Global Analysis of Ankyrin Repeat Domain C3HC4-Type RING Finger Gene Family in Plants

<div><p>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 (<i>Oryza sativa</i>) XB3. A phylogenetic relationship analysis suggested that the <i>XB3</i>-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 <i>XB3</i>-like genes of <i>Arabidopsis</i>, <i>Oryza sative</i>, <i>Zea mays</i> and <i>Glycine max</i> revealed that the expression of <i>XB3</i>-like genes was in different tissues and during different life stages. The preferential expression of <i>XB3</i>-like genes in specified tissues and the response to phytohormone and abiotic stress treatments of <i>Arabidopsis</i> and <i>Zea mays</i> 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.</p>