RNA-Seq transcriptome data. a Plot comparing total ABC transporter unique genes observed in the flax genome and the three 1KP transcriptomes for flax (shoot sample 1, shoot sample 2, shoot sample 3). b Plot comparing total ABC transporter unique genes observed in the castor bean genome and the 1KP transcriptomes for castor bean (mixed tissue sample). Searches based on hmmscan searches for the PF00005 pfam domain and subsequent BLAST queries against a custom BLAST database of ABC transporters from Arabidopsis and rice

Fig. 2

Number of unique ABC transporter gene members distributed over plant taxa inferred from RNA-Seq transcriptome data. a Box and whisker plot of subfamily ABC transporter unique genes among each set of samples in indicated plant groups: Chromista, rhodophytes, glaucophytes, charophytes, chlorophytes, hornworts, liverworts, mosses, lycophytes, ferns, conifers, and anigosperms. b ABCB transporter gene members. c ABCC transporter gene members. d ABCG transporter gene members. e ABCD transporter gene members. f ABCE transporter gene members. g ABCI transporter gene members. h ABCF transporter gene members. i ABCA transporter gene members. Classifications are based on hmmscan searches for the PF00005 pfam domain. Significant differences between unique gene counts of the twelve groups were determined by a comparison of means using the Wilcoxon method. Filled circles indicate outliers. The total samples per plant group are indicated in parentheses beside each label along the x-axis. Statistical differences are indicated by letter groupings (p < 0.005)