Abstract
RBR (RING1-IBR-RING2) proteins play an important role in protein ubiquitination and are involved in many cellular processes. Recent studies showed plant RBR genes were induced by abiotic and biotic stresses. However, detailed studies on RBR genes in the important oil crop, soybean (Glycine max (L.) Merr.), is still lacking. Here we performed a genome-wide search and identified 24 RBR domain-containing genes from the soybean genome sequence and cloned 11 of them. Most soybean RBR proteins contain a highly conserved RBR supra-domain. Phylogenetic analyses indicated all 24 soybean RBR proteins are most related to the RBR proteins from Phaseolus vulgaris, and could be classified into seven groups including Ariadne A, Ariadne B, ARA54, Plant IIA, Plant IIB, Plant IIC, and Helicase. Tandem duplication and block duplication were found among the Ariadne B and Plant IIC group of soybean RBR genes. Despite the conserved RBR supra-domain, there are extensive variations in the additional protein motifs and exon-intron structures between different groups, which indicate they might have diverse functions. Most soybean RBR proteins are predicted to localize in nucleus, and four of them were experimentally confirmed by GFP fusion proteins. Soybean RBR genes are broadly expressed in many tissue types with a little more abundant in the roots and flowers than leaves, stems, and seeds. The expression of GmRTRTP3 (Plant IIB) and GmRTRTP5 (Plant IIC) are induced by NaCl treatment, which suggests these RBR genes might be involved in soybean response to abiotic stresses.
Highlights
In eukaryotes, protein ubiquitination is a key biochemical mechanism and play a fundamental role in multiple cellular processes, such as protein homeostasis [1], signal transduction [2,3,4,5], development [6,7], differentiations and programmed cell death (PCD) [2]
A new E3 protein family involved in ubiquitination, which is a subset of RING (Really Interesting New Gene) proteins,is characterized by the presence of a RING1-IBR-RING2 (RBR) supra-domain
This tripartite domain is known as a TRIAD [8], which is composed of three consecutive domains including a N-terminal RING1, an IBR (In Between Ring), and a C-terminal RING2 domain
Summary
Protein ubiquitination is a key biochemical mechanism and play a fundamental role in multiple cellular processes, such as protein homeostasis [1], signal transduction [2,3,4,5], development [6,7], differentiations and programmed cell death (PCD) [2]. A new E3 protein family involved in ubiquitination, which is a subset of RING (Really Interesting New Gene) proteins,is characterized by the presence of a RING1-IBR-RING2 (RBR) supra-domain. This tripartite domain is known as a TRIAD (for two RING fingers and a DRIL) [8], which is composed of three consecutive domains including a N-terminal RING1, an IBR (In Between Ring), and a C-terminal RING2 domain. The IBR domain has a typical C6HC signature with a shorter and strict formula: C–X2–C–X(9– 11)–C–X–H– X2–C–X(1–4)–C–X4–C–X2–C, which is found only in RBR proteins [9,10]. The C-terminal domain, often called as RING2, resembles a much shorter RING finger with C3HC4 signature
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