Genome-wide Comparative Phylogenetic Analysis Of Mrs2 And Shaker Gene Families In Arabidopsis And Rice

mrs2 (mitochondrial RNA splicing2) genes were discovered as a suppressor of self-splicing defects of group II introns in mitochondria. The mrs2 gene product (mrs2p) is an integral protein of the inner mitochondrial membrane. It has been shown to be a transporter for the movement of Mg2+ in plants. Channel proteins were coded by Shaker channel genes. The uptake of K+ and its redistribution throughout the plant is accomplished by channel proteins. They belong to a kind of membrane transport protein of K+ transport systems in the plant.In this study, we performed the genome-wide comparative phylogenetic analysis according to the structural characteristics of the two gene families. Based on the HMM model, all the members of the two gene families in Arabidopsis and rice were identified at genome level. The sequences of the proteins were obtained. A phylogenetic tree was reconstructed based on the each protein family from Arabidopsis and rice to estimate the evolutionary trace between the monocot and dicot model plants. The analysis of conserved domains of these proteins was carried out and the results revealed the characteristics of the domain organization. Conserved motifs of these protein sequences were identified statistically using MEME. Ka (nonsynonymous substitution rate) and Ks (synonymous substitution rate) analysis of the paralogous nucleotide sequences was conducted using the K-Estimator program, which was used to show environmental selection-pressure involved in the driving gene divergence after duplication and to reveal the basic of molecule evolution. Finally the expression information of these genes was searched from the Genbank EST database. The results are as follows:(1) 11 and 9 mrs2 genes were detected in Arabidopsis and rice, respectively. 9 and 11 members of Shaker gene family were identified in Arabidopsis and rice. Phylogenetic trees were constructed for these two families. Both mrs2 proteins and Shaker proteins could be divided into 2 major groups, and each group contained at least one Arabidopsis and rice protein, which indicated that the main characteristics of these two families were formed before the split of Arabidopsis and rice. We found only one pair of orthologous proteins and 6 pairs of paralogous proteins in mrs2 gene family, 2 pairs of orthologous proteins and 4 pairs of paralogous proteins in Shaker gene family. It indicated that most mrs2 and Shaker genes in Arabidopsis and rice expanded in a species-specific manner.(2) All the members of the MRS2 proteins contain a conserved MRS2 domain. We identified the Ion_trans domains and CNBD contained in all the Shaker proteins. MEME analysis indicated that the motifs in the mrs2 protein and Shaker channel protein were all highly conservative, and the order of these motifs in each protein family was quite similar.(3) The coding regions of the paralogous proteins were used to calculate the nonsynonymous/synonynmous substitution ratio (Ka/Ks). The high ratios were always in the regions outside the motifs and domains, suggesting positive selections had taken place in these regions. While Ka/Ks ratios were obviously smaller even near zero for the motifs and domains regions. It suggested that these regions had gone through strong purifying selection.(4) In Arabidopsis and rice, most mrs2 genes were expressed mainly in the tissue of flower, root and leaf. And there were more than half of Shaker genes expressing in the tissue of flower, root, stem and shoot. These genes kept consistency in some expressions in Arabidopsis and rice. In Arabidopsis, nearly half of mrs2 and Shaker genes were expressed in silique, while many mrs2 genes were expressed in shoots and callus in rice. It suggested that there were tissue-specific expressions of the two gene families in Arabidopsis and rice.These results will lay solid foundation for cloning these genes or verifying their functions.