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Genome-Wide Sequence Characterization and Expression Analysis of Major Intrinsic Proteins in Soybean (Glycine max L.)

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 classi...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3577755/
https://www.ncbi.nlm.nih.gov/pubmed/23437113
http://dx.doi.org/10.1371/journal.pone.0056312
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author 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
author_facet 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
author_sort Zhang, Da Yong
collection PubMed
description 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.
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spelling pubmed-35777552013-02-22 Genome-Wide Sequence Characterization and Expression Analysis of Major Intrinsic Proteins in Soybean (Glycine max L.) 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 PLoS One Research Article 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. Public Library of Science 2013-02-20 /pmc/articles/PMC3577755/ /pubmed/23437113 http://dx.doi.org/10.1371/journal.pone.0056312 Text en © 2013 Zhang et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
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
Genome-Wide Sequence Characterization and Expression Analysis of Major Intrinsic Proteins in Soybean (Glycine max L.)
title Genome-Wide Sequence Characterization and Expression Analysis of Major Intrinsic Proteins in Soybean (Glycine max L.)
title_full Genome-Wide Sequence Characterization and Expression Analysis of Major Intrinsic Proteins in Soybean (Glycine max L.)
title_fullStr Genome-Wide Sequence Characterization and Expression Analysis of Major Intrinsic Proteins in Soybean (Glycine max L.)
title_full_unstemmed Genome-Wide Sequence Characterization and Expression Analysis of Major Intrinsic Proteins in Soybean (Glycine max L.)
title_short Genome-Wide Sequence Characterization and Expression Analysis of Major Intrinsic Proteins in Soybean (Glycine max L.)
title_sort genome-wide sequence characterization and expression analysis of major intrinsic proteins in soybean (glycine max l.)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3577755/
https://www.ncbi.nlm.nih.gov/pubmed/23437113
http://dx.doi.org/10.1371/journal.pone.0056312
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