Replication-involved genes of pAL1, the linear plasmid of Arthrobacter nitroguajacolicus Rü61a - Phylogenetic and transcriptional analysis

Plasmid

Volumn 65, Issue 2, 2011, Pages 176-184

  Wagenknecht, Martin ^a   Meinhardt, Friedhelm ^a  

^a UNIVERSITY OF MÜNSTER   (Germany)

Author keywords

Actinomycetes; Arthrobacter; Linear plasmid; Replication; Telomere associated protein; Terminal protein

Indexed keywords

ARTHROBACTER; ARTHROBACTER NITROGUAJACOLICUS; ARTICLE; BACTERIAL GENE; CONTROLLED STUDY; DNA REPLICATION; DNA REPLICATION ORIGIN; GENETIC TRANSCRIPTION; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; PLASMID; REPLICON; RHODOCOCCUS; STREPTOMYCES; TELOMERE;

AMINO ACID SEQUENCE; ARTHROBACTER; BACTERIAL PROTEINS; DNA REPLICATION; GENE ORDER; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; OPERON; PHYLOGENY; PLASMIDS; REPLICATION ORIGIN; SEQUENCE ALIGNMENT;

ACTINOBACTERIA; ACTINOBACTERIA (CLASS); ARTHROBACTER; ARTHROBACTER NITROGUAJACOLICUS; STREPTOMYCES; STREPTOMYCINEAE;

EID: 79551482446     PISSN: 0147619X     EISSN: 10959890     Source Type: Journal    
DOI: 10.1016/j.plasmid.2010.12.005     Document Type: Article

References (59)

1. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
2. Arakawa K., Tomita M. The GC skew index: a measure of genomic compositional asymmetry and the degree of replicational selection. Evol. Bioinform. Online 2007, 3:159-168.
3. Bagwell C.E., Bhat S., Hawkins G.M., Smith B.W., Biswas T., Hoover T.R., Saunders E., et al. Survival in nuclear waste, extreme resistance, and potential applications gleaned from the genome sequence of Kineococcus radiotolerans SRS30216. PLoS One 2008, 3:e3878.
4. Bao K., Cohen S.N. Terminal proteins essential for the replication of linear plasmids and chromosomes in Streptomyces. Genes Dev. 2001, 15:1518-1527.
5. Bao K., Cohen S.N. 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. 2003, 17:774-785.
6. Bao K., Cohen S.N. Reverse transcriptase activity innate to DNA polymerase I and DNA topoisomerase I proteins of Streptomyces telomere complex. Proc. Natl. Acad. Sci. USA 2004, 101:14361-14366.
7. Bentley S.D., Brown S., Murphy L.D., Harris D.E., Quail M.A., Parkhill J., Barrell B.G., et al. SCP1, a 356,023 bp linear plasmid adapted to the ecology and developmental biology of its host, Streptomyces coelicolor A3(2). Mol. Microbiol. 2004, 51:1615-1628.
8. Brown S.E., Knudson D.L., Ishimaru C.A. Linear plasmid in the genome of Clavibacter michiganensis subsp. sepedonicus. J. Bacteriol. 2002, 184:2841-2844.
9. Chang P.C., Cohen S.N. Bidirectional replication from an internal origin in a linear Streptomyces plasmid. Science 1994, 265:952-954.
10. Chater K.F., Kinashi H. Streptomyces linear plasmids: their discovery, functions, interactions with other replicons, and evolutionary significance. Microbial Linear Plasmids 2007, 1-32. Springer, Berlin, Heidelberg, New York. F. Meinhardt, R. Klassen (Eds.).
11. Chen C.W. Streptomyces linear plasmids: replication and telomeres. Microbial Linear Plasmids 2007, 33-62. Springer, Berlin, Heidelberg, New York. F. Meinhardt, R. Klassen (Eds.).
12. Dib J.R., Wagenknecht M., Hill R.T., Farias M.E., Meinhardt F. First report of linear megaplasmids in the genus Micrococcus. Plasmid 2010, 63:40-45.
13. Dib J.R., Wagenknecht M., Hill R.T., Farias M.E., Meinhardt F. Novel linear megaplasmid from Brevibacterium sp. isolated from extreme environment. J. Basic Microbiol. 2010, 50:280-284.
14. Gartemann K.H., Eichenlaub R. 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. 2001, 183:3729-3736.
15. Grigoriev A. Analyzing genomes with cumulative skew diagrams. Nucleic Acids Res. 1998, 26:2286-2290.
16. Hamoen L.W., Eshuis H., Jongbloed J., Venema G., van Sinderen D. A small gene, designated comS, located within the coding region of the fourth amino acid-activation domain of srfA, is required for competence development in Bacillus subtilis. Mol. Microbiol. 1995, 15:55-63.
17. Hanahan D. Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol. 1983, 166:557-580.
18. Hiratsu K., Mochizuki S., Kinashi H. Cloning and analysis of the replication origin and the telomeres of the large linear plasmid pSLA2-L in Streptomyces rochei. Mol. Gen. Genet. 2000, 263:1015-1021.
19. Hosted T.J., Wang T., Horan A.C. Characterization of the Streptomyces lavendulae IMRU 3455 linear plasmid pSLV45. Microbiology 2004, 150:1819-1827.
20. Huang C.H., Lin Y.S., Yang Y.L., Huang S.W., Chen C.W. The telomeres of Streptomyces chromosomes contain conserved palindromic sequences with potential to form complex secondary structures. Mol. Microbiol. 1998, 28:905-916.
21. Huang C.H., Tsai H.H., Tsay Y.G., Chien Y.N., Wang S.L., Cheng M.Y., Ke C.H., Chen C.W. The telomere system of the Streptomyces linear plasmid SCP1 represents a novel class. Mol. Microbiol. 2007, 63:1710-1718.
22. Huang T.W., Chen C.W. DNA polymerase I is not required for replication of linear chromosomes in Streptomyces. J. Bacteriol. 2008, 190:755-758.
23. Kalkus J., Reh M., Schlegel H.G. Hydrogen autotrophy of Nocardia opaca strains is encoded by linear megaplasmids. J. Gen. Microbiol. 1990, 136:1145-1151.
24. Kinashi H., Shimaji-Murayama M., Hanafusa T. Nucleotide sequence analysis of the unusually long terminal inverted repeats of a giant linear plasmid, SCP1. Plasmid 1991, 26:123-130.
25. Kolkenbrock S., Naumann B., Hippler M., Fetzner S. A novel replicative enzyme encoded by the linear Arthrobacter plasmid pAL1. J. Bacteriol. 2010, 192:4935-4943.
26. Kolkenbrock S., Fetzner S. Identification and in vitro deoxynucleotidylation of the terminal protein of the linear plasmid pAL1 of Arthrobacter nitroguajacolicus Rü61a. FEMS Microbiol. Lett. 2010, 304:169-176.
27. Le Dantec C., Winter N., Gicquel B., Vincent V., Picardeau M. Genomic sequence and transcriptional analysis of a 23-kilobase mycobacterial linear plasmid: evidence for horizontal transfer and identification of plasmid maintenance systems. J. Bacteriol. 2001, 183:2157-2164.
28. McLeod M.P., Warren R.L., Hsiao W.W., Araki N., Myhre M., Fernandes C., Miyazawa, et al. The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc. Natl. Acad. Sci. USA 2006, 103:15582-15587.
29. Meinhardt F., Klassen R. Microbial linear plasmids. Microbiology Monographs 2007, vol. 7. Springer, Berlin, Heidelberg, New York.
30. Mochizuki S., Hiratsu K., Suwa M., Ishii T., Sugino F., Yamada K., Kinashi H. The large linear plasmid pSLA2-L of Streptomyces rochei has an unusually condensed gene organization for secondary metabolism. Mol. Microbiol. 2003, 48:1501-1510.
31. Overhage J., Sielker S., Homburg S., Parschat K., Fetzner S. Identification of large linear plasmids in Arthrobacter spp. encoding the degradation of quinaldine to anthranilate. Microbiology 2005, 151:491-500.
32. Parschat K., Hauer B., Kappl R., Kraft R., Huttermann J., Fetzner S. Gene cluster of Arthrobacter ilicis Rü61a involved in the degradation of quinaldine to anthranilate: characterization and functional expression of the quinaldine 4-oxidase qoxLMS genes. J. Biol. Chem. 2003, 278:27483-27494.
33. Parschat K., Overhage J., Strittmatter A.W., Henne A., Gottschalk G., Fetzner S. 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. 2007, 189:3855-3867.
34. Picardeau M., Le Dantec C., Vincent V. Analysis of the internal replication region of a mycobacterial linear plasmid. Microbiology 2000, 146:305-313.
35. Picardeau M., Vincent V. Characterization of large linear plasmids in mycobacteria. J. Bacteriol. 1997, 179:2753-2756.
36. Polo S., Guerini O., Sosio M., Deho G. Identification of two linear plasmids in the actinomycete Planobispora rosea. Microbiology 1998, 144:2819-2825.
37. Qin Z., Cohen S.N. Replication at the telomeres of the Streptomyces linear plasmid pSLA2. Mol. Microbiol. 1998, 28:893-903.
38. Rainey F.A., Ward-Rainey N., Kroppenstedt R.M., Stackebrandt E. The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage: proposal of Nocardiopsaceae fam. Nov. Int. J. Syst. Bacteriol. 1996, 46:1088-1092.
39. Ravel J., Schrempf H., Hill R.T. Mercury resistance is encoded by transferable giant linear plasmids in two Chesapeake Bay Streptomyces strains. Appl. Environ. Microbiol. 1998, 64:3383-3388.
40. Redenbach M., Bibb M., Gust B., Seitz B., Spychaj A. The linear plasmid SCP1 of Streptomyces coelicolor A3(2) possesses a centrally located replication origin and shows significant homology to the transposon Tn4811. Plasmid 1999, 42:174-185.
41. Sakaguchi K. Invertrons, a class of structurally and functionally related genetic elements that includes linear DNA plasmids, transposable elements, and genomes of adeno-type viruses. Microbiol. Rev. 1990, 54:66-74.
42. Salas M. Protein-priming of DNA replication. Annu. Rev. Biochem. 1991, 60:39-71.
43. Sambrook J., Fritsch E.F., Maniatis T. Molecular Cloning: A Laboratory Manual 1989, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York. second ed.
44. Sambrook J., Russell D.W. Molecular Cloning: A Laboratory Manual 2001, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York. third ed.
45. Sekine M., Tanikawa S., Omata S., Saito M., Fujisawa T., Tsukatani N., Tajima T., et al. Sequence analysis of three plasmids harboured in Rhodococcus erythropolis strain PR4. Environ. Microbiol. 2006, 8:334-346.
46. Shiffman D., Cohen S.N. Reconstruction of a Streptomyces linear replicon from separately cloned DNA fragments: existence of a cryptic origin of circular replication within the linear plasmid. Proc. Natl. Acad. Sci. USA 1992, 89:6129-6133.
47. Stecker C., Johann A., Herzberg C., Averhoff B., Gottschalk G. Complete nucleotide sequence and genetic organization of the 210-kilobase linear plasmid of Rhodococcus erythropolis BD2. J. Bacteriol. 2003, 185:5269-5274.
48. Stephan I., Tshisuaka B., Fetzner S., Lingens F. Quinaldine 4-oxidase from Arthrobacter sp. Rü61a, a versatile procaryotic molybdenum-containing hydroxylase active towards N-containing heterocyclic compounds and aromatic aldehydes. Eur. J. Biochem. 1996, 236:155-162.
49. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
50. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22:4673-4680.
51. Vieira J., Messing J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene 1982, 19:259-268.
52. Wagenknecht, M., Meinhardt, F., 2010. Copy number determination, expression analysis of genes potentially involved in replication, and stability assays of pAL1 - the linear megaplasmid of Arthrobacter nitroguajacolicus Rü61a. doi:10.1016/j.micres.2009.12.005.
53. Wagenknecht M., Dib J.R., Thürmer A., Daniel R., Farias M.E., Meinhardt F. Structural peculiarities of linear megaplasmid, pLMA1, from Micrococcus luteus interfere with pyrosequencing reads assembly. Biotechnol. Lett. 2010, 32:1853-1862.
54. Warren R., Hsiao W.W., Kudo H., Myhre M., Dosanjh M., Petrescu A., Kobayashi H., et al. Functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading Rhodococcus sp. strain RHA1. J. Bacteriol. 2004, 186:7783-7795.
55. Xu M., Zhu Y., Zhang R., Shen M., Jiang W., Zhao G., Qin Z. Characterization of the genetic components of Streptomyces lividans linear plasmid SLP2 for replication in circular and linear modes. J. Bacteriol. 2006, 188:6851-6857.
56. Yang C.C., Huang C.H., Li C.Y., Tsay Y.G., Lee S.C., Chen C.W. The terminal proteins of linear Streptomyces chromosomes and plasmids: a novel class of replication priming proteins. Mol. Microbiol. 2002, 43:297-305.
57. Yang C.C., Chen Y.H., Tsai H.H., Huang C.H., Huang T.W., Chen C.W. In vitro deoxynucleotidylation of the terminal protein of Streptomyces linear chromosomes. Appl. Environ. Microbiol. 2006, 72:7959-7961.
58. Zhang R., Yang Y., Fang P., Jiang C., Xu L., Zhu Y., Shen M., et al. Diversity of telomere palindromic sequences and replication genes among Streptomyces linear plasmids. Appl. Environ. Microbiol. 2006, 72:5728-5733.
59. Zhang R., Xia H., Guo P., Qin Z. Variation in the replication loci of Streptomyces linear plasmids. FEMS Microbiol. Lett. 2009, 290:209-216.