Genome-wide analysis of major intrinsic proteins in the tree plant Populus trichocarpa: Characterization of XIP subfamily of aquaporins from evolutionary perspective
Identifieur interne : 000A76 ( Ncbi/Checkpoint ); précédent : 000A75; suivant : 000A77Genome-wide analysis of major intrinsic proteins in the tree plant Populus trichocarpa: Characterization of XIP subfamily of aquaporins from evolutionary perspective
Auteurs : Anjali Bansal Gupta [Inde] ; Ramasubbu Sankararamakrishnan [Inde]Source :
- BMC Plant Biology [ 1471-2229 ] ; 2009.
Abstract
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
Fifty five full-length MIPs have been identified in
Due to whole genome duplication,
Url:
DOI: 10.1186/1471-2229-9-134
PubMed: 19930558
PubMed Central: 2789079
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genome-wide analysis of major intrinsic proteins in the tree plant <italic>Populus trichocarpa</italic>: Characterization of XIP subfamily of aquaporins from evolutionary perspective</title><author><name sortKey="Gupta, Anjali Bansal" sort="Gupta, Anjali Bansal" uniqKey="Gupta A" first="Anjali Bansal" last="Gupta">Anjali Bansal Gupta</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016</wicri:regionArea><wicri:noRegion>Kanpur 208016</wicri:noRegion></affiliation></author><author><name sortKey="Sankararamakrishnan, Ramasubbu" sort="Sankararamakrishnan, Ramasubbu" uniqKey="Sankararamakrishnan R" first="Ramasubbu" last="Sankararamakrishnan">Ramasubbu Sankararamakrishnan</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016</wicri:regionArea><wicri:noRegion>Kanpur 208016</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">19930558</idno><idno type="pmc">2789079</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789079</idno><idno type="RBID">PMC:2789079</idno><idno type="doi">10.1186/1471-2229-9-134</idno><date when="2009">2009</date><idno type="wicri:Area/Pmc/Corpus">000E24</idno><idno type="wicri:Area/Pmc/Curation">000E23</idno><idno type="wicri:Area/Pmc/Checkpoint">001018</idno><idno type="wicri:Area/Ncbi/Merge">000A76</idno><idno type="wicri:Area/Ncbi/Curation">000A76</idno><idno type="wicri:Area/Ncbi/Checkpoint">000A76</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genome-wide analysis of major intrinsic proteins in the tree plant <italic>Populus trichocarpa</italic>: Characterization of XIP subfamily of aquaporins from evolutionary perspective</title><author><name sortKey="Gupta, Anjali Bansal" sort="Gupta, Anjali Bansal" uniqKey="Gupta A" first="Anjali Bansal" last="Gupta">Anjali Bansal Gupta</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016</wicri:regionArea><wicri:noRegion>Kanpur 208016</wicri:noRegion></affiliation></author><author><name sortKey="Sankararamakrishnan, Ramasubbu" sort="Sankararamakrishnan, Ramasubbu" uniqKey="Sankararamakrishnan R" first="Ramasubbu" last="Sankararamakrishnan">Ramasubbu Sankararamakrishnan</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016</wicri:regionArea><wicri:noRegion>Kanpur 208016</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Plant Biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2009">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>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 <italic>Arabidopsis thaliana</italic>, rice and maize contain more than 30 MIPs and based on phylogenetic analysis they can be divided into at least four subfamilies. <italic>Populus trichocarpa </italic>is a model tree species and provides an opportunity to investigate several tree-specific traits. In this study, we have investigated <italic>Populus </italic>MIPs (PtMIPs) and compared them with their counterparts in <italic>Arabidopsis</italic>, rice and maize.</p></sec><sec><title>Results</title><p>Fifty five full-length MIPs have been identified in <italic>Populus </italic>genome. Phylogenetic analysis reveals that <italic>Populus </italic>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 <italic>Arabidopsis</italic>, 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 <italic>Populus </italic>MIPs indicates that <italic>Populus </italic>XIPs don't show any tissue-specific transcript abundance.</p></sec><sec><title>Conclusion</title><p>Due to whole genome duplication, <italic>Populus </italic>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.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Zhou, Y" uniqKey="Zhou Y">Y Zhou</name></author><author><name sortKey="Setz, N" uniqKey="Setz N">N Setz</name></author><author><name sortKey="Niemietz, C" uniqKey="Niemietz C">C Niemietz</name></author><author><name sortKey="Qu, H" uniqKey="Qu H">H Qu</name></author><author><name sortKey="Offler, Ce" uniqKey="Offler C">CE Offler</name></author><author><name sortKey="Tyerman, Sd" uniqKey="Tyerman S">SD Tyerman</name></author><author><name sortKey="Patrick, Jw" uniqKey="Patrick J">JW Patrick</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Siefritz, F" uniqKey="Siefritz F">F Siefritz</name></author><author><name sortKey="Tyree, Mt" uniqKey="Tyree M">MT 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Thompson</name></author><author><name sortKey="Higgins, Dg" uniqKey="Higgins D">DG Higgins</name></author><author><name sortKey="Gibson, Tj" uniqKey="Gibson T">TJ Gibson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Page, Rdm" uniqKey="Page R">RDM Page</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sali, A" uniqKey="Sali A">A Sali</name></author><author><name sortKey="Blundell, Tl" uniqKey="Blundell T">TL Blundell</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Canutescu, Aa" uniqKey="Canutescu A">AA Canutescu</name></author><author><name sortKey="Shelenkov, Aa" uniqKey="Shelenkov A">AA Shelenkov</name></author><author><name sortKey="Rl, Dunbrack" uniqKey="Rl D">Dunbrack RL</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lindahl, E" uniqKey="Lindahl E">E Lindahl</name></author><author><name sortKey="Hess, B" uniqKey="Hess B">B Hess</name></author><author><name sortKey="Spoel, D Van Der" uniqKey="Spoel D">D van der Spoel</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Laskowski, Ra" uniqKey="Laskowski R">RA Laskowski</name></author><author><name sortKey="Macarthur, Mw" uniqKey="Macarthur M">MW MacArthur</name></author><author><name sortKey="Moss, Ds" uniqKey="Moss D">DS Moss</name></author><author><name sortKey="Thornton, Jm" uniqKey="Thornton J">JM Thornton</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Smart, Os" uniqKey="Smart O">OS Smart</name></author><author><name sortKey="Neduvelil, Jg" uniqKey="Neduvelil J">JG Neduvelil</name></author><author><name sortKey="Wang, X" uniqKey="Wang X">X Wang</name></author><author><name sortKey="Wallace, Ba" uniqKey="Wallace B">BA Wallace</name></author><author><name sortKey="Sansom, Msp" uniqKey="Sansom M">MSP Sansom</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Inde</li></country></list><tree><country name="Inde"><noRegion><name sortKey="Gupta, Anjali Bansal" sort="Gupta, Anjali Bansal" uniqKey="Gupta A" first="Anjali Bansal" last="Gupta">Anjali Bansal Gupta</name></noRegion><name sortKey="Sankararamakrishnan, Ramasubbu" sort="Sankararamakrishnan, Ramasubbu" uniqKey="Sankararamakrishnan R" first="Ramasubbu" last="Sankararamakrishnan">Ramasubbu Sankararamakrishnan</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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