Genome-wide identification and characterization of ATP-binding cassette transporters in the silkworm, Bombyx mori

Shumin Liu,Ling Tian,Sheng Li,Shun Zhou,Jianzhen Zhang,Yunxia Luan,Enen Guo

doi:10.1186/1471-2164-12-491

Abstract

BackgroundThe ATP-binding cassette (ABC) transporter superfamily is the largest transporter gene family responsible for transporting specific molecules across lipid membranes in all living organisms. In insects, ABC transporters not only have important functions in molecule transport, but also play roles in insecticide resistance, metabolism and development.ResultsFrom the genome of the silkworm, Bombyx mori, we have identified 51 putative ABC genes which are classified into eight subfamilies (A-H) by phylogenetic analysis. Gene duplication is very evident in the ABCC and ABCG subfamilies, whereas gene numbers and structures are well conserved in the ABCD, ABCE, ABCF, and ABCH subfamilies. Microarray analysis revealed that expression of 32 silkworm ABC genes can be detected in at least one tissue during different developmental stages, and the expression patterns of some of them were confirmed by quantitative real-time PCR. A large number of ABC genes were highly expressed in the testis compared to other tissues. One of the ABCG genes, BmABC002712, was exclusively and abundantly expressed in the Malpighian tubule implying that BmABC002712 plays a tissue-specific role. At least 5 ABCG genes, including BmABC005226, BmABC005203, BmABC005202, BmABC010555, and BmABC010557, were preferentially expressed in the midgut, showing similar developmental expression profiles to those of 20-hydroxyecdysone (20E)-response genes. 20E treatment induced the expression of these ABCG genes in the midgut and RNA interference-mediated knockdown of USP, a component of the 20E receptor, decreased their expression, indicating that these midgut-specific ABCG genes are 20E-responsive.ConclusionIn this study, a genome-wide analysis of the silkworm ABC transporters has been conducted. A comparison of ABC transporters from 5 insect species provides an overview of this vital gene superfamily in insects. Moreover, tissue- and stage-specific expression data of the silkworm ABCG genes lay a foundation for future analysis of their physiological function and hormonal regulation.

Highlights

The ATP-binding cassette (ABC) transporter superfamily is the largest transporter gene family responsible for transporting specific molecules across lipid membranes in all living organisms
Identification of the silkworm ABC transporters The nucleotide binding domains (NBDs) of all the D. melanogaster ABC transporters were used as queries for BLASTP search against the two silkworm genome databases, SilkDB and KAIKObase
Each potential silkworm ABC transporter was validated by searching its known orthologs from the protein database of NCBI and further searching its NBD and transmembrane domains (TMD) with the Pfam program

Summary

Introduction

The ATP-binding cassette (ABC) transporter superfamily is the largest transporter gene family responsible for transporting specific molecules across lipid membranes in all living organisms. The ATP-binding cassette (ABC) transporters form one of the largest family of membrane proteins [1]. With 48 members in total, the ABC transporter family from animals was first identified in the human genome [2]. Ranging from 28 to ~200 members, the ABC transporter family is present in all organisms [3]. Based on sequence similarity of the ATPbinding sites, the 48 human ABC transporters can be classified into seven subfamilies (A to G, ABCA to ABCG). In addition to the fruitfly [2], the ABC transporters have been previously analyzed in another insect species, the mosquito, Anopheles gambiae (Diptera), at the genome-wide level [4]

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