Abstract
ATP-binding cassette (ABC) transporters constitute one of the largest gene families in all living organisms, most of which mediate transport across biological membranes by hydrolyzing ATP. However, detailed studies of ABC transporter genes in the important oil crop, soybean, are still lacking. In the present study, we carried out genome-wide identification and phylogenetic and transcriptional analyses of the ABC gene family in G. max. A total of 261 G. max ABC (GmABCs) genes were identified and unevenly localized onto 20 chromosomes. Referring to protein-domain orientation and phylogeny, the GmABC family could be classified into eight (ABCA-ABCG and ABCI) subfamilies and ABCG were the most abundantly present. Further, investigation of whole genome duplication (WGD) signifies the role of segmental duplication in the expansion of the ABC transporter gene family in soybean. The Ka/Ks ratio indicates that several duplicated genes are governed by intense purifying selection during evolution. In addition, in silico expression analysis based on RNA-sequence using publicly available database revealed that ABC transporters are differentially expressed in tissues and developmental stages and in dehydration. Overall, we provide an extensive overview of the GmABC transporter gene family and it promises the primary basis for the study in development and response to dehydration tolerance.
Highlights
IntroductionActive transport mechanisms require the intake of energy and can be operated by either of two mechanisms: (1) free energy change associated with ATP hydrolysis (primary transport), or (2) assisted by the potential energy of the chemical gradient of another molecule (secondary transport)
Active transport mechanisms require the intake of energy and can be operated by either of two mechanisms: (1) free energy change associated with ATP hydrolysis, or (2) assisted by the potential energy of the chemical gradient of another molecule
The analysis identified the presence of several stress-related, development and hormone inducible motifs, such as Homeo Box/ leucine Zipper, MBS (MYB Binding Site), WRKYdomain, NAC-domain, GT1consensus, dehydration responsive element binding factors (DREB), ABRE (Abscisic AcidResponsive Element), GATA-box, AT-hook containing transcription factors, DNA binding with one finger (DOF), GCN4, TC-rich, and Skn-1
Summary
Active transport mechanisms require the intake of energy and can be operated by either of two mechanisms: (1) free energy change associated with ATP hydrolysis (primary transport), or (2) assisted by the potential energy of the chemical gradient of another molecule (secondary transport). Depending on structural homology and transport mechanism, primary transporters are subdivided into three classes — rotary motor ATPases (F-, V-, and A-ATPases), P-type ATPases, and a large family of integral membrane proteins named ATP-binding cassette (ABC) transporters [1]. The ABC transporters represent one of the largest families of membrane proteins, ubiquitously found within the kingdoms of eukarya, eubacteria, and archaea [1,2,3]. These proteins employ ATP hydrolysis to transport various substrates (e.g., heavy metals, endogenous metabolites, inorganic anions, drugs, lipids, sterols, hormones, amino acids, peptides, vitamins, and sugars) in and out of cells across biological membranes [2, 4]. Genome-wide surveys and expression analysis of this gene family have not been performed in G. max
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