NPA Boxes Research Articles

Classification and Gene Structure of Aquaporins.

Aquaporins (AQPs) are a family of membrane water channels that basically function as regulators of intracellular and intercellular water flow. To date, 13 AQPs, distributed widely in specific cell types in various organs and tissues, have been characterized in humans. A pair of NPA boxes forming a pore is highly conserved among all aquaporins and is also key residues for the classification of AQP superfamily into four groups according to primary sequences. AQPs may also be classified based on their transport properties. So far, chromosome localization and gene structure of 13 human AQPs have been identified, which is definitely helpful for studying phenotypes and potential targets in naturally occurring and synthetic mutations in human or cells.

Evolutionary Overview of Aquaporin Superfamily.

Aquaporins (AQPs) are present not only in three domains of life, bacteria, eukaryotes, and archaea, but also in viruses. With the accumulating arrays of AQP superfamily, the evolutional relationship has attracted much attention with multiple publications on "the genome-wide identification and phylogenetic analysis" of AQP superfamily. A pair of NPA boxes forming a pore is highly conserved throughout the evolution and renders key residues for the classification of AQP superfamily into four groups: AQP1-like, AQP3-like, AQP8-like, and AQP11-like. The complexity of AQP family has mostly been achieved in nematodes and subsequent evolution has been directed toward increasing the number of AQPs through whole-genome duplications (WGDs) to extend the tissue specific expression and regulation. The discovery of the intracellular AQP (iAQP: AQP8-like and AQP11-like) and substrate transports by the plasma membrane AQP (pAQP: AQP1-like and AQP3-like) have accelerated the AQP research much more toward the transport of substrates with complex profiles. This evolutionary overview based on a simple classification of AQPs into four subfamilies will provide putative structural, functional, and localization information and insights into the role of AQP as well as clues to understand the complex diversity of AQP superfamily.

Perspectives on the evolution of aquaporin superfamily.

Aquaporins (AQPs) belong to a transmembrane protein superfamily composed of an internal repeat of a three membrane-spanning domain and each has a highly conserved NPA box. Based on the more variable carboxyl-terminal NPA box, AQPs can be divided into three subfamilies: (1) glycerol-channel aquaglyceroporin (gAQP) (2) water-selective AQP (wAQP), and (3) deviated superaquaporin (sAQP) in the order of passible evolution. This classification has functional and localization relevance: most wAQPs transports water selectively whereas gAQPs and sAQPs also transport small molecules with sAQPs mostly localized inside the cell. As this classification is not based on the function, some wAQPs functioning as glycerol channels will not be included in gAQPs. AQP ancestors may have first originated in eubacteria as gAQPs to transport small molecules such as glycerol. Later some of them may have acquired a water-selective filter to become wAQPs. Although AQPs are absent in many bacteria, especially in archaea, both gAQPs and wAQPs may have been carried over to eukaryotes or horizontally transferred. Finally, multicellular organisms have obtained new sAQPs, which are curiously absent in fungi and plants. Interestingly, both plants and higher insects independently have lost gAQPs, whose functions, however, have been taken over by functionally modified wAQPs partly obtained by horizontal gene transfers from bacteria. This evolutionary viewpoints on AQPs will facilitate further functional analysis of AQP-like sequences and expand our viewpoints on AQP superfamily.

Characterization of Leishmania donovani Aquaporins Shows Presence of Subcellular Aquaporins Similar to Tonoplast Intrinsic Proteins of Plants

Leishmania donovani, a protozoan parasite, resides in the macrophages of the mammalian host. The aquaporin family of proteins form important components of the parasite-host interface. The parasite-host interface could be a potential target for chemotherapy. Analysis of L. major and L. infantum genomes showed the presence of five aquaporins (AQPs) annotated as AQP9 (230aa), AQP putative (294aa), AQP-like protein (279aa), AQP1 (314aa) and AQP-like protein (596aa). We report here the structural modeling, localization and functional characterization of the AQPs from L. donovani. LdAQP1, LdAQP9, LdAQP2860 and LdAQP2870 have the canonical NPA-NPA motifs, whereas LdAQP putative has a non-canonical NPM-NPA motif. In the carboxyl terminal to the second NPA box of all AQPs except AQP1, a valine/alanine residue was found instead of the arginine. In that respect these four AQPs are similar to tonoplast intrinsic proteins in plants, which are localized to intracellular organelles. Confocal microscopy of L. donovani expressing GFP-tagged AQPs showed an intracellular localization of LdAQP9 and LdAQP2870. Real-time PCR assays showed expression of all aquaporins except LdAQP2860, whose level was undetectable. Three-dimensional homology modeling of the AQPs showed that LdAQP1 structure bears greater topological similarity to the aquaglyceroporin than to aquaporin of E. coli. The pore of LdAQP1 was very different from the rest in shape and size. The cavity of LdAQP2860 was highly irregular and undefined in geometry. For functional characterization, four AQP proteins were heterologously expressed in yeast. In the fps1Δ yeast cells, which lacked the key aquaglyceroporin, LdAQP1 alone displayed an osmosensitive phenotype indicating glycerol transport activity. However, expression of LdAQP1 and LdAQP putative in a yeast gpd1Δ strain, deleted for glycerol production, conferred osmosensitive phenotype indicating water transport activity or aquaporin function. Our analysis for the first time shows the presence of subcellular aquaporins and provides structural and functional characterization of aquaporins in Leishmania donovani.

The evolutionary aspects of aquaporin family

Aquaporins (AQPs) were originally identified as channels facilitating water transport across the plasma membrane. They have a pair of highly conserved signature sequences, asparagine-proline-alanine (NPA) boxes, to form a pore. However, some have little conserved amino acid sequences around the NPA boxes unclassifiable to two previous AQP subfamilies, classical AQPs and aquaglyceroporins. These will be called unorthodox AQPs in this review. Interestingly, these unorthodox AQPs have a highly conserved cysteine residue downstream of the second NPA box. AQPs also have a diversity of functions: some related to water transport such as fluid secretion, fluid absorption, and cell volume regulation, and the others not directly related to water transport such as cell adhesion, cell migration, cell proliferation, and cell differentiation. Some AQPs even permeate nonionic small molecules, ions, metals, and possibly gasses. AQP gene disruption studies have revealed their physiological roles: water transport in the kidney and exocrine glands, glycerol transport in fat metabolism and in skin moisture, and nutrient uptakes in plants. Furthermore, AQPs are also present at intracellular organelles, including tonoplasts, mitochondria, and the endoplasmic reticulum. This review focuses on the evolutionary aspects of AQPs from bacteria to humans in view of the structural and functional diversities of AQPs.

The role of a group III AQP, AQP11 in intracellular organelle homeostasis

AQP11 is a member of a new aquaporin subfamily which includes many aquaporin homologs with low amino acid identities, around 20% of previously identified AQPs. Although these AQPs have unusual NPA sequences, these AQPs have a completely conserved and functionally indispensable cysteine residue downstream of the second NPA box, suggesting that they belong to a specific AQP subfamily, which we propose to name the group III AQPs. On the other hand, the NPA boxes are highly conserved in previous AQP subfamilies: the group I AQPs, original water-selective aquaporin family and the group II AQPs, aquaglyceroporin family. Currently the roles of the group III AQPs are only known with AQP11 as the disruption of intracellularly located AQP11 in mice produced huge vacuoles in the proximal tubule leading to fatal polycystic kidneys at one month old. This review focused on the classification of AQPs based on primary structures to obtain insights into the function and the role of AQPs. With the accumulation of new AQP-like sequences through genome projects, this classification will be useful to predict their functions as each group may have specific characteristics in its function, distribution and regulation.

Developmental expression and physiological roles of aquaporin‐11 in mice

Aquaporin-11 (AQP11) has low homology with conventional aquaporins especially at NPA boxes which constitute the pore. Its localization in the cytosol makes its functional studies difficult. To get insights into its physiological roles we examined its expression in developmental stages and water-deprived conditions. New born mice expressed AQP11 mRNA in the intestines, liver and kidney but not in the testis. Its expression in the testis was first observed after three weeks. AQP11 appeared after AQP8 and before AQP7. It was expressed in Sertoli cells. AQP11 KO mice (Mol. Cell. Biol. 25: 7770, 2005) had decreased cellularity in seminiferous tubules but were fertile. Dehydration and rehydration of adult mice did not change AQP11 mRNA expression in the kidney cortex and jejunum. It was expressed intracellularly in the proximal tubules, epithelia of intestines and hepatocytes. AQP11 KO mice developed vacuoles in these epithelia and had growth defect. The thymus and brain of AQP11 KO mice appeared normal. In summary, AQP11 is developmentally regulated in the testis and its function may be a nutrients transport.

Disruption of Aquaporin-11 Produces Polycystic Kidneys following Vacuolization of the Proximal Tubule

Aquaporin-11 (AQP11) has been identified with unusual pore-forming NPA (asparagine-proline-alanine) boxes, but its function is unknown. We investigated its potential contribution to the kidney. Immunohistochemistry revealed that AQP11 was localized intracellularly in the proximal tubule. When AQP11 was transfected in CHO-K1 cells, it was localized in intracellular organelles. AQP11-null mice were generated; these mice exhibited vacuolization and cyst formation of the proximal tubule. AQP11-null mice were born normally but died before weaning due to advanced renal failure with polycystic kidneys, in which cysts occupied the whole cortex. Remarkably, cyst epithelia contained vacuoles. These vacuoles were present in the proximal tubules of newborn mice. In 3-week-old mice, these tubules contained multiple cysts. Primary cultured cells of the proximal tubule revealed an endosomal acidification defect in AQP11-null mice. These data demonstrate that AQP11 is essential for the proximal tubular function. AQP11-null mice are a novel model for polycystic kidney diseases and will provide a new mechanism for cystogenesis.

Expression of aquaporin 1 in human cardiac and skeletal muscle

Aquaporins (AQPs) are a family of water channel proteins that assist in maintenance of the cellular osmotic environment and whole body fluid balance. Specialized organ-specific AQPs are important in physiologic and pathologic processes but little is known about AQPs in the human heart. AQP1 has been identified in rodent heart. We investigated the presence and localization of AQP1 in human heart and skeletal muscle using immunohistochemistry and confocal microscopy, western blot and reverse transcriptase-polymerase chain reaction. There was abundant AQP1 present in both cardiac and skeletal muscle. Immunohistochemistry revealed co-localization of AQP1 with vinculin, a t-tubule marker, and caveolin-3. No novel sequences bearing an NPA box motif common to other AQPs were identified in human heart using degenerative PCR analysis. We conclude that AQP1 is present in the human heart. AQP1 co-localizes with t-tubular and caveolar proteins. Cardiac AQPs may have a role during osmotic stresses including ischemia/reperfusion and cardiopulmonary bypass.

Molecular Mechanisms and Drug Development in Aquaporin Water Channel Diseases: Aquaporin Superfamily (Superaquaporins): Expansion of Aquaporins Restricted to Multicellular Organisms

Eleven aquaporins are identified in mammals. They all have highly conserved two asparagine-proline-alanine (NPA) boxes that are important for the formation of the water permeating pore. Recently we identified two new proteins in mammals distantly related to aquaporins (AQPs) with poorly conserved NPA boxes. Similarly poorly conserved AQP-like proteins were found in several genome projects of multicellular organisms. They may be subgrouped as the AQP superfamily or superaquaporins. Their function is still unknown. AQP11 knockout mice suffer from polycystic kidneys and neonatal fatality. The identification of superaquaporins will provide new insights into the role of AQPs in organogenesis.

Heterologous expression and topography of the main intrinsic protein (MIP) from rat lens

Wild type rat lens main intrinsic protein (MIP) and MIP mutated (F73I, F75L) to resemble the glycerol facilitator of Escherichia coli in the region of the NPA1 box were used to investigate the topology of MIP in the membrane of Spodoptera frugiperda (Sf21) cells using the baculovirus expression system and expression in mouse erythroid leukaemia cells (MEL C88). Differential fixation for staining was used, with paraformaldehyde for externally exposed antigenic sites, and acetone for both externally and internally exposed protein antigenic sites. Immunofluorescence using antibodies to synthetic MIP peptides showed that wild type MIP had a six transmembrane topography. The N- and C-termini were intracellular in both expression systems, and both NPA boxes were found to be extracellular. These results show that residues around the NPA1 box can influence the folding of the MIP in the membrane, and provide structural evidence for the poor water transport properties of MIP, as the NPA boxes lie outside the plane of the membrane.

A phylogenetic framework for the aquaporin family in eukaryotes.

A comprehensive evolutionary analysis of aquaporins, a family of intrinsic membrane proteins that function as water channels, was conducted to establish groups of homology (i.e., to identify orthologues and paralogues) within the family and to gain insights into the functional constraints acting on the structure of the aquaporin molecule structure. Aquaporins are present in all living organisms, and therefore, they provide an excellent opportunity to further our understanding of the broader biological significance of molecular evolution by gene duplication followed by functional and structural specialization. Based on the resulting phylogeny, the 153 channel proteins analyzed were classified into six major paralogous groups: (1) GLPs, or glycerol-transporting channel proteins, which include mammalian AQP3, AQP7, and AQP9, several nematode paralogues, a yeast paralogue, and Escherichia coli GLP; (2) AQPs, or aquaporins, which include metazoan AQP0, AQP1, AQP2, AQP4, AQP5, and AQP6; (3) PIPs, or plasma membrane intrinsic proteins of plants, which include PIP1 and PIP2; (4) TIPs, or tonoplast intrinsic proteins of plants, which include alphaTIP, gammaTIP, and deltaTIP; (5) NODs, or nodulins of plants; and (6) AQP8s, or metazoan aquaporin 8 proteins. Of these groups, AQPs, PIPs, and TIPs cluster together. According to the results, the capacity to transport glycerol shown by several members of the family was acquired only early in the history of the family. The new phylogeny reveals that several water channel proteins are misclassified and require reassignment, whereas several previously undetermined ones can now be classified with confidence. The deduced phylogenetic framework was used to characterize the molecular features of water channel proteins. Three motifs are common to all family members: AEF (Ala-Glu-Phe), which is located in the N-terminal domain; and two NPA (Asp-Pro-Ala) boxes, which are located in the center and C-terminal domains, respectively. Other residues are found to be conserved within the major groups but not among them. Overall, the PIP subfamily showed the least variation. In general, no radical amino acid replacements affecting tertiary structure were identified, with the exception of Ala-->Ser in the TIP subfamily. Constancy of rates of evolution was demonstrated within the different paralogues but rejected among several of them (GLP and NOD).

Three-dimensional fold of the human AQP1 water channel determined at 4 Å resolution by electron crystallography of two-dimensional crystals embedded in ice

Here, we present a three-dimensional (3D) density map of deglycosylated, human erythrocyte aquaporin 1 (AQP1) determined at 4 Å resolution in plane and ∼7 Å resolution perpendicular to the bilayer. The map was calculated by analyzing images and electron diffraction patterns recorded from tilted (up to 60 °), ice-embedded, frozen-hydrated 2D crystals of AQP1 in lipid bilayer membranes. This map significantly extends the findings related to the folding of the AQP1 polypeptide chain determined by us at a lower, 7 Å by ∼20 Å, resolution. The solvent-accessible volume within a monomer has a vestibular architecture, with a narrow, ∼6.5 Å diameter constriction near the center of the bilayer, where the location of the water-selective channel is postulated to exist. The clearly resolved densities for the transmembrane helices display the protrusions expected for bulky side-chains. The density in the interior of the helix barrel (putative NPA box region) is better resolved compared to our previous map, suggesting clearer linkage to some of the helices, and it may harbor short stretches of α-helix. At the bilayer extremities, densities for some of the inter-helix hydrophilic loops are visible. Consistent with these observed inter-helix connections, possible models for the threading of the AQP1 polypeptide chain are presented. A preferred model is deduced that agrees with the putative locations of a group of aromatic residues in the amino acid sequence and in the 3D density map.

Role of aquaporins in renal water handling: physiology and pathophysiology.

the six bilayer spanning domains are connected by fiveloops (A–E in Figure 1). The molecule consists of twoAn essential function of the mammalian kidney is its repeats of three a-helices which are 180°mirror imagesability to conserve or excrete free water independent of each other (Figure 1). Each repeat contains theof changes in solute excretion. Early physiological highly conserved family characteristic asparagine-studies have provided evidence for constitutive absorp- proline-alanine (NPA) sequence in loops B and E.tion of about 90% of the GFR volume in proximal LoopsBandEarepostulatedtofoldbackintothetubules and descending limbs of Henle’s loop, whereas membrane and form the water pore. Recently, the three-facultative water reabsorption occurs in collecting dimensional structure of AQP1 was determined at 6A˚ducts under control of the antidiuretic hormone argin- resolution by cryo-electron crystallography [8]. AQP1ine vasopressin (AVP). Although all cell membranes is a homotetramer containing four independent aqueoushave a surpringly high diVusive water permeability, it channels. It was shown that each monomer is composedis now clear that water transport in the nephron is of six tilted a-helices which form a barrel that enclosesfacilitated by water channels [1]. a central density which is attributed to the functionallyDiscovery of the aquaporin family of water channels important NPA boxes in loops B and E. Given thehas provided insight in the molecular mechanisms by highly homologues primary structures of AQP1 and thewhich rapid osmotic water flow occurs in kidney and other aquaporins, it is likely that all AQPs have a morein other organs. Nine mammalian aquaporins, AQPs, or less similar three-dimensional structure. The lesshave been cloned to date, of which AQP1, 2, 3, 4, 6, conserved region among the aquaporins is the carboxy-7 are expressed in kidney (for review see [1–3], new terminus and this property has been exploited to gener-aquaporins [4–6]). Aquaporins belong to an old ubi- ate highly specific polyclonal antibodies which havequitous major intrinsic protein (MIP) family of trans- been very useful for localization studies.membrane channel proteins of which at present closeto hundred members have been identified [7]. The

Three-dimensional organization of a human water channel.

Aquaporins (AQP) are members of the major intrinsic protein (MIP) superfamily of integral membrane proteins and facilitate water transport in various eukaryotes and prokaryotes. The archetypal aquaporin AQP1 is a partly glycosylated water-selective channel that is widely expressed in the plasma membranes of several water-permeable epithelial and endothelial cells. Here we report the three-dimensional structure of deglycosylated, human erythrocyte AQP1, determined at 7 A resolution in the membrane plane by electron crystallography of frozen-hydrated two-dimensional crystals. The structure has an inplane, intramolecular 2-fold axis of symmetry located in the hydrophobic core of the bilayer. The AQP1 monomer is composed of six membrane-spanning, tilted alpha-helices. These helices form a barrel that encloses a vestibular region leading to the water-selective channel, which is outlined by densities attributed to the functionally important NPA boxes and their bridges to the surrounding helices. The intramolecular symmetry within the AQP1 molecule represents a new motif for the topology and design of membrane protein channels, and is a simple and elegant solution to the problem of bidirectional transport across the bilayer.

Topological Structure of Lens Fibre Cell Membrane Protein MIP

The topological structure of the MIP (major intrinsic protein) family was investigated. The MIP family is a group of transmenbrane proteins which are also known as aquaporins because of their role as water channels. To enable study of the topological structure of MIP, a heterologous-expression cell system using Escherichia coli was used as a tool for the production and assembly of MIP into the cytoplasmic membrane. A set of specific antibodies was used to establish the topological model of lens MIP. Antipeptide antisera were prepared for four hydrophilic regions of rat MIP according to its predicted residues (1). Monoclonal Anti-Flag M2 antibody was used against the PCR based FLAG peptide fused to either the N- or C-terminal end of MIP. Two peptides, HNPA l (Ser-Gly-Ala-His-Val-Asn-Pro-Ala-Val-Thr) and NPAR 2 (Thr-Gly-Ala-Gly-Met-Asn-Pro-Ala-Arg-Ser), were synthesised according to NPA boxes HNPA1 amino acids 61-70 represent a portion of the second cytoplasmic loop of rat MIP while NPAR 2 amino acids 178-187 represent a portion of the fifth extracellular loop of MIP containing a predominance of polar and charged amino acids. The data presented in this study are not consistent with all aspects of the previously proposed model. Based on the data in this work, and previously reported information regarding MIP, a new topological model is proposed for the assembly of MIP in the lens fibre cel membrane. This may provide a revised model for investigating the role of MIP in the formation of cararacts with age and diabetes.

Cloning of a Novel cDNA Homologous to CHIP28 Water Channel from Ocular Ciliary Epithelium

Water channel protein (CHIP28) has been initially identified from human erythrocyte and subsequently localized in human kidney, rat kidney and bovine corneal endothelium. We report here cloning of homologous cDNA (CHIP29) from an expression cDNA library constructed from bovine ciliary epithelium poly A+ that codes a 271 amino acid, 28.8 kDa protein. At the amino acid level, bovine CHIP29 is 91% identical to the CHIP28 protein. Analysis of the deduced amino acid sequence indicated a hydrophobic protein with six membrane spanning domains, one N-linked glycosylation site, two consented NPA boxes common to MIP26 family proteins, and conserved amino acid residue cysteine 189 common to water channels. Northern blotting revealed a major mRNA of 2.8 Kb size expressed in bovine ciliary epithelium. The results presented here confirm the presence of water channel gene in the bovine ciliary epithelium, a primary site for the aqueous humor production.

Cloning of a Novel Rat Kidney cDNA Homologous to CHIP28 and WCH-CD Water Channels

Two kidney water channels have been identified: CHIP28 in proximal tubule and thin descending limb, and WCH-CD in collecting duct apical membrane. An homologous cDNA (WCH3) was obtained from rat kidney and found to encode a 276 amino acid, 29 kDa protein with 39% amino acid identity to rat CHIP28, 50% to WCH-CD and 49% to MIP26. The WCH3 transcript of 2.5 kb was expressed exclusively in kidney and was upregulated in dehydrated rats. Cell-free translation produced an ∼28 kDa protein. Analysis of the predicted amino acid sequence indicated a hydrophobic protein with 4-6 membrane-spanning domains, with one N-linked glycosylation site, two conserved NPA boxes common to MIP26 family proteins, and conserved residue C189 common to water channels. WCH3 is a new member of the MIP26 family of channel-forming proteins in mammalian kidney.