An archaeal histone is required for transformation of Thermococcus kodakarensis

Journal of Bacteriology

Volumn 194, Issue 24, 2012, Pages 6864-6874

  Čuboňová, Lubomira ^a   Katano, Masahiro ^b,c   Kanai, Tamotsu ^b,c   Atomi, Haruyuki ^b,c   Reeve, John N ^a   Santangelo, Thomas J ^a  

^a OHIO STATE UNIVERSITY   (United States)

^b KYOTO UNIVERSITY   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEAL PROTEIN; GENOMIC DNA; HISTONE; PROTEIN HTKA; PROTEIN HTKB; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GROWTH; BACTERIAL STRAIN; BIOTRANSFORMATION; CODON; DNA RECOMBINATION; GENE DELETION; GENETIC TRANSCRIPTION; MICROARRAY ANALYSIS; NONHUMAN; PLASMID; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN STRUCTURE; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; THERMOCOCCUS KODAKARENSIS; WILD TYPE;

AMINO ACID SEQUENCE; ARCHAEAL PROTEINS; DNA, ARCHAEAL; DNA-BINDING PROTEINS; GENE DELETION; GENE EXPRESSION REGULATION, ARCHAEAL; HISTONES; NUCLEOSOMES; PROTEIN FOLDING; SEQUENCE ALIGNMENT; THERMOCOCCUS; TRANSCRIPTION, GENETIC; TRANSFORMATION, GENETIC;

ARCHAEA; EUKARYOTA; THERMOCOCCUS KODAKARENSIS;

EID: 84870724169     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.01523-12     Document Type: Article

References (44)

1. Brogaard K, Xi L, Wang JP, Widom J. 2012. A map of nucleosome positions in yeast at base-pair resolution. Nature 486:496-501.
2. Čuboňová L, Sandman K, Hallam SJ, DeLong EF, Reeve JN. 2005. Histones in Crenarchaea. J. Bacteriol. 187:5482-5485.
3. Decanniere K, Babu AM, Sandman K, Reeve JN, Heinemann U. 2000. Crystal structures of recombinant histones HMfA and HMfB from the hyperthermophilic archaeon Methanothermus fervidus. J. Mol. Biol. 303: 35-47.
4. Dinger ME, Baillie GJ, Musgrave DR. 2000. Growth phase-dependent expression and degradation of histones in the thermophilic archaeon Thermococcus zilligii. Mol. Microbiol. 36:876-885.
5. Forbes AJ, et al. 2004. Targeted analysis and discovery of posttranslational modifications in proteins from methanogenic archaea by top-down MS. Proc. Natl. Acad. Sci. U. S. A. 101:2678-2683.
6. Fukui T, et al. 2005. Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. Genome Res. 15:352-363.
7. Geiduschek EP, Ouhammouch M. 2005. Archaeal transcription and its regulators. Mol. Microbiol. 56:1397-1407.
8. Grayling RA, Bailey KA, Reeve JN. 1997. DNA binding and nuclease protection by the HMf histones from the hyperthermophilic archaeon Methanothermus fervidus. Extremophiles 1:79-88.
9. Hadjithomas M, Moudrianakis EN. 2011. Experimental evidence for the role of domain swapping in the evolution of the histone fold. Proc. Natl. Acad. Sci. U. S. A. 108:13462-13467.
10. Heinicke I, Müller J, Pittelkow M, Klein A. 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.
11. Higashibata H, Fujiwara S, Takagi M, Imanaka T. 1999. Analysis of DNA compaction profile and intracellular contents of archaeal histones from Pyrococcus kodakaraensis KOD1. Biochem. Biophys. Res. Commun. 258:416-424.
12. Hileman TH, Santangelo TJ. 2012. Genetics techniques for Thermococcus kodakarensis. Front. Microbiol. 3:195. doi:10.3389/fmicb.2012.00195.
13. Imanaka T. 2011. Molecular bases of thermophily in hyperthermophiles. Proc. Jpn. Acad. Ser. B Phys. Biol. Sci. 87:587-602.
14. Jahn U, Aigner J, Längst G, Reeve JN, Huber H. 2009. Nanoarchaeal origin of histone H3? J. Bacteriol. 191:1092-1096.
15. Kanai T, et al. 2005. Continuous hydrogen production by the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J. Biotechnol. 116: 271-282.
16. Kanai T, Takedomi S, Fujiwara S, Atomi H, Imanaka T. 2010. Identification of the Phr-dependent heat shock regulon in the hyperthermophilic archaeon, Thermococcus kodakaraensis. J. Biochem. 147:361-370.
17. Li Z, et al. 2011. A novel DNA nuclease is stimulated by association with the GINS complex. Nucleic Acids Res. 39:6114-6123.
18. Li Z, Santangelo TJ, Cuboňová L, Reeve JN, Kelman Z. 2010. Affinity purification of an archaeal DNA replication protein network. mBio 1(5): e00221-10. doi:10.1128/mBio.00221-10.
19. Li T, Sun F, Ji X, Feng Y, Rao Z. 2003. Structure based hyperthermostability of archaeal histone HPhA from Pyrococcus horikoshii. J. Mol. Biol. 325:1031-1037.
20. Marc F, Sandman K, Lurz R, Reeve JN. 2002. Archaeal histone tetramer formation determines DNA affinity, and the direction of DNA supercoiling. J. Biol. Chem. 277:30879-30886.
21. Mariño-Ramírez L, et al. 2011. The Histone Database: an integrated resource for histones and histone fold-containing proteins. Database 2011:bar048. doi:10.1093/database/bar048.
22. Maruyama H, et al. 2011. Histone and TK0471/TrmBL2 form a novel heterogeneous genome architecture in the hyperthermophilic archaeon Thermococcus kodakarensis. Mol. Biol. Cell 22:386-398.
23. Pan M, Santangelo TJ, Li Z, Reeve JN, Kelman Z. 2011. Thermococcus kodakarensis encodes threeMCMhomologs but only one is essential. Nucleic Acids Res. 39:9671-9680.
24. Pereira S, Grayling RA, Lurz R, Reeve JN. 1997. Archaeal nucleosomes. Proc. Natl. Acad. Sci. U. S. A. 94:12633-12637.
25. Sandman K, Grayling RA, Dobrinski B, Lurz R, Reeve JN. 1994. Growth phase dependent synthesis of histones in the archaeon Methanothermus fervidus. Proc. Natl. Acad. Sci. U. S. A. 91:12624-12628.
26. Sandman K, Krzycki JA, Dobrinski B, Lurz R, Reeve JN. 1990. DNA binding protein HMf, from the hyperthermophilic archaebacterium Methanothermus fervidus, is most closely related to histones. Proc. Natl. Acad. Sci. U. S. A. 87:5788-5791.
27. Sandman K, Louvel H, Samson RY, Pereira SL, Reeve JN. 2008. Archaeal chromatin proteins histone HMtB and Alba have lost DNAbinding ability in laboratory strains of Methanothermobacter thermautotrophicus. Extremophiles 12:811-817.
28. Sandman K, Reeve JN. 2000. Structure and functional relationships of archaeal and eukaryal histones and nucleosomes. Arch. Microbiol. 173: 165-169.
29. Sandman K, Reeve JN. 2005. Archaeal chromatin proteins: different structures but common function? Curr. Opin. Microbiol. 8:656-661.
30. Sandman K, Reeve JN. 2006. Archaeal histones and the origin of the histone fold. Curr. Opin. Microbiol. 9:520-525.
31. Santangelo TJ, Cuboňová L, James CL, Reeve JN. 2007. TFB1 or TFB2 is sufficient for Thermococcus kodakarensis viability and basal transcription in vitro. J. Mol. Biol. 367:344-357.
32. Santangelo TJ, Cuboňová L, Reeve JN. 2008. Shuttle vector expression in Thermococcus kodakaraensis: contributions of cis elements to protein synthesis in a hyperthermophilic archaeon. Appl. Environ. Microbiol. 74: 3099-3104.
33. Santangelo TJ, Cuboňová L, Reeve JN. 2010. Thermococcus kodakarensis genetics: TK1827-encoded beta-glycosidase, new positive-selection protocol, and targeted and repetitive deletion technology. Appl. Environ. Microbiol. 74:1044-1052.
34. Santangelo TJ, Cuboňová L, Reeve JN. 2011. Deletion of alternative pathways for reductant recycling in Thermococcus kodakarensis increases hydrogen production. Mol. Microbiol. 81:897-911.
35. Santangelo TJ, Reeve JN. 2010. Deletion of switch 3 results in an archaeal RNA polymerase that is defective in transcript elongation. J. Biol. Chem. 285:23908-23915.
36. Sato T, Fukui T, Atomi H, Imanaka T. 2003. Targeted gene disruption by homologous recombination in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J. Bacteriol. 185:210-220.
37. Shin J-H, Santangelo TJ, Xie Y, Reeve JN, Kelman Z. 2007. Archaeal MCM helicase can unwind DNA bound by archaeal histones and transcription factors. J. Biol. Chem. 282:4908-4915.
38. Slesarev AI, Belova GI, Kozyavkin SA, Lake JA. 1998. Evidence for an early prokaryotic origin of histones H2A and H4 prior to the emergence of eukaryotes. Nucleic Acids Res. 26:427-430.
39. Soares DJ, Sandman K, Reeve JN. 2000. Mutational analysis of archaeal histone-DNA interactions. J. Mol. Biol. 297:39-47.
40. Soler N, et al. 2007. The rolling-circle plasmid pTN1 from the hyperthermophilic archaeon Thermococcus nautilus. Mol. Microbiol. 66:357-370.
41. Weidenbach K, et al. 2008. Deletion of the archaeal histone in Methanosarcina mazei Gö1 results in reduced growth and genomic transcription. Mol. Microbiol. 67:662-671.
42. Weng L, Liu D, Li Y, Cao S, Feng Y. 2004. An archaeal histone-like protein as an efficient DNA carrier in gene transfer. Biochim. Biophys. Acta 1702:209-216.
43. Wilkinson SP, Ouhammouch M, Geiduschek EP. 2010. Transcriptional activation in the context of repression mediated by archaeal histones. Proc. Natl. Acad. Sci. U. S. A. 107:6777-6781.
44. Xie Y, Reeve JN. 2004. Transcription by an archaeal RNA polymerase is slowed but not blocked by an archaeal nucleosome. J. Bacteriol. 186:3492-3498.