1887

Abstract

The genome contains a cluster of genes that are predicted to encode Fe–S cluster assembly proteins, and this cluster is known as the operon. is the first gene in the operon, and it was inactivated to determine its physiological function. The mutant exhibited a small colony phenotype, grew slower than the wild-type strain and was more sensitive to various oxidants including peroxide, organic hydroperoxide and superoxide. The gene was negatively regulated by iron response regulator (Irr) and rhizobial iron regulator (RirA) under low and high iron conditions, respectively, and was inducible in response to oxidative stress. The oxidant-induced expression of was controlled by Irr, RirA and an additional but not yet identified mechanism. was required for RirA activity in the repression of a promoter- fusion. RirA may use Fe–S as its cofactor. disruption may cause a defect in the Fe–S supply and could thereby affect the RirA activity. The three conserved cysteine residues (C91, C99 and C105) in RirA were predicted to coordinate with the Fe–S cluster and were shown to be essential for RirA repression of the - fusion. These results suggested that is important for the survival of .

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2014-01-01
2019-10-17
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References

  1. Alexeyev M. F. . ( 1999; ). The pKNOCK series of broad-host-range mobilizable suicide vectors for gene knockout and targeted DNA insertion into the chromosome of gram-negative bacteria. . Biotechniques 26:, 824–826, 828.[PubMed]
    [Google Scholar]
  2. Ayala-Castro C. , Saini A. , Outten F. W. . ( 2008; ). Fe-S cluster assembly pathways in bacteria. . Microbiol Mol Biol Rev 72:, 110–125. [CrossRef]
    [Google Scholar]
  3. Beaumont H. J. , Lens S. I. , Reijnders W. N. , Westerhoff H. V. , van Spanning R. J. . ( 2004; ). Expression of nitrite reductase in Nitrosomonas europaea involves NsrR, a novel nitrite-sensitive transcription repressor. . Mol Microbiol 54:, 148–158. [CrossRef] [PubMed]
    [Google Scholar]
  4. Behshad E. , Parkin S. E. , Bollinger J. M. Jr . ( 2004; ). Mechanism of cysteine desulfurase Slr0387 from Synechocystis sp. PCC 6803: kinetic analysis of cleavage of the persulfide intermediate by chemical reductants. . Biochemistry 43:, 12220–12226. [CrossRef] [PubMed]
    [Google Scholar]
  5. Bhubhanil S. , Ruangkiattikul N. , Niamyim P. , Chamsing J. , Ngok-Ngam P. , Sukchawalit R. , Mongkolsuk S. . ( 2012; ). Identification of amino acid residues important for the function of Agrobacterium tumefaciens Irr protein. . FEMS Microbiol Lett 335:, 68–77. [CrossRef] [PubMed]
    [Google Scholar]
  6. Cangelosi G. A. , Best E. A. , Martinetti G. , Nester E. W. . ( 1991; ). Genetic analysis of Agrobacterium. . Methods Enzymol 204:, 384–397. [CrossRef] [PubMed]
    [Google Scholar]
  7. Chuchue T. , Tanboon W. , Prapagdee B. , Dubbs J. M. , Vattanaviboon P. , Mongkolsuk S. . ( 2006; ). ohrR and ohr are the primary sensor/regulator and protective genes against organic hydroperoxide stress in Agrobacterium tumefaciens. . J Bacteriol 188:, 842–851. [CrossRef] [PubMed]
    [Google Scholar]
  8. Crack J. C. , Green J. , Thomson A. J. , Le Brun N. E. . ( 2012; ). Iron-sulfur cluster sensor-regulators. . Curr Opin Chem Biol 16:, 35–44. [CrossRef] [PubMed]
    [Google Scholar]
  9. Cupp-Vickery J. R. , Urbina H. , Vickery L. E. . ( 2003; ). Crystal structure of IscS, a cysteine desulfurase from Escherichia coli. . J Mol Biol 330:, 1049–1059. [CrossRef] [PubMed]
    [Google Scholar]
  10. DeFeyter R. , Kado C. I. , Gabriel D. W. . ( 1990; ). Small, stable shuttle vectors for use in Xanthomonas. . Gene 88:, 65–72. [CrossRef] [PubMed]
    [Google Scholar]
  11. Eiamphungporn W. , Charoenlap N. , Vattanaviboon P. , Mongkolsuk S. . ( 2006; ). Agrobacterium tumefaciens soxR is involved in superoxide stress protection and also directly regulates superoxide-inducible expression of itself and a target gene. . J Bacteriol 188:, 8669–8673. [CrossRef] [PubMed]
    [Google Scholar]
  12. Giel J. L. , Nesbit A. D. , Mettert E. L. , Fleischhacker A. S. , Wanta B. T. , Kiley P. J. . ( 2013; ). Regulation of iron–sulphur cluster homeostasis through transcriptional control of the Isc pathway by [2Fe-2S]-IscR in Escherichia coli. . Mol Microbiol 87:, 478–492. [CrossRef] [PubMed]
    [Google Scholar]
  13. Grant S. G. , Jessee J. , Bloom F. R. , Hanahan D. . ( 1990; ). Differential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants. . Proc Natl Acad Sci U S A 87:, 4645–4649. [CrossRef] [PubMed]
    [Google Scholar]
  14. Hibbing M. E. , Fuqua C. . ( 2011; ). Antiparallel and interlinked control of cellular iron levels by the Irr and RirA regulators of Agrobacterium tumefaciens. . J Bacteriol 193:, 3461–3472. [CrossRef] [PubMed]
    [Google Scholar]
  15. Jacobson M. R. , Brigle K. E. , Bennett L. T. , Setterquist R. A. , Wilson M. S. , Cash V. L. , Beynon J. , Newton W. E. , Dean D. R. . ( 1989a; ). Physical and genetic map of the major nif gene cluster from Azotobacter vinelandii. . J Bacteriol 171:, 1017–1027.[PubMed]
    [Google Scholar]
  16. Jacobson M. R. , Cash V. L. , Weiss M. C. , Laird N. F. , Newton W. E. , Dean D. R. . ( 1989b; ). Biochemical and genetic analysis of the nifUSVWZM cluster from Azotobacter vinelandii. . Mol Gen Genet 219:, 49–57. [CrossRef] [PubMed]
    [Google Scholar]
  17. Jang S. , Imlay J. A. . ( 2010; ). Hydrogen peroxide inactivates the Escherichia coli Isc iron–sulphur assembly system, and OxyR induces the Suf system to compensate. . Mol Microbiol 78:, 1448–1467. [CrossRef] [PubMed]
    [Google Scholar]
  18. Johnson D. C. , Dean D. R. , Smith A. D. , Johnson M. K. . ( 2005; ). Structure, function, and formation of biological iron-sulfur clusters. . Annu Rev Biochem 74:, 247–281. [CrossRef] [PubMed]
    [Google Scholar]
  19. Kitphati W. , Ngok-Ngam P. , Suwanmaneerat S. , Sukchawalit R. , Mongkolsuk S. . ( 2007; ). Agrobacterium tumefaciens fur has important physiological roles in iron and manganese homeostasis, the oxidative stress response, and full virulence. . Appl Environ Microbiol 73:, 4760–4768. [CrossRef] [PubMed]
    [Google Scholar]
  20. Kovach M. E. , Elzer P. H. , Hill D. S. , Robertson G. T. , Farris M. A. , Roop R. M. II , Peterson K. M. . ( 1995; ). Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. . Gene 166:, 175–176. [CrossRef] [PubMed]
    [Google Scholar]
  21. Lauhon C. T. , Kambampati R. . ( 2000; ). The iscS gene in Escherichia coli is required for the biosynthesis of 4-thiouridine, thiamin, and NAD. . J Biol Chem 275:, 20096–20103. [CrossRef] [PubMed]
    [Google Scholar]
  22. Lee J. H. , Yeo W. S. , Roe J. H. . ( 2004; ). Induction of the sufA operon encoding Fe-S assembly proteins by superoxide generators and hydrogen peroxide: involvement of OxyR, IHF and an unidentified oxidant-responsive factor. . Mol Microbiol 51:, 1745–1755. [CrossRef] [PubMed]
    [Google Scholar]
  23. Lee K. C. , Yeo W. S. , Roe J. H. . ( 2008; ). Oxidant-responsive induction of the suf operon, encoding a Fe-S assembly system, through Fur and IscR in Escherichia coli. . J Bacteriol 190:, 8244–8247. [CrossRef] [PubMed]
    [Google Scholar]
  24. Livak K. J. , Schmittgen T. D. . ( 2001; ). Analysis of relative gene expression data using real-time quantitative PCR and the 2(-ΔΔCT) Method. . Methods 25:, 402–408. [CrossRef] [PubMed]
    [Google Scholar]
  25. Luo Z. Q. , Clemente T. E. , Farrand S. K. . ( 2001; ). Construction of a derivative of Agrobacterium tumefaciens C58 that does not mutate to tetracycline resistance. . Mol Plant Microbe Interact 14:, 98–103. [CrossRef] [PubMed]
    [Google Scholar]
  26. Metcalf W. W. , Jiang W. , Daniels L. L. , Kim S. K. , Haldimann A. , Wanner B. L. . ( 1996; ). Conditionally replicative and conjugative plasmids carrying lacZ alpha for cloning, mutagenesis, and allele replacement in bacteria. . Plasmid 35:, 1–13. [CrossRef] [PubMed]
    [Google Scholar]
  27. Mihara H. , Esaki N. . ( 2002; ). Bacterial cysteine desulfurases: their function and mechanisms. . Appl Microbiol Biotechnol 60:, 12–23. [CrossRef] [PubMed]
    [Google Scholar]
  28. Miller J. H. . ( 1972; ). Experiments in Molecular Genetics. Cold Spring Harbor, NY:: Cold Spring Harbor Laboratory Press;.
    [Google Scholar]
  29. Nakjarung K. , Mongkolsuk S. , Vattanaviboon P. . ( 2003; ). The oxyR from Agrobacterium tumefaciens: evaluation of its role in the regulation of catalase and peroxide responses. . Biochem Biophys Res Commun 304:, 41–47. [CrossRef] [PubMed]
    [Google Scholar]
  30. Ngok-Ngam P. , Ruangkiattikul N. , Mahavihakanont A. , Virgem S. S. , Sukchawalit R. , Mongkolsuk S. . ( 2009; ). Roles of Agrobacterium tumefaciens RirA in iron regulation, oxidative stress response, and virulence. . J Bacteriol 191:, 2083–2090. [CrossRef] [PubMed]
    [Google Scholar]
  31. Outten F. W. , Djaman O. , Storz G. . ( 2004; ). A suf operon requirement for Fe-S cluster assembly during iron starvation in Escherichia coli. . Mol Microbiol 52:, 861–872. [CrossRef] [PubMed]
    [Google Scholar]
  32. Patzer S. I. , Hantke K. . ( 1999; ). SufS is a NifS-like protein, and SufD is necessary for stability of the [2Fe-2S] FhuF protein in Escherichia coli. . J Bacteriol 181:, 3307–3309.[PubMed]
    [Google Scholar]
  33. Roche B. , Aussel L. , Ezraty B. , Mandin P. , Py B. , Barras F. . ( 2013; ). Iron/sulfur proteins biogenesis in prokaryotes: formation, regulation and diversity. . Biochim Biophys Acta 1827:, 455–469. [CrossRef] [PubMed]
    [Google Scholar]
  34. Rodionov D. A. , Gelfand M. S. , Todd J. D. , Curson A. R. , Johnston A. W. . ( 2006; ). Computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria. . PLOS Comput Biol 2:, e163. [CrossRef] [PubMed]
    [Google Scholar]
  35. Ruangkiattikul N. , Bhubhanil S. , Chamsing J. , Niamyim P. , Sukchawalit R. , Mongkolsuk S. . ( 2012; ). Agrobacterium tumefaciens membrane-bound ferritin plays a role in protection against hydrogen peroxide toxicity and is negatively regulated by the iron response regulator. . FEMS Microbiol Lett 329:, 87–92. [CrossRef] [PubMed]
    [Google Scholar]
  36. Saenkham P. , Eiamphungporn W. , Farrand S. K. , Vattanaviboon P. , Mongkolsuk S. . ( 2007; ). Multiple superoxide dismutases in Agrobacterium tumefaciens: functional analysis, gene regulation, and influence on tumorigenesis. . J Bacteriol 189:, 8807–8817. [CrossRef] [PubMed]
    [Google Scholar]
  37. Sambrook J. , Fritsch E. F. , Maniatis T. . ( 1989; ). Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY:: Cold Spring Harbor Laboratory Press;.
    [Google Scholar]
  38. Schwartz C. J. , Djaman O. , Imlay J. A. , Kiley P. J. . ( 2000; ). The cysteine desulfurase, IscS, has a major role in in vivo Fe-S cluster formation in Escherichia coli. . Proc Natl Acad Sci U S A 97:, 9009–9014. [CrossRef] [PubMed]
    [Google Scholar]
  39. Schwartz C. J. , Giel J. L. , Patschkowski T. , Luther C. , Ruzicka F. J. , Beinert H. , Kiley P. J. . ( 2001; ). IscR, an Fe-S cluster-containing transcription factor, represses expression of Escherichia coli genes encoding Fe-S cluster assembly proteins. . Proc Natl Acad Sci U S A 98:, 14895–14900. [CrossRef] [PubMed]
    [Google Scholar]
  40. Skovran E. , Downs D. M. . ( 2000; ). Metabolic defects caused by mutations in the isc gene cluster in Salmonella enterica serovar typhimurium: implications for thiamine synthesis. . J Bacteriol 182:, 3896–3903. [CrossRef] [PubMed]
    [Google Scholar]
  41. Sun D. , Setlow P. . ( 1993; ). Cloning, nucleotide sequence, and regulation of the Bacillus subtilis nadB gene and a nifS-like gene, both of which are essential for NAD biosynthesis. . J Bacteriol 175:, 1423–1432.[PubMed]
    [Google Scholar]
  42. Takahashi Y. , Nakamura M. . ( 1999; ). Functional assignment of the ORF2-iscS-iscU-iscA-hscB-hscA-fdx-ORF3 gene cluster involved in the assembly of Fe-S clusters in Escherichia coli. . J Biochem 126:, 917–926. [CrossRef] [PubMed]
    [Google Scholar]
  43. Tirupati B. , Vey J. L. , Drennan C. L. , Bollinger J. M. Jr . ( 2004; ). Kinetic and structural characterization of Slr0077/SufS, the essential cysteine desulfurase from Synechocystis sp. PCC 6803. . Biochemistry 43:, 12210–12219. [CrossRef] [PubMed]
    [Google Scholar]
  44. Todd J. D. , Sawers G. , Rodionov D. A. , Johnston A. W. . ( 2006; ). The Rhizobium leguminosarum regulator IrrA affects the transcription of a wide range of genes in response to Fe availability. . Mol Genet Genomics 275:, 564–577. [CrossRef] [PubMed]
    [Google Scholar]
  45. Wojtaszek P. . ( 1997; ). Oxidative burst: an early plant response to pathogen infection. . Biochem J 322:, 681–692.[PubMed]
    [Google Scholar]
  46. Wood D. W. , Setubal J. C. , Kaul R. , Monks D. E. , Kitajima J. P. , Okura V. K. , Zhou Y. , Chen L. , Wood G. E. . & other authors ( 2001; ). The genome of the natural genetic engineer Agrobacterium tumefaciens C58. . Science 294:, 2317–2323. [CrossRef] [PubMed]
    [Google Scholar]
  47. Yang J. , Panek H. R. , O’Brian M. R. . ( 2006; ). Oxidative stress promotes degradation of the Irr protein to regulate haem biosynthesis in Bradyrhizobium japonicum. . Mol Microbiol 60:, 209–218. [CrossRef] [PubMed]
    [Google Scholar]
  48. Yeo W. S. , Lee J. H. , Lee K. C. , Roe J. H. . ( 2006; ). IscR acts as an activator in response to oxidative stress for the suf operon encoding Fe-S assembly proteins. . Mol Microbiol 61:, 206–218. [CrossRef] [PubMed]
    [Google Scholar]
  49. Zheng L. , Cash V. L. , Flint D. H. , Dean D. R. . ( 1998; ). Assembly of iron-sulfur clusters. Identification of an iscSUA-hscBA-fdx gene cluster from Azotobacter vinelandii. . J Biol Chem 273:, 13264–13272. [CrossRef] [PubMed]
    [Google Scholar]
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