Genome-Wide Characterization of Major Intrinsic Proteins in Four Grass Plants and Their Non-Aqua Transport Selectivity Profiles with Comparative Perspective.
Major intrinsic proteins (MIPs), commonly known as aquaporins, transport not only water in plants but also other substrates of physiological significance and heavy metals. In most of the higher plants, MIPs are divided into five subfamilies (PIPs, TIPs, NIPs, SIPs and XIPs). Herein, we identified 68, 42, 38 and 28 full-length MIPs, respectively in the genomes of four monocot grass plants, specifically Panicum virgatum, Setaria italica, Sorghum bicolor and Brachypodium distachyon. Phylogenetic analysis showed that the grass plants had only four MIP subfamilies including PIPs, TIPs, NIPs and SIPs without XIPs. Based on structural analysis of the homology models and comparing the primary selectivity-related motifs [two NPA regions, aromatic/arginine (ar/R) selectivity filter and Froger's positions (FPs)] of all plant MIPs that have been experimentally proven to transport non-aqua substrates, we predicted the transport profiles of all MIPs in the four grass plants and also in eight other plants. Groups of MIP subfamilies based on ar/R selectivity filter and FPs were linked to the non-aqua transport profiles. We further deciphered the substrate selectivity profiles of the MIPs in the four grass plants and compared them with their counterparts in rice, maize, soybean, poplar, cotton, Arabidopsis thaliana, Physcomitrella patens and Selaginella moellendorffii. In addition to two NPA regions, ar/R filter and FPs, certain residues, especially in loops B and C, contribute to the functional distinctiveness of MIP groups. Expression analysis of transcripts in different organs indicated that non-aqua transport was related to expression of MIPs since most of the unexpressed MIPs were not predicted to facilitate the transport of non-aqua molecules. Among all MIPs in every plant, TIP (BdTIP1;1, SiTIP1;2, SbTIP2;1 and PvTIP1;2) had the overall highest mean expression. Our study generates significant information for understanding the diversity, evolution, non-aqua transport profiles and insight into comparative transport selectivity of plant MIPs, and provides tools for the development of transgenic plants.
Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
Abul Kalam
AK
Azad
Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
Jahed
J
Ahmed
Forensic DNA Laboratory of Bangladesh Police, Malibagh, Dhaka, Bangladesh.
Md Asraful
MA
Alum
Department of Genetic Engineering and Biotechnology, University of Chittagong, Chittagong 4331, Bangladesh.
Md Mahbub
MM
Hasan
Department of Life Science and Biotechnology, Shimane University, Shimane 690-8504, Japan.
Takahiro
T
Ishikawa
Department of Life Science and Biotechnology, Shimane University, Shimane 690-8504, Japan.
Yoshihiro
Y
Sawa
Institute of Plant Science and Resources, Okayama University, Chuo-2-chome, Kurashiki 710-0046, Japan.
Maki
M
Katsuhara
D020816:Amino Acid Motifs; D020346:Aquaporins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D018515:Plant Leaves / Q000235:genetics; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics; D018520:Plant Shoots / Q000235:genetics; D006109:Poaceae / Q000235:genetics* / Q000378:metabolism*; D021381:Protein Transport; D013347:Subcellular Fractions / Q000378:metabolism; D013379:Substrate Specificity; D009626:Terminology as Topic; D014867:Water / Q000378:metabolism*
D020346:Aquaporins; D010940:Plant Proteins; C110065:major intrinsic protein, plant; D014867:Water