Prediction of Aquaporin Function by Integrating Evolutionary and Functional Analyses

Abstract

Aquaporins (AQPs) are a family of channel proteins, which transport water and/or small solutes across cell membranes. AQPs are present in Bacteria, Eukarya, and Archaea. The classical AQP evolution paradigm explains the inconsistent phylogenetic trees by multiple transfer events and emphasizes that the assignment of orthologous AQPs is not possible, making it difficult to integrate functional information. Recently, a novel phylogenetic framework of eukaryotic AQP evolution showed congruence between eukaryotic AQPs and organismal trees identifying 32 orthologous clusters in plants and animals (Soto et al. Gene 503:165-176, 2012). In this article, we discuss in depth the methodological strength, the ability to predict functionality and the AQP community perception about the different paradigms of AQP evolution. Moreover, we show an updated review of AQPs transport functions in association with phylogenetic analyses. Finally, we discuss the possible effect of AQP data integration in the understanding of water and solute transport in eukaryotic cells.

Pollen-Specific Aquaporins NIP4;1 and NIP4;2 Are Required for Pollen Development and Pollination in Arabidopsis thaliana

“…According to the ar/R filter, NIPs can be further divided into three groups (Rougé and Barre, 2008). Group 1 is characterized by residues W V/I A R with permeability to water, glycerol, lactic acid, ammonia, arsenite, and hydrogen peroxide (Wallace and Roberts, 2004;Rougé and Barre, 2008;Perez Di Giorgio et al, 2014). NIP4;1 and NIP4;2 have the same conserved residues, also for other specificity motifs ( Figure 1B), suggesting similar substrate transport specificity and, thus, possibly, functional redundancy.…”

“…This is probably due to the expression of other pollen AQPs (TIP5;1, TIP1;3, SIP1;1, SIP2;1, PIP2;8, TIP1;1, NIP2;1, and NIP7;1; Supplemental Figure 2) apart from NIP4;1 and NIP4;2, which may have some functional redundancy masking more pronounced phenotypes. TIP5;1 and TIP1;3 were shown to transport water and urea; SIP1;1, water; TIP1;1, water, urea, arsenite, and H 2 O 2 ; NIP2;1, water, glycerol, and H 2 O 2 ; and NIP7;1, water, glycerol, urea, boron, arsenite, and H 2 O 2 (revised in Perez Di Giorgio et al, 2014). It has been shown that aquaporin mutantassociated phenotypes were mostly observed under nutrient limiting growth conditions Schnurbusch et al, 2010;Li et al, 2011a;Hanaoka et al, 2014;Wudick et al, 2014;Xu et al, 2015), while the nip4;1 and nip4;2 phenotypes described here are under normal growth conditions.…”

“…Aquaporins (AQPs), also named membrane intrinsic proteins, are highly diversified channel proteins, which facilitate the bidirectional transport of water, small solutes such as H 2 O 2 , urea, glycerol, metalloids (boric, silicic, and arsenious acid), lactic acid, and/or dissolved gas molecules (CO 2 and NH 3 ) across cell membranes in all living organisms (Soto et al, 2012;Perez Di Giorgio et al, 2014;Abascal et al, 2014). Plant AQPs are classified into seven subfamilies: plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), NOD26-like intrinsic proteins (NIPs), small basic intrinsic proteins (SIPs), X intrinsic proteins (XIPs), hybrid intrinsic proteins, and GlpF-like intrinsic proteins (Abascal et al, 2014).…”

Fungal aquaporins: cellular functions and ecophysiological perspectives

“…As the first (transmembrane helices 1 to 3) and the second half (transmembrane helices 4 to 6) of the protein are imperfect repeats of opposite orientation, intragenic tandem duplication of a precursor has been supposed (Reizer et al 1993; for a structural overview, see Perez Di Giorgio et al 2014). The transmembrane helices form an hourglass-like pore (Jung et al 1994) with a central channel that is crossed by water and solute molecules in a single-file line (Gena et al 2011).…”

“…Major intrinsic proteins (MIPs) or aquaporins (AQPs) are synonyms that are often used in literature (Perez Di Giorgio et al 2014). Such proteins have been discovered in all kingdoms, from Archaea and eubacteria to fungi, animals, and plants (Engel and Stahlberg 2002).…”