LdrP, a cAMP receptor protein/FNR family transcriptional regulator, serves as a positive regulator for the light-inducible gene cluster in the megaplasmid of Thermus thermophilus

Microbiology (United Kingdom)

Volumn 160, Issue , 2014, Pages 2650-2660

  Takano, Hideaki ^a   Agari, Yoshihiro ^b   Hagiwara, Kenta ^a   Watanabe, Ren ^a   Yamazaki, Ryuta ^a   Beppu, Teruhiko ^a   Shinkai, Akeo ^b,c   Ueda, Kenji ^a  

^a NIHON UNIVERSITY   (Japan)

^b RIKEN SPring 8 Center ^*  (Japan)

^c RIKEN   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; LIGHT INDUCED TRANSCRIPTION REGULATOR; LITR DEPENDENT REGULATORY PROTEIN; MESSENGER RNA; NUCLEASE S1; RECEPTOR PROTEIN; RNA POLYMERASE; TRANSCRIPTION FACTOR; TRANSCRIPTOME; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENE; BACTERIUM MUTANT; CONTROLLED STUDY; GENE CLUSTER; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; ILLUMINATION; IN VITRO STUDY; MESSENGER RNA SYNTHESIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PROMOTER REGION; THERMUS THERMOPHILUS; TRANSCRIPTION REGULATION; DNA SEQUENCE; GENE EXPRESSION PROFILING; GENE INACTIVATION; GENETIC TRANSCRIPTION; GENETICS; LIGHT; METABOLISM; MOLECULAR GENETICS; MULTIGENE FAMILY; PLASMID; RADIATION RESPONSE; TRANSCRIPTION INITIATION;

THERMUS THERMOPHILUS;

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; GENE KNOCKOUT TECHNIQUES; LIGHT; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PLASMIDS; PROMOTER REGIONS, GENETIC; SEQUENCE ANALYSIS, DNA; THERMUS THERMOPHILUS; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC; TRANSCRIPTIONAL ACTIVATION;

EID: 84915749294     PISSN: 13500872     EISSN: 14652080     Source Type: Journal    
DOI: 10.1099/mic.0.082263-0     Document Type: Article

References (35)

1. Agari, Y., Kashihara, A., Yokoyama, S., Kuramitsu, S. & Shinkai, A. (2008). Global gene expression mediated by Thermus thermophilus SdrP, a CRP/FNR family transcriptional regulator. Mol Microbiol 70, 60-75.
2. Agari, Y., Kuramitsu, S. & Shinkai, A. (2012). X-ray crystal structure of TTHB099, a CRP/FNR superfamily transcriptional regulator from Thermus thermophilus HB8, reveals a DNA-binding protein with no required allosteric effector molecule. Proteins 80, 1490-1494.
3. Brüggemann, H. & Chen, C. (2006). Comparative genomics of Thermus thermophilus: plasticity of the megaplasmid and its contribution to a thermophilic lifestyle. J Biotechnol 124, 654-661.
4. Busby, S. & Ebright, R. H. (1999). Transcription activation by catabolite activator protein (CAP). J Mol Biol 293, 199-213.
5. Díez, A. I., Ortiz-Guerrero, J. M., Ortega, A., Elías-Arnanz, M., Padmanabhan, S. & García de la Torre, J. (2013). Analytical ultracentrifugation studies of oligomerization and DNA-binding of TtCarH, a Thermus thermophilus coenzyme B12-based photosensory regulator. Eur Biophys J 42, 463-476.
6. Ebright, R. H., Ebright, Y. W. & Gunasekera, A. (1989). Consensus DNA site for the Escherichia coli catabolite gene activator protein (CAP): CAP exhibits a 450-fold higher affinity for the consensusDNA site than for the E. coli lac DNA site. Nucleic Acids Res 17, 10295-10305.
7. Edge, R., McGarvey, D. J. & Truscott, T. G. (1997). The carotenoids as anti-oxidants - a review. J Photochem Photobiol B 41, 189-200.
8. Glaeser, J., Nuss, A. M., Berghoff, B. A. & Klug, G. (2011). Singlet oxygen stress in microorganisms. Adv Microb Physiol 58, 141-173.
9. Hashimoto, Y., Yano, T., Kuramitsu, S. & Kagamiyama, H. (2001). Disruption of Thermus thermophilus genes by homologous recombination using a thermostable kanamycin-resistantmarker. FEBS Lett 506, 231-234.
10. Hayes, J. D. & McLellan, L. I. (1999). Glutathione and glutathionedependent enzymes represent a co-ordinately regulated defence against oxidative stress. Free Radic Res 31, 273-300.
11. Hendrischk, A. K., Braatsch, S., Glaeser, J. & Klug, G. (2007). The phrA gene of Rhodobacter sphaeroides encodes a photolyase and is regulated by singlet oxygen and peroxide in a sE-dependent manner. Microbiology 153, 1842-1851.
12. Henne, A., Brüggemann, H., Raasch, C., Wiezer, A., Hartsch, T., Liesegang, H., Johann, A., Lienard, T., Gohl, O. & other authors (2004). The genome sequence of the extreme thermophile Thermus thermophilus. Nat Biotechnol 22, 547-553.
13. Hoseki, J., Yano, T., Koyama, Y., Kuramitsu, S. & Kagamiyama, H. (1999). Directed evolution of thermostable kanamycin-resistance gene: a convenient selectionmarker for Thermus thermophilus. J Biochem 126, 951-956.
14. Hoshino, T., Kosuge, T., Hidaka, Y., Tabata, K. & Nakahara, T. (1994). Molecular cloning and sequence analysis of the proC gene encoding delta 1-pyrroline-5-carboxylate reductase from an extremely thermophilic eubacterium Thermus thermophilus. Biochem Biophys Res Commun 199, 410-417.
15. Koyama, Y., Hoshino, T., Tomizuka, N. & Furukawa, K. (1986). Genetic transformation of the extreme thermophile Thermus thermophilus and of other Thermus spp. J Bacteriol 166, 338-340.
16. Lawson, C. L., Swigon, D., Murakami, K. S., Darst, S. A., Berman, H. M. & Ebright, R. H. (2004). Catabolite activator protein: DNA binding and transcription activation. Curr Opin Struct Biol 14, 10-20.
17. Maniatis, T., Fritsch, E. F. & Sambrook, J. (1982). Molecular Cloning: A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
18. Moll, I., Grill, S., Gualerzi, C. O. & Bläsi, U. (2002). Leaderless mRNAs in bacteria: surprises in ribosomal recruitment and translational control. Mol Microbiol 43, 239-246.
19. Nishiyama, M., Kobashi, N., Tanaka, K., Takahashi, H. & Tanokura, M. (1999). Cloning and characterization in Escherichia coli of the gene encoding the principal sigma factor of an extreme thermophile, Thermus thermophilus. FEMS Microbiol Lett 172, 179-186.
20. Ohtani, N., Tomita, M. & Itaya, M. (2012). The third plasmid pVV8 from Thermus thermophilus HB8: isolation, characterization, and sequence determination. Extremophiles 16, 237-244.
21. Ortiz-Guerrero, J. M., Polanco, M. C., Murillo, F. J., Padmanabhan, S. & Elías-Arnanz, M. (2011). Light-dependent gene regulation by a coenzyme B12-based photoreceptor. Proc Natl Acad Sci U S A 108, 7565-7570.
22. Oshima, T. (1974). [Comparative studies on biochemical properties of an extreme thermophile, Thermus thermophilus HB 8 (author's transl)]. Seikagaku 46, 887-907.
23. Pepper, S. D., Saunders, E. K., Edwards, L. E., Wilson, C. L. & Miller, C. J. (2007). The utility of MAS5 expression summary and detection call algorithms. BMC Bioinformatics 8, 273.
24. Pérez-Marín, M. C., Padmanabhan, S., Polanco, M. C., Murillo, F. J. & Elías-Arnanz, M. (2008). Vitamin B12 partners the CarH repressor to downregulate a photoinducible promoter in Myxococcus xanthus. Mol Microbiol 67, 804-819.
25. Sevostyanova, A., Djordjevic, M., Kuznedelov, K., Naryshkina, T., Gelfand, M. S., Severinov, K. & Minakhin, L. (2007). Temporal regulation of viral transcription during development of Thermus thermophilus bacteriophage phiYS40. J Mol Biol 366, 420-435.
26. Shinkai, A., Kira, S., Nakagawa, N., Kashihara, A., Kuramitsu, S. & Yokoyama, S. (2007). Transcription activation mediated by a cyclic AMP receptor protein from Thermus thermophilus HB8. J Bacteriol 189, 3891-3901.
27. Sikorski, J., Tindall, B. J., Lowry, S., Lucas, S., Nolan, M., Copeland, A., Glavina Del Rio, T., Tice, H., Cheng, J. F. & other authors (2010). Complete genome sequence of Meiothermus silvanus type strain (VIR2). Stand Genomic Sci 3, 37-46.
28. Sollner-Webb, B. & Reeder, R. H. (1979). The nucleotide sequence of the initiation and termination sites for ribosomal RNA transcription in X. laevis. Cell 18, 485-499.
29. Storey, J. D. & Tibshirani, R. (2003). Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100, 9440-9445.
30. Takano, H., Obitsu, S., Beppu, T. & Ueda, K. (2005). Light-induced carotenogenesis in Streptomyces coelicolor A3(2): identification of an extracytoplasmic function sigma factor that directs photodependent transcription of the carotenoid biosynthesis gene cluster. J Bacteriol 187, 1825-1832.
31. Takano, H., Asker, D., Beppu, T. & Ueda, K. (2006a). Genetic control for light-induced carotenoid production in non-phototrophic bacteria. J Ind Microbiol Biotechnol 33, 88-93.
32. Takano, H., Beppu, T. & Ueda, K. (2006b). The CarA/LitR-family transcriptional regulator: its possible role as a photosensor and wide distribution in non-phototrophic bacteria. Biosci Biotechnol Biochem 70, 2320-2324.
33. Takano, H., Kondo, M., Usui, N., Usui, T., Ohzeki, H., Yamazaki, R., Washioka, M., Nakamura, A., Hoshino, T. & other authors (2011). Involvement of CarA/LitR and CRP/FNR family transcriptional regulators in light-induced carotenoid production in Thermus thermophilus. J Bacteriol 193, 2451-2459.
34. Takayama, G., Kosuge, T., Maseda, H., Nakamura, A. & Hoshino, T. (2004). Nucleotide sequence of the cryptic plasmid pTT8 from Thermus thermophilus HB8 and isolation and characterization of its high-copy-number mutant. Plasmid 51, 227-237.
35. Tindall, B. J., Sikorski, J., Lucas, S., Goltsman, E., Copeland, A., Glavina Del Rio, T., Nolan, M., Tice, H., Cheng, J. F. & other authors (2010). Complete genome sequence of Meiothermus ruber type strain (21). Stand Genomic Sci 3, 26-36.