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Genome-wide sequence characterization and expression analysis of major intrinsic proteins in soybean (Glycine max L.).
PLoS One. 2013; 8(2):e56312.Plos

Abstract

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.

Authors+Show Affiliations

Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

23437113

Citation

Zhang, Da Yong, et al. "Genome-wide Sequence Characterization and Expression Analysis of Major Intrinsic Proteins in Soybean (Glycine Max L.)." PloS One, vol. 8, no. 2, 2013, pp. e56312.
Zhang DY, Ali Z, Wang CB, et al. Genome-wide sequence characterization and expression analysis of major intrinsic proteins in soybean (Glycine max L.). PLoS One. 2013;8(2):e56312.
Zhang, D. Y., Ali, Z., Wang, C. B., Xu, L., Yi, J. X., Xu, Z. L., Liu, X. Q., He, X. L., Huang, Y. H., Khan, I. A., Trethowan, R. M., & Ma, H. X. (2013). Genome-wide sequence characterization and expression analysis of major intrinsic proteins in soybean (Glycine max L.). PloS One, 8(2), e56312. https://doi.org/10.1371/journal.pone.0056312
Zhang DY, et al. Genome-wide Sequence Characterization and Expression Analysis of Major Intrinsic Proteins in Soybean (Glycine Max L.). PLoS One. 2013;8(2):e56312. PubMed PMID: 23437113.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide sequence characterization and expression analysis of major intrinsic proteins in soybean (Glycine max L.). AU - Zhang,Da Yong, AU - Ali,Zulfiqar, AU - Wang,Chang Biao, AU - Xu,Ling, AU - Yi,Jin Xin, AU - Xu,Zhao Long, AU - Liu,Xiao Qing, AU - He,Xiao Lan, AU - Huang,Yi Hong, AU - Khan,Iqrar Ahmad, AU - Trethowan,Richard M, AU - Ma,Hong Xiang, Y1 - 2013/02/20/ PY - 2012/08/13/received PY - 2013/01/08/accepted PY - 2013/2/26/entrez PY - 2013/2/26/pubmed PY - 2013/8/22/medline SP - e56312 EP - e56312 JF - PloS one JO - PLoS One VL - 8 IS - 2 N2 - 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. SN - 1932-6203 UR - https://www.unboundmedicine.com/medline/citation/23437113/Genome_wide_sequence_characterization_and_expression_analysis_of_major_intrinsic_proteins_in_soybean__Glycine_max_L___ L2 - https://dx.plos.org/10.1371/journal.pone.0056312 DB - PRIME DP - Unbound Medicine ER -