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1.
Int J Biol Macromol ; 107(Pt B): 2630-2642, 2018 Feb.
Article in English | MEDLINE | ID: mdl-29080824

ABSTRACT

Major intrinsic proteins (MIPs), commonly known as aquaporins, transport water and non-polar small solutes. Comparing the 3D models and the primary selectivity-related motifs (two Asn-Pro-Ala (NPA) regions, the aromatic/arginine (ar/R) selectivity filter, and Froger's positions (FPs)) of all plant MIPs that have been experimentally proven to transport arsenic (As) and antimony (Sb), some substrate-specific signature sequences (SSSS) or specificity determining sites (SDPs) have been predicted. These SSSS or SDPs were determined in 543 MIPs found in the genomes of 12 crop plants; the As and Sb transporters were predicted to be distributed in noduline-26 like intrinsic proteins (NIPs), and every plant had one or several As and Sb transporter NIPs. Phylogenetic grouping of the NIP subfamily based on the ar/R selectivity filter and FPs were linked to As and Sb transport. We further determined the group-wise substrate selectivity profiles of the NIPs in the 12 crop plants. In addition to two NPA regions, the ar/R filter, and FPs, certain amino acids especially in the pore line, loop D, and termini contribute to the functional distinctiveness of the NIP groups. Expression analysis of transcripts in different organs indicated that most of the As and Sb transporter NIPs were expressed in roots.


Subject(s)
Antimony/metabolism , Aquaporins/metabolism , Arsenic/metabolism , Crops, Agricultural/genetics , Genome, Plant , Aquaporins/chemistry , Aquaporins/genetics , Biological Transport , Gene Expression Profiling , Gene Expression Regulation, Plant , Hydrogen Bonding , Models, Molecular , Organ Specificity/genetics , Phylogeny , Sequence Homology, Amino Acid
2.
PLoS One ; 11(6): e0157735, 2016.
Article in English | MEDLINE | ID: mdl-27327960

ABSTRACT

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.


Subject(s)
Aquaporins/genetics , Genome, Plant , Plant Proteins/genetics , Poaceae/genetics , Poaceae/metabolism , Water/metabolism , Amino Acid Motifs , Aquaporins/chemistry , Aquaporins/metabolism , Evolution, Molecular , Gene Expression Regulation, Plant , Genes, Plant , Plant Leaves/genetics , Plant Proteins/chemistry , Plant Proteins/metabolism , Plant Roots/genetics , Plant Shoots/genetics , Protein Transport , Subcellular Fractions/metabolism , Substrate Specificity , Terminology as Topic
3.
J Microbiol Biotechnol ; 20(11): 1500-5, 2010 Nov.
Article in English | MEDLINE | ID: mdl-21124053

ABSTRACT

The novel swine-origin influenza A/H1N1 virus (S-OIV) first detected in April 2009 has been identified to transmit from human to human directly and is the cause of currently emerged pandemic. In this study, nucleotide and deduced amino acid sequences of hemagglutinin (HA) and neuraminidase (NA) of the S-OIV and other influenza A viruses were analyzed through bioinformatic tools for phylogenetic analysis, genetic recombination and point mutation to investigate the emergence and adaptation of the S-OIV in human. The phylogenetic analysis showed that the HA comes from triple reassortant influenza A/H1N2 and the NA from Eurasian swine influenza A/H1N1 indicating HA and NA to descend from different lineages during the genesis of the S-OIV. Recombination analysis nullified the possibility of occurrence of recombination in HA and NA denoting the role of reassortment in the outbreak. Several conservative mutations are observed in the amino acid sequences of the HA and NA and this mutated residues are identical in the S-OIV. The results reported herein suggested the notion that the recent pandemic is the result of reassortment of different genes from different lineages of two envelope proteins, HA and NA which are responsible for antigenic activity of virus. This study further suggests that the adaptive capability of the S-OIV in human is acquired by the unique mutations generated during emergence.


Subject(s)
Evolution, Molecular , Hemagglutinin Glycoproteins, Influenza Virus/genetics , Influenza A Virus, H1N1 Subtype/genetics , Influenza, Human/virology , Neuraminidase/genetics , Viral Proteins/genetics , Adaptation, Physiological , Amino Acid Sequence , Hemagglutinin Glycoproteins, Influenza Virus/chemistry , Hemagglutinin Glycoproteins, Influenza Virus/metabolism , Humans , Influenza A Virus, H1N1 Subtype/chemistry , Influenza A Virus, H1N1 Subtype/classification , Influenza A Virus, H1N1 Subtype/physiology , Influenza A virus/chemistry , Influenza A virus/classification , Influenza A virus/genetics , Influenza A virus/physiology , Molecular Sequence Data , Mutation , Neuraminidase/chemistry , Neuraminidase/metabolism , Phylogeny , Sequence Alignment , Viral Proteins/chemistry , Viral Proteins/metabolism
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