Structure and transcriptional regulation of the major intrinsic protein gene family in grapevine

Abstract

BackgroundThe major intrinsic protein (MIP) family is a family of proteins, including aquaporins, which facilitate water and small molecule transport across plasma membranes. In plants, MIPs function in a huge variety of processes including water transport, growth, stress response, and fruit development. In this study, we characterize the structure and transcriptional regulation of the MIP family in grapevine, describing the putative genome duplication events leading to the family structure and characterizing the family’s tissue and developmental specific expression patterns across numerous preexisting microarray and RNAseq datasets. Gene co-expression network (GCN) analyses were carried out across these datasets and the promoters of each family member were analyzed for cis-regulatory element structure in order to provide insight into their transcriptional regulation.ResultsA total of 29 Vitis vinifera MIP family members (excluding putative pseudogenes) were identified of which all but two were mapped onto Vitis vinifera chromosomes. In this study, segmental duplication events were identified for five plasma membrane intrinsic protein (PIP) and four tonoplast intrinsic protein (TIP) genes, contributing to the expansion of PIPs and TIPs in grapevine. Grapevine MIP family members have distinct tissue and developmental expression patterns and hierarchical clustering revealed two primary groups regardless of the datasets analyzed. Composite microarray and RNA-seq gene co-expression networks (GCNs) highlighted the relationships between MIP genes and functional categories involved in cell wall modification and transport, as well as with other MIPs revealing a strong co-regulation within the family itself. Some duplicated MIP family members have undergone sub-functionalization and exhibit distinct expression patterns and GCNs. Cis-regulatory element (CRE) analyses of the MIP promoters and their associated GCN members revealed enrichment for numerous CREs including AP2/ERFs and NACs.ConclusionsCombining phylogenetic analyses, gene expression profiling, gene co-expression network analyses, and cis-regulatory element enrichment, this study provides a comprehensive overview of the structure and transcriptional regulation of the grapevine MIP family. The study highlights the duplication and sub-functionalization of the family, its strong coordinated expression with genes involved in growth and transport, and the putative classes of TFs responsible for its regulation.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4638-5) contains supplementary material, which is available to authorized users.

The physiology of drought stress in grapevine: towards an integrative definition of drought tolerance

“… Gambetta et al , 2017 ; Maurel and Prado, 2017 ). Aquaporins comprise a large gene family whose regulation is complex, and they are expressed in all grapevine tissues ( Wong et al , 2018 ). As in other plant species, aquaporins have been linked to grapevine stomatal regulation and to differences in this regulation between varieties ( Vandeleur et al , 2009 ; Vitali et al , 2016 ; Coupel-Ledru et al , 2017 ).…”

Whole Genome Re-sequencing Reveals Natural Variation and Adaptive Evolution of Phytophthora sojae

“…NADH oxidases are involved in sexual differentiation (Malagnac et al, 2004), virulence (Segmuller et al, 2008), cell degeneration and host defense (Haedens et al, 2005). MIP transporters are involved in a wide range of cellular processes in human (Preston et al, 1992), plant (Wong et al, 2018) and protozoan parasites (Dean et al, 2014). They are attractive targets for antifungal drugs in pathogenic fungi (Verma et al, 2014).…”

ABA Alleviates Uptake and Accumulation of Zinc in Grapevine (Vitis vinifera L.) by Inducing Expression of ZIP and Detoxification-Related Genes

“…The expression levels of 10 Zn-related genes, whose functions will be introduced in discussion, VviZIP2, VviZIP6, VviZIP7, VviZIP13, VviHMA2, VviNAS, VviNRAMP3, VviYSL1, VviPCR2 , and VvibZIP23 , were determined in root and leaf tissues by using an Applied Biosystems TM 7500 Fast Dx Real-Time PCR Instrument (Thermo Fisher Scientific, MA, United States) and a PowerUP SYBR Green Master Mix (Thermo Fisher Scientific, TX, United States). The genes were selected according to whole-genome array data organized from publicly available RNA-sequencing experiments in our previous publication (Wong et al, 2018). The primers were designed with PrimerQuest Tool (Integrated DNA Technologies, IA, United States) (Supplementary Table S2), and the annealing temperature was 60°C for all primer pairs except VviUbiquitin , which annealed at 56°C.…”