Abstract
Ankyrin repeat (ANK) C3HC4-type RING finger (RF) genes comprise a large family in plants and play important roles in various physiological processes of plant life. In this study, we identified 187 ANK C3HC4-type RF proteins from 29 species with complete genomes and named the ANK C3HC4-type RF proteins the XB3-like proteins because they are structurally related to the rice (Oryza sativa) XB3. A phylogenetic relationship analysis suggested that the XB3-like genes originated from ferns, and the encoded proteins fell into 3 major groups. Among these groups, we found that the spacing between the metal ligand position 6 and 7, and the conserved residues, which was in addition to the metal ligand amino acids, in the C3HC4-type RF were different. Using a wide range of protein structural analyses, protein models were established, and all XB3-like proteins were found to contain two to seven ANKs and a C3HC4-type RF. The microarray data for the XB3-like genes of Arabidopsis, Oryza sative, Zea mays and Glycine max revealed that the expression of XB3-like genes was in different tissues and during different life stages. The preferential expression of XB3-like genes in specified tissues and the response to phytohormone and abiotic stress treatments of Arabidopsis and Zea mays not only confirmed the microarray analysis data but also demonstrated that the XB3-like proteins play roles in plant growth and development as well as in stress responses. Our data provide a very useful reference for the identification and functional analysis of members of this gene family and also provide a new method for the genome-wide analysis of gene families.
Highlights
Ankyrin repeat (ANK), which is a 33-residue motif in proteins consisting of two alpha helices separated by loops [1], is one of the most common protein domains and is widely distributed in organisms ranging from viruses to human [2]
Our result demonstrated that all twelve proteins contained a conserved C3HC4 RING finger (RF) domain and no fewer than two ANK domains (XBAT34 and XBAT35 contain two ANK domains; XBOS34 contains three ANK domains; XBAT31, XBAT32, XBAT33, XBOS31, XBOS33 and XBOS36 contain five ANK domains; and XB3, XBOS32 and XBOS35 contain six ANK domains; Fig. 1)
To clarify the phylogenetic relationship among the XB3-like genes and to infer functions as well as the evolutionary history of this gene family, we identified 187 genes in 27 land plants with completely sequenced genomes
Summary
Ankyrin repeat (ANK), which is a 33-residue motif in proteins consisting of two alpha helices separated by loops [1], is one of the most common protein domains and is widely distributed in organisms ranging from viruses to human [2]. RF is a member of the zinc finger domain protein family, which was first identified as a DNA-binding motif in the transcription factor TFIIIA from Xenopus laevis [12]. This domain was identified as functionally binding to RNA [13], protein or lipid substrates [14]. In addition to the two canonical RING types (C3H2C3 or C3HC4), additional types of modified RING domains, known as RING-V, RING-D, RING-S/T, RING-G and RING-C2, were characterised on the basis of the spacing between their metal ligands or by the different substitutions at one or more of the metal ligand positions [15]
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