In Silico Analysis of Natural Resistance-Associated Macrophage Protein (NRAMP) Family of Transporters in Rice

The Protein Journal - Tập 37 Số 3 - Trang 237-247 - 2018
Anitha Mani1, Kavitha Sankaranarayanan1
1Ion Channel Biology Laboratory, AU-KBC Research Centre, Madras Institute of Technology, Anna University, Chromepet, Chennai, Tamil Nadu, 600 044, India

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Tài liệu tham khảo

Nelson N (1999) Metal ion transporters and homeostasis. EMBO J 18(16):4361–4371

Cellier M, Prive G, Belouchi A, Kwan T, Rodrigues V, Chia W, Gros P (1995) Nramp defines a family of membrane proteins. Proc Natl Acad Sci USA 92(22):10089–10093

Migeon A, Blaudez D, Wilkins O, Montanini B, Campbell MM, Richaud P, Thomine S, Chalot M (2010) Genome-wide analysis of plant metal transporters, with an emphasis on poplar. Cell Mol Life Sci 67(22):3763–3784

Narayanan NN, Vasconcellos MW, Grusak MA (2007) Expression profiling of Oryza sativa metal homeostasis genes in different rice cultivars using a cDNA macroarray. Plant Physiol Biochem 45:277–286

Xia J, Yamaji N, Kasai T, Ma JF (2010) Plasma membrane localized transporter for aluminum in rice. Proc Natl Acad Sci USA 107:18381–18385

Xia J, Yamaji N, Ma JF (2011) Further characterization of an aluminum influx transporter in rice. Plant Signal Behav 6:160–163

Yamaji N, Sasaki A, Xia JX, Yokosho K, Ma JF (2013) Anode based switch for preferential distribution of manganese in rice. Nat Commun 4:2442

Sasaki A, Yamaji N, Yokosho K, Ma JF (2012) Nramp5 is a major transporter responsible for manganese and cadmium uptake in rice. Plant Cell 24:2155–2167

Peris-Peris C, Serra-Cardona A, Sánchez-Sanuy F, Campo S, Ariño J, San Segundo B (2016) Two NRAMP6 isoforms function as iron and manganese transporters and contribute to disease resistance in rice. Mol Plant Microbe Interact. https://doi.org/10.1094/MPMI-01-17-0005-R

Thomine S, Wang R, Ward JM, Crawford NM, Schroeder JI (2000) Cadmium and iron transport by members of a plant metal transporter family in Arabidopsis with homology to Nramp genes. Proc Natl Acad Sci USA 97:4991–4996

Sakai H, Lee SS et al (2013) Rice annotation project database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol 54(2):e6

Kawahara Y, Bastide M et al (2013) Improvement of the Oryza sativa nipponbare reference genome using next generation sequence and optical map data. Rice 6:4

Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD et al (2005) Protein identification and analysis tools on the ExPASy server. In: Walker JM (ed) The proteomics protocols handbook. Humana, Louisville, pp 571–607

Sonnhammer EL, Eddy SR, Durbin R (1997) Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 28:405–420

Krogh A, Larsson B, Heijne GV, Sonnhammer ELL (2001) Predicting transmembrane protein topology with a hidden markov model: application to complete genomes. J Mol Biol 305:567–580

Yu CS, Chen YC, Lu CH, Hwang JK (2006) Prediction of protein subcellular localization. Proteins 64:643–651

Timothy L, Mikael B, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37:202–208

Grant CE, Timothy L, Bailey, Noble WS (2011) FIMO: Scanning for occurrences of a given motif, Bioinformatics 27(7):1017–1018

Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539

Von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA, Bork P (2005) STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res 33:D433-437

Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C (2009) STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 37:D412–D416

Roy A, Kucukural A, Zhang Y (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 5:725–738

David E, Kim D, Chivian, Baker D (2004) Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res 32(Web Server issue): W526–W531. https://doi.org/10.1093/nar/gkh468

Wu S, Skolnick J, Zhang Y (2007) Ab initio modelling of small proteins by iterative TASSER simulations. BMC Biol 5:17. https://doi.org/10.1186/1741-7007-5-17

Zang Y (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9:40. https://doi.org/10.1186/1471-2105-9-40

DeLano WL (2002) The PyMOL molecular graphics system

Lovell SC, Davis IW, Arendall WB, de Bakker PI, Word JM et al (2003) Structure validation by C-alpha geometry: phi, psi and beta deviation. Proteins 50:437–450

Colovos C, Yeates TO (1993) Verification of protein structures: patterns of non bonded atomic interactions. Protein Sci 2:1511–1519

Wallner B, Elofsson A (2003) Can correct protein models be identified? Protein Sci 12:1073–1086

Holm L, Rosenström P (2010) Dali server: conservation mapping in 3D. Nucl. Acids Res 38:W545-549

Hasegawa H, Holm L (2009) Advances and pitfalls of protein structural alignment. Curr Opin Struct Biol 19:341–348

Sato Y, Antonio B, Namiki N, Takehisa H, Minami H, Kamatsuki K, Sugimoto K, Shimizu Y, Hirochika H, Nagamura Y (2011) RiceXpro: a platform for monitoring gene expression in japonica rice grown under natural field conditions. Nucleic Acids Res 39:D1141–D1148

Sato Y, Takehisa H, Kamatsuki K, Minami H, Namiki N, Ikawa H, Ohyanagi H, Sugimoto K, Antonio B, Nagamura Y (2013) RiceXPro Version 3.0: expanding the informatics resource for rice transcriptome. Nucleic Acids Res 41:D1206–D1213

Weinstein JN et al (1994) Predictive statistics and artificial intelligence in the U.S. National cancer institute’s drug discovery program for cancer and AIDS. Stem Cells 12:13–22

Weinstein JN, Myers TG, O’Connor PM, Friend SH, Fornace AJ Jr, Kohn KW, Fojo T, Bates SE, Rubinstein LV, Anderson NL, Buolamwini JK, van Osdol WW, Monks AP, Scudiero DA, Sausville EA, Zaharevitz DW, Bunow B, Viswanadhan VN, Johnson GS, Wittes RE, Paull KD (1997) An information intensive approach to the molecular pharmacology of cancer. Science 17:343–349

Cristobal S, Zemla A, Fischer D, Rychlewski L, Elofsson A (2001) A study of quality measures for protein threading models. BMC Bioinformatics 2(1):5

Belouchi A, Kwan T, Gros P (1997) Cloning and characterization of the OsNRAMP family from Oryza sativa, a new family of membrane proteins possibly implicated in the transport of metal ions. Plant Mol Bio 33(6):1085–1092

Courville P et al (2008) Solute carrier 11 cation symport requires distinct residues in transmembrane helices 1 and 6. J Biol Chem 283:9651–9658

Haemig HA, Brooker RJ (2004) Importance of conserved acidic residues in mntH, the Nramp homolog of Escherichia coli. J Membr Biol 201:97–107

Ehrnstorfer IA, Manatschal C, Arnold FM, Laederach J, Dutzler R (2017) Structural and mechanistic basis of proton-coupled metal ion transport in the SLC11/NRAMP family. Nat Commun 8:14033. https://doi.org/10.1038/ncomms14033