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

BMC Biotechnology

Research Article

Patrick P. Edger¹  Ying Zhu¹  Gane Ka-Shu Wong²  Yinlong Xie³  J. Chris Pires⁴  Jun Yu⁵  Tao Liu⁶  Eric Carpenter⁷  James H. Leebens-Mack⁸  Michael Melkonian⁹  Michael Deyholos^1,10  Douglas Edward Soltis^1,11  Sean W. Graham^1,12  Yong Zhang^1,13  Margaret E. Staton^1,14  Jack Davitt^1,14  Carl J. Rothfels^1,15  Yanhui Peng^1,16  Mark Chase^1,17  Dennis Stevenson^1,18  Caroline S. Rempe^1,19  Thomas S. Lane^1,19  C. Neal Stewart^1,19 

[1] BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083, Shenzhen, China;BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083, Shenzhen, China;Department of Biological Sciences, University of Alberta, T6G 2E9, Edmonton, AB, Canada;Department of Medicine, University of Alberta, T6G 2E1, Edmonton, AB, Canada;BGI-Shenzhen, Beishan Industrial Zone, Yantian District, 518083, Shenzhen, China;Department of Computer Science, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, University of Hong Kong, Pokfulam, Hong Kong;School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China;Bond Life Sciences Center, Division of Biological Sciences, University of Missouri, Columbia, MO, USA;CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, People’s Republic of China;College of Marine Life Sciences, Ocean University of China, 266003, Qingdao, People’s Republic of China;Department of Biological Sciences, University of Alberta, T6G 2E9, Edmonton, AB, Canada;Department of Biological Sciences, University of Georgia, 30602, Athens, GA, USA;Department of Biology, Cologne Biocenter, University of Cologne, 50674, Cologne, Germany;Department of Biology, University of British Columbia, V1V 1V7, Kelowna, BC, Canada;Department of Biology, University of Florida, 32611, Gainesville, FL, USA;Florida Museum of Natural History, 32611, Gainesville, FL, USA;Genetics Institute, University of Florida, 32611, Gainesville, FL, USA;Department of Botany, University of British Columbia, Vancouver, BC, Canada;Department of Computer Science, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, University of Hong Kong, Pokfulam, Hong Kong;Department of Entomology and Plant Pathology, University of Tennessee, 37996, Knoxville, TN, USA;Department of Integrative Biology, University of California, University Herbarium, 94720-2465, Berkeley, CA, USA;Department of Plant Sciences, University of Tennessee, 37996, Knoxville, TN, USA;Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, TW9 3AE, Surrey, UK;Department of Biology, Duke University, 27708, Durham, NC, USA;New York Botanical Garden, Bronx, 10458, New York, NY, USA;The Graduate School of Genome Science and Technology, University of Tennessee, 37996, Knoxville, TN, USA;Department of Plant Sciences, University of Tennessee, 37996, Knoxville, TN, USA;

关键词: ABC transporter;    Transcriptomics;    Computational biology;    Taxonomic diversity;   

DOI  :  10.1186/s12896-016-0277-6

 received in 2016-03-01, accepted in 2016-05-23,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsWe 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).ConclusionsWe 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.

【 授权许可】

CC BY   
© The Author(s). 2016