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Daniel M Roberts - One of the best experts on this subject based on the ideXlab platform.
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interaction of cytosolic glutamine synthetase of soybean root nodules with the c terminal domain of the symbiosome membrane nodulin 26 aquaglyceroporin
Journal of Biological Chemistry, 2010Co-Authors: Pintu D Masalkar, Ian S Wallace, Jin Ha Hwang, Daniel M RobertsAbstract:Nodulin 26 (nod26) is a Major Intrinsic protein that constitutes the Major protein component on the symbiosome membrane (SM) of N2-fixing soybean nodules. Functionally, nod26 forms a low energy transport pathway for water, osmolytes, and NH3 across the SM. Besides their transport functions, emerging evidence suggests that high concentrations of Major Intrinsic Proteins on membranes provide interaction and docking targets for various cytosolic Proteins. Here it is shown that the C-terminal domain peptide of nod26 interacts with a 40-kDa protein from soybean nodule extracts, which was identified as soybean cytosolic glutamine synthetase GS1β1 by mass spectrometry. Fluorescence spectroscopy assays show that recombinant soybean GS1β1 binds the nod26 C-terminal domain with a 1:1 stoichiometry (Kd = 266 nm). GS1β1 also binds to isolated SMs, and this binding can be blocked by preincubation with the C-terminal peptide of nod26. In vivo experiments using either a split ubiquitin yeast two-hybrid system or bimolecular fluorescence complementation show that the four cytosolic GS isoforms expressed in soybean nodules interact with full-length nod26. The binding of GS, the principal ammonia assimilatory enzyme, to the conserved C-terminal domain of nod26, a transporter of NH3, is proposed to promote efficient assimilation of fixed nitrogen, as well as prevent potential ammonia toxicity, by localizing the enzyme to the cytosolic side of the symbiosome membrane.
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the structure function and regulation of the nodulin 26 like Intrinsic protein family of plant aquaglyceroporins
Biochimica et Biophysica Acta, 2006Co-Authors: Ian S Wallace, Wongyu Choi, Daniel M RobertsAbstract:The nodulin 26-like Intrinsic protein family is a group of highly conserved multifunctional Major Intrinsic Proteins that are unique to plants, and which transport a variety of uncharged solutes ranging from water to ammonia to glycerol. Based on structure–function studies, the NIP family can be subdivided into two subgroups (I and II) based on the identity of the amino acids in the selectivity-determining filter (ar/R region) of the transport pore. Both subgroups appear to contain multifunctional transporters with low to no water permeability and the ability to flux multiple uncharged solutes of varying sizes depending upon the composition of the residues of the ar/R filter. NIPs are subject to posttranslational phosphorylation by calcium-dependent protein kinases. In the case of the family archetype, soybean nodulin 26, phosphorylation has been shown to stimulate its transport activity and to be regulated in response to developmental as well as environmental cues, including osmotic stresses. NIPs tend to be expressed at low levels in the plant compared to other MIPs, and several exhibit cell or tissue specific expression that is subject to spatial and temporal regulation during development.
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distinct transport selectivity of two structural subclasses of the nodulin like Intrinsic protein family of plant aquaglyceroporin channels
Biochemistry, 2005Co-Authors: Ian S Wallace, Daniel M RobertsAbstract:Major Intrinsic Proteins (MIPs) are a diverse class of integral membrane Proteins that facilitate the transport of water and some small solutes across cellular membranes. X-ray structures of MIPs indicate that a tetrad of residues (the ar/R region) form a narrow pore constriction that constitutes the selectivity filter. In comparison with mammalian and microbial species, plants have a greater number and diversity of MIPs with greater than 30 genes encoding four phylogenetic subfamilies with eight different classes of ar/R sequences. The nodulin 26-like Intrinsic protein (NIP) subfamily in Arabidopsis can be subdivided into two ar/R subgroups: the NIP subgroup I, which resembles the archetype of the family, soybean nodulin 26, and the NIP subgroup II, which is represented by the Arabidopsis protein AtNIP6;1. These two NIPs differ principally by the substitution of a conserved alanine (NIP subgroup II) for a conserved tryptophan (NIP subgroup I) in the helix 2 position (H2) of the ar/R filter. A comparison of the water and solute tranport properties of the two Proteins was performed by expression in Xenopus laevis oocytes. Nodulin 26 is an aquaglyceroporin with a modest osmotic water permeability (P(f)) and the ability to transport uncharged solutes such as glycerol and formamide. In constrast, AtNIP6;1 showed no measurable water permeability but transported glycerol, formamide, as well as larger solutes that were impermeable to nodulin 26. By site-directed mutagenesis, we show that the H2 position is the crucial determinant that confers these transport behaviors. A comparison of the NIPs and tonoplast-Intrinsic Proteins (TIP) shows that the H2 residue can predict the transport profile for water and glycerol with histidine found in TIP-like aquaporins, tryptophan found in aquaglyceroporins (NIP I), and alanine found in water-impermeable glyceroporins (AtNIP6;1).
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distinct transport selectivity of two structural subclasses of the nodulin like Intrinsic protein family of plant aquaglyceroporin channels
Biochemistry, 2005Co-Authors: Ian S Wallace, Daniel M RobertsAbstract:Major Intrinsic Proteins (MIPs) are a diverse class of integral membrane Proteins that facilitate the transport of water and some small solutes across cellular membranes. X-ray structures of MIPs indicate that a tetrad of residues (the ar/R region) form a narrow pore constriction that constitutes the selectivity filter. In comparison with mammalian and microbial species, plants have a greater number and diversity of MIPs with greater than 30 genes encoding four phylogenetic subfamilies with eight different classes of ar/R sequences. The nodulin 26-like Intrinsic protein (NIP) subfamily in Arabidopsis can be subdivided into two ar/R subgroups: the NIP subgroup I, which resembles the archetype of the family, soybean nodulin 26, and the NIP subgroup II, which is represented by the Arabidopsis protein AtNIP6;1. These two NIPs differ principally by the substitution of a conserved alanine (NIP subgroup II) for a conserved tryptophan (NIP subgroup I) in the helix 2 position (H2) of the ar/R filter. A comparison...
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homology modeling of representative subfamilies of arabidopsis Major Intrinsic Proteins classification based on the aromatic arginine selectivity filter
Plant Physiology, 2004Co-Authors: Ian S Wallace, Daniel M RobertsAbstract: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.
Pierreemmanuel Courty - One of the best experts on this subject based on the ideXlab platform.
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expression of Major Intrinsic protein genes in sorghum bicolor roots under water deficit depends on arbuscular mycorrhizal fungal species
Soil Biology & Biochemistry, 2020Co-Authors: Sarah Symanczik, Jennifer Krutzmann, Uwe Nehls, Thomas Boller, Pierreemmanuel CourtyAbstract:Abstract Drought is a limiting factor for crop plant production, especially in arid and semi-arid climates. In this study, sorghum (Sorghum bicolor) was inoculated with two arbuscular mycorrhizal fungi, either the standard Rhizophagus irregularis or the desert-adapted Rhizophagus arabicus, and grown in experimental microcosms under well-watered or drought conditions. We investigated gene expression of selected Major Intrinsic Proteins (MIPs) of sorghum in these mycorrhizal plants in comparison to non-inoculated, well-watered controls. Colonization with R. irregularis resulted in the induction of the MIPs SbPIP2.2 and SbPIP2.5, regardless of whether sorghum plants were well watered or not. Root colonization with R. arabicus, however, caused an exclusive, strong reduction in the transcript levels of three MIP genes (SbTIP2.1, SbNIP1.2, SbNIP2.2) under drought conditions. . We also studied water transport properties of mycorrhiza-regulated MIPs. One particular MIP, SbPIP2.8, was found to mediate particularly high water permeability. Expression of this gene was strongly repressed upon drought, irrespectively on whether plants were mycorrhized or not.
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Expression of Major Intrinsic protein genes in Sorghum bicolor roots under water deficit depends on arbuscular mycorrhizal fungal species
Soil Biology and Biochemistry, 2020Co-Authors: Sarah Symanczik, Jennifer Krutzmann, Uwe Nehls, Thomas Boller, Pierreemmanuel CourtyAbstract:Drought is a limiting factor for crop plant production, especially in arid and semi-arid climates. In this study, sorghum (Sorghum bicolor) was inoculated with two arbuscular mycorrhizal fungi, either the standard Rhizophagus irregularis or the desert-adapted Rhizophagus arabicus, and grown in experimental microcosms under well-watered or drought conditions. We investigated gene expression of selected Major Intrinsic Proteins (MIPs) of sorghum in these mycorrhizal plants, compared to non-inoculated, well-watered sorghum (control). Colonization with R. irregularis induced the MIPs SbPIP2.2 and SbPIP2.5, regardless of whether sorghum plants were well watered or not. Root colonization with R. arabicus, however, caused an exclusive, strong reduction in the transcript levels of three MIP genes (SbTIP2.1, SbNIP1.2, SbNIP2.2) under drought conditions. We also studied water transport properties of mycorrhiza-regulated MIPs. One particular MIP, SbPIP2.8, was associated with high water permeability of roots. Expression of this gene was strongly repressed in all sorghum plants (mycorrhizal and non-inoculated) that experienced drought conditions.
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Developmental and Environmental Regulation of Aquaporin Gene Expression across Populus Species: Divergence or Redundancy?
PLoS ONE, 2013Co-Authors: David Cohen, Pierreemmanuel Courty, Marie-béatrice Bogeat-triboulot, Silvère Vialet-chabrand, Rémy Merret, Sebastien Moretti, François Bizet, Agnès Guilliot, Irène HummelAbstract:Aquaporins (AQPs) are membrane channels belonging to the Major Intrinsic Proteins family and are known for their ability to facilitate water movement. While in Populus trichocarpa, AQP Proteins form a large family encompassing fifty-five genes, most of the experimental work focused on a few genes or subfamilies. The current work was undertaken to develop a comprehensive picture of the whole AQP gene family in Populus species by delineating gene expression domain and distinguishing responsiveness to developmental and environmental cues. Since duplication events amplified the poplar AQP family, we addressed the question of expression redundancy between gene duplicates. On these purposes, we carried a meta-analysis of all publicly available Affymetrix experiments. Our in-silico strategy controlled for previously identified biases in cross-species transcriptomics, a necessary step for any comparative transcriptomics based on multispecies design chips. Three poplar AQPs were not supported by any expression data, even in a large collection of situations (abiotic and biotic constraints, temporal oscillations and mutants). The expression of 11 AQPs was never or poorly regulated whatever the wideness of their expression domain and their expression level. Our work highlighted that PtTIP1;4 was the most responsive gene of the AQP family. A high functional divergence between gene duplicates was detected across species and in response to tested cues, except for the root-expressed PtTIP2;3/PtTIP2;4 pair exhibiting 80% convergent responses. Our meta-analysis assessed key features of aquaporin expression which had remained hidden in single experiments, such as expression wideness, response specificity and genotype and environment interactions. By consolidating expression profiles using independent experimental series, we showed that the large expansion of AQP family in poplar was accompanied with a strong divergence of gene expression, even if some cases of functional redundancy could be suspected.
Ramasubbu Sankararamakrishnan - One of the best experts on this subject based on the ideXlab platform.
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genome wide analysis of Major Intrinsic Proteins in the tree plant populus trichocarpa characterization of xip subfamily of aquaporins from evolutionary perspective
BMC Plant Biology, 2009Co-Authors: Anjali Gupta, Ramasubbu SankararamakrishnanAbstract:Background Members of Major Intrinsic Proteins (MIPs) include water-conducting aquaporins and glycerol-transporting aquaglyceroporins. MIPs play important role in plant-water relations. The model plants Arabidopsis thaliana, rice and maize contain more than 30 MIPs and based on phylogenetic analysis they can be divided into at least four subfamilies. Populus trichocarpa is a model tree species and provides an opportunity to investigate several tree-specific traits. In this study, we have investigated Populus MIPs (PtMIPs) and compared them with their counterparts in Arabidopsis, rice and maize.
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genome wide analysis of Major Intrinsic Proteins in the tree plant populus trichocarpa characterization of xip subfamily of aquaporins from evolutionary perspective
BMC Plant Biology, 2009Co-Authors: Anjali Gupta, Ramasubbu SankararamakrishnanAbstract:Members of Major Intrinsic Proteins (MIPs) include water-conducting aquaporins and glycerol-transporting aquaglyceroporins. MIPs play important role in plant-water relations. The model plants Arabidopsis thaliana, rice and maize contain more than 30 MIPs and based on phylogenetic analysis they can be divided into at least four subfamilies. Populus trichocarpa is a model tree species and provides an opportunity to investigate several tree-specific traits. In this study, we have investigated Populus MIPs (PtMIPs) and compared them with their counterparts in Arabidopsis, rice and maize. Fifty five full-length MIPs have been identified in Populus genome. Phylogenetic analysis reveals that Populus has a fifth uncharacterized subfamily (XIPs). Three-dimensional models of all 55 PtMIPs were constructed using homology modeling technique. Aromatic/arginine (ar/R) selectivity filters, characteristics of loops responsible for solute selectivity (loop C) and gating (loop D) and group conservation of small and weakly polar interfacial residues have been analyzed. Majority of the non-XIP PtMIPs are similar to those in Arabidopsis, rice and maize. Additional XIPs were identified from database search and 35 XIP sequences from dicots, fungi, moss and protozoa were analyzed. Ar/R selectivity filters of dicots XIPs are more hydrophobic compared to fungi and moss XIPs and hence they are likely to transport hydrophobic solutes. Loop C is longer in one of the subgroups of dicot XIPs and most probably has a significant role in solute selectivity. Loop D in dicot XIPs has higher number of basic residues. Intron loss is observed on two occasions: once between two subfamilies of eudicots and monocot and in the second instance, when dicot and moss XIPs diverged from fungi. Expression analysis of Populus MIPs indicates that Populus XIPs don't show any tissue-specific transcript abundance. Due to whole genome duplication, Populus has the largest number of MIPs identified in any single species. Non-XIP MIPs are similar in all four plant species considered in this study. Small and weakly polar residues at the helix-helix interface are group conserved presumably to maintain the hourglass fold of MIP channels. Substitutions in ar/R selectivity filter, insertion/deletion in loop C, increasing basic nature of loop D and loss of introns are some of the events occurred during the evolution of dicot XIPs.
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homology modeling of Major Intrinsic Proteins in rice maize and arabidopsis comparative analysis of transmembrane helix association and aromatic arginine selectivity filters
BMC Structural Biology, 2007Co-Authors: Anjali Bansal, Ramasubbu SankararamakrishnanAbstract:Background The Major Intrinsic Proteins (MIPs) facilitate the transport of water and neutral solutes across the lipid bilayers. Plant MIPs are believed to be important in cell division and expansion and in water transport properties in response to environmental conditions. More than 30 MIP sequences have been identified in Arabidopsis thaliana, maize and rice. Plasma membrane Intrinsic Proteins (PIPs), tonoplast Intrinsic Proteins (TIPs), Nod26-like Intrinsic protein (NIPs) and small and basic Intrinsic Proteins (SIPs) are subfamilies of plant MIPs. Despite sequence diversity, all the experimentally determined structures belonging to the MIP superfamily have the same "hour-glass" fold.
Ian S Wallace - One of the best experts on this subject based on the ideXlab platform.
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interaction of cytosolic glutamine synthetase of soybean root nodules with the c terminal domain of the symbiosome membrane nodulin 26 aquaglyceroporin
Journal of Biological Chemistry, 2010Co-Authors: Pintu D Masalkar, Ian S Wallace, Jin Ha Hwang, Daniel M RobertsAbstract:Nodulin 26 (nod26) is a Major Intrinsic protein that constitutes the Major protein component on the symbiosome membrane (SM) of N2-fixing soybean nodules. Functionally, nod26 forms a low energy transport pathway for water, osmolytes, and NH3 across the SM. Besides their transport functions, emerging evidence suggests that high concentrations of Major Intrinsic Proteins on membranes provide interaction and docking targets for various cytosolic Proteins. Here it is shown that the C-terminal domain peptide of nod26 interacts with a 40-kDa protein from soybean nodule extracts, which was identified as soybean cytosolic glutamine synthetase GS1β1 by mass spectrometry. Fluorescence spectroscopy assays show that recombinant soybean GS1β1 binds the nod26 C-terminal domain with a 1:1 stoichiometry (Kd = 266 nm). GS1β1 also binds to isolated SMs, and this binding can be blocked by preincubation with the C-terminal peptide of nod26. In vivo experiments using either a split ubiquitin yeast two-hybrid system or bimolecular fluorescence complementation show that the four cytosolic GS isoforms expressed in soybean nodules interact with full-length nod26. The binding of GS, the principal ammonia assimilatory enzyme, to the conserved C-terminal domain of nod26, a transporter of NH3, is proposed to promote efficient assimilation of fixed nitrogen, as well as prevent potential ammonia toxicity, by localizing the enzyme to the cytosolic side of the symbiosome membrane.
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the structure function and regulation of the nodulin 26 like Intrinsic protein family of plant aquaglyceroporins
Biochimica et Biophysica Acta, 2006Co-Authors: Ian S Wallace, Wongyu Choi, Daniel M RobertsAbstract:The nodulin 26-like Intrinsic protein family is a group of highly conserved multifunctional Major Intrinsic Proteins that are unique to plants, and which transport a variety of uncharged solutes ranging from water to ammonia to glycerol. Based on structure–function studies, the NIP family can be subdivided into two subgroups (I and II) based on the identity of the amino acids in the selectivity-determining filter (ar/R region) of the transport pore. Both subgroups appear to contain multifunctional transporters with low to no water permeability and the ability to flux multiple uncharged solutes of varying sizes depending upon the composition of the residues of the ar/R filter. NIPs are subject to posttranslational phosphorylation by calcium-dependent protein kinases. In the case of the family archetype, soybean nodulin 26, phosphorylation has been shown to stimulate its transport activity and to be regulated in response to developmental as well as environmental cues, including osmotic stresses. NIPs tend to be expressed at low levels in the plant compared to other MIPs, and several exhibit cell or tissue specific expression that is subject to spatial and temporal regulation during development.
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distinct transport selectivity of two structural subclasses of the nodulin like Intrinsic protein family of plant aquaglyceroporin channels
Biochemistry, 2005Co-Authors: Ian S Wallace, Daniel M RobertsAbstract:Major Intrinsic Proteins (MIPs) are a diverse class of integral membrane Proteins that facilitate the transport of water and some small solutes across cellular membranes. X-ray structures of MIPs indicate that a tetrad of residues (the ar/R region) form a narrow pore constriction that constitutes the selectivity filter. In comparison with mammalian and microbial species, plants have a greater number and diversity of MIPs with greater than 30 genes encoding four phylogenetic subfamilies with eight different classes of ar/R sequences. The nodulin 26-like Intrinsic protein (NIP) subfamily in Arabidopsis can be subdivided into two ar/R subgroups: the NIP subgroup I, which resembles the archetype of the family, soybean nodulin 26, and the NIP subgroup II, which is represented by the Arabidopsis protein AtNIP6;1. These two NIPs differ principally by the substitution of a conserved alanine (NIP subgroup II) for a conserved tryptophan (NIP subgroup I) in the helix 2 position (H2) of the ar/R filter. A comparison of the water and solute tranport properties of the two Proteins was performed by expression in Xenopus laevis oocytes. Nodulin 26 is an aquaglyceroporin with a modest osmotic water permeability (P(f)) and the ability to transport uncharged solutes such as glycerol and formamide. In constrast, AtNIP6;1 showed no measurable water permeability but transported glycerol, formamide, as well as larger solutes that were impermeable to nodulin 26. By site-directed mutagenesis, we show that the H2 position is the crucial determinant that confers these transport behaviors. A comparison of the NIPs and tonoplast-Intrinsic Proteins (TIP) shows that the H2 residue can predict the transport profile for water and glycerol with histidine found in TIP-like aquaporins, tryptophan found in aquaglyceroporins (NIP I), and alanine found in water-impermeable glyceroporins (AtNIP6;1).
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distinct transport selectivity of two structural subclasses of the nodulin like Intrinsic protein family of plant aquaglyceroporin channels
Biochemistry, 2005Co-Authors: Ian S Wallace, Daniel M RobertsAbstract:Major Intrinsic Proteins (MIPs) are a diverse class of integral membrane Proteins that facilitate the transport of water and some small solutes across cellular membranes. X-ray structures of MIPs indicate that a tetrad of residues (the ar/R region) form a narrow pore constriction that constitutes the selectivity filter. In comparison with mammalian and microbial species, plants have a greater number and diversity of MIPs with greater than 30 genes encoding four phylogenetic subfamilies with eight different classes of ar/R sequences. The nodulin 26-like Intrinsic protein (NIP) subfamily in Arabidopsis can be subdivided into two ar/R subgroups: the NIP subgroup I, which resembles the archetype of the family, soybean nodulin 26, and the NIP subgroup II, which is represented by the Arabidopsis protein AtNIP6;1. These two NIPs differ principally by the substitution of a conserved alanine (NIP subgroup II) for a conserved tryptophan (NIP subgroup I) in the helix 2 position (H2) of the ar/R filter. A comparison...
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homology modeling of representative subfamilies of arabidopsis Major Intrinsic Proteins classification based on the aromatic arginine selectivity filter
Plant Physiology, 2004Co-Authors: Ian S Wallace, Daniel M RobertsAbstract: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.
Anjali Gupta - One of the best experts on this subject based on the ideXlab platform.
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genome wide analysis of Major Intrinsic Proteins in the tree plant populus trichocarpa characterization of xip subfamily of aquaporins from evolutionary perspective
BMC Plant Biology, 2009Co-Authors: Anjali Gupta, Ramasubbu SankararamakrishnanAbstract:Background Members of Major Intrinsic Proteins (MIPs) include water-conducting aquaporins and glycerol-transporting aquaglyceroporins. MIPs play important role in plant-water relations. The model plants Arabidopsis thaliana, rice and maize contain more than 30 MIPs and based on phylogenetic analysis they can be divided into at least four subfamilies. Populus trichocarpa is a model tree species and provides an opportunity to investigate several tree-specific traits. In this study, we have investigated Populus MIPs (PtMIPs) and compared them with their counterparts in Arabidopsis, rice and maize.
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genome wide analysis of Major Intrinsic Proteins in the tree plant populus trichocarpa characterization of xip subfamily of aquaporins from evolutionary perspective
BMC Plant Biology, 2009Co-Authors: Anjali Gupta, Ramasubbu SankararamakrishnanAbstract:Members of Major Intrinsic Proteins (MIPs) include water-conducting aquaporins and glycerol-transporting aquaglyceroporins. MIPs play important role in plant-water relations. The model plants Arabidopsis thaliana, rice and maize contain more than 30 MIPs and based on phylogenetic analysis they can be divided into at least four subfamilies. Populus trichocarpa is a model tree species and provides an opportunity to investigate several tree-specific traits. In this study, we have investigated Populus MIPs (PtMIPs) and compared them with their counterparts in Arabidopsis, rice and maize. Fifty five full-length MIPs have been identified in Populus genome. Phylogenetic analysis reveals that Populus has a fifth uncharacterized subfamily (XIPs). Three-dimensional models of all 55 PtMIPs were constructed using homology modeling technique. Aromatic/arginine (ar/R) selectivity filters, characteristics of loops responsible for solute selectivity (loop C) and gating (loop D) and group conservation of small and weakly polar interfacial residues have been analyzed. Majority of the non-XIP PtMIPs are similar to those in Arabidopsis, rice and maize. Additional XIPs were identified from database search and 35 XIP sequences from dicots, fungi, moss and protozoa were analyzed. Ar/R selectivity filters of dicots XIPs are more hydrophobic compared to fungi and moss XIPs and hence they are likely to transport hydrophobic solutes. Loop C is longer in one of the subgroups of dicot XIPs and most probably has a significant role in solute selectivity. Loop D in dicot XIPs has higher number of basic residues. Intron loss is observed on two occasions: once between two subfamilies of eudicots and monocot and in the second instance, when dicot and moss XIPs diverged from fungi. Expression analysis of Populus MIPs indicates that Populus XIPs don't show any tissue-specific transcript abundance. Due to whole genome duplication, Populus has the largest number of MIPs identified in any single species. Non-XIP MIPs are similar in all four plant species considered in this study. Small and weakly polar residues at the helix-helix interface are group conserved presumably to maintain the hourglass fold of MIP channels. Substitutions in ar/R selectivity filter, insertion/deletion in loop C, increasing basic nature of loop D and loss of introns are some of the events occurred during the evolution of dicot XIPs.
