Genome-wide sequence characterization and expression analysis of major intrinsic proteins in soybean (Glycine max L.)

• Published in: PloS one Vol. 8; no. 2; p. e56312
• Main Authors: Zhang, Da Yong, Ali, Zulfiqar, Wang, Chang Biao, Xu, Ling, Yi, Jin Xin, Xu, Zhao Long, Liu, Xiao Qing, He, Xiao Lan, Huang, Yi Hong, Khan, Iqrar Ahmad, Trethowan, Richard M, Ma, Hong Xiang
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 20.02.2013; Public Library of Science (PLoS)
• Subjects: Agriculture; Amino Acid Sequence; Amino acids; Analysis; Aquaporins; Aquaporins - chemistry; Aquaporins - genetics; Aquaporins - metabolism; Arabidopsis; Biology; Biotechnology; Cell membranes; Chromosomes, Plant - genetics; Cladistic analysis; Dehydration; Exons - genetics; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Plant - drug effects; Gene sequencing; Genes; Genes, Plant - genetics; Genetic aspects; Genome, Plant - genetics; Genomes; Genomics; Glycine max; Glycine max - drug effects; Glycine max - genetics; Homology; Introns - genetics; Mammals; Membranes; Molecular Sequence Data; Next-generation sequencing; Nucleotide sequence; Organ Specificity - drug effects; Organ Specificity - genetics; Phosphorylation; Phosphorylation - drug effects; Phylogeny; Physiology; Plant Proteins - chemistry; Plant Proteins - genetics; Plant Proteins - metabolism; Plant Roots - drug effects; Plant Roots - genetics; Plants (botany); Plasma; Polyethylene Glycols - pharmacology; Protein Structure, Tertiary; Proteins; Reverse transcription; Selectivity; Sequence Alignment; Sequence Analysis, DNA; Similarity; Soybeans; Studies; Subgroups; Substrate Specificity - drug effects; Substrates; Terminology as Topic; Transport; Water transport; China
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0056312

Water is essential for all living organisms. Aquaporin proteins are the major facilitator of water transport activity through cell membranes of plants including soybean. These proteins are diverse in plants and belong to a large major intrinsic (MIP) protein family. In higher plants, MIPs are classified into five subfamilies including plasma membrane intrinsic proteins (PIP), tonoplast intrinsic proteins (TIP), NOD26-like intrinsic proteins (NIP), small basic intrinsic proteins (SIP), and the recently discovered X intrinsic proteins (XIP). This paper reports genome wide assembly of soybean MIPs, their functional prediction and expression analysis. Using a bioinformatic homology search, 66 GmMIPs were identified in the soybean genome. Phylogenetic analysis of amino acid sequences of GmMIPs divided the large and highly similar multi-gene family into 5 subfamilies: GmPIPs, GmTIPs, GmNIPs, GmSIPs and GmXIPs. GmPIPs consisted of 22 genes and GmTIPs 23, which showed high sequence similarity within subfamilies. GmNIPs contained 13 and GmSIPs 6 members which were diverse. In addition, we also identified a two member GmXIP, a distinct 5(th) subfamily. GmMIPs were further classified into twelve subgroups based on substrate selectivity filter analysis. Expression analyses were performed for a selected set of GmMIPs using semi-quantitative reverse transcription (semi-RT-qPCR) and qPCR. Our results suggested that many GmMIPs have high sequence similarity but diverse roles as evidenced by analysis of sequences and their expression. It can be speculated that GmMIPs contains true aquaporins, glyceroporins, aquaglyceroporins and mixed transport facilitators.