The sac10b homolog in methanococcus maripaludis binds DNA at specific sites

Journal of Bacteriology

Volumn 191, Issue 7, 2009, Pages 2315-2329

  Liu, Yuchen ^a   Guo, Li ^b   Guo, Rong ^b   Wong, Richard L ^a   Hernandez, Hilda ^a   Hu, Jinchuan ^b   Chu, Yindi ^b   Amster, I Jonathan ^a   Whitman, William B ^a   Huang, Li ^a,b  

^a UNIVERSITY OF GEORGIA   (United States)

^b INSTITUTE OF MICROBIOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN; RECOMBINANT PROTEIN; SAC10B PROTEIN; UNCLASSIFIED DRUG; ARCHAEAL PROTEIN; DNA BINDING PROTEIN;

ARTICLE; AUTOTROPHY; BACTERIAL GENE; BACTERIAL GROWTH; BACTERIUM CULTURE; BACTERIUM MUTANT; BINDING AFFINITY; BINDING SITE; CARBON DIOXIDE FIXATION; CULTURE MEDIUM; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENE FUNCTION; GENETIC VARIABILITY; METHANOCOCCUS MARIPALUDIS; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN DNA BINDING; PROTEIN MOTIF; PROTEIN RNA BINDING; SEQUENCE HOMOLOGY; TEMPERATURE; CHEMISTRY; GENE EXPRESSION; GENETICS; METABOLISM; METHANOCOCCUS; PROTEIN BINDING;

EURYARCHAEOTA; METHANOCOCCI; METHANOCOCCUS MARIPALUDIS; SULFOLOBUS;

ARCHAEAL PROTEINS; BINDING SITES; DNA-BINDING PROTEINS; GENE EXPRESSION; METHANOCOCCUS; PROTEIN BINDING;

EID: 64049111620     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.01534-08     Document Type: Article

References (51)

1. Ali Azam, T., A. Iwata, A. Nishimura, S. Ueda, and A. Ishihama. 1999. Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J. Bacteriol. 181:6361-6370.
2. Aravind, L., L. M. Iyer, and V. Anantharaman. 2003. The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism. Genome Biol. 4:R64.
3. Balch, W. E., G. E. Fox, L. J. Magrum, C. R. Woese, and R. S. Wolfe. 1979. Methanogens: reevaluation of a unique biological group. Microbiol. Mol. Biol. Rev. 43:260-296.
4. Bell, S. D., C. H. Botting, B. N. Wardleworth, S. P. Jackson, and M. F. White. 2002. The interaction of Alba, a conserved archaeal chromatin protein, with Sir2 and its regulation by acetylation. Science 296:148-151.
5. Beloin, C., J. Jeusset, B. Revet, G. Mirambeau, F. Le Hegarat, and E. Le Cam. 2003. Contribution of DNA conformation and topology in righthanded DNA wrapping by the Bacillus subtilis LrpC Protein. J. Biol. Chem. 278:5333-5342.
6. Bremer, H., and P. P. Dennis. 1996. Modulation of chemical composition and other parameters of the cell by growth, p. 1553-1569. In F. C. Neidhardt, R. Curtiss, J. L. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella, 2nd ed., vol. 2. ASM Press, Washington, DC.
7. Cui, Q., Y. Tong, H. Xue, L. Huang, Y. Feng, and J. Wang. 2003. Two conformations of archaeal Ssh10b: the origin of its temperature-dependent interaction with DNA. J. Biol. Chem. 278:51015-51022.
8. Dame, R. T. 2005. The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin. Mol. Microbiol. 56:858-870.
9. Dybas, M., and J. Konisky. 1992. Energy transduction in the methanogen Methanococcus voltae is based on a sodium current. J. Bacteriol. 174:5575- 5583.
10. Forterre, P., F. Confalonieri, and S. Knapp. 1999. Identification of the gene encoding archeal-specific DNA-binding proteins of the Sac10b family. Mol. Microbiol. 32:669-670.
11. Gernhardt, P., O. Possot, M. Foglino, L. Sibold, and A. Klein. 1990. Construction of an integration vector for use in the archaebacterium Methanococcus voltae and expression of a eubacterial resistance gene. Mol. Gen. Genet. 221:273-279.
12. Guo, R., H. Xue, and L. Huang. 2003. Ssh10b, a conserved thermophilic archaeal protein, binds RNA in vivo. Mol. Microbiol. 50:1605-1615.
13. Hecht, A., S. Strahl-Bolsinger, and M. Grunstein. 1996. Spreading of transcriptional represser SIR3 from telomeric heterochromatin. Nature 383:92- 96.
14. Heinicke, I., J. Muller, M. Pittelkow, and A. Klein. 2004. Mutational analysis of genes encoding chromatin proteins in the archaeon Methanococcus voltae indicates their involvement in the regulation of gene expression. Mol. Genet. Genomics 272:76-87.
15. Hendrickson, E. L., R. Kaul, Y. Zhou, D. Bovee, P. Chapman, J. Chung, E. Conway de Macario, J. A. Dodsworth, W. Gillett, D. E. Graham, M. Hackett, A. K. Haydock, A. Kang, M. L. Land, R. Levy, T. J. Lie, T. A. Major, B. C. Moore, I. Porat, A. Palmeiri, G. Rouse, C. Saenphimmachak, D. Soll, S. Van Dien, T. Wang, W. B. Whitman, Q. Xia, Y. Zhang, F. W. Larimer, M. V. Olson, and J. A. Leigh. 2004. Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis. J. Bacteriol. 186:6956-6969.
16. Hendrickson, E. L., Y. Liu, G. Rosas-Sandoval, I. Porat, D. Soll, W. B. Whitman, and J. A. Leigh. 2008. Global responses of Methanococcus maripaludis to specific nutrient limitations and growth rate. J. Bacteriol. 190: 2198-2205.
17. Hennigan, A. N., and J. N. Reeve. 1994. mRNAs in the methanogenic archaeon Methanococcus vannielii: numbers, half-lives and processing. Mol. Microbiol. 11:655-670.
18. Huber, H., M. Thomm, H. König, G. Thies, and K. O. Stetter. 1982. Methanococcus thermolithotrophicus, a novel thermophilic lithotrophic methanogen. Arch. Microbiol. 132:47-50.
19. Jelinska, C., M. J. Conroy, C. J. Craven, A. M. Hounslow, P. A. Bullough, J. P. Waltho, G. L. Taylor, and M. F. White. 2005. Obligate heterodimerization of the archaeal Alba2 protein with Alba1 provides a mechanism for control of DNA packaging. Structure 13:963-971.
20. Jones, W. J., J. A. Leigh, F. Mayer, C. R. Woese, and R. S. Wolfe. 1983. Methanococcus jannaschii sp. nov., an extremely thermophilic methanogen from a submarine hydrothermal vent. Arch. Microbiol. 136:254-261.
21. Lie, T. J., G. E. Wood, and J. A. Leigh. 2005. Regulation of nif expression in Methanococcus maripaludis: roles of the euryarchaeal repressor NrpR, 2-oxoglutarate, and two operators. J. Biol. Chem. 280:5236-5241.
22. Lin, W., and W. Whitman. 2004. The importance of porE and porF in the anabolic pyruvate oxidoreductase of Methanococcus maripaludis. Arch. Microbiol. 181:68-73.
23. Lin, W. C., Y.-L. Yang, and W. B. Whitman. 2003. The anabolic pyruvate oxidoreductase from Methanococcus maripaludis. Arch. Microbiol. 179:444- 456.
24. Lopez-Torrejon, G., M. I. Martinez-Jimenez, and S. Ayora. 2006. Role of LrpC from Bacillus subtilis in DNA transactions during DNA repair and recombination. Nucleic Acids Res. 34:120-129.
25. Lurz, R., M. Grote, J. Dijk, R. Reinhardt, and B. Dobrinski. 1986. Electron microscopic study of DNA complexes with proteins from the Archaebacterium Sulfolobus acidocaldarius. EMBO J. 5:3715-3721.
26. Malandrin, L., H. Huber, and R. Bernander. 1999. Nucleoid structure and partition in Methanococcus jannaschii: an archaeon with multiple copies of the chromosome. Genetics 152:1315-1323.
27. Marsh, V. L., S. Y. Peak-Chew, and S. D. Bell. 2005. Sir2 and the acetyltransferase, Pat, regulate the archaeal chromatin protein, Alba. J. Biol. Chem. 280:21122-21128.
28. Mrazek, J., S. Xie, X. Guo, and A. Srivastava. 2008. AIMIE: a web-based environment for detection and interpretation of significant sequence motifs in prokaryotic genomes. Bioinformatics 24:1041-1048.
29. Neidhardt, F. C., and H. E. Umbarger. 1996. Chemical composition of Escherichia coli, p. 143-170. In F. C. Neidhardt, R. Curtiss, J. L. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella, 2nd ed., vol. 1. ASM Press, Washington, DC.
30. Porat, I., W. Kim, E. L. Hendrickson, Q. Xia, Y. Zhang, T. Wang, F. Taub, B. C. Moore, I. J. Anderson, M. Hackett, J. A. Leigh, and W. B. Whitman. 2006. Disruption of the operon encoding Ehb hydrogenase limits anabolic CO2 assimilation in the archaeon Methanococcus maripaludis. J. Bacteriol. 188:1373-1380.
31. Postow, L., C. D. Hardy, J. Arsuaga, and N. R. Cozzarelli. 2004. Topological domain structure of the Escherichia coli chromosome. Genes Dev. 18:1766- 1779.
32. Robertson, D. E., D. Noll, and M. F. Roberts. 1992. Free amino acid dynamics in marine methanogens. Beta-amino acids as compatible solutes. J. Biol. Chem. 267:14893-14901.
33. Sandman, K., and J. N. Reeve. 2006. Archaeal histones and the origin of the histone fold. Curr. Opin. Microbiol. 9:520-525.
34. Shieh, J., and W. B. Whitman. 1988. Autotrophic acetyl coenzyme A biosynthesis in Methanococcus maripaludis. J. Bacteriol. 170:3072-3079.
35. Soares, D., I. Dahlke, W. T. Li, K. Sandman, C. Hethke, M. Thomm, and J. N. Reeve. 1998. Archaeal histone stability, DNA binding, and transcription inhibition above 90 degrees C. Extremophiles 2:75-81.
36. Sprott, G. D., and K. F. Jarrell. 1981. K+, Na+, and Mg2+ content and permeability of Methanospirillum hungatei and Methanobacterium thermoautotrophicum. Can. J. Microbiol. 27:444-451.
37. Stathopoulos, C., W. Kim, T. Li, I. Anderson, B. Deutsch, S. Palioura, W. Whitman, and D. Soll. 2001. Cysteinyl-tRNA synthetase is not essential for viability of the archaeon Methanococcus maripaludis. Proc. Natl. Acad. Sci. USA 98:14292-14297.
38. Stetter, K. O. 1994. The lesson of Archaeabacteria, p. 143-151. In S. Boengtson (ed.), Early life on earth. Columbia University Press, New York, NY.
39. Tapias, A., G. Lopez, and S. Ayora. 2000. Bacillus subtilis LrpC is a sequenceindependent DNA-binding and DNA-bending protein which bridges DNA. Nucleic Acids Res. 28:552-559.
40. Thompson, W., E. C. Rouchka, and C. E. Lawrence. 2003. Gibbs Recursive Sampler: finding transcription factor binding sites. Nucleic Acids Res. 31: 3580-3585.
41. Tumbula, D. L., J. Keswani, J. Shieh, and W. B. Whitman. 1995. Maintenance of methanogen stock cultures in glycerol at -70oC, p. 85-87. In F. T. Robb, A. R. Place, K. R. Sowers, H. J. Schreir, S. DasSarma, E. M. Fleis chmann (ed.), Archaea-a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
42. Tumbula, D. L., R. A. Makula, and W. B. Whitman. 1994. Transformation of Methanococcus maripaludis and identification of a PstI-like restriction system. FEMS Microbiol. Lett. 121:309-314.
43. Wang, G., R. Guo, M. Bartlam, H. Yang, H. Xue, Y. Liu, L. Huang, and Z. Rao. 2003. Crystal structure of a DNA binding protein from the hyperthermophilic euryarchaeon Methanococcus jannaschii. Protein Sci. 12:2815-2822.
44. Wardleworth, B. N., R. J. M. Russell, S. D. Bell, G. L. Taylor, and M. F. White. 2002. Structure of Alba: an archaeal chromatin protein modulated by acetylation. EMBO J. 21:4654-4662.
45. White, M. F., and S. D. Bell. 2002. Holding it together: chromatin in the Archaea. Trends Genet. 18:621-626.
46. Whitman, W. B. 2001. Genus I. Methanococcus, p. 236-240. In D. R. Boone, R. W. Castenholz, and G. M. Garrity (ed.), Bergey's mannual of systematic bacteriology, vol. 1. Springer, New York, NY.
47. Whitman, W. B., J. Shieh, S. Sohn, D. S. Caras, and U. Premachandran. 1986. Isolation and characterization of 22 mesophilic methanococci. Syst. Appl. Microbiol. 7:235-240.
48. Wong, R. L., and I. J. Amster. 2006. Combining low and high mass ion accumulation for enhancing shotgun proteome analysis by accurate mass measurement. J. Am. Soc. Mass Spectrom. 17:205-212.
49. Xia, Q., E. L. Hendrickson, Y. Zhang, T. Wang, F. Taub, B. C. Moore, I. Porat, W. B. Whitman, M. Hackett, and J. A. Leigh. 2006. Quantitative proteomics of the archaeon Methanococcus maripaludis validated by microarray analysis and real time PCR. Mol. Cell Proteomics 5:868-881.
50. Xue, H., R. Guo, Y. Wen, D. Liu, and L. Huang. 2000. An abundant DNA binding protein from the hyperthermophilic archaeon Sulfolobus shibatae affects DNA supercoiling in a temperature-dependent fashion. J. Bacteriol. 182:3929-3933.
51. Yindeeyoungyeon, W., and M. A. Schell. 2000. Footprinting with an automated capillary DNA sequencer. BioTechniques 29:1034-1041.