A novel replicative enzyme encoded by the linear Arthrobacter plasmid pAL1

Journal of Bacteriology

Volumn 192, Issue 19, 2010, Pages 4935-4943

  Kolkenbrock, Stephan ^a   Naumann, Bianca ^a   Hippler, Michael ^a   Fetzner, Susanne ^a  

^a UNIVERSITY OF MÜNSTER   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; DNA POLYMERASE; DNA TOPOISOMERASE; HELICASE; HYBRID PROTEIN; SINGLE STRANDED DNA; ZINC FINGER PROTEIN; BACTERIAL PROTEIN; DNA DIRECTED DNA POLYMERASE;

AMINO TERMINAL SEQUENCE; ARTHROBACTER; ARTICLE; BACTERIAL GENE; BIOINFORMATICS; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; DNA TEMPLATE; ENZYME ACTIVITY; ENZYME ASSAY; INVERTED REPEAT; NONHUMAN; PAL1 BACTERIAL GENE; PLASMID; POLYMERIZATION; PRIORITY JOURNAL; PROTEIN DOMAIN; REPLICON; AMINO ACID SEQUENCE; BIOLOGY; CHEMISTRY; ENZYMOLOGY; GENETICS; METABOLISM; MOLECULAR GENETICS; PROTEIN BINDING; SEQUENCE HOMOLOGY;

ACTINOBACTERIA (CLASS); ARTHROBACTER; ARTHROBACTER NITROGUAJACOLICUS; BACTERIA (MICROORGANISMS);

AMINO ACID SEQUENCE; ARTHROBACTER; BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; DNA HELICASES; DNA TOPOISOMERASES, TYPE I; DNA-DIRECTED DNA POLYMERASE; MOLECULAR SEQUENCE DATA; PLASMIDS; PROTEIN BINDING; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 77957367115     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.00614-10     Document Type: Article

References (60)

1. Aravind, L., D. D. Leipe, and E. V. Koonin. 1998. Toprim: a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. Nucleic Acids Res. 26:4205-4213.
2. Bao, K., and S. N. Cohen. 2001. Terminal proteins essential for the replication of linear plasmids and chromosomes in Streptomyces. Genes Dev. 15:1518-1527.
3. Bao, K., and S. N. Cohen. 2003. Recruitment of terminal protein to the ends of Streptomyces linear plasmids and chromosomes by a novel telomere-binding protein essential for linear DNA replication. Genes Dev. 17:774-785.
4. Bianco, P. R., L. R. Brewer, M. Corzett, R. Balhorn, Y. Yeh, S. C. Kowalczykowski, and R. J. Baskin. 2001. Processive translocation and DNA unwinding by individual RecBCD enzyme molecules. Nature 409:374-378.
5. Blanco, L., A. Bernad, J. M. Lázaro, G. Martín, C. Garmendia, and M. Salas. 1989. Highly efficient DNA synthesis by the phage φ29 DNA polymerase. Symmetrical mode of DNA replication. J. Biol. Chem. 264:8935-8940.
6. Blanco, L., J. M. Lázaro, M. De Vega, A. Bonnin, and M. Salas. 1994. Terminal protein-primed DNA amplification. Proc. Natl. Acad. Sci. U. S. A. 91:12198-12202.
7. Blanco, L., and M. Salas. 1996. Relating structure to function in φ29 DNA polymerase. J. Biol. Chem. 271:8509-8512.
8. Caruthers, J. M., and D. B. McKay. 2002. Helicase structure and mechanism. Curr. Opin. Struct. Biol. 12:123-133.
9. Chang, P.-C., and S. N. Cohen. 1994. Bidirectional replication from an internal origin in a linear Streptomyces plasmid. Science 265:952-954.
10. Choi, J. K., K. H. Tak, L. T. Jin, S. Y. Hwang, T. I. Kwon, and G. S. Yoo. 2002. Background-free fast protein staining in sodium dodecyl sulfate polyacrylamide gel using counterion dyes, zincon and ethyl violet. Electrophoresis 23:4053-4059.
11. Dexheimer, T. S., and Y. Pommier. 2008. DNA cleavage assay for the identification of topoisomerase I inhibitors. Nat. Protoc. 3:1736-1750.
12. Dillingham, M. S., M. R. Webb, and S. C. Kowalczykowski. 2005. Bipolar DNA translocation contributes to highly processive DNA unwinding by RecBCD enzyme. J. Biol. Chem. 280:37069-37077.
13. Dong, F., S. E. Weitzel, and P. H. von Hippel. 1996. A coupled complex of T4 DNA replication helicase (gp41) and polymerase (gp43) can perform rapid and processive DNA strand-displacement synthesis. Proc. Natl. Acad. Sci. U. S. A. 93:14445-14461.
14. Dufour, E., J. Méndez, J. M. Lázaro, M. de Vega, L. Blanco, and M. Salas. 2000. An aspartic acid residue in TPR-1, a specific region of protein-priming DNA polymerases, is required for the functional interaction with primer terminal protein. J. Biol. Chem. 304:289-300.
15. Dufour, E., I. Rodríguez, J. M. Lázaro, M. de Vega, and M. Salas. 2003. A conserved insertion in protein-primed DNA polymerases is involved in primer terminus stabilisation. J. Mol. Biol. 331:781-794.
16. Eggleston, A. K., N. A. Rahim, and S. C. Kowalczykowski. 1996. A helicase assay based on the displacement of fluorescent, nucleic-acid binding ligands. Nucleic Acids Res. 24:1179-1186.
17. Gartemann, K. H., and R. Eichenlaub. 2001. Isolation and characterization of IS1409, an insertion element of 4-chlorobenzoate-degrading Arthrobacter sp. strain TM1, and development of a system for transposon mutagenesis. J. Bacteriol. 183:3729-3736.
18. Grigoriev, A. 1998. Analyzing genomes with cumulative skew diagrams. Nucleic Acids Res. 26:2286-2290.
19. Grishin, N. V. 2000. C-terminal domains of Escherichia coli topoisomerase I belong to the zinc-ribbon superfamily. J. Mol. Biol. 299:1165-1177.
20. Hall, M. C., and S. W. Matson. 1999. Helicase motifs: the engine that powers DNA unwinding. Mol. Microbiol. 34:867-877.
21. Hamdan, S. M., and C. C. Richardson. 2009. Motors, switches, and contacts in the replisome. Annu. Rev. Biochem. 78:205-243.
22. Hanahan, D. 1983. Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol. 166:557-580.
23. Hiratsu, K., S. Mochizuki, and H. Kinashi. 2000. Cloning and analysis of the replication origin and the telomeres of the large linear plasmid pSLA2-L in Streptomyces rochei. Mol. Gen. Genet. 263:1015-1021.
24. Huang, C.-H., H.-H. Tsai, Y.-G. Tsay, Y.-N. Chien, S.-L. Wang, M.-Y. Cheng, C.-H. Ke, and C. W. Chen. 2007. The telomere system of the Streptomyces linear plasmid SCP1 represents a novel class. Mol. Microbiol. 63:1710-1718.
25. Illana, B., L. Blanco, and M. Salas. 1996. Functional characterization of the genes coding for the terminal protein and DNA polymerase from bacteriophage GA-1. Evidence for a sliding-back mechanism during protein-primed GA-1 DNA replication. J. Mol. Biol. 264:453-464.
26. Kamtekar, S., A. J. Berman, J. Wang, J. M. Lázaro, M. de Vega, L. Blanco, M. Salas, and T. A. Steitz. 2004. Insights into strand displacement and processivity from the crystal structure of the protein-primed DNA polymerase of bacteriophage φ29. Mol. Cell 16:609-618.
27. Kamtekar, S., J. Méndez, J. M. Lázaro, M. de Vega, L. Blanco, and M. Salas. 2006. The φ29 DNA polymerase:protein-primer structure suggests a model for the initiation to elongation transition. EMBO J. 25:1335-1343.
28. Kim, S., H. G. Dallmann, C. S. McHenry, and K. J. Marians. 1996. Coupling of a replicative polymerase and helicase: a Τ-DnaB interaction mediates rapid replication fork movement. Cell 84:643-650.
29. Klassen, R., and F. Meinhardt. 2007. Linear protein-primed replicating plasmids in eukaryotic microbes, p. 187-226. In F. Meinhardt and R. Klassen (ed.), Microbial linear plasmids. Microbiology monograph 7. Springer, Heidelberg, Germany.
30. Kolkenbrock, S., and S. Fetzner. 2010. Identification and in vitro deoxynucleotidylation of the terminal protein of the linear plasmid pAL1 of Arthrobacter nitroguajacolicus Rü61a. FEMS Microbiol. Lett. 304:169-176.
31. Lohman, T. M., and K. P. Bjornson. 1996. Mechanisms of helicase-catalyzed DNA unwinding. Annu. Rev. Biochem. 65:169-214.
32. Martín, A. C., L. Blanco, P. García, and M. Salas. 1996. In vitro initiation of pneumococcal phage Cp-1 DNA replication occurs at the third 3′ nucleotide of the linear template: a stepwise sliding-back mechanism. J. Mol. Biol. 260:369-377.
33. Méndez, J., L. Blanco, J. A. Esteban, A. Bernad, and M. Salas. 1992. Initiation of φ29 DNA replication occurs at the second 3′-nucleotide of the linear template: a sliding-back mechanism for protein-primed DNA replication. Proc. Natl. Acad. Sci. U. S. A. 89:9579-9583.
34. Overhage, J., S. Sielker, S. Homburg, K. Parschat, and S. Fetzner. 2005. Identification of large linear plasmids in Arthrobacter spp. encoding the degradation of quinaldine to anthranilate. Microbiology 151:491-500.
35. Parschat, K., B. Hauer, R. Kappl, R. Kraft, J. Hüttermann, and S. Fetzner. 2003. Gene cluster of Arthrobacter ilicis Rü61a involved in the degradation of quinaldine to anthranilate. J. Biol. Chem. 278:27483-27494.
36. Parschat, K., J. Overhage, A. W. Strittmatter, A. Henne, G. Gottschalk, and S. Fetzner. 2007. Complete nucleotide sequence of the 113-kilobase linear catabolic plasmid pAL1 of Arthrobacter nitroguajacolicus Rü61a and transcriptional analysis of genes involved in quinaldine degradation. J. Bacteriol. 189:3855-3867.
37. Pérez-Arnaiz, P., E. Longás, L. Villar, J. M. Lázaro, M. Salas, and M. de Vega. 2007. Involvement of phage φ29 DNA polymerase and terminal protein subdomains in conferring specificity during initiation of protein-primed DNA replication. Nucleic Acids Res. 35:7061-7073.
38. Picardeau, M., C. Le Dantec, and V. Vincent. 2000. Analysis of the internal replication region of a mycobacterial linear plasmid. Microbiology 146:305-313.
39. Rainey, F. A., N. Ward-Rainey, R. M. Kroppenstedt, and E. Stackebrandt. 1996. The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage: proposal of Nocardiopsaceae fam. nov. Int. J. Syst. Bacteriol. 46:1088-1092.
40. Roche Molecular Biochemicals. 1995. The DIG system user's guide for filter hybridization. Boehringer Mannheim GmbH, Mannheim, Germany.
41. Roman, L. J., and S. C. Kowalczykowski. 1989. Characterization of the helicase activity of the Escherichia coli RecBCD enzyme using a novel helicase assay. Biochemistry 28:2863-2873.
42. Salas, M. 1991. Protein-priming of DNA replication. Annu. Rev. Biochem. 60:39-71.
43. Salas, M., L. Blanco, J. M. Lázaro, and M. de Vega. 2008. The bacteriophage φ29 DNA polymerase. IUBMB Life 60:82-85.
44. Salas, M., R. Freire, M. S. Soengas, J. A. Esteban, J. Méndez, A. Bravo, M. Serrano, M. A. Blasco, J. M. Lázaro, L. Blanco, C. Gutiérrez, and J. M. Hermoso. 1995. Protein-nucleic acid interactions in bacteriophage φ29 DNA replication. FEMS Microbiol. Rev. 17:73-82.
45. Sambrook, J., and D. W. Russell. 2001. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
46. Singleton, M. R., and D. B. Wigley. 2002. Modularity and specialization in superfamily 1 and 2 helicases. J. Bacteriol. 184:1819-1826.
47. Sissi, C., and M. Palumbo. 2009. Effects of magnesium and related divalent metal ions in topoisomerase structure and function. Nucleic Acids Res. 37:702-711.
48. Smith, P. K., R. I. Krohn, G. T. Hermanson, A. K. Mallia, F. H. Gartner, M. D. Provenzano, E. K. Fujimoto, N. M. Goeke, B. J. Olson, and D. C. Klenk. 1985. Measurement of protein using bicinchoninic acid. Anal. Biochem. 150:76-85.
49. Stauber, E. J., A. Busch, B. Naumann, A. Svatos, and M. Hippler. 2009. Proteotypic profiling of LHCI from Chlamydomonas reinhardtii provides new insights into structure and function of the complex. Proteomics 9:398-408.
50. Stauber, E. J., A. Fink, C. Markert, O. Kruse, U. Johanningmeier, and M. Hippler. 2003. Proteomics of Chlamydomonas reinhardtii light-harvesting proteins. Eukaryot. Cell 2:978-994.
51. Steitz, T. A. 1999. DNA polymerases: structural diversity and common mechanisms. J. Biol. Chem. 274:17395-17398.
52. Stoll, A., M. Redenbach, and J. Cullum. 2007. Identification of essential genes for linear replication of an SCP1 composite plasmid. FEMS Microbiol. Lett. 270:146-154.
53. Studier, F. W. 2005. Protein production by auto-induction in high-density shaking cultures. Protein Expr. Purif. 41:207-234.
54. Suzuki, H., K. Marushima, Y. Ohnishi, and S. Horinouchi. 2008. A novel pair of terminal protein and telomere-associated protein for replication of the linear chromosome of Streptomyces griseus IFO13350. Biosci. Biotechnol. Biochem. 72:2973-2980.
55. Trego, K. S., and D. S. Parris. 2003. Functional interaction between the herpes simplex virus type 1 polymerase processivity factor and origin-binding proteins: Enhancement of UL9 helicase activity. J. Virol. 77:12646-12659.
56. Walker, J. E., M. Saraste, M. J. Runswick, and N. J. Gay. 1982. Distantly related sequences in the α- and β-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1:945-951.
57. Warren, R., W. W. L. Hsiao, H. Kudo, M. Myhre, M. Dosanjh, A. Petrescu, H. Kobayashi, S. Shimizu, K. Miyauchi, E. Masai, G. Yang, J. M. Stott, J. E. Schein, H. Shin, J. Khattra, D. Smailus, Y. S. Butterfield, A. Siddiqui, R. Holt, M. A. Marra, S. J. M. Jones, W. W. Mohn, F. S. L. Brinkman, M. Fukuda, J. Davies, and L. D. Eltis. 2004. Functional characterization of a catabolic plasmid from polychlorinated-biphenyl-degrading Rhodococcus sp. strain RHA1. J. Bacteriol. 186:7783-7795.
58. Yang, C.-C., Y.-H. Chen, H.-H. Tsai, C.-H. Huang, T.-W. Huang, and C. W. Chen. 2006. In vitro deoxynucleotidylation of the terminal protein of Streptomyces linear chromosomes. Appl. Environ. Microbiol. 72:7959-7961.
59. Zhang, R., Y. Yang, P. Fang, C. Jiang, L. Xu, Y. Zhu, M. Shen, H. Xia, J. Zhao, T. Chen, and Z. Qin. 2006. Diversity of telomere palindromic sequences and replication genes among Streptomyces linear plasmids. Appl. Environ. Microbiol. 72:5728-5733.
60. Zhang, R., H. Xia, P. Guo, and Z. Qin. 2009. Variation in the replication loci of Streptomyces linear plasmids. FEMS Microbiol. Lett. 290:209-216.