Arsenic and cadmium are inhibitors of cyanobacterial dinitrogenase reductase (nifH1) gene

Functional and Integrative Genomics

Volumn 14, Issue 3, 2014, Pages 571-580

  Singh, Shilpi ^a,b   Shrivastava, A K ^a,b   Singh, V K ^a  

^a BANARAS HINDU UNIVERSITY   (India)

^b SHOBHIT UNIVERSITY   (India)

Author keywords

Anabaena sp. PCC7120; Docking; Homology modelling; nifH1; Promoter; qRT PCR

Indexed keywords

ARSENIC; BACTERIAL PROTEIN; CADMIUM; COPPER; DINITROGENASE REDUCTASE; GLUTAMATE AMMONIA LIGASE; GLUTAMATE DEHYDROGENASE; NICOTINAMIDE ADENINE DINUCLEOTIDE SYNTHASE; NIRA PROTEIN; NITROGEN FIXATION PROTEIN; SODIUM; SYNTHETASE; UNCLASSIFIED DRUG;

ANABAENA; ARTICLE; BINDING SITE; CONTROLLED STUDY; DINITROGENASE REDUCTASE GENE; ENZYME INHIBITION; GENE FUNCTION; MOLECULAR DOCKING; NITROGEN FIXATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; REAL TIME POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; STRUCTURAL HOMOLOGY; BIOSYNTHESIS; CHEMICAL STRUCTURE; CHEMISTRY; DRUG EFFECTS; ENZYMOLOGY; GENE EXPRESSION; GENETICS; PHYLOGENY; PROMOTER REGION;

ANABAENA; ARSENIC; BACTERIAL PROTEINS; CADMIUM; DINITROGENASE REDUCTASE; GENE EXPRESSION; MODELS, MOLECULAR; NITROGEN FIXATION; PHYLOGENY; PROMOTER REGIONS, GENETIC; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 84906317010     PISSN: 1438793X     EISSN: 14387948     Source Type: Journal    
DOI: 10.1007/s10142-014-0375-2     Document Type: Article

References (41)

1. Angove HC, Yoo SJ, Burgess BK, Muinck E (1997) Mossbauer and EPR evidence for an all-ferrous Fe4S4 cluster with S-4 in the Fe protein of nitrogenase. J Am Chem Soc 119:8730-8731
2. Arnott S, Campbell-Smith PJ, Chandrasekaran R (1976) Handbook of biochemistry and molecular biology. In: Fasman GP (ed) Nucleic acids, vol II, 3rd edn. CRC Press, Cleveland, pp 411-422
3. Atri N, Rai LC (2003) Differential responses of three cyanobacteria to UV-B and Cd. J Microbiol Biotech 13:544-551 (Pubitemid 37099003)
4. Benkert P, Tosatto SCE, Schomburg D (2008) QMEAN: a comprehensive scoring function for model quality assessment. Proteins: Struct, Funct, Bioinf 71:261-277 (Pubitemid 351358609)
5. Berjanskii M, Zhou J, Liang Y, Lin G, Wishart DS (2012) Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures. J Biomol NMR 3:167-180
6. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28:235-242 (Pubitemid 30047768)
7. Bhargava P, Mishra Y, Srivastava AK, Narayan OP, Rai LC (2008) Excess copper induces anoxygenic photosynthesis in Anabaena doliolum: a homology based proteomic assessment of its survival strategy. Photosynth Res 96(1):61-74
8. Colovos C, Yeates TO (1993) Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 9:1511-1519 (Pubitemid 23262844)
9. David WR, Vishwesh V (2010) Ultra-fast FFT protein docking on graphics processors. Bioinformatics 26:2398-2405
10. Dean DR, Jacobson MR (1992) Biochemical genetics of nitrogenase. In: Stacey G, Burris RH, Evans HJ (eds) Biological nitrogen fixation. Chapman and Hall, New York, pp 763-834
11. Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy server. In:Walker JM (ed) The proteomics protocols handbook. Humana Press, pp. 571-607
12. Gouy M, Guindon S, Gascuel O (2010) SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27:221-224
13. Hahn M, Meyer L, Studer D, Regensburger B, Hennecke H (1984) Insertion and deletion mutations within the nif region of Rhizobium japonicum. Plant Mol Bio 3:159-168
14. Halbleib CM, Ludden PW (2000) Regulation of biological nitrogen fixation. J Nutr 130:1081-1084 (Pubitemid 30233250)
15. Kallas T, Coursin T, Rippka R (1985) Different organization of nif genes in non-heterocystous and heterocystous cyanobacteria. Plant Mol Biol 5:321-329
16. Kaneko T, Nakamura Y, Wolk CP, Kuritz T, Sasamoto S, Watanabe A, Iriguchi M, Ishikawa A, Kawashima K, Kimura T et al (2001) Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120. DNA Res 8(205-213):227-253
17. Kumari N, Narayan OP, Rai LC (2009) Understanding butachlor toxicity in Aulosira fertilissima using physiological, biochemical and proteomic approaches. Chemosphere 77:1501-1507
18. Laskowski RA (2001) PDBsum: summaries and analyses of PDB structures. Nucleic Acids Res 29:221-222
19. Laurie AT, Jackson RM (2005) Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 21:1908-1916 (Pubitemid 40668026)
20. Leigh W, Anuj R, Haiyan Z, Hassan M, Robert FB, Brian DS, David SW (2003) VADAR: a web server for quantitative evaluation of protein structure quality. Nucleic Acids Res 31:3316-3319
21. Marchler-Bauer A, Zheng C, Chitsaz F, Derbyshire MK, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Lanczycki CJ et al (2013) CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Res 41:348-352
22. Moshe M, Rice D, Haselkorn R (1980) Nucleotide sequence of a cyanobacterial NifH gene coding for nitrogenase reductase. Proc Natl Acad Sci U S A 77:6476-6480 (Pubitemid 11219154)
23. Münch R, Hiller K, Grote A, Scheer M, Klein J, Schobert M, Jahn D (2005) Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. Bioinformatics 21:4187-4189 (Pubitemid 41672111)
24. Oláh B, Kiss E, Györgypál Z, Borzi J, Cinege G, Csanádi G, Batut J, Kondorosi A, Dusha I (2001) Mutation in the ntrR gene, a member of the vap gene family, increases the symbiotic efficiency of Sinorhizobium meliloti. Mol Plant Microbe Interact 14:887-894 (Pubitemid 32575666)
25. Pandey S, Rai R, Rai LC (2012a) Proteomics combines morphological, physiological and biochemical attributes to unravel the survival strategy of Anabaena sp. PCC7120 under arsenic stress. J Prot 75:921-937
26. Pandey S, Shrivastava AK, Singh VK, Rai R, Singh PK, Rai S, Rai LC (2012b) A new arsenate reductase involved in arsenic detoxification in Anabaena sp. PCC7120. Funct Integr Genomic 13:43-55
27. Pandey S, Shrivastava AK, Rai R, Rai LC (2013) Molecular characterization of Alr1105 a novel arsenate reductase of the diazotrophic cyanobacterium Anabaena sp. PCC7120 and decoding its role in abiotic stress management in Escherichia coli. Plant Mol Biol 83:417-432
28. Pau RN (1989) Nitrogenases without molybdenum. Trends Biochem Sci 5:183-186
29. Rai LC, Raizada M (1985) Effect of nickel and silver ions on survival, growth, carbon fixation and nitrogenase activity of Nostoc muscorum: regulation of toxicity by EDTA and calcium. J Gen Appl Microbiol 31:329-337 (Pubitemid 16162221)
30. Rice D, Mazur BJ, Haselkorn R (1982) Isolation and physicalmapping of nitrogen fixation genes from the cyanobacterium Anabaena 7120. J Biol Chem 257:13157-13163
31. Salamov AA, Solovyev VV (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res 10:516-522 (Pubitemid 30259081)
32. Shahi SK, Singh VK, Kumar A, Gupta SK, Singh SK (2013) Interaction of dihydrofolate reductase and aminoglycoside adenyltransferase enzyme from Klebsiella pneumoniae multidrug resistant strain DF12SA with clindamycin: a molecular modelling and docking study. J Mol Model 19:973-983
33. Snel B, Lehmann G, Bork P, Huynen MA (2000) STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res 28:3442-3444
34. Srivastava AK, Bhargava P, Thapar R, Rai LC (2008) Salinity-induced physiological and proteomic changes in Anabaena doliolum. Environ Exp Bot 64:49-57
35. Srivastava AK, Bhargava P, Kumar A, Rai LC, Neilan BA (2009) Molecular characterization of the effect of salinity on cyanobacterial diversity in the rice fields of EasternUttar Pradesh, India. Saline Syst 5:4
36. Stewart WDP, Fipzgerald GP, Burris RH (1968) Acetylene reduction by nitrogen fixing blue-green algae. Arch Microbiol 62:336-348
37. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 8:1596-1599 (Pubitemid 47236692)
38. 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. Nucleic Acids Res 22:4673-4680 (Pubitemid 24354800)
39. Ueda T, Suga Y, Yashiro N, Matsuguchi T (1995) Remarkable N 2-fixing bacterial diversity detected in rice roots by molecular evolutionary analysis of NifH gene sequences. J Bacteriol 177:1414-1417
40. Weinman JJ, Fellows FF, Gresshoff PM, Shine J, Scott KF (1984) Structural analysis of the genes encoding the molybdenum-iron protein of nitrogenase in the Parasponia rhizobium strain ANU289. Nucleic Acids Res 12:8329-8344
41. Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35:407-410