MORC Domain Definition and Evolutionary Analysis of the MORC Gene Family in Green Plants

Abstract

Microrchidia (MORC) proteins have been described as epigenetic regulators and plant immune mediators in Arabidopsis. Typically, plant and animal MORC proteins contain a hallmark GHKL-type (Gyrase, Hsp90, Histidine kinase, MutL) ATPase domain in their N-terminus. Here, 356 and 83 MORC orthologues were identified in 60 plant and 27 animal genomes. Large-scale MORC sequence analyses revealed the presence of a highly conserved motif composition that defined as the MORC domain. The MORC domain was present in both plants and animals, indicating that it originated in the common ancestor before the divergence of plants and animals. Phylogenetic analyses showed that MORC genes in both plant and animal lineages were clearly classified into two major groups, named Plants-Group I, Plants-Group II and Animals-Group I, Animals-Group II, respectively. Further analyses of MORC genes in green plants uncovered that Group I can be subdivided into Group I-1 and Group I-2. Group I-1 only contains seed plant genes, suggesting that Group I-1 and I-2 divergence occurred at least before the emergence of spermatophytes. Group I-2 and Group II have undergone several gene duplications, resulting in the expansion of MORC gene family in angiosperms. Additionally, MORC gene expression analyses in Arabidopsis, soybean, and rice revealed a higher expression level in reproductive tissues compared with other organs, and showed divergent expression patterns for several paralogous gene pairs. Our studies offered new insights into the origins, phylogenetic relationships, and expressional patterns of MORC family members in green plants, which would help to further reveal their functions as plant epigenetic regulators.

Fig. 1.

—Phylogenetic classification of MORC genes in plant and animal lineages. Phylogenetic tree was constructed using the ML method implemented in RaxML-HPC2 through the online CIPRES Science Gateway website. The topology of ML tree showed that MORC genes in plants and animals can be clearly classified into two major groups, respectively, which is designed as Plants-Group I, Plants-Group II and Animals-Group I, Animals-Group II. The green algae were located in the base of these two plant groups. Seven and four canonical MORC genes in Arabidopsis and human were labeled with red triangle and circle.

Fig. 2.

—Phylogenetic relationships and motif compositions of some representative MORC genes in plants and animals. The phylogenetic tree was reconstructed using some representative species based on the ML method implemented in RaxML-HPC2 through the online CIPRES Science Gateway website. For major nodes, ML bootstrap values >70% are labeled based on 1,000 replications. Motifs conserved across MORC proteins were identified through a MEME analysis and each motif composition is presented in supplementary figure S3, Supplementary Material online. Based on their highly conserved motif composition, we proposed a characteristic MORC domain that was marked in red box on the right.

Fig. 3.

—Homologous modeling of MORC1 protein and MORC domain in several representative species. The 3D structure of MORC1 protein and MORC domain in Arabidopsis and human were predicted based on the Swiss-model database according to mice MORC3 protein crystal structure (A). Sequence logo of MORC domain was generated on the Weblogo website using all aligned MORC domain sequences (B). Some conserved secondary structures in MORC domain were labeled (on the logo bottom) according to human MORC1 domain modeling result (on the logo top).

Fig. 4.

—Phylogenetic relationships of MORC gene family in major groups of green lineage. The phylogenetic tree was built using the ML method implemented in RaxML-HPC2 through the online CIPRES Science Gateway and the Chlorophyta was rooted as outgroup. Two major groups (Group I-1 and 2 and Group II) and two major gene duplication events (D1 and D2) are recognized. Numbers above each branch indicates bootstrap support percentage values based on 1,000 replications and values >50% are shown. Gene lineages composed of angiosperms, gymnosperms, monilophytes, lycophytes, bryophytes, charophyta, and chlorophyta are labeled on the right.

Fig. 5.

—Maximum likelihood tree of detailed phylogenetic relationships among each group in representative angiosperm MORC genes. Phylogenetic trees of the Group II (A), Group I-2 (B), and Group I-1 (C) from representative angiosperms were reconstructed by ML method using in RaxML-HPC2 program through the online CIPRES Science Gateway with default parameters. For each clade, numbers above branches indicate bootstrap support percentage values based on 1,000 replications. The red asterisks indicate the family-specific gene duplication event and other different color asterisks represent several ancient whole genome duplication (WGD) events.

Fig. 6.

—A proposed model for the evolution of MORC genes in plants and animals. Based on sequence similarity, exon–intron organization and MORC domain, MORC genes in plants and animals can be divided into two major groups, respectively. The MORC gene is present in both plants and animals and its origin can be traced back to the common ancestor before the divergence of plants and animals. Animal MORCs underwent a gene duplication during the evolution of vertebrates in each subgroups and thus produced multiple gene copies in vertebrate lineages. Plant MORCs encountered several rounds of gene duplication events in the long-term evolutionary courses, eventually generating large-scale expansion in most species.