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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.
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