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Front Plant Sci
2016 Jan 01;7:1896. doi: 10.3389/fpls.2016.01896.
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Plant Aquaporins: Genome-Wide Identification, Transcriptomics, Proteomics, and Advanced Analytical Tools.
Deshmukh RK
,
Sonah H
,
Bélanger RR
.
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Aquaporins (AQPs) are channel-forming integral membrane proteins that facilitate the movement of water and many other small molecules. Compared to animals, plants contain a much higher number of AQPs in their genome. Homology-based identification of AQPs in sequenced species is feasible because of the high level of conservation of protein sequences across plant species. Genome-wide characterization of AQPs has highlighted several important aspects such as distribution, genetic organization, evolution and conserved features governing solute specificity. From a functional point of view, the understanding of AQP transport system has expanded rapidly with the help of transcriptomics and proteomics data. The efficient analysis of enormous amounts of data generated through omic scale studies has been facilitated through computational advancements. Prediction of protein tertiary structures, pore architecture, cavities, phosphorylation sites, heterodimerization, and co-expression networks has become more sophisticated and accurate with increasing computational tools and pipelines. However, the effectiveness of computational approaches is based on the understanding of physiological and biochemical properties, transport kinetics, solute specificity, molecular interactions, sequence variations, phylogeny and evolution of aquaporins. For this purpose, tools like Xenopus oocyte assays, yeast expression systems, artificial proteoliposomes, and lipid membranes have been efficiently exploited to study the many facets that influence solute transport by AQPs. In the present review, we discuss genome-wide identification of AQPs in plants in relation with recent advancements in analytical tools, and their availability and technological challenges as they apply to AQPs. An exhaustive review of omics resources available for AQP research is also provided in order to optimize their efficient utilization. Finally, a detailed catalog of computational tools and analytical pipelines is offered as a resource for AQP research.
Figure 1. Co-expression network developed for rice and Arabidopsis aquaporin genes: (A) Network analyzed with RiceFREND tool (http://ricefrend.dna.affrc.go.jp) showing interdependency of PIP1-1, PIP1-2, and PIP2-1 in rice; and (B) Network of Arabidopsis visualized with GENEMANIA tool (http://genemania.org) showing interaction of PIP1A with PIP2 and other genes. Network for all rice AQPs at the third hierarchical level is provided in Supplementary Data 2.
Figure 2. Simplified workflow of Xenopus oocyte assay used for the evaluation of solute transport by heterologously expressed foreign transporters including aquaporins.
Figure 3. Yeast heterologous expression system used to evaluate aquaporins. Aquaporin cloned in the expression vector can be easily transferred in yeasts for different assays like growth and survival tests, protein localization, and/or stopped-flow spectrometry.
Agre,
Aquaporin water channels (Nobel Lecture).
2004, Pubmed
Agre,
Aquaporin water channels (Nobel Lecture).
2004,
Pubmed
Aharon,
Overexpression of a plasma membrane aquaporin in transgenic tobacco improves plant vigor under favorable growth conditions but not under drought or salt stress.
2003,
Pubmed
Anderberg,
Annotation of Selaginella moellendorffii Major Intrinsic Proteins and the Evolution of the Protein Family in Terrestrial Plants.
2012,
Pubmed
Ariani,
Genome-wide identification and characterization of aquaporin gene family in common bean (Phaseolus vulgaris L.).
2015,
Pubmed
Benga,
On the definition, nomenclature and classification of water channel proteins (aquaporins and relatives).
2012,
Pubmed
Benga,
Brain water channel proteins in health and disease.
2012,
Pubmed
Benga,
p-(Chloromercuri)benzenesulfonate binding by membrane proteins and the inhibition of water transport in human erythrocytes.
1986,
Pubmed
Benga,
Comparative studies of water permeability of red blood cells from humans and over 30 animal species: an overview of 20 years of collaboration with Philip Kuchel.
2013,
Pubmed
Benga,
Water permeability in human erythrocytes: identification of membrane proteins involved in water transport.
1986,
Pubmed
Bertl,
Function of a separate NH3-pore in Aquaporin TIP2;2 from wheat.
2007,
Pubmed
Besserer,
Selective regulation of maize plasma membrane aquaporin trafficking and activity by the SNARE SYP121.
2012,
Pubmed
,
Xenbase
Biela,
The Nicotiana tabacum plasma membrane aquaporin NtAQP1 is mercury-insensitive and permeable for glycerol.
1999,
Pubmed
,
Xenbase
Bienert,
Solanaceae XIPs are plasma membrane aquaporins that facilitate the transport of many uncharged substrates.
2011,
Pubmed
,
Xenbase
Bienert,
Maize plasma membrane aquaporin ZmPIP2;5, but not ZmPIP1;2, facilitates transmembrane diffusion of hydrogen peroxide.
2014,
Pubmed
Bienert,
Specific aquaporins facilitate the diffusion of hydrogen peroxide across membranes.
2007,
Pubmed
Bienert,
A subgroup of plant aquaporins facilitate the bi-directional diffusion of As(OH)3 and Sb(OH)3 across membranes.
2008,
Pubmed
Burgess,
Gene expression: A space for transcriptomics.
2016,
Pubmed
Carpentier,
Identification of key residues involved in Si transport by the aquaglyceroporins.
2016,
Pubmed
,
Xenbase
Chaumont,
Plasma membrane intrinsic proteins from maize cluster in two sequence subgroups with differential aquaporin activity.
2000,
Pubmed
,
Xenbase
Chen,
Identification and Comparative Analysis of Differential Gene Expression in Soybean Leaf Tissue under Drought and Flooding Stress Revealed by RNA-Seq.
2016,
Pubmed
Chevalier,
A new LxxxA motif in the transmembrane Helix3 of maize aquaporins belonging to the plasma membrane intrinsic protein PIP2 group is required for their trafficking to the plasma membrane.
2014,
Pubmed
Chiba,
HvLsi1 is a silicon influx transporter in barley.
2009,
Pubmed
,
Xenbase
Daniels,
Projection structure of a plant vacuole membrane aquaporin by electron cryo-crystallography.
1999,
Pubmed
Danielson,
Unexpected complexity of the aquaporin gene family in the moss Physcomitrella patens.
2008,
Pubmed
Dean,
Purification and functional reconstitution of soybean nodulin 26. An aquaporin with water and glycerol transport properties.
1999,
Pubmed
,
Xenbase
Deokar,
Genome-Wide Analysis of the Aquaporin Gene Family in Chickpea (Cicer arietinum L.).
2016,
Pubmed
Deshmukh,
Integrating omic approaches for abiotic stress tolerance in soybean.
2014,
Pubmed
Deshmukh,
Identification and functional characterization of silicon transporters in soybean using comparative genomics of major intrinsic proteins in Arabidopsis and rice.
2013,
Pubmed
,
Xenbase
Deshmukh,
A precise spacing between the NPA domains of aquaporins is essential for silicon permeability in plants.
2015,
Pubmed
,
Xenbase
Di Giorgio,
Pollen-Specific Aquaporins NIP4;1 and NIP4;2 Are Required for Pollen Development and Pollination in Arabidopsis thaliana.
2016,
Pubmed
Dordas,
Permeability and channel-mediated transport of boric acid across membrane vesicles isolated from squash roots.
2000,
Pubmed
,
Xenbase
Feng,
Optimizing plant transporter expression in Xenopus oocytes.
2013,
Pubmed
,
Xenbase
Giovannetti,
Two putative-aquaporin genes are differentially expressed during arbuscular mycorrhizal symbiosis in Lotus japonicus.
2012,
Pubmed
Grégoire,
Discovery of a multigene family of aquaporin silicon transporters in the primitive plant Equisetum arvense.
2012,
Pubmed
,
Xenbase
Gupta,
Genome-wide analysis of major intrinsic proteins in the tree plant Populus trichocarpa: characterization of XIP subfamily of aquaporins from evolutionary perspective.
2009,
Pubmed
He,
An aquaporin PvTIP4;1 from Pteris vittata may mediate arsenite uptake.
2016,
Pubmed
Heckwolf,
The Arabidopsis thaliana aquaporin AtPIP1;2 is a physiologically relevant CO₂ transport facilitator.
2011,
Pubmed
Higuchi,
Molecular cloning, water channel activity and tissue specific expression of two isoforms of radish vacuolar aquaporin.
1998,
Pubmed
,
Xenbase
Hove,
Identification and Expression Analysis of the Barley (Hordeum vulgare L.) Aquaporin Gene Family.
2015,
Pubmed
Hu,
Genome-Wide Identification and Expression Analyses of Aquaporin Gene Family during Development and Abiotic Stress in Banana.
2015,
Pubmed
Huang,
The genome of the cucumber, Cucumis sativus L.
2009,
Pubmed
Isayenkov,
The Arabidopsis thaliana aquaglyceroporin AtNIP7;1 is a pathway for arsenite uptake.
2008,
Pubmed
Ishikawa,
Novel type aquaporin SIPs are mainly localized to the ER membrane and show cell-specific expression in Arabidopsis thaliana.
2005,
Pubmed
Jang,
Transgenic Arabidopsis and tobacco plants overexpressing an aquaporin respond differently to various abiotic stresses.
2007,
Pubmed
Johansson,
Water transport activity of the plasma membrane aquaporin PM28A is regulated by phosphorylation.
1998,
Pubmed
,
Xenbase
Jung,
Molecular structure of the water channel through aquaporin CHIP. The hourglass model.
1994,
Pubmed
,
Xenbase
Katsuhara,
Barley plasma membrane intrinsic proteins (PIP Aquaporins) as water and CO2 transporters.
2008,
Pubmed
Kirscht,
Crystal Structure of an Ammonia-Permeable Aquaporin.
2016,
Pubmed
Kitchen,
Beyond water homeostasis: Diverse functional roles of mammalian aquaporins.
2015,
Pubmed
Koonin,
The structure of the protein universe and genome evolution.
2002,
Pubmed
Lindahl,
Membrane proteins: molecular dynamics simulations.
2008,
Pubmed
Liu,
Aquaporin OsPIP1;1 promotes rice salt resistance and seed germination.
2013,
Pubmed
,
Xenbase
Loqué,
Tonoplast intrinsic proteins AtTIP2;1 and AtTIP2;3 facilitate NH3 transport into the vacuole.
2005,
Pubmed
,
Xenbase
Ma,
Do phosphoinositides regulate membrane water permeability of tobacco protoplasts by enhancing the aquaporin pathway?
2015,
Pubmed
Ma,
An efflux transporter of silicon in rice.
2007,
Pubmed
Ma,
A silicon transporter in rice.
2006,
Pubmed
Maurel,
Aquaporins in Plants.
2015,
Pubmed
Mirzaei,
Differential regulation of aquaporins, small GTPases and V-ATPases proteins in rice leaves subjected to drought stress and recovery.
2012,
Pubmed
Movahedi,
Comparative co-expression analysis in plant biology.
2012,
Pubmed
Murata,
Structural determinants of water permeation through aquaporin-1.
2000,
Pubmed
Navarro-Ródenas,
Expression analysis of aquaporins from desert truffle mycorrhizal symbiosis reveals a fine-tuned regulation under drought.
2013,
Pubmed
Negishi,
Tonoplast- and plasma membrane-localized aquaporin-family transporters in blue hydrangea sepals of aluminum hyperaccumulating plant.
2012,
Pubmed
Palmgren,
Sealed inside-out and right-side-out plasma membrane vesicles : optimal conditions for formation and separation.
1990,
Pubmed
Papadopoulos,
Aquaporin water channels in the nervous system.
2013,
Pubmed
Patil,
Soybean (Glycine max) SWEET gene family: insights through comparative genomics, transcriptome profiling and whole genome re-sequence analysis.
2015,
Pubmed
Peng,
Overexpression of a Panax ginseng tonoplast aquaporin alters salt tolerance, drought tolerance and cold acclimation ability in transgenic Arabidopsis plants.
2007,
Pubmed
Peng,
Rhododendron catawbiense plasma membrane intrinsic proteins are aquaporins, and their over-expression compromises constitutive freezing tolerance and cold acclimation ability of transgenic Arabidopsis plants.
2008,
Pubmed
Preston,
Appearance of water channels in Xenopus oocytes expressing red cell CHIP28 protein.
1992,
Pubmed
,
Xenbase
Preston,
Membrane topology of aquaporin CHIP. Analysis of functional epitope-scanning mutants by vectorial proteolysis.
1994,
Pubmed
,
Xenbase
Quigley,
From genome to function: the Arabidopsis aquaporins.
2002,
Pubmed
Reuscher,
Genome-wide identification and expression analysis of aquaporins in tomato.
2013,
Pubmed
Sabir,
Exploring three PIPs and three TIPs of grapevine for transport of water and atypical substrates through heterologous expression in aqy-null yeast.
2014,
Pubmed
Sade,
Improving plant stress tolerance and yield production: is the tonoplast aquaporin SlTIP2;2 a key to isohydric to anisohydric conversion?
2009,
Pubmed
Sakr,
Plasma membrane aquaporins are involved in winter embolism recovery in walnut tree.
2003,
Pubmed
,
Xenbase
Sakurai,
Identification of 33 rice aquaporin genes and analysis of their expression and function.
2005,
Pubmed
Sakurai,
In silico simulation modeling reveals the importance of the Casparian strip for efficient silicon uptake in rice roots.
2015,
Pubmed
Santoni,
A proteomic study reveals novel insights into the diversity of aquaporin forms expressed in the plasma membrane of plant roots.
2003,
Pubmed
Schey,
Matrix-assisted laser desorption mass spectrometry of rhodopsin and bacteriorhodopsin.
1992,
Pubmed
Schindler,
Analysis of hydrophobic proteins and peptides by electrospray ionization mass spectrometry.
1993,
Pubmed
Schnurbusch,
Boron toxicity tolerance in barley through reduced expression of the multifunctional aquaporin HvNIP2;1.
2010,
Pubmed
,
Xenbase
Schulze,
Navigating gene expression using microarrays--a technology review.
2001,
Pubmed
Secchi,
Isolation and functional characterization of three aquaporins from olive (Olea europaea L.).
2007,
Pubmed
,
Xenbase
Shen,
Isolation, culture, and transient transformation of plant protoplasts.
2014,
Pubmed
Song,
Soybean TIP Gene Family Analysis and Characterization of GmTIP1;5 and GmTIP2;5 Water Transport Activity.
2016,
Pubmed
,
Xenbase
Srivastava,
Multifaceted roles of aquaporins as molecular conduits in plant responses to abiotic stresses.
2016,
Pubmed
Suga,
Water channel activity of radish plasma membrane aquaporins heterologously expressed in yeast and their modification by site-directed mutagenesis.
2004,
Pubmed
Sun,
Genome-wide identification and characterization of aquaporin gene family in moso bamboo (Phyllostachys edulis).
2016,
Pubmed
Sutka,
Tonoplast vesicles of Beta vulgaris storage root show functional aquaporins regulated by protons.
2005,
Pubmed
Takano,
The Arabidopsis major intrinsic protein NIP5;1 is essential for efficient boron uptake and plant development under boron limitation.
2006,
Pubmed
,
Xenbase
Tan,
Membrane proteins and membrane proteomics.
2008,
Pubmed
Tanaka,
NIP6;1 is a boric acid channel for preferential transport of boron to growing shoot tissues in Arabidopsis.
2008,
Pubmed
,
Xenbase
Tanghe,
Why do microorganisms have aquaporins?
2006,
Pubmed
To,
A generic high-throughput assay to detect aquaporin functional mutants: Potential application to discovery of aquaporin inhibitors.
2015,
Pubmed
Törnroth-Horsefield,
Structural mechanism of plant aquaporin gating.
2006,
Pubmed
Uehlein,
The tobacco aquaporin NtAQP1 is a membrane CO2 pore with physiological functions.
2003,
Pubmed
,
Xenbase
Venkatesh,
Genome-wide analysis and expression profiling of the Solanum tuberosum aquaporins.
2013,
Pubmed
Verkman,
Aquaporins: translating bench research to human disease.
2009,
Pubmed
Vivancos,
Silicon-mediated resistance of Arabidopsis against powdery mildew involves mechanisms other than the salicylic acid (SA)-dependent defence pathway.
2015,
Pubmed
Vivancos,
Identification and characterization of silicon efflux transporters in horsetail (Equisetum arvense).
2016,
Pubmed
,
Xenbase
Wang,
MzPIP2;1: An Aquaporin Involved in Radial Water Movement in Both Water Uptake and Transportation, Altered the Drought and Salt Tolerance of Transgenic Arabidopsis.
2015,
Pubmed
Wang,
The Thellungiella salsuginea tonoplast aquaporin TsTIP1;2 functions in protection against multiple abiotic stresses.
2014,
Pubmed
,
Xenbase
Werner,
Characterization of two tomato aquaporins and expression during the incompatible interaction of tomato with the plant parasite Cuscuta reflexa.
2001,
Pubmed
,
Xenbase
Yaneff,
Heteromerization of PIP aquaporins affects their intrinsic permeability.
2014,
Pubmed
,
Xenbase
Yoo,
Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis.
2007,
Pubmed
Zhao,
The role of the rice aquaporin Lsi1 in arsenite efflux from roots.
2010,
Pubmed
,
Xenbase
Zou,
Genome-Wide Identification of Jatropha curcas Aquaporin Genes and the Comparative Analysis Provides Insights into the Gene Family Expansion and Evolution in Hevea brasiliensis.
2016,
Pubmed
Zou,
Genome-wide identification of rubber tree (Hevea brasiliensis Muell. Arg.) aquaporin genes and their response to ethephon stimulation in the laticifer, a rubber-producing tissue.
2015,
Pubmed
di Pietro,
Coordinated post-translational responses of aquaporins to abiotic and nutritional stimuli in Arabidopsis roots.
2013,
Pubmed