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Short Communication

In silico characterization of a nitrate reductase gene family and analysis of the predicted proteins from the moss Physcomitrella patens

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Pages 19-25 | Published online: 01 Jan 2012

References

  • Campbell WH. Nitrate reductase structure, function and regulation: bridging the gap between biochemistry and physiology. Annu Rev Plant Physiol Plant Mol Biol 1999; 50:277 - 303; http://dx.doi.org/10.1146/annurev.arplant.50.1.277; PMID: 15012211
  • Campbell WH, Kinghorn KR. Functional domains of assimilatory nitrate reductases and nitrite reductases. Trends Biochem Sci 1990; 15:315 - 9; http://dx.doi.org/10.1016/0968-0004(90)90021-3; PMID: 2204158
  • Fischer K, Barbier GG, Hecht H-J, Mendel RR, Campbell WH, Schwarz G. Structural basis of eukaryotic nitrate reduction: crystal structures of the nitrate reductase active site. Plant Cell 2005; 17:1167 - 79; http://dx.doi.org/10.1105/tpc.104.029694; PMID: 15772287
  • Lu G, Campbell WH, Schneider G, Lindqvist Y. Crystal structure of the FAD-containing fragment of corn nitrate reductase at 2.5 A resolution: relationship to other flavoprotein reductases. Structure 1994; 2:809 - 21; http://dx.doi.org/10.1016/S0969-2126(94)00082-4; PMID: 7812715
  • Dean JV, Harper JE. The conversion of nitrite to nitrogen oxide(s) by the constitutive NAD(P)H-Nitrate reductase enzyme from soybean. Plant Physiol 1988; 88:389 - 95; http://dx.doi.org/10.1104/pp.88.2.389; PMID: 16666314
  • Yamasaki H, Sakihama Y, Takahashi S. An alternative pathway for nitric oxide production in plants: new features of an old enzyme. Trends Plant Sci 1999; 4:128 - 9; http://dx.doi.org/10.1016/S1360-1385(99)01393-X; PMID: 10322545
  • Garcia-Mata C, Gay R, Sokolovski S, Hills A, Lamattina L, Blatt MR. Nitric oxide regulates K+ and Cl- channels in guard cells through a subset of abscisic acid-evoked signaling pathways. Proc Natl Acad Sci U S A 2003; 100:11116 - 21; http://dx.doi.org/10.1073/pnas.1434381100; PMID: 12949257
  • Kolbert Z, Bartha B, Erdei L. Exogenous auxin-induced NO synthesis is nitrate reductase-associated in Arabidopsis thaliana root primordia. J Plant Physiol 2008; 165:967 - 75; http://dx.doi.org/10.1016/j.jplph.2007.07.019; PMID: 17936409
  • Seligman K, Saviani EE, Oliveira HC, Pinto-Maglio CAF, Salgado I. Floral transition and nitric oxide emission during flower development in Arabidopsis thaliana is affected in nitrate reductase-deficient plants. Plant Cell Physiol 2008; 49:1112 - 21; http://dx.doi.org/10.1093/pcp/pcn089; PMID: 18540030
  • Sakihama Y, Nakamura S, Yamasaki H. Nitric oxide production mediated by nitrate reductase in the green alga Chlamydomonas reinhardtii: an alternative NO production pathway in photosynthetic organisms. Plant Cell Physiol 2002; 43:290 - 7; http://dx.doi.org/10.1093/pcp/pcf034; PMID: 11917083
  • Kaiser WM, Huber SC. Post-translational regulation of nitrate reductase: mechanism, physiological relevance and environmental triggers. J Exp Bot 2001; 52:1981 - 9; http://dx.doi.org/10.1093/jexbot/52.363.1981; PMID: 11559733
  • Riens B, Heldt HW. Decrease of nitrate reductase activity in spinach leaves during a light-dark transition. Plant Physiol 1992; 98:573 - 7; http://dx.doi.org/10.1104/pp.98.2.573; PMID: 16668679
  • MacKintosh C, Meek SEM. Regulation of plant NR activity by reversible phosphorylation, 14-3-3 proteins and proteolysis. Cell Mol Life Sci 2001; 58:205 - 14; http://dx.doi.org/10.1007/PL00000848; PMID: 11289302
  • Stolz JF, Basu P. Evolution of nitrate reductase: molecular and structural variations on a common function. Chembiochem 2002; 3:198 - 206; http://dx.doi.org/10.1002/1439-7633(20020301)3:2/3<198::AID-CBIC198>3.0.CO;2-C; PMID: 11921398
  • Pozuelo M, MacKintosh C, Galván A, Fernández E. Cytosolic glutamine synthetase and not nitrate reductase from the green alga Chlamydomonas reinhardtii is phosphorylated and binds 14-3-3 proteins. Planta 2001; 212:264 - 9; http://dx.doi.org/10.1007/s004250000388; PMID: 11216847
  • Falcão RF, Oliveira MC, Colepicolo P. Molecular characterization of nitrate reductase gene and its expression in the marine red alga Gracilaria tenuistipitata (Rhodophyta). J Appl Phycol 2010; 22:613 - 22; http://dx.doi.org/10.1007/s10811-010-9501-2
  • Song B, Ward BB. Molecular characterization of the assimilatory nitrate reductase gene and its expression in the marine green alga Dunaliella tertiolecta (chlorophyceae). J Phycol 2004; 40:721 - 31; http://dx.doi.org/10.1111/j.1529-8817.2004.03078.x
  • Coyne KJ. Nitrate reductase (NR1) sequence and expression in the harmful alga Heterostigma akashiwo (Raphidophyceae). J Phycol 2010; 46:135 - 42; http://dx.doi.org/10.1111/j.1529-8817.2009.00781.x
  • Young EB, Dring MJ, Berges JA. Distinct patterns of nitrate reductase activity in brown algae: light and ammonium sensitivity in Laminaria digitata is absent in Fucus species. J Phycol 2007; 43:1200 - 8; http://dx.doi.org/10.1111/j.1529-8817.2007.00403.x
  • Dawson HN, Pendleton LC, Solomonson LP, Cannons AC. Cloning and characterization of the nitrate reductase-encoding gene from Chlorella vulgaris: structure and identification of transcription start points and initiator sequences. Gene 1996; 171:139 - 45; http://dx.doi.org/10.1016/0378-1119(96)00063-7; PMID: 8666264
  • Gruber H, Goetinck SD, Kirk DL, Schmitt RD. The nitrate reductase-encoding gene of Volvox carteri: map location, sequence and induction kinetics. Gene 1992; 120:75 - 83; http://dx.doi.org/10.1016/0378-1119(92)90011-D; PMID: 1398126
  • Howarth DG, Baum DA. Phylogenetic utility of a nuclear intron from nitrate reductase for the study of closely related plant species. Mol Phylogenet Evol 2002; 23:525 - 8; http://dx.doi.org/10.1016/S1055-7903(02)00035-0; PMID: 12099803
  • Mishler BD, Oliver MJ. Putting Physcomitrella patens on the Tree of Life: The evolution and ecology of mosses. In: Knight C, Perroud PF, Cove D eds. Annual Plant Reviews Volume 36: The Moss Physcomitrella patens. West Sussex, UK: Wiley-Blackwell, 2009:1-15.
  • Shaw J, Renzaglia K. Phylogeny and diversification of bryophytes. Am J Bot 2004; 91:1557 - 81; http://dx.doi.org/10.3732/ajb.91.10.1557; PMID: 21652309
  • Cove D, Bezanilla M, Harries P, Quatrano R. Mosses as model systems for the study of metabolism and development. Annu Rev Plant Biol 2006; 57:497 - 520; http://dx.doi.org/10.1146/annurev.arplant.57.032905.105338; PMID: 16669772
  • Cove DJ. The moss Physcomitrella patens. Annu Rev Genet 2005; 39:339 - 58; http://dx.doi.org/10.1146/annurev.genet.39.073003.110214; PMID: 16285864
  • Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, et al. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 2008; 319:64 - 9; http://dx.doi.org/10.1126/science.1150646; PMID: 18079367
  • Irimia M, Roy SW. Spliceosomal introns as tools for genomic and evolutionary analysis. Nucleic Acids Res 2008; 36:1703 - 12; http://dx.doi.org/10.1093/nar/gkn012; PMID: 18263615
  • Bachmann M, Huber JL, Liao P-C, Gage DA, Huber SC. The inhibitor protein of phosphorylated nitrate reductase from spinach (Spinacia oleracea) leaves is a 14-3-3 protein. FEBS Lett 1996; 387:127 - 31; http://dx.doi.org/10.1016/0014-5793(96)00478-4; PMID: 8674533
  • Huber SC, Bachmann M, Huber JL. Post-translational regulation of nitrate reductase activity: a role for Ca2+ and 14-3-3 proteins. Trends Plant Sci 1996; 1:432 - 8; http://dx.doi.org/10.1016/S1360-1385(96)10046-7
  • Lea US, Ten Hoopen F, Provan F, Kaiser WM, Meyer C, Lillo C. Mutation of the regulatory phosphorylation site of tobacco nitrate reductase results in high nitrite excretion and NO emission from leaf and root tissue. Planta 2004; 219:59 - 65; http://dx.doi.org/10.1007/s00425-004-1209-6; PMID: 14767769
  • Lillo C, Lea US, Leydecker M-T, Meyer C. Mutation of the regulatory phosphorylation site of tobacco nitrate reductase results in constitutive activation of the enzyme in vivo and nitrite accumulation. Plant J 2003; 35:566 - 73; http://dx.doi.org/10.1046/j.1365-313X.2003.01828.x; PMID: 12940950
  • Balandani T, Aparicio PJ. Regulation of nitrate reductase in Acetabularia mediterranea. J Exp Bot 1992; 43:625 - 31; http://dx.doi.org/10.1093/jxb/43.5.625
  • Chow F, Cabral de Oliveira M. Rapid and slow modulation of nitrate reductase acivity in the red macro alga Gracilaria chilensis (Gracilariales, Rhodophyta): influence of different nitrogen sources. J Appl Phycol 2008; 20:775 - 82; http://dx.doi.org/10.1007/s10811-008-9310-z
  • Kaiser WM, Spill D. Rapid Modulation of Spinach Leaf Nitrate Reductase by Photosynthesis : II. In Vitro Modulation by ATP and AMP. Plant Physiol 1991; 96:368 - 75; http://dx.doi.org/10.1104/pp.96.2.368; PMID: 16668195
  • Becker B, Marin B. Steptophyte algae and the origin of embryophytes. Ann Bot (Lond) 2009; 103:999 - 1004; http://dx.doi.org/10.1093/aob/mcp044
  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389 - 402; http://dx.doi.org/10.1093/nar/25.17.3389; PMID: 9254694
  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876 - 82; http://dx.doi.org/10.1093/nar/25.24.4876; PMID: 9396791
  • Campanella JJ, Bitincka L, Smalley J. MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences. BMC Bioinformatics 2003; 4:29; http://dx.doi.org/10.1186/1471-2105-4-29; PMID: 12854978
  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731 - 9; http://dx.doi.org/10.1093/molbev/msr121; PMID: 21546353
  • Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406 - 25; PMID: 3447015