Erratum to: Genome-wide exploration of silicon (Si) transporter genes, Lsi1 and Lsi2 in plants; insights into Si-accumulation status/capacity of plants (BioMetals, (2017), 30, 2, (185-200), 10.1007/s10534-017-9992-2);Genome-wide exploration of silicon (Si) transporter genes, Lsi1 and Lsi2 in plants; insights into Si-accumulation status/capacity of plants

BioMetals

Volumn 30, Issue 2, 2017, Pages 185-200

  Vatansever, Recep ^a   Ozyigit, Ibrahim Ilker ^a   Filiz, Ertugrul ^b   Gozukara, Nermin ^c  

^a MARMARA UNIVERSITY   (Turkey)

^b DUZCE UNIVERSITY   (Turkey)

^c ISTANBUL UNIVERSITY   (Turkey)

Author keywords

Accumulator; ar R Selectivity filter; Motifs; Perturbation; Silicic acid

Indexed keywords

CARRIER PROTEIN; CITRATE-BINDING TRANSPORT PROTEIN; PLANT PROTEIN; SILICON;

ADAPTATION; ALPHA HELIX; AMINO ACID SEQUENCE; BETA SHEET; CHEMISTRY; CLASSIFICATION; GENETICS; METABOLISM; MOLECULAR MODEL; PHYLOGENY; PHYSIOLOGICAL STRESS; PLANT; PLANT GENOME; PLANT ROOT; PROTEIN DOMAIN; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; TRANSPORT AT THE CELLULAR LEVEL;

ADAPTATION, PHYSIOLOGICAL; AMINO ACID SEQUENCE; BIOLOGICAL TRANSPORT; CARRIER PROTEINS; GENOME, PLANT; MODELS, MOLECULAR; PHYLOGENY; PLANT PROTEINS; PLANT ROOTS; PLANTS; PROTEIN CONFORMATION, ALPHA-HELICAL; PROTEIN CONFORMATION, BETA-STRAND; PROTEIN DOMAINS; PROTEIN INTERACTION DOMAINS AND MOTIFS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SILICON; SPECIES SPECIFICITY; STRESS, PHYSIOLOGICAL;

EID: 85010712183     PISSN: 09660844     EISSN: 15728773     Source Type: Journal    
DOI: 10.1007/s10534-017-9995-z     Document Type: Erratum

References (56)

1. Ashraf MA, Morshed MM, Ahammad AS, Morshed MN (2013) Computational study of silicon transporter protein in rice and wheat. Int J Comput Bioinform Silico Model 2:199–205
2. Bernsel A, Viklund H, Falk J, Lindahl E, von Heijne G, Elofsson A (2008) Prediction of membrane-protein topology from first principles. Proc Natl Acad Sci 105:7177–7181 DOI: 10.1073/pnas.0711151105
3. Bienert G, Chaumont F (2011) Plant aquaporins: roles in water homeostasis, nutrition, and signaling processes. In: Geisler M, Venema K (eds) Transporters and pumps in plant signaling processes. Springer, Berlin, pp 3–36 DOI: 10.1007/978-3-642-14369-4_1
4. Brodersen P, Petersen M, Bjørn Nielsen H et al (2006) Arabidopsis MAP kinase 4 regulates salicylic acid-and jasmonic acid/ethylene-dependent responses via EDS1 and PAD4. Plant J 47:532–546 DOI: 10.1111/j.1365-313X.2006.02806.x
5. Chiba Y, Mitani N, Yamaji N, Ma JF (2009) HvLsi1 is a silicon influx transporter in barley. Plant J 57:810–818 DOI: 10.1111/j.1365-313X.2008.03728.x
6. DeLano WL (2002) The PyMOL molecular graphics system. DeLano Scientific, San Carlos
7. Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, Liang J (2006) CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucl Acids Res 34:W116–W118 DOI: 10.1093/nar/gkl282
8. Eastmond PJ, Li Y, Graham IA (2003) Is trehalose-6-phosphate a regulator of sugar metabolism in plants? J Exp Bot 54:533–537 DOI: 10.1093/jxb/erg039
9. Facchini PJ, Bird DA, St-Pierre B (2004) Can Arabidopsis make complex alkaloids? Trends Plant Sci 9:116–122 DOI: 10.1016/j.tplants.2004.01.004
10. Fauteux F, Rémus-Borel W, Menzies JG, Bélanger RR (2005) Silicon and plant disease resistance against pathogenic fungi. FEMS Microbiol Lett 249:1–6 DOI: 10.1016/j.femsle.2005.06.034
11. Feng J, Shi Q, Wang X, Wei M, Yang F, Xu H (2010) Silicon supplementation ameliorated the inhibition of photosynthesis and nitrate metabolism by cadmium (Cd) toxicity in Cucumis sativus L. Sci Hortic Amst 123:521–530 DOI: 10.1016/j.scienta.2009.10.013
12. Forrest KL, Bhave M (2007) Major intrinsic proteins (MIPs) in plants: a complex gene family with major impacts on plant phenotype. Func Integr Genom 7:263–289 DOI: 10.1007/s10142-007-0049-4
13. Franceschini A, Szklarczyk D, Frankild S et al (2013) STRING v9. 1: protein-protein interaction networks, with increased coverage and integration. Nucl Acids Res 41:D808–D815 DOI: 10.1093/nar/gks1094
14. Fu D, Libson A, Miercke LJ, Weitzman C, Nollert P, Krucinski J, Stroud RM (2000) Structure of a glycerol conducting channel and the basis for its selectivity. Science 290:481–486 DOI: 10.1126/science.290.5491.481
15. 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 DOI: 10.1385/1-59259-890-0:571
16. Geourjon C, Deleage G (1995) SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Comput Appl Biosci 11:681–684
17. Goodstein DM, Shu S, Howson R et al (2012) Phytozome: a comparative platform for green plant genomics. Nucl Acids Res 40:D1178–D1186 DOI: 10.1093/nar/gkr944
18. Guo AY, Zhu QH, Chen X, Luo JC (2007) [GSDS: a gene structure display server]. Yi chuan = Hereditas/Zhongguo yi chuan xue hui bian ji 29:1023–1026 DOI: 10.1360/yc-007-1023
19. Harries WE, Akhavan D, Miercke LJ, Khademi S, Stroud RM (2004) The channel architecture of aquaporin 0 at a 2.2 Å resolution. Proc Natl Acad Sci 101:14045–14050 DOI: 10.1073/pnas.0405274101
20. Hruz T, Laule O, Szabo G et al (2008) Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. Adv Bioinform 2008:420747 DOI: 10.1155/2008/420747
21. Ilan B, Tajkhorshid E, Schulten K, Voth GA (2004) The mechanism of proton exclusion in aquaporin channels. Proteins 55:223–228 DOI: 10.1002/prot.20038
22. Jia-Wen WU, Yu SHI, Yong-Xing ZHU, Yi-Chao WA, Hai-Jun GO (2013) Mechanisms of enhanced heavy metal tolerance in plants by silicon: a review. Pedosphere 23:815–825 DOI: 10.1016/S1002-0160(13)60073-9
23. Kelley LA, Sternberg MJ (2009) Protein structure prediction on the web: a case study using the Phyre server. Nat Protoc 4:363–371 DOI: 10.1038/nprot.2009.2
24. Kim YH, Khan AL, Kim DH et al (2014) Silicon mitigates heavy metal stress by regulating P-type heavy metal ATPases, Oryza sativa low silicon genes, and endogenous phytohormones. BMC Plant Biol 14:13 DOI: 10.1186/1471-2229-14-13
25. Kliebenstein DJ (2012) Plant defense compounds: systems approaches to metabolic analysis. Annu Rev Phytopathol 50:155–173 DOI: 10.1146/annurev-phyto-081211-172950
26. Krogh A, Larsson B, Von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305:567–580 DOI: 10.1006/jmbi.2000.4315
27. Lovell SC, Davis IW, Arendall WB et al (2003) Structure validation by Cα geometry: ϕ, ψ and Cβ deviation. Proteins 50:437–450 DOI: 10.1002/prot.10286
28. Lunn JE, Delorge I, Figueroa CM, Van Dijck P, Stitt M (2014) Trehalose metabolism in plants. Plant J 79:544–567 DOI: 10.1111/tpj.12509
29. Lux A, Luxová M, Hattori T, Inanaga S, Sugimoto Y (2002) Silicification in sorghum (Sorghum bicolor) cultivars with different drought tolerance. Physiol Plant 115:87–92 DOI: 10.1034/j.1399-3054.2002.1150110.x
30. Ma JF (2004) Role of silicon in enhancing the resistance of plants to biotic and abiotic stresses. Soil Sci Plant Nutr 50:11–18 DOI: 10.1080/00380768.2004.10408447
31. Ma JF (2010) Si transporters in higher plant. In: Jhon PT, Bienert PG (eds) MIPs and their role in the exchange of materials. Landes Bioscience, Austin, pp 99–109 DOI: 10.1007/978-1-4419-6315-4_8
32. Ma JF, Yamaji N (2006) Silicon uptake and accumulation in higher plants. Trends Plant Sci 11:392–397 DOI: 10.1016/j.tplants.2006.06.007
33. Ma JF, Yamaji N (2008) Functions and transport of silicon in plants. Cell Mol Life Sci 65:3049–3057 DOI: 10.1007/s00018-008-7580-x
34. Ma JF, Tamai K, Yamaji N, Mitani N, Konishi S, Katsuhara M, Ishiguro M, Murata Y, Yano M (2006) A silicon transporter in rice. Nature 440:688–691 DOI: 10.1038/nature04590
35. Ma JF, Yamaji N, Mitani N, Kazunori T, Konishi S, Fujiwara T, Katsuhara M, Yano M (2007) An efflux transporter of silicon in rice. Nature 448:209–212 DOI: 10.1038/nature05964
36. Marchler-Bauer A, Lu S, Anderson JB et al (2011) CDD: a conserved domain database for the functional annotation of proteins. Nucl Acids Res 39:D225–D229 DOI: 10.1093/nar/gkq1189
37. Mitani N, Yamaji N, Ma JF (2008) Characterization of substrate specificity of a rice silicon transporter, Lsi1. Pflüger Arch Eur J Phy 456:679–686 DOI: 10.1007/s00424-007-0408-y
38. Mitani N, Chiba Y, Yamaji N, Ma JF (2009a) Identification and characterization of maize and barley Lsi2-like silicon efflux transporters reveals a distinct silicon uptake system from that in rice. Plant Cell 21:2133–2142 DOI: 10.1105/tpc.109.067884
39. Mitani N, Yamaji N, Ma JF (2009b) Identification of maize silicon influx transporters. Plant Cell Physiol 50:5–12 DOI: 10.1093/pcp/pcn110
40. Mitani N, Yamaji N, Ago Y, Iwasaki K, Ma JF (2011) Isolation and functional characterization of an influx silicon transporter in two pumpkin cultivars contrasting in silicon accumulation. Plant J 66:231–240 DOI: 10.1111/j.1365-313X.2011.04483.x
41. Mitani-Ueno N, Yamaji N, Zhao FJ, Ma JF (2011) The aromatic/arginine selectivity filter of NIP aquaporins plays a critical role in substrate selectivity for silicon, boron, and arsenic. J Exp Bot 62:4391–4398 DOI: 10.1093/jxb/err158
42. Mithöfer A, Boland W (2012) Plant defense against herbivores: chemical aspects. Annu Rev Plant Biol 63:431–450 DOI: 10.1146/annurev-arplant-042110-103854
43. Montpetit J, Vivancos J, Mitani-Ueno N et al (2012) Cloning, functional characterization and heterologous expression of TaLsi1, a wheat silicon transporter gene. Plant Mol Biol 79:35–46 DOI: 10.1007/s11103-012-9892-3
44. Romiti M (2010) Entrez nucleotide and entrez protein FAQs. Gene 1:270
45. Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27:431–432 DOI: 10.1093/bioinformatics/btq675
46. Sonnhammer EL, Eddy SR, Durbin R (1997) Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 28:405–420 DOI: 10.1002/(SICI)1097-0134(199707)28:3<405::AID-PROT10>3.0.CO;2-L
47. Sui H, Han BG, Lee JK, Walian P, Jap BK (2001) Structural basis of water-specific transport through the AQP1 water channel. Nature 414:872–878 DOI: 10.1038/414872a
48. Tamai K, Ma JF (2003) Characterization of silicon uptake by rice roots. New Phytol 158:431–436 DOI: 10.1046/j.1469-8137.2003.00773.x
49. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729 DOI: 10.1093/molbev/mst197
50. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res 22:4673–4680 DOI: 10.1093/nar/22.22.4673
51. Timothy TL, Bodén BM, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009) MEME SUITE: tools for motif discovery and searching. Nucl Acids Res 37:202–208 DOI: 10.1093/nar/gkp335
52. Wallace IS, Roberts DM (2004) Homology modeling of representative subfamilies of Arabidopsis major intrinsic proteins. Classification based on the aromatic/arginine selectivity filter. Plant Physiol 135:1059–1068 DOI: 10.1104/pp.103.033415
53. Wu B, Beitz E (2007) Aquaporins with selectivity for unconventional permeants. Cell Mol Life Sci 64:2413–2421 DOI: 10.1007/s00018-007-7163-2
54. Yu CS, Chen YC, Lu CH, Hwang JK (2006) Prediction of protein subcellular localization. Proteins 64:643–651 DOI: 10.1002/prot.21018
55. Zhang C, Wang L, Nie Q, Zhang W, Zhang F (2008) Long-term effects of exogenous silicon on cadmium translocation and toxicity in rice (Oryza sativa L.). Environ Exp Bot 62:300–307 DOI: 10.1016/j.envexpbot.2007.10.024
56. Zhu Y, Gong H (2014) Beneficial effects of silicon on salt and drought tolerance in plants. Agron Sustain Dev 34:455–472 DOI: 10.1007/s13593-013-0194-1