Genome-wide analysis and expression profiling of the Solanum tuberosum aquaporins

Venkatesh, Jelli; Yu, Jae‐Woong; Park, Se Won

doi:10.1016/j.plaphy.2013.10.025

Cited by 87 publications

(72 citation statements)

References 44 publications

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“…We identified a total of 40 putative aquaporin encoding genes chickpea genome, namely, thereafter, as CaAQPs (Table 1 and Supplementary File S1). The number of AQP identified in this study are slightly higher than the 35 AQP genes reported in Arabidopsis (Johanson et al, 2001), 33 in rice (Sakurai et al, 2005), 35 in Medicago and 30 in lotus genome, then again almost same in number as reported 41 AQP genes in potato (Venkatesh et al, 2013), Sorghum (Reddy et al, 2015), common bean (Ariani and Gepts, 2015), and 40 AQP genes in Pigeonpea (Deshmukh et al, 2015). …”

Section: Resultssupporting

confidence: 48%

Genome-Wide Analysis of the Aquaporin Gene Family in Chickpea (Cicer arietinum L.)

Deokar

Tar’an

2016

Front. Plant Sci.

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Aquaporins (AQPs) are essential membrane proteins that play critical role in the transport of water and many other solutes across cell membranes. In this study, a comprehensive genome-wide analysis identified 40 AQP genes in chickpea (Cicer arietinum L.). A complete overview of the chickpea AQP (CaAQP) gene family is presented, including their chromosomal locations, gene structure, phylogeny, gene duplication, conserved functional motifs, gene expression, and conserved promoter motifs. To understand AQP's evolution, a comparative analysis of chickpea AQPs with AQP orthologs from soybean, Medicago, common bean, and Arabidopsis was performed. The chickpea AQP genes were found on all of the chickpea chromosomes, except chromosome 7, with a maximum of six genes on chromosome 6, and a minimum of one gene on chromosome 5. Gene duplication analysis indicated that the expansion of chickpea AQP gene family might have been due to segmental and tandem duplications. CaAQPs were grouped into four subfamilies including 15 NOD26-like intrinsic proteins (NIPs), 13 tonoplast intrinsic proteins (TIPs), eight plasma membrane intrinsic proteins (PIPs), and four small basic intrinsic proteins (SIPs) based on sequence similarities and phylogenetic position. Gene structure analysis revealed a highly conserved exon-intron pattern within CaAQP subfamilies supporting the CaAQP family classification. Functional prediction based on conserved Ar/R selectivity filters, Froger's residues, and specificity-determining positions suggested wide differences in substrate specificity among the subfamilies of CaAQPs. Expression analysis of the AQP genes indicated that some of the genes are tissue-specific, whereas few other AQP genes showed differential expression in response to biotic and abiotic stresses. Promoter profiling of CaAQP genes for conserved cis-acting regulatory elements revealed enrichment of cis-elements involved in circadian control, light response, defense and stress responsiveness reflecting their varying pattern of gene expression and potential involvement in biotic and abiotic stress responses. The current study presents the first detailed genome-wide analysis of the AQP gene family in chickpea and provides valuable information for further functional analysis to infer the role of AQP in the adaptation of chickpea in diverse environmental conditions.

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Section: Resultssupporting

confidence: 48%

Genome-Wide Analysis of the Aquaporin Gene Family in Chickpea (Cicer arietinum L.)

Deokar

Tar’an

2016

Front. Plant Sci.

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“…On the other hand, an increase in the amount of PIPs may facilitate water loses from the cell when the water potential is reversed and, due to salt administration, becomes higher inside cells than outside them. As mentioned above, the suppression of AQPs activity may protect cells from dehydration and reductions in AQPs expression under short term salt treatments were reported (Horie et al 2011;Boursiac et al 2005;Venkatesh et al 2013). However, it was also reported that an increase in the PIP expression and the accumulation of PIP proteins in salt exposed roots occurs in roots, during the later stages of salt stress, when root tissues re-establish their hydraulic conductivity, after its initial decline caused by osmotic shock.…”

Section: Discussionmentioning

confidence: 84%

The expression patterns of plasma membrane aquaporins in leaves of sugar beet and its halophyte relative, Beta vulgaris ssp. maritima, in response to salt stress

et al. 2015

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Salt tolerance is largely dependent on a plant’s ability to maintain optimal water status in leaves. The adjustment of water relations under salinity involves changes in the transcriptional activity of genes encoding plasma membrane aquaporins (PIPs). Here, we report the effects of long-term or short-term treatments with moderate or strong salt stress on the expression of BvPIP1;1, BvPIP2;1 and BvPIP2;2 in the leaves of sugar beet, Beta vulgaris cv. Huzar, and its halophyte relative, Beta vulgaris ssp. maritima. Plants subjected to long-term treatment were watered with salt-supplemented media during a 32 day long culture period. Short-term salt treatments were executed either by immersing the petioles of excised leaves into salt solutions for 48h, or incubating excised leaf blades in salt-supplemented media for 20h. B. vulgaris ssp. maritima reacted to long-term salt treatment with a decrease in BvPIP1;1, BvPIP2;1 and BvPIP2;2 expression. Contrastingly, only BvPIP2;2 transcript was down-regulated by salinity in leaves of B. vulgaris cv. Huzar, whereas BvPIP1;1 and BvPIP2;1 did not vary in response to salt-treatments. On the other hand, the expression of BvPIP1;1, BvPIP2;1 and BvPIP2;2 was enhanced by salinity if salt solutions was supplied through leaf petioles, irrespective of genotype. PIP expression in excised leaf blades revealed a complex pattern of changes. BvPIP1;1 and BvPIP2;1 expression underwent a period of transient increase in both the control and salt-treated leaves. Furthermore, BvPIP1;1 expression was enhanced by strong salinity. BvPIP2;2 expression was up-regulated by strong salinity or up- or down-regulated by moderate salinity during the treatment period.

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“…Available transcriptomic resources are helpful to integrate information with genomics data for a better comprehension of gene functions (Movahedi et al, 2012; Patil et al, 2015; Sonah et al, 2016; Song et al, 2016). For instance, many of the recent studies highlighting genome-wide identification of AQPs have relied on transcriptomic resources to explain tissue-specific expression of those genes (Gupta and Sankararamakrishnan, 2009; Reuscher et al, 2013; Venkatesh et al, 2013; Deshmukh et al, 2015; Hu et al, 2015; Deokar and Tar'an, 2016; Deshmukh and Bélanger, 2016; Zou et al, 2016). …”

Section: Transcriptomics Studies For Aqpsmentioning

confidence: 99%

Plant Aquaporins: Genome-Wide Identification, Transcriptomics, Proteomics, and Advanced Analytical Tools

2016

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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.

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Genome-wide analysis and expression profiling of the Solanum tuberosum aquaporins

Cited by 87 publications

References 44 publications

Genome-Wide Analysis of the Aquaporin Gene Family in Chickpea (Cicer arietinum L.)

Genome-Wide Analysis of the Aquaporin Gene Family in Chickpea (Cicer arietinum L.)

The expression patterns of plasma membrane aquaporins in leaves of sugar beet and its halophyte relative, Beta vulgaris ssp. maritima, in response to salt stress

Plant Aquaporins: Genome-Wide Identification, Transcriptomics, Proteomics, and Advanced Analytical Tools

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