Deshmukh Rupesh K, Sonah Humira, Bélanger Richard R
Département de Phytologie-Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval Québec, QC, Canada.
Front Plant Sci. 2016 Dec 20;7:1896. doi: 10.3389/fpls.2016.01896. eCollection 2016.
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 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.
水通道蛋白（AQPs）是形成通道的整合膜蛋白，可促进水和许多其他小分子的移动。与动物相比，植物基因组中AQPs的数量要多得多。由于植物物种间蛋白质序列的高度保守性，基于同源性在已测序物种中鉴定AQPs是可行的。对AQPs进行全基因组特征分析突出了几个重要方面，如分布、基因组织、进化以及决定溶质特异性的保守特征。从功能角度来看，借助转录组学和蛋白质组学数据，对AQP转运系统的理解迅速扩展。通过计算技术的进步，有助于对通过组学规模研究产生的大量数据进行有效分析。随着计算工具和流程的增加，蛋白质三级结构、孔结构、腔、磷酸化位点、异源二聚化以及共表达网络的预测变得更加精细和准确。然而，计算方法的有效性基于对水通道蛋白的生理和生化特性、转运动力学、溶质特异性、分子相互作用、序列变异、系统发育和进化的理解。为此，已有效利用卵母细胞测定、酵母表达系统、人工蛋白脂质体和脂质膜等工具来研究影响AQPs溶质转运的多个方面。在本综述中，我们讨论了植物中AQPs的全基因组鉴定与分析工具的最新进展，以及它们在应用于AQPs时的可用性和技术挑战。还提供了对可用于AQP研究的组学资源的详尽综述，以优化其有效利用。最后，提供了一份详细的计算工具和分析流程目录，作为AQP研究的资源。
