Genome-Wide Sequence Characterization and Expression Analysis of Major Intrinsic Proteins in Soybean (Glycine max L.)

Abstract

Water is essential for all living organisms. Aquaporin proteins are the major facilitator of water transport activity through cell membranes of plants including soybean. These proteins are diverse in plants and belong to a large major intrinsic (MIP) protein family. In higher plants, MIPs are classified into five subfamilies including plasma membrane intrinsic proteins (PIP), tonoplast intrinsic proteins (TIP), NOD26-like intrinsic proteins (NIP), small basic intrinsic proteins (SIP), and the recently discovered X intrinsic proteins (XIP). This paper reports genome wide assembly of soybean MIPs, their functional prediction and expression analysis. Using a bioinformatic homology search, 66 GmMIPs were identified in the soybean genome. Phylogenetic analysis of amino acid sequences of GmMIPs divided the large and highly similar multi-gene family into 5 subfamilies: GmPIPs, GmTIPs, GmNIPs, GmSIPs and GmXIPs. GmPIPs consisted of 22 genes and GmTIPs 23, which showed high sequence similarity within subfamilies. GmNIPs contained 13 and GmSIPs 6 members which were diverse. In addition, we also identified a two member GmXIP, a distinct 5th subfamily. GmMIPs were further classified into twelve subgroups based on substrate selectivity filter analysis. Expression analyses were performed for a selected set of GmMIPs using semi-quantitative reverse transcription (semi-RT-qPCR) and qPCR. Our results suggested that many GmMIPs have high sequence similarity but diverse roles as evidenced by analysis of sequences and their expression. It can be speculated that GmMIPs contains true aquaporins, glyceroporins, aquaglyceroporins and mixed transport facilitators.

Genome-wide identification and characterization of aquaporin gene family in common bean (Phaseolus vulgaris L.)

“…In addition, the ar/R selectivity filter is highly conserved and typical of watertransporting aquaporins (F/H/T/R). The same ar/R selectivity filter sequence is shared by the PIP sub-family in different plant species such as Z. mays, A. thaliana, P. trichocarpa, S. lycopersicum, G. max and B. rapa (Chaumont et al 2001;Johanson et al 2001;Gupta and Sankararamakrishnan 2009;Reuscher et al 2013;Zhang et al 2013;Tao et al 2014). SIn plants,everal researchers hypothesize PIP aquaporins have a central role in roots water absorption in rootsfor plant PIP aquaporins, suggesting thatand this proteins could also actively regulate root and leaf hydraulics (Maurel et al 2008;Li et al 2014).…”

Heteromerization of PIP aquaporins affects their intrinsic permeability

“…Plant PIP aquaporins represent a conserved subfamily that has been historically divided into two subgroups due to their differences in primary structure, PIP1 and PIP2. Interestingly, PIP aquaporins compose ∼40% of the total aquaporin set, and the PIP1 and PIP2 ratio among different species is relatively constant (5)(6)(7)(8)(9)(10)(11)(12). Fig.…”

Identification and Characterization of Plasma Membrane Intrinsic Protein (PIP) Aquaporin Genes in Petals of Opening Carnation Flowers

“…org/). The amino acid sequences of XIPs from tobacco (XIP1;1α and XIP1;1β; Bienert et al, 2011), soybeans (GmXIP1;1 and GmXIP1;2; Zhang et al, 2013), and tomatoes (SlXIP1;1-SlXIP1;6; Reuscher et al, 2013) were also retrieved from the Ensembl Genomes. These sequences were used as queries for a BLAST (Altschul et al, 1997) search to identify open reading frames (ORFs) encoding AQP in the carnation genome sequence database (Carnation DB; Yagi et al, 2014; http://carnation.kazusa.or.jp/index.html).…”

“…Plant AQPs are encoded by a large family (35 AQPs in Arabidopsis, 31 in maize, and 33 in rice; Chaumont et al, 2000;Johanson et al, 2001;Sakurai et al, 2005), and divided into 5 subfamilies; the plasma membrane intrinsic proteins (PIPs), the tonoplast intrinsic proteins (TIPs), the nodulin-26-like intrinsic membrane proteins (NIPs), the small basic intrinsic proteins (SIPs), and the X-intrinsic proteins (XIPs) (Danielson and Johanson, 2008;Maurel et al, 2008). Although XIPs are absent in Arabidopsis, maize, and rice, they are found in a moss, Physcomitrella patens (Danielson and Johanson, 2008), some Solanaceae species including tobacco and tomatoes (Bienert et al, 2011;Reuscher et al, 2013), and soybeans (Zhang et al, 2013). Water transport across the plasma membrane is mediated by PIPs, which are divided into PIP1 and PIP2 subgroups according to their differences in primary structure.…”