A Systematic Analysis Of Structure And Evolution Of HECT And U-box Genes In Plants

E3 ubiquitin ligases comprise a highly diverse and important group of enzymes that act within the 26 S ubiquitin proteasome pathway. They facilitate the transfer of ubiquitin to substrate proteins which may be marked for degradation by this way. As such they perform as central regulators in many cellular and physiological processes in plants. HECT(homologous to E6-associated protein C-terminus) and U-box(a modified RING motif without the full complement of Zn2+-binding ligands) are two essential classes of E3 ubiquitin ligases. Currently, the gene numbers, structures, evolution and potential functions of these two E3 enzymes were not fully understood in plant genomes. In this study, we focused on the prediction of the HECT and U-box genes in plant genomes and comprehensively analyzed the structures, evolution and potential functions of these plant genes.Part 1. Structure and evolution of HECT genes in soybean genome In this part, we systematically analyzed the sequences, structures, evolution and functions of HECT genes in soybean genome. Using high-quality genome sequences, we predicted 19 soybean HECT genes. The predicted HECT genes were distributed unevenly across 15 of 20 chromosomes. Nineteen of these genes were inferred to be segmentally duplicated gene pairs, suggesting that segmental duplications have made a significant contribution to the expansion of the HECT gene family in soybean. Phylogenetic analysis showed that these HECT genes can be divided into seven groups, among which gene structure and domain architecture were relatively well-conserved. Moreover, expression analysis revealed that 15 of the HECT genes in soybean were differentially expressed in 14 tissues, and were often highly expressed in the flowers and roots. In summary, this work provides useful information on which further functional studies of soybean HECT genes can be based.Part 2. Structure and evolution of HECT genes in other plants In this part, we systematically analyzed the sequences, structures, evolution and functions of HECT genes in 40 other plant genomes. All the detected plant genomes contain HECT genes, but varied substantially. Totally, 365 plant HECT genes were predicted(included that predicted in soybean genome). The HECT genes in higher plants were classified into seven groups as in soybean based on phylogenetic relationships. Except for group II, all plant HECT gene groups have orthologous genes in Arabidopsis thaliana. Our analysis of 365 plant HECT domains shows that many highly conserved residues are present, suggesting that these conserved residues still play key roles in structural maintenance, and are involved in plant ubiquitination processes. The dN/dS ratios showed that seven HECT orthologous groups are under strong negative selection. The three paralogous clusters among these HECT genes-(UPL1/2/UPL8, UPL3/UPL4, and UPL6/UPL7) in plants diverged into functional divergences in angiosperm evolution.Part 3. Structure and evolution of U-box genes in soybean genome In this part, we systematically analyzed the sequences, structures, evolution and functions of U-box genes in soybean genome. We predicted 127 U-box genes in soybean genome. These soybean U-box genes were divided into three main subfamilies based on phylogenetic relationships and domain architectures. Subfamily I mainly contains Kinase domain, subfamily II mainly contains ARM repeats domain, and Subfamily III contains U-box domain only. Segmentally replication events and tandem replication events contributed significantly to the expansion of the soybean U-box gene family. Expression analysis showed that 98 U-box genes in 14 soybean tissues expressed. These soybean U-box genes mostly expressed relatively highly in root, flower, young leaf, nodule, and pod shell tissues, while expressed relatively lowly in seed tissues in different stages.In summary, in the present work, I conducted a comprehensively analysis on the structure and evolution of HECT and U-box genes in plant genomes. The results could provide new insights to the study of the functions and evolution of E3 ubiquitin ligases in plant genomes.