The phrA gene of Rhodobacter sphaeroides encodes a photolyase and is regulated by singlet oxygen and peroxide in a σ E-dependent manner

References

1. Anthony J. R., Newman J. D., Donohue T. J. 2004; Interactions between the Rhodobacter sphaeroides ECF sigma factor, σ ^E, and its anti-sigma factor, ChrR. J Mol Biol 341:345–360 [CrossRef]
   [Google Scholar]
2. Anthony J. R., Warczak K. L., Donohue T. J. 2005; A transcriptional response to singlet oxygen, a toxic byproduct of photosynthesis. Proc Natl Acad Sci U S A 102:6502–6507 [CrossRef]
   [Google Scholar]
3. Berrocal-Tito G., Sametz-Baron L., Eichenberg K., Horwitz B. A., Herrera-Estrella A. 1999; Rapid blue light regulation of a Trichoderma harzianum photolyase gene. J Biol Chem 274:14288–14294 [CrossRef]
   [Google Scholar]
4. Borland C. F., McGarvey D. J., Truscott T. G., Cogdell R. J., Land E. J. 1987; Photophysical studies of bacteriochlorophyll a and bacteriopheophytin a – singlet oxygen generation. J Photochem Photobiol B 1:93–101 [CrossRef]
   [Google Scholar]
5. Borland C. F., Cogdell R. J., Land E. J., Truscott T. G. 1989; Bacteriochlorophyll a triplet state and its interactions with bacterial carotenoids and oxygen. J Photochem Photobiol B 3:237–245 [CrossRef]
   [Google Scholar]
6. Braatsch S., Klug G. 2004; ORF90, a gene required for photoreactivation in Rhodobacter capsulatus SB1003 encodes a cyclobutane pyrimidine dimer photolyase. Photosynth Res 79:167–177 [CrossRef]
   [Google Scholar]
7. Braatsch S., Gomelsky M., Kuphal S., Klug G. 2002; A single flavoprotein, AppA, integrates both redox and light signals in Rhodobacter sphaeroides. Mol Microbiol 45:827–836 [CrossRef]
   [Google Scholar]
8. Braatsch S., Moskvin O. V., Klug G., Gomelsky M. 2004; Responses of the Rhodobacter sphaeroides transcriptome to blue light under semiaerobic conditions. J Bacteriol 186:7726–7735 [CrossRef]
   [Google Scholar]
9. Brudler R., Hitomi K., Daiyasu H., Toh H., Kucho K., Ishiura M., Kanehisa M., Roberts V. A., Todo T. other authors 2003; Identification of a new cryptochrome class: structure, function and evolution. Mol Cell 11:59–67 [CrossRef]
   [Google Scholar]
10. Byrdin M., Eker A. P., Vos M. H., Brettel K. 2003; Dissection of the triple tryptophan electron transfer chain in Escherichia coli DNA photolyase: Trp382 is the primary donor in photoactivation. Proc Natl Acad Sci U S A 100:8676–8681 [CrossRef]
    [Google Scholar]
11. Casadaban M. J., Chou J., Cohen S. N. 1980; In vitro gene fusions that join an enzymatically active β -galactosidase segment to amino-terminal fragments of exogenous proteins: Escherichia coli plasmid vectors for the detection and cloning of translational initiation signals. J Bacteriol 143:971–980
    [Google Scholar]
12. Cashmore A. R., Jarillo J. A., Wu Y. J., Liu D. 1999; Cryptochromes: blue light receptors for plants and animals. Science 284:760–765 [CrossRef]
    [Google Scholar]
13. Daiyasu H., Iskikawa T., Kuma K., Iwai S., Todo T., Toh H. 2004; Identification of cryptochrome DASH from vertebrates. Genes Cells 9:479–495 [CrossRef]
    [Google Scholar]
14. Debus R. J., Feher G., Okamura M. Y. 1985; LM complex of reaction centers from Rhodopseudomonas-sphaeroides R-26: characterization and reconstitution with the H-subunit. Biochemistry 24:2488–2500 [CrossRef]
    [Google Scholar]
15. Ditta G., Schmidhauser T., Yakobsen E., Lu P., Liang X. W., Finlay D. R., Guiney D., Helinski D. R. 1985; Plasmids related to the broad host range vector, pRK290, useful for gene cloning and monitoring gene expression. Plasmid 13:149–153 [CrossRef]
    [Google Scholar]
16. Drews G. 1983 Mikrobiologisches Praktikum Heidelberg, Germany: Springer-Verlag;
    [Google Scholar]
17. Fujihashi M., Numoto N., Kobayashi Y., Mizushima A., Tsujimura M., Nakamura A., Kawarabayasi Y., Miki K. 2007; Crystal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules: implication of a novel light-harvesting cofactor. J Mol Biol 365:903–910 [CrossRef]
    [Google Scholar]
18. Glaeser J., Klug G. 2005; Photo-oxidative stress in Rhodobacter sphaeroides : protective role of carotenoids and expression of selected genes. Microbiology 151:1927–1938 [CrossRef]
    [Google Scholar]
19. Happ H. N., Braatsch S., Broschek V., Osterloh L., Klug G. 2005; Light-dependent regulation of photosynthesis genes in Rhodobacter sphaeroides 2.4.1 is coordinately controlled by photosynthetic electron transport via the PrrBA two-component system and the photoreceptor AppA. Mol Microbiol 58:903–914 [CrossRef]
    [Google Scholar]
20. Hu P., Brodie E. L., Suzuki Y., McAdams H. H., Andersen G. L. 2005; Whole-genome transcriptional analysis of heavy metal stresses in Caulobacter crescentus. J Bacteriol 187:8437–8449 [CrossRef]
    [Google Scholar]
21. Hübner P., Willison J. C., Vignais P. M., Bickle T. A. 1991; Expression of regulatory nif genes in Rhodobacter capsulatus. J Bacteriol 173:2993–2999
    [Google Scholar]
22. Hübner P., Masepohl B., Klipp W., Bickle T. A. 1993; nif gene expression studies in Rhodobacter capsulatus : ntrC -independent repression by high ammonium concentrations. Mol Microbiol 10:123–132 [CrossRef]
    [Google Scholar]
23. Kavakli I. H., Sancar A. 2004; Analysis of the role of intraprotein electron transfer in photoreactivation by DNA photolyase in vivo. Biochemistry 43:15103–15110 [CrossRef]
    [Google Scholar]
24. Keen N. T., Tamaki S., Kobayashi D., Trollinger D. 1988; Improved broad-host-range plasmids for DNA cloning in gram-negative bacteria. Gene 70:191–197 [CrossRef]
    [Google Scholar]
25. Kihara J., Moriwaki A., Matsuo N., Arase S., Honda Y. 2004; Cloning, functional characterization, and near-ultraviolet radiation-enhanced expression of a photolyase gene ( PHR1 ) from the phytopathogenic fungus Bipolaris oryzae. Curr Genet 46:37–46
    [Google Scholar]
26. Klug G., Drews G. 1984; Construction of a gene bank of Rhodopseudomonas capsulata using a broad host range DNA cloning system. Arch Microbiol 139:319–325 [CrossRef]
    [Google Scholar]
27. Lang H. P., Cogdell R. J., Takaichi S., Hunter C. N. 1995; Complete DNA sequence, specific Tn5 insertion map, and gene assignment of the carotenoid biosynthesis pathway of Rhodobacter sphaeroides. J Bacteriol 177:2064–2073
    [Google Scholar]
28. Lin C., Shalitin D. 2003; Cryptochrome structure and signal transduction. Annu Rev Plant Biol 54:469–496 [CrossRef]
    [Google Scholar]
29. Mitani H., Shima A. 1995; Induction of cyclobutane pyrimidine dimer photolyase in cultured fish cells by fluorescent light and oxygen stress. Photochem Photobiol 61:373–377 [CrossRef]
    [Google Scholar]
30. Mitani H., Uchida N., Shima A. 1996; Induction of cyclobutane pyrimidine dimer photolyase in cultured fish cells by UVA and blue light. Photochem Photobiol 64:943–948 [CrossRef]
    [Google Scholar]
31. Newman J. D., Falkowski M. J., Schilke B. A., Anthony L. C., Donohue T. J. 1999; The Rhodobacter sphaeroides ECF sigma factor, σ ^E, and the target promoters cycA P3 and rpoE P1. J Mol Biol 294:307–320 [CrossRef]
    [Google Scholar]
32. Newman J. D., Anthony J. R., Donohue T. J. 2001; The importance of zinc-binding to the function of Rhodobacter sphaeroides ChrR as an anti-sigma factor. J Mol Biol 313:485–499 [CrossRef]
    [Google Scholar]
33. Nies D. H. 1999; Microbial heavy-metal resistance. Appl Microbiol Biotechnol 51:730–750 [CrossRef]
    [Google Scholar]
34. Nieuwlandt D. T., Palmer J. R., Armbruster D. T., Kuo Y.-P., Oda W., Daniels C. J. 1995; A rapid procedure for the isolation of RNA from Haloferax volcanii . In Archaea: A Laboratory Manual pp 161–162 Edited by Robb F. T., Place A. R. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press;
    [Google Scholar]
35. Page K. A., Connon S. A., Giovannoni S. J. 2004; Representative freshwater bacterioplankton isolated from Crater Lake, Oregon. Appl Environ Microbiol 70:6542–6550 [CrossRef]
    [Google Scholar]
36. Partch C. L., Sancar A. 2005; Photochemistry and photobiology of cryptochrome blue-light photopigments: the search for a photocycle. Photochem Photobiol 81:1291–1304 [CrossRef]
    [Google Scholar]
37. Pfaffl M. W. 2001; A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29:2002–2007
    [Google Scholar]
38. Rupert C. S., Goodgal S. H., Herriott R. M. 1958; Photoreactivation in vitro of ultraviolet-inactivated Hemophilus influenzae transforming factor. J Gen Physiol 41:451–471 [CrossRef]
    [Google Scholar]
39. Sambrook J., Russell D. W. 2001 Molecular Cloning: A Laboratory Manual Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press;
    [Google Scholar]
40. Sancar A. 2003; Structure and function of DNA photolyase and cryptochrome blue-light photoreceptors. Chem Rev 103:2203–2237 [CrossRef]
    [Google Scholar]
41. Schilke B. A., Donohue T. J. 1995; ChrR positively regulates transcription of the Rhodobacter sphaeroides cytochrome c ₂ gene. J Bacteriol 177:1929–1937
    [Google Scholar]
42. Selby C. P., Sancar A. 2006; A cryptochrome/photolyase class of enzymes with single-stranded DNA-specific photolyase activity. Proc Natl Acad Sci U S A 21:17696–17700
    [Google Scholar]
43. Simon R., Priefer U., Pühler A. 1983; A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in gram-negative bacteria. Biotechnology 1:784–791 [CrossRef]
    [Google Scholar]
44. Sockett R. E., Donohue T. J., Varga A. R., Kaplan S. 1989; Control of photosynthetic membrane assembly in Rhodobacter sphaeroides mediated by puhA and flanking sequences. J Bacteriol 171:436–446
    [Google Scholar]
45. Tamada T., Kitadoroko K., Higuchi Y., Inaka K., Yasui A., Eker A. P., Miki K., de Ruiter P. E. 1997; Crystal structure of DNA photolyase from Anacystis nidulans. Nat Struct Biol 4:887–891 [CrossRef]
    [Google Scholar]
46. Tehrani A., Prince R. C., Beatty J. T. 2003; Effects of photosynthetic reaction center H protein domain mutations on photosynthetic properties and reaction center assembly in Rhodobacter sphaeroides. Biochemistry 42:8919–8928 [CrossRef]
    [Google Scholar]
47. Toptchieva A., Sisson G., Bryden L. J., Taylor D. E., Hoffman P. S. 2003; An inducible tellurite-resistance operon in Proteus mirabilis. Microbiology 149:1285–1295 [CrossRef]
    [Google Scholar]
48. Ueda T., Kato A., Kuramitsu S., Terasawa H., Shimada I. 2005; Identification and characterization of a second chromophore of DNA photolyase from Thermus thermophilus HB27. J Biol Chem 280:36237–36243 [CrossRef]
    [Google Scholar]
49. van Niel C. B. 1944; The culture, general physiology, morphology, and classification of the non-sulfur purple and brown bacteria. Bacteriol Rev 8:1–118
    [Google Scholar]
50. Vieira J., Messing J. 1982; The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene 19:259–268 [CrossRef]
    [Google Scholar]
51. Yang H. Q., Tang R. H., Cashmore A. R. 2001; The signaling mechanism of Arabidopsis CRY1 involves direct interaction with COP1. Plant Cell 13:2573–2587 [CrossRef]
    [Google Scholar]
52. Yasuhira S., Mitani H., Shima A. 1991; Enhancement of photorepair of ultraviolet-damage by preillumination with fluorescent light in cultured fish cells. Photochem Photobiol 53:211–215 [CrossRef]
    [Google Scholar]
53. Zeilstra-Ryalls J., Gomelsky M., Eraso J. M., Yeliseev A., O'Gara J., Kaplan S. 1998; Control of photosystem formation in Rhodobacter sphaeroides. J Bacteriol 180:2801–2809
    [Google Scholar]
54. Zeller T., Klug G. 2004; Detoxification of hydrogen peroxide and expression of catalase genes in Rhodobacter. Microbiology 150:3451–3462 [CrossRef]
    [Google Scholar]
55. Zeller T., Moskvin O. V., Li K., Klug G., Gomelsky M. 2005; Transcriptome and physiological responses to hydrogen peroxide of the facultatively phototrophic bacterium Rhodobacter sphaeroides. J Bacteriol 187:7232–7242 [CrossRef]
    [Google Scholar]