Structural organization of DNA in chlorella viruses

PLoS ONE

Volumn 7, Issue 2, 2012, Pages

  Wulfmeyer, Timo ^a   Polzer, Christian ^a   Hiepler, Gregor ^a   Hamacher, Kay ^a   Shoeman, Robert ^b   Dunigan, David D ^c   van Etten, James L ^c   Lolicato, Marco ^d   Moroni, Anna ^d   Thiel, Gerhard ^a   Meckel, Tobias ^a  

^a DARMSTADT UNIVERSITY OF TECHNOLOGY   (Germany)

^b MAX PLANCK INSTITUTE FOR MEDICAL RESEARCH   (Germany)

^c UNIVERSITY OF NEBRASKA LINCOLN   (United States)

^d UNIVERSITY OF MILAN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; PROTEIN A278L; PROTEIN A282L; UNCLASSIFIED DRUG; VIRUS DNA; CAPSID PROTEIN; VIRUS PROTEIN;

ARTICLE; ATOMIC FORCE MICROSCOPY; BINDING SITE; CHLORELLA VIRUS; CONTROLLED STUDY; DNA DETERMINATION; DNA PACKAGING; DNA STRUCTURE; FLUORESCENCE; GENE CONTROL; NONHUMAN; NUCLEOTIDE SEQUENCE; PARTICLE SIZE; PROTEIN AGGREGATION; PROTEIN ANALYSIS; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION; PROTEOMICS; VIRUS GENOME; CHEMISTRY; CHLORELLA; GC RICH SEQUENCE; GREEN ALGA; VIROLOGY;

ALGAE; CHLORELLA VIRUS; EUKARYOTA; MIRIDAE;

CAPSID PROTEINS; CHLORELLA; CHLOROPHYTA; DNA PACKAGING; DNA, VIRAL; DNA-BINDING PROTEINS; FLUORESCENCE; GC RICH SEQUENCE; GENOME, VIRAL; VIRAL PROTEINS;

EID: 84857125476     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0030133     Document Type: Article

References (45)

1. Iyer LM, Balaji S, Koonin EV, Aravind L, (2006) Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Virus Res 117: 156-184.
2. Raoult D, Audic S, Robert C, Abergel C, Renesto P, et al. (2004) The 1.2-megabase genome sequence of mimivirus. Science 306: 1344-1350.
3. Villarreal LP, DeFilippis VR, (2000) A hypothesis for DNA viruses as the origin of eukaryotic replication proteins. J Virol 74: 7079-7084.
4. Iyer LM, Aravind L, Koonin EV, (2001) Common origin of four diverse families of large eukaryotic DNA viruses. J Virol 75: 11720-11734.
5. Koonin EV, Yutin N, (2010) Origin and evolution of eukaryotic large nucleo-cytoplasmic DNA viruses. Intervirology 53: 284-292.
6. Yan X, Olson NH, Van Etten JL, Bergoin M, Rossmann MG, et al. (2000) Structure and assembly of large lipid-containing dsDNA viruses. Nat Struct Biol 7: 101-103.
7. Cherrier MV, Kostyuchenko VA, Xiao C, Bowman VD, Battisti AJ, et al. (2009) An icosahedral alga virus has a complex unique vertex decorated by a spike. Proc Natl Sci USA 106: 11085-11089.
8. Zhang X, Xiang Y, Dunigan DD, Klose T, Chipman PR, et al. (2011) The structure and function of the Paramecium bursaria chlorella virus capsid. Proc Natl Acad Sci USA 108: 14837-14842.
9. Meints RH, Lee K, Burbank DE, VanEtten JL, (1984) Infection of a Chlorella-like alga with the virus PBCV-1: ultrastructural studies. Virology 138: 341-346.
10. Frohns F, Käsmann A, Kramer D, Schäfer B, Mehmel M, et al. (2006) Potassium ion channels of chlorella viruses cause rapid depolarization of host cells during infection. J Virol 80: 2437-2444.
11. Neupärtl M, Meyer C, Woll I, Frohns F, Kang M, et al. (2008) Chlorella viruses evoke a rapid release of K+ from host cells during early phase of infection. Virology 372: 340-348.
12. Agarkova I, Dunigan DD, Gurnon J, Greiner T, Barres J, et al. (2008) Chlorovirus-mediated membrane depolarization of chlorella alters secondary active transport of solutes. J Virol 82: 12181-12190.
13. Thiel G, Moroni A, Dunigan D, Van Etten JL, (2010) Initial Events Associated with Virus PBCV-1 Infection of Chlorella NC64A. Prog Bot 71: 169-183.
14. Grayson P, Han L, Winther T, Philips R, (2007) Real-time observations of single bacteriophage lambda DNA ejection in vitro. Proc Natl Acad Sci USA 104: 14652-14657.
15. Cordova A, Deserno M, Gelbart WM, Ben-Shaul A, (2003) Osmotic shock and the strength of viral capsids. Biophys J 85: 70-74.
16. Earnshaw WC, Casjens SR, (1980) DNA packaging by the double-stranded DNA bacteriophages. Cell 21: 319-331.
17. Kuznetsov Y, Gershon PD, McPherson A, (2008) Atomic force microscopy investigation of vaccinia virus structure. J Virol 82: 7551-7566.
18. Kuznetsov YG, Xiao C, Sun S, Raoult D, Rossmann M, et al. (2010) Atomic force microscopy investigation of the giant mimivirus. Virology 404: 127-137.
19. Li Z, Wu J, Wang Z-G, (2008) Osmotic pressure and packing structure of caged DNA. Biophys J 94: 737-746.
20. Kindt J, Tzlil S, Ben-Shaul A, Gelbart WM, (2001) DNA packaging and ejection forces in bacteriophage. Proc Natl Acad Sci USA 98: 13671-13674.
21. Mangenot S, Hochrein M, Räder J, Letellier L, (2005) Real-time imaging of DNA ejection from single phage particles. Curr Biol 15: 430-435.
22. Grayson P, Molineux IJ, (2007) Is phage DNA 'injected' into cells- biologists and physicists can agree. Current Opin Microbiol 10: 401-409.
23. Bloomfield VA, (1997) DNA condensation by multivalent cations. Biopolymers 44: 269-282.
24. Ames BN, Dubin DT, (1960) The role of polyamines in the neutralization of bacteriophage deoxyribonucleic acid. J Biol Chem 235: 769-775.
25. Hass R, Murphy RF, Cantor CR, (1982) Testing models of the arrangement of DNA inside bacteriophage lamda by crosslinking the packaged DNA. J Mol Biol 159: 71-92.
26. Serwer P, (1986) Arrangement of double-stranded DNA packaged in bacteriophage capsids. An alternative model. J Mol Biol 190: 509-512.
27. Casjens SR, (2011) The DNA-packaging nanomotor of tailed bacteriophages. Nature Reviews 9: 647-657.
28. Tan KB, (1977) Histones: metabolism in simian virus 40-infected cells and incorporation into virions. Proc. Natl Acad Sci USA 74: 2805-2809.
29. Pfister H, zur Hausen H, (1978) Characterization of proteins of human papilloma viruses (HPV) and antibody response to HPV 1. Med. Microbiol Immunol 166: 13-19.
30. Tweeten KA, Bulla LA, Consigli RA, (1980) Characterization of an extremely basic protein derived from granulosis virus nucleocapsids. J Virol 33: 866-876.
31. Wang M, Tuladhar E, Shen S, Wang H, van Oers MM, et al. (2010) Specificity of Baculovirus P6.9 basic DNA-binding proteins and critical role oft he c terminus in virion formation. J Virol 84: 8821-8828.
32. Yamada T, Furukawa S, Hamazaki T, Songsri P, (1996) Characterization of DNA-binding proteins and protein kinase activities in Chlorella virus CVK2. Virology 219: 395-406.
33. Meints RH, Burbank DE, Van Etten JL, Lamport DT, (1988) Properties of the Chlorella receptor for the virus PBCV-1. Virology 164: 15-21.
34. Greiner T, Frohns F, Kang M, Van Etten JL, Käsmann, et al. (2009) Chlorella viruses prevent multiple infections by depolarizing the host membranes. J Gen Virol 90: 2033-2039.
35. Ore A, Pollard E, (1956) Physical mechanism of bacteriophage injection. Science 124: 430-432.
36. Kuznetsov YG, Gurnon JR, Van Etten JL, McPherson A, (2005) Atomic force microscopy investigation of a chlorella virus, PBCV-1. J Struc Biol 149: 256-263.
37. Schneider SW, Lärmer J, Henderson RM, Oberleithner H, (1998) Molecular weights of individual proteins correlate with molecular volumes measured by atomic force microscopy. Pflügers Arch- Eur J Physiol 435: 362-367.
38. Cavalcanti MC, Rizgalla M, Geyer J, Failing K, Litzke LF, et al. (2009) Expression of histone 1 (H1) and testis-specific histone 1 (H1t) genes during stallion spermatogenesis. Animal Reprod Sci 111: 220-234.
39. Funk CJ, Consigli RA, (1993) Phosphate cycling on the basic protein of Plodia interpunctella granulosis virus. Virology 193: 396-402.
40. Ishihama Y, Oda Y, Tabata T, Sato T, Nagasu T, et al. (2005) Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol & Cell Proteomics 4: 1265-1272.
41. Hoshina R, Iwataki M, Imamura N, (2010) Chlorella variabilis and Micractinium reisseri sp. nov. (Chlorellaceae, Trebouxiophyceae): Redescription of the endosymbiotic green algae of Paramecium bursaria (Peniculia, Oligohymenophorea) in the 120th year. Phycol Res 58: 188-210.
42. Van Etten JL, Burbank DE, Kuczmarski D, Meints RH, (1983) virus infection of culturable chlorella-like algae and development of a plaque assay. Science 219: 994-996.
43. Hamacher K, (2008) Relating Sequence Evolution of HIV1-Protease to Its Underlying Molecular Mechanics. Gene 422: 30-36.
44. Bremm S, Schreck T, Boba P, Held S, Hamacher K, (2010) Computing and Visually Analyzing Mutual Information in Molecular Co-Evolution. BMC Bioinform 11: 330.
45. Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, et al. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25: 1422-1423.