C68 from the Sulfolobus islandicus plasmid-virus pSSVx is a novel member of the AbrB-like transcription factor family

Biochemical Journal

Volumn 435, Issue 1, 2011, Pages 157-166

  Contursi, Patrizia ^a,c   D'Ambrosio, Katia ^b   Pirone, Luciano ^b   Pedone, Emilia ^b   Aucelli, Tiziana ^a   She, Qunxin ^c   De Simone, Giuseppina ^b   Bartolucci, Simonetta ^a  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^b CNR   (Italy)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

AbrB; C68; Plasmid virus hybrid; pSSVx; Sulfolobus islandicus; Transcription factor

Indexed keywords

ABRB PROTEIN; BACTERIAL PROTEIN; C68 PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ARTICLE; CIRCULAR DICHROISM; DNA FOOTPRINTING; ESCHERICHIA COLI; GEL FILTRATION CHROMATOGRAPHY; GEL MOBILITY SHIFT ASSAY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; SULFOLOBUS; SULFOLOBUS ISLANDICUS; X RAY DIFFRACTION;

AMINO ACID SEQUENCE; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; DNA FOOTPRINTING; DNA, INTERGENIC; DNA-BINDING PROTEINS; FUSELLOVIRIDAE; MOLECULAR SEQUENCE DATA; OPERATOR REGIONS, GENETIC; PLASMIDS; PROMOTER REGIONS, GENETIC; PROTEIN CONFORMATION; RECOMBINANT PROTEINS; SATELLITE VIRUSES; SELENOMETHIONINE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SULFOLOBUS; TRANSCRIPTION FACTORS; VIRAL PROTEINS;

BACILLUS SUBTILIS; CRENARCHAEOTA; ESCHERICHIA COLI; FUSELLOVIRUS; PROKARYOTA; SULFOLOBUS; SULFOLOBUS ISLANDICUS;

EID: 79952859902     PISSN: 02646021     EISSN: 14708728     Source Type: Journal    
DOI: 10.1042/BJ20101334     Document Type: Article

References (50)

1. Prangishvili, D., Forterre, P. and Garrett, R. A. (2006) Viruses of the Archaea: a unifying view. Nat. Rev. Microbiol. 4, 837-848
2. Arnold, H. P., She, Q., Phan, H., Stedman, K., Prangishvili, D., Holz, I., Kristjansson, J. K., Garrett, R. and Zillig, W. (1999) The genetic element pSSVx of the extremely thermophilic crenarchaeon Sulfolobus is a hybrid between a plasmid and a virus. Mol. Microbiol. 34, 217-226
3. Contursi, P., Jensen, S., Aucelli, T., Rossi, M., Bartolucci, S. and She, Q. (2006) Characterization of the Sulfolobus host-SSV2 virus interaction. Extremophiles 10, 615-627 (Pubitemid 44764319)
4. Contursi, P., Cannio, R., Prato, S., She, Q., Rossi, M. and Bartolucci, S. (2007) Transcriptional analysis of the genetic element pSSVx: differential and temporal regulation of gene expression reveals correlation between transcription and replication. J. Bacteriol. 189, 6339-6350 (Pubitemid 47378642)
5. Lipps, G. (2009) Molecular biology of the pRN1 plasmid from Sulfolobus islandicus. Biochem. Soc. Trans. 37, 42-45
6. Keeling, P. J., Klenk, H. P., Singh, R. K., Schenk, M. E., Sensen, C. W., Zillig, W. and Doolittle, W. F. (1998) Sulfolobus islandicus plasmids pRN1 and pRN2 share distant but common evolutionary ancestry. Extremophiles 2, 391-393
7. Peng, X., Holz, I., Zillig, W., Garrett, R. A. and She, Q. (2000) Evolution of the family of pRN plasmids and their integrase-mediated insertion into the chromosome of the crenarchaeon Sulfolobus solfataricus. J. Mol. Biol. 303, 449-454
8. Kletzin, A., Lieke, A., Urich, T., Charlebois, R. L. and Sensen, C. W. (1999) Molecular analysis of pDL10 from Acidianus ambivalens reveals a family of related plasmids from extremely thermophilic and acidophilic archaea. Genetics 152, 1307-1314
9. She, Q., Singh, R. K., Confalonieri, F., Zivanovic, Y., Allard, G., Awayez, M. J., Chan-Weiher, C. C. Y., Clausen, I. G., Curtis, B. A., De Moors, A. et al. (2001) The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc. Natl. Acad. Sci. U.S.A. 98, 7835-7840
10. Lipps, G. (2006) Plasmids and viruses of the thermoacidophilic crenarchaeote Sulfolobus. Extremophiles 10, 17-28
11. Wang, Y., Duan, Z., Zhu, H., Guo, X., Wang, Z., Zhou, J., She, Q. and Huang, L. (2007) A novel Sulfolobus non-conjugative extrachromosomal genetic element capable of integration into the host genome and spreading in the presence of a fusellovirus. Virology 363, 124-133 (Pubitemid 46678173)
12. Kawarabayasi, Y., Hino, Y., Horikawa, H., Jin-no, K., Takahashi, M., Sekine, M., Baba, S., Ankai, A., Kosugi, H., Hosoyama, A. et al. (2001) Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7. DNA Res. 8, 123-140
13. Chen, L., Brugger, K., Skovgaard, M., Redder, P., She, Q., Torarinsson, E., Greve, B., Awayez, M., Zibat, A., Klenk, H. P. and Garrett, R. A. (2005) The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota. J. Bacteriol. 187, 4992-4999
14. Reno, M. L., Held, N. L., Fields, C. J., Burke, P. V. and Whitaker, R. J. (2009) Biogeography of the Sulfolobus islandicus pan-genome. Proc. Natl. Acad. Sci. U.S.A. 106, 8605-8610
15. Aucelli, T., Contursi, P., Girfoglio, M., Rossi, M. and Cannio, R. (2006) A spreadable, non-integrative and high copy number shuttle vector for Sulfolobus solfataricus based on the genetic element pSSVx from Sulfolobus islandicus. Nucleic Acids Res. 34, e114
16. +-dependent bacillar alcohol dehydrogenase. Eur. J. Biochem. 222, 345-352
17. D'Ambrosio, K., Limauro, D., Pedone, E., Galdi, I., Pedone, C., Bartolucci, S. and De Simone, G. (2009) Insights into the catalytic mechanism of the Bcp family: functional and structural analysis of Bcp1 from Sulfolobus solfataricus. Proteins 76, 995-1006
18. McPherson, A. (1990) Current approaches to macromolecular crystallization. Eur. J. Biochem. 189, 1-23
19. Cudney, R., Patel, S., Weisgraber, K., Newhouse, Y. and McPherson, A. (1994) Screening and optimization strategies for macromolecular crystal growth. Acta Crystallogr. Sect. D Biol. Crystallogr. 50, 414-423
20. Otwinowsky, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326
21. Terwilliger, T. C. and Berendzen, J. (1999) Automated MAD and MIR structure solution. Acta Crystallogr. Sect. D Biol. Crystallogr. 55, 849-861
22. Terwilliger, T. C. (2000) Maximum likelihood density modification. Acta Crystallogr. Sect. D Biol. Crystallogr. 56, 965-972
23. Terwilliger, T. C. (2003) Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallogr. Sect. D Biol. Crystallogr. 59, 38-44
24. Jones, T. A., Zou, J. Y., Cowan, S. W. and Kjeldgaard, M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. Sect. A Found. Crystallogr. 47, 110-119
25. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunsteleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S. et al. (1998) Crystallography and NMR system (CNS): a new software system for macromolecular structure determination. Acta Crystallogr. Sect. D Biol. Crystallogr. 54, 905-921
26. Laskowski, R. A., MacArthur, M. W., Moss, M. D. and Thorton, J. M. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291
27. Holm, L. and Rosenström, P. (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res. 38, 545-549
28. Coles, M., Djuranovic, S., Soding, J., Frickey, T., Koretke, K., Truffault, V., Martin, J. and Lupas, A. N. (2005) AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi β barrels. Structure 13, 919-928
29. Bobay, B. G., Andreeva, A., Mueller, G. A., Cavanagh, J. and Murzin, A. G. (2005) Revised structure of the AbrB N-terminal domain unifies a diverse superfamily of putative DNA-binding proteins. FEBS Lett. 579, 5669-5674
30. Sullivan, D. M., Bobay, B. G., Kojetin, D. J., Thompson, R. J., Rance, M., Strauch, M. A. and Cavanagh, J. (2008) Insights into the nature of DNA binding of AbrB-like transcription factors. Structure 16, 1702-1713
31. Bobay, B. G., Mueller, G. A., Thompson, R. J., Murzin, A. G., Venters, R. A., Strauch, M. A. and Cavanagh, J. (2006) NMR structure of AbhN and comparison with AbrBN: first insights into the DNA binding promiscuity and specificity of AbrB-like transition state regulator proteins. J. Biol. Chem. 281, 21399-21409
32. Asen, I., Djuranovic, S., Lupas, A. N. and Zeth, K. (2009) Crystal structure of SpoVT, the final modulator of gene expression during spore development in Bacillus subtilis. J. Mol. Biol. 386, 962-975
33. Kamada, K., Hanaoka, F. and Burley, S. K. (2003) Crystal structure of the MazE/MazF complex: molecular bases of antidote-toxin recognition. Mol. Cell 11, 875-884
34. Loris, R., Marianovsky, I., Lah, J., Laeremans, T., Engelberg-Kulka, H., Glaser, G., Muyldermans, S. and Wyns, L. (2003) Crystal structure of the intrinsically flexible addiction antidote MazE. J. Biol. Chem. 278, 28252-2825
35. Aravind, L. and Koonin, E. V. (1999) DNA-binding proteins and evolution of transcription regulation in the archaea. Nucleic Acids Res. 27, 4658-4670
36. Bell, S. D., Magill, C. P. and Jackson, S. P. (2001) Basal and regulated transcription in Archaea. Biochem. Soc. Trans. 29, 392-395
37. Geiduschek, E. P. and Ouhammouch, M. (2005) Archaeal transcription and its regulators. Mol. Microbiol. 56, 1397-1407
38. Ouhammouch, M. and Geiduschek, E. P. (2005) An expanding family of archaeal transcriptional activators. Proc. Natl. Acad. Sci. U.S.A. 102, 15423-15428
39. Ouhammouch, M., Dewhurst, R. E., Hausner, W., Thomm, M. and Geiduschek, E. P. (2003) Activation of archaeal transcription by recruitment of the TATA-binding protein. Proc. Natl. Acad. Sci. U.S.A. 100, 5097-5102
40. Fiorentino, G., Ronca, R., Cannio, R., Rossi, M. and Bartolucci, S. (2007) MarR-like transcriptional regulator involved in detoxification of aromatic compounds in Sulfolobus solfataricus. J. Bacteriol. 189, 7351-7360 (Pubitemid 47557350)
41. Kessler, A., Sezonov, G., Guijarro, J. I., Desnoues, N., Rose, T., Delepierre, M., Bell, S. D. and Prangishvili, D. (2006) A novel archaeal regulatory protein, Sta1, activates transcription from viral promoters. Nucleic Acids Res. 34, 4837-4845 (Pubitemid 44605627)
42. Ouhammouch, M., Langham, G. E., Hausner, W., Simpson, A. J., El-Sayed, N. M. and Geiduschek, E. P. (2005) Promoter architecture and response to a positive regulator of archaeal transcription. Mol. Microbiol. 56, 625-637
43. Bobay, B. G., Benson, L., Naylor, S., Feeney, B., Clark, A. C., Goshe, M. B., Strauch, M. A., Thompson, R. and Cavanagh, J. (2004) Evaluation of the DNA binding tendencies of the transition state regulator AbrB. Biochemistry 43, 16106-16118 (Pubitemid 40041024)
44. Strauch, M. A., Ballar, P., Rowshan, A. J. and Zoller, K. L. (2005) The DNA-binding specificity of the Bacillus anthracis AbrB protein. Microbiology 151, 1751-1759
45. Dong, T. C., Cutting, S. M. and Lewis, R. J. (2004) DNA-binding studies on the Bacillus subtilis transcriptional regulator and AbrB homologue, SpoVT. FEMS Microbiol. Lett. 233, 247-256 (Pubitemid 38452627)
46. Marianovsky, I., Aizenman, E., Engelberg-Kulka, H. and Glaser, G. (2001) The regulation of the Escherichia coli mazEF promoter involves an unusual alternating palindrome. J. Biol. Chem. 276, 5975-5984
47. Xu, K. and Strauch, M. A. (1996) In vitro selection of optimal AbrB-binding sites: comparison to known in vivo sites indicates flexibility in AbrB binding and recognition of three-dimensional DNA structures. Mol. Microbiol. 19, 145-158
48. Fink, A. L. (2005) Natively unfolded proteins. Curr. Opin. Struct. Biol. 15, 35-41
49. Karginov, F. V. and Hannon, G. J. (2010) The CRISPR system: small RNA-guided defense in bacteria and archaea. Mol. Cell 37, 7-19
50. Horvath, P. and Barrangou, R. (2010) CRISPR/Cas, the immune system of bacteria and archaea. Science 327, 167-170