In silico Analysis of Acyl-CoA-Binding Protein Expression in Soybean

Abstract

Plant acyl-CoA-binding proteins (ACBPs) form a highly conserved protein family that binds to acyl-CoA esters as well as other lipid and protein interactors to function in developmental and stress responses. This protein family had been extensively studied in non-leguminous species such as Arabidopsis thaliana (thale cress), Oryza sativa (rice), and Brassica napus (oilseed rape). However, the characterization of soybean (Glycine max) ACBPs, designated GmACBPs, has remained unreported although this legume is a globally important crop cultivated for its high oil and protein content, and plays a significant role in the food and chemical industries. In this study, 11 members of the GmACBP family from four classes, comprising Class I (small), Class II (ankyrin repeats), Class III (large), and Class IV (kelch motif), were identified. For each class, more than one copy occurred and their domain architecture including the acyl-CoA-binding domain was compared with Arabidopsis and rice. The expression profile, tertiary structure and subcellular localization of each GmACBP were predicted, and the similarities and differences between GmACBPs and other plant ACBPs were deduced. A potential role for some Class III GmACBPs in nodulation, not previously encountered in non-leguminous ACBPs, has emerged. Interestingly, the sole member of Class III ACBP in each of non-leguminous Arabidopsis and rice had been previously identified in plant-pathogen interactions. As plant ACBPs are known to play important roles in development and responses to abiotic and biotic stresses, the in silico expression profiles on GmACBPs, gathered from data mining of RNA-sequencing and microarray analyses, will lay the foundation for future studies in their applications in biotechnology.

Plant Acyl-CoA-Binding Proteins—Their Lipid and Protein Interactors in Abiotic and Biotic Stresses

“…Following the discovery of BnACBP, similar 10-kDa ACBPs emerged in Arabidopsis thaliana [ 95 ], Gossypium hirsutum (cotton) [ 96 ], Ricinus communis (castor bean) [ 97 ], Digitalis lanata Ehrh. (Wolly Foxglove) [ 98 ], Oryza sativa (rice) [ 89 ], Vernicia fordii (tung tree) [ 99 ], Vitis vinifera (grape) [ 100 ], Helianthus annuus (sunflower) [ 101 ], Elaeis guineensis (oil palm) [ 102 ], Zea mays (maize) [ 103 ] and Glycine max (soybean) [ 104 ].…”

“…In plants such as Arabidopsis, rice, oilseed rape, oil palm, maize and soybean, ACBPs are classified into four main groups according to size and domains: Class I small ACBPs, Class II ACBPs containing ankyrin repeats, Class III large ACBPs and Class IV ACBPs containing kelch motifs ( Table 1 ) [ 89 , 102 , 103 , 104 , 105 ]. Table 1 shows that Class I ACBPs range from 10 to 17 kDa, whereas the others comprised of a transmembrane domain, ankyrin repeats and/or kelch motifs, have molecular weights of 34 to 85 kDa [ 89 , 103 ].…”

“…These changes in expression levels depicted the potential roles of ZmACBPs in cold stress response which remain to be further elucidated. RNA-seq data analysis of the expression of soybean GmACBPs showed that only Class IV GmACBP11 was downregulated at 24 h after cold stress, whereas other GmACBPs displayed a lack of significant changes of expression in comparison to the nontreated control [ 104 ].…”

“…In soybean, expression profiles of roots were analysed by RNA-seq following dehydration stress [ 153 ]. Data mining of GmACBP expression by Azlan et al [ 104 ] revealed that Class II ( GmACBP3 and GmACBP4 ), Class III ( GmACBP7 ) as well as Class IV ( GmACBP9 ) were induced, suggesting that these GmACBPs play a role in drought response.…”

“…These results suggested that ZmACBP3 overexpression may enhance stress tolerance through changes in lipid metabolism which led to the induction of stress-responsive genes [ 103 ]. In soybean response to NaCl stress, in silico analysis of GmACBP expression from RNA-seq data exhibited induction of Class II GmACBP3 , Class III GmACBP7 and Class IV GmACBP9 , but decreases in Class I GmACBP2 and Class IV GmACBP10 [ 104 ]. As only Arabidopsis and rice Class II ACBPs have been reported in the NaCl response, the greater increase of Class III GmACBP7 than Class II GmACBP3 expression implied different roles for GmACBPs in soybean [ 104 ].…”