Unveiling the role of Dps in the organization of mycobacterial nucleoid

PLoS ONE

Volumn 6, Issue 1, 2011, Pages

  Ghatak, Payel ^a   Karmakar, Kajari ^a,b   Kasetty, Sanjay ^a   Chatterji, Dipankar ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

^b FRIEDRICH MIESCHER INSTITUTE FOR BIOMEDICAL RESEARCH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; DPS PROTEIN; DPS1 PROTEIN; DPS2 PROTEIN; GLUCOSE; MAGNESIUM ION; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; DNA BINDING PROTEIN; DPS PROTEIN, BACTERIA;

ARTICLE; ATOMIC FORCE MICROSCOPY; BACTERIAL CELL; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; CONTROLLED STUDY; CORAL REEF; MYCOBACTERIAL NUCLEOID; MYCOBACTERIUM SMEGMATIS; NONHUMAN; PROTEIN DNA BINDING; PROTEIN FUNCTION; CELL NUCLEUS; PHYSIOLOGY; ULTRASTRUCTURE;

ANTHOZOA; BACTERIA (MICROORGANISMS); MYCOBACTERIUM SMEGMATIS;

BACTERIAL PROTEINS; CELL NUCLEUS; CORAL REEFS; DNA-BINDING PROTEINS; MICROSCOPY, ATOMIC FORCE; MYCOBACTERIUM SMEGMATIS;

EID: 79551529436     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0016019     Document Type: Article

References (48)

1. Thanky NR, Young DB, Robertson BD (2007) Unusual features of the cell cycle in mycobacteria: polar-restricted growth and the snapping-model of cell division. Tuberculosis (Edinb) 87: 231-236.
2. Enright HU, Miller WJ, Hebbel RP (1992) Nucleosomal histone protein protects DNA from iron-mediated damage. Nucleic Acids Res 20: 3341-3346.
3. Kornberg RD (1999) Twenty-Five Years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98: 285-294.
4. Luijsterburg MS, Noom MC, Wuite GJ, Dame RT (2006) The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective. J Struct Biol 156: 262-272.
5. Kornberg RD (1974) Chromatin structure: a repeating unit of histones and DNA. Science 184: 868-871.
6. Drlica K, Rouviere-Yaniv J (1987) Histonelike proteins of bacteria. Microbiol Rev 51: 301-319.
7. Dillon SC, Dorman CJ (2010) Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nat Rev Microbiol 8: 185-195.
8. Ishihama A (1999) Modulation of the nucleoid, the transcription apparatus, and the translation machinery in bacteria for stationary phase survival. Genes Cells 4: 135-143.
9. Azam TA, Ishihama A (1999) Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity. J Biol Chem 274: 33105-33113.
10. Kim J, Yoshimura SH, Hizume K, Ohniwa RL, Ishihama A, et al. (2004) Fundamental structural units of the Escherichia coli nucleoid revealed by atomic force microscopy. Nucleic Acids Res 32: 1982-1992.
11. Minsky A, Shimoni E, Frenkiel-Krispin D (2002) Stress, order and survival. Nat Rev Mol Cell Biol 3: 50-60.
12. Mukherjee A, DiMario PJ, Grove A (2009) Mycobacterium smegmatis histone-like protein Hlp is nucleoid associated. FEMS Microbiol Lett 291: 232-240.
13. Grant RA, Filman DJ, Finkel SE, Kolter R, Hogle JM (1998) The crystal structure of Dps, a ferritin homolog that binds and protects DNA. Nat Struct Biol 5: 294-303.
14. Gupta S, Chatterji D (2005) Stress responses in mycobacteria. IUBMB Life 57: 149-159.
15. Gupta S, Chatterji D (2003) Bimodal protection of DNA by Mycobacterium smegmatis DNA-binding protein from stationary phase cells. J Biol Chem 278: 5235-5241.
16. Morikawa K, Ohniwa RL, Kim J, Maruyama A, Ohta T, et al. (2006) Bacterial nucleoid dynamics: oxidative stress response in Staphylococcus aureus. Genes Cells 11: 409-423.
17. Frenkiel-Krispin D, Ben-Avraham I, Englander J, Shimoni E, Wolf SG, et al. (2004) Nucleoid restructuring in stationary-state bacteria. Mol Microbiol 51: 395-405.
18. Roy S, Saraswathi R, Chatterji D, Vijayan M (2008) Structural studies on the second Mycobacterium smegmatis Dps: invariant and variable features of structure, assembly and function. J Mol Biol 375: 948-959.
19. Chowdhury RP, Saraswathi R, Chatterji D (2010) Mycobacterial stress regulation: The Dps "twin sister" defense mechanism and structure-function relationship. IUBMB Life 62: 67-77.
20. Saraswathi R, Chowdhury RP, Williams SM, Ghatak P, Chatterji D (2009) The mycobacterial MsDps2 protein is a nucleoid-forming DNA binding protein regulated by sigma factors sA and sB. PLoS One 4: e8017.
21. Cunha S, Odijk T, Süleymanoglu E, Woldringh CL (2001) Isolation of the Escherichia coli nucleoid. Biochimie 83: 149-154.
22. Yoshimura SH, Kim J, Takeyasu K (2003) On-substrate lysis treatment combined with scanning probe microscopy revealed chromosome structures in eukaryotes and prokaryotes. J Electron Microsc (Tokyo) 52: 415-423.
23. Hamon L, Pastré D, Dupaigne P, Le Breton C, Le Cam E, et al. (2007) Highresolution AFM imaging of single-stranded DNA-binding (SSB) protein-DNA complexes. Nucleic Acids Res 35: e58.
24. Rezwan M, Lanéelle MA, Sander P, Daffé M (2007) Breaking down the wall: fractionation of mycobacteria. J Microbiol Methods 68: 32-39.
25. Kleppe K, Ovrebö S, Lossius I (1979) The bacterial nucleoid. J Gen Microbiol 112: 1-13.
26. Fang Y, Spisz TS, Hoh JH (1999) Ethanol-induced structural transitions of DNA on mica. Nucleic Acids Res 27: 1943-1949.
27. Ojha AK, Mukherjee TK, Chatterji D (2000) High intracellular level of guanosine tetraphosphate in Mycobacterium smegmatis changes the morphology of the bacterium. Infect Immun 68: 4084-4091.
28. Ojha AK, Varma S, Chatterji D (2002) Synthesis of an unusual polar glycopeptidolipid in glucose-limited culture of Mycobacterium smegmatis. Microbiology 148: 3039-3048.
29. Ohniwa RL, Morikawa K, Takeshita SL, Kim J, Ohta T, et al. (2007) Transcription-coupled nucleoid architecture in bacteria. Genes Cells 12: 1141-1152.
30. Hecht RM, Pettijohn DE (1976) Studies of DNA bound RNA molecules isolated from nucleoids of Escherichia coli. Nucleic Acids Res 3: 767-788.
31. Facey PD, Hitchings MD, Saavedra-Garcia P, Fernandez-Martinez L, Dyson PJ, et al. (2009) Streptomyces coelicolor Dps-like proteins: differential dual roles in response to stress during vegetative growth and in nucleoid condensation during reproductive cell division. Mol Microbiol 73: 1186-1202.
32. Zamore PD, Haley B (2005) Ribo-gnome: the big world of small RNAs. Science 309: 1519-1524.
33. Frenkiel-Krispin D, Levin-Zaidman S, Shimoni E, Wolf SG, Wachtel EJ, et al. (2001) Regulated phase transitions of bacterial chromatin: a non-enzymatic pathway for generic DNA protection. Embo J 20: 1184-1191.
34. Ceci P, Cellai S, Falvo E, Rivetti C, Rossi GL, et al. (2004) DNA condensation and self-aggregation of Escherichia coli Dps are coupled phenomena related to the properties of the N-terminus. Nucleic Acids Res 32: 5935-5944.
35. Allen MJ, Bradbury EM, Balhorn R (1997) AFM analysis of DNA-protamine complexes bound to mica. Nucleic Acids Res 25: 2221-2226.
36. Balhorn R, Brewer L, Corzett M (2000) DNA condensation by protamine and arginine-rich peptides: analysis of toroid stability using single DNA molecules. Mol Reprod Dev 56: 230-234.
37. Roy S, Gupta S, Das S, Sekar K, Chatterji D, et al. (2004) X-ray analysis of Mycobacterium smegmatis Dps and a comparative study involving other Dps and Dps-like molecules. J Mol Biol 339: 1103-1113.
38. Frenkiel-Krispin D, Minsky A (2002) Biocrystallization: a last-resort survival strategy in bacteria. ASM News 68: 277-283.
39. Allison SA, Herr JC, Schurr JM (1981) Structure of viral phi 29 DNA condensed by simple triamines: a light-scattering and electron-microscopy study. Biopolymers 20: 469-488.
40. Hud NV, Vilfan ID (2005) Toroidal DNA condensates: unraveling the fine structure and the role of nucleation in determining size. Annu Rev Biophys Biomol Struct 34: 295-318.
41. Yoshikawa Y, Yoshikawa K, Kanbe T (1999) Formation of a giant toroid from long duplex DNA. Langmuir 15: 4085-4088.
42. Conwell CC, Vilfan ID, Hud NV (2003) Controlling the size of nanoscale toroidal DNA condensates with static curvature and ionic strength. Proc Natl Acad Sci USA 100: 9296-9301.
43. Lange R, Hengge-Aronis R (1991) Growth phase-regulated expression of bolA and morphology of stationary-phase Escherichia coli cells are controlled by the novel sigma factor sS. J Bacteriol 173: 4474-4481.
44. Basu D, Khare G, Singh S, Tyagi A, Khosla S, et al. (2009) A novel nucleoidassociated protein of Mycobacterium tuberculosis is a sequence homolog of GroEL. Nucleic Acids Res 37: 4944-4954.
45. Kumar M, Chatterji D (2008) Cyclic di-GMP: a second messenger required for long-term survival, but not for biofilm formation, in Mycobacterium smegmatis. Microbiology 154: 2942-2955.
46. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning: a laboratory manual. 2nd ed. NY: Cold Spring Harbor Laboratory, in Cold Spring Harbor Laboratory Press. 1659 p.
47. Pelicic V, Jackson M, Reyrat JM, Jacobs WR, Jr., Gicquel B, et al. (1997) Efficient allelic exchange and transposon mutagenesis in Mycobacterium tuberculosis. Proc Natl Acad Sci USA 94: 10955-10960.
48. Stover CK, de la Cruz VF, Fuerst TR, Burlein JE, Benson LA, et al. (1991) New use of BCG for recombinant vaccines. Nature 351: 456-460.