Homology Modeling of Representative Subfamilies of Arabidopsis Major Intrinsic Proteins. Classification Based on the Aromatic/Arginine Selectivity Filter

Abstract

Major intrinsic proteins (MIPs) are a family of membrane channels that facilitate the bidirectional transport of water and small uncharged solutes such as glycerol. The 35 full-length members of the MIP family in Arabidopsis are segregated into four structurally homologous subfamilies: plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), nodulin 26-like intrinsic membrane proteins (NIPs), and small basic intrinsic proteins (SIPs). Computational methods were used to construct structural models of the putative pore regions of various plant MIPs based on homology modeling with the atomic resolution crystal structures of mammalian aquaporin 1 and the bacterial glycerol permease GlpF. Based on comparisons of the narrow selectivity filter regions (the aromatic/Arg [ar/R] filter), the members of the four phylogenetic subfamilies of Arabidopsis MIPs can be classified into eight groups. PIPs possess a uniform ar/R signature characteristic of high water transport aquaporins, whereas TIPs are highly diverse with three separate conserved ar/R regions. NIPs possess two separate conserved ar/R regions, one that is similar to the archetype, soybean (Glycine max) nodulin 26, and another that is characteristic of Arabidopsis NIP6;1. The SIP subfamily possesses two ar/R subgroups, characteristic of either SIP1 or SIP2. Both SIP ar/R residues are divergent from all other MIPs in plants and other kingdoms. Overall, these findings suggest that higher plant MIPs have a common fold but show distinct differences in proposed pore apertures, potential to form hydrogen bonds with transported molecules, and amphiphilicity that likely results in divergent transport selectivities.Members of the major intrinsic protein (MIP) family form a large and diverse group of membrane proteins that facilitate the bidirectional transport of water and some small solutes across cellular membranes (Agre et al., 2002;Thomas et al., 2002). MIPs are widely distributed in organisms from bacteria to higher eukaryotes, and these proteins are especially abundant in plants, with 35 full-length genes present in Arabidopsis (Johanson et al., 2001;Quigley et al., 2001). Members of the plant MIP family have been implicated in cell elongation and development, changes in hydraulic conductivity in response to environmental cues, and numerous other processes that require rapid transmembrane movements of water (for review, see Johansson et al., 2000;Maurel et al., 2002;Tyerman et al., 2002).MIP family members in Arabidopsis are subdivided into four subfamilies: the plasma membrane intrinsic proteins (PIPs; 13 genes), the tonoplast intrinsic membrane proteins (TIPs; 10 genes), the nodulin 26-like intrinsic membrane proteins (NIPs; 9 genes), and the small basic intrinsic proteins (SIPs; 3 genes) (Weig et al., 1997;Johanson et al., 2001;Quigley et al., 2001). By contrast, mammals have only two functional subfamilies of MIPs: water-specific aquaporins and solute-transporting glyceroporins and aquaglyceroporins (Agre et al., 2002). This disparity leads...

AtTIP1;3 and AtTIP5;1, the only highly expressed Arabidopsis pollen‐specific aquaporins, transport water and urea

“…On the contrary, the ar/R region of AtTIP5;1 is unique. Because of this, AtTIP5;1 would have a larger apparent pore aperture and a reduced ability to form hydrogen bonds with transported solutes [26]. Therefore, AtTIP5;1 may have transport properties that are unlike conventional aquaporins, although we showed here that AtTIP5;1 transports water and specifically urea, since no transport of glycerol or boric acid was observed.…”

Arabidopsis NIP2;1, a Major Intrinsic Protein Transporter of Lactic Acid Induced by Anoxic Stress

“…In contrast, NIP II proteins, which differ principally at one residue within the aromatic/arginine selectivity filter, show little water permeability (17,19) but do transport a variety of uncharged solutes, including glycerol and urea (17), as well as metalloid compounds, including boron and silicon (19,20). With respect to pore determinant sequences, AtNIP2;1 resembles the nodulin 26-like NIP I pore group (9), showing the conserved aromatic/arginine selectivity sequence of this group. Nevertheless, the results of the present study show that AtNIP2;1 is clearly distinct from nodulin 26 and other NIP I proteins, such as AtNIP1;1 and -1;2 (10, 11), not only in its ability to transport lactic acid instead of glycerol but also in its unusually low permeability to water.…”

“…As pointed out previously, the pore properties and multifunctional transport signature of this subfamily of plant MIPs are unique (15). Based on modeling, there are two general pore subfamilies of NIP, NIP I and NIP II (9). NIP I proteins are typified by soybean nodulin 26 and form aquaglyceroporins that transport glycerol as well as water (4).…”

“…For example, among the 35 MIP genes in Arabidopsis thaliana (1), there are nine members of the NIP subfamily. Based on molecular modeling of the pore selectivity sequences, these nine NIPs are subdivided into the following two groups: NIP subgroup I proteins are encoded by NIP1;1, NIP1;2, NIP2;1, NIP3;1, NIP4;1, and NIP4;2, and NIP subgroup II proteins are encoded by NIP5;1, NIP6;1, and NIP7;1 (9).…”

Ammonia permeability of the soybean nodulin 26 channel

“…The results show that several NIPlike mutants of both the NIP I and NIP II ar/R subclasses show the ability to complement yeast ammonia auxotrophs but that this ability also depends upon additional residues in other regions of the pore [20]. In the present study it is shown that purified soybean nod26, the NIP family archetype which has an ar/R region characteristic of NIP I pores [22], exhibits the ability to transport NH 3 and shows an approximately fourfold stronger preference for this substrate over water. Additionally, the use of purified nod26 liposomes allowed a determination of the single channel rate for ammonia transport.…”