Functional characterization of the origin of replication of pRN1 from Sulfolobus islandicus REN1H1

PLoS ONE

Volumn 8, Issue 12, 2013, Pages

  Joshua, Chijioke J ^a,b,c   Perez, Luis D ^a,b,c   Keasling, Jay D ^a,b,c,d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c JOINT BIOENERGY INSTITUTE   (United States)

^d University of California at Berkeley   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; GUANINE; THYMINE; URACIL;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; AUXOTROPHY; CONTROLLED STUDY; EXPRESSION VECTOR; GENE; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE REPLICATION; GENE STRUCTURE; GENETIC TRANSFORMATION; HETEROLOGOUS EXPRESSION; NONHUMAN; ORF56 GENE; ORF904 GENE; PLASMID; PROTEIN MOTIF; REPLICON; SHUTTLE VECTOR; START CODON; SULFOLOBUS; SULFOLOBUS ISLANDICUS REN1H1;

ANIMALS; BASE SEQUENCE; DNA REPLICATION; GENETIC VECTORS; MOLECULAR SEQUENCE DATA; PLASMIDS; REPLICATION ORIGIN; SULFOLOBUS;

EID: 84893193766     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0084664     Document Type: Article

References (43)

1. Chen L, Brügger K, Skovgaard M, Redder P, She Q et al. (2005) The Genome of Sulfolobus acidocaldarius, a Model Organism of the Crenarchaeota. J Bacteriol 187: 4992-4999. doi:10.1128/JB.187.14.4992-4999.2005. PubMed: 15995215.
2. Joshua CJ, Dahl R, Benke PI, Keasling JD (2011) Absence of Diauxie during Simultaneous Utilization of Glucose and Xylose by Sulfolobus acidocaldarius. J Bacteriol 193: 1293-1301. doi:10.1128/JB.01219-10. PubMed: 21239580.
3. Magasanik B (1961) Catabolite repression. Cold Spring Harb Symp Quant Biol 26: 249-256. doi:10.1101/SQB.1961.026.01.031. PubMed: 14468226.
4. Grogan DW (1989) Phenotypic characterization of the archaebacterial genus Sulfolobus : comparison of five wild-type strains. J Bacteriol 171: 6710-6719. PubMed: 2512283.
5. Hatzinikolaou DG, Kalogeris E, Christakopoulos P, Kekos D, Macris BJ (2001) Comparative growth studies of the extreme thermophile Sulfolobus acidocaldarius in submerged and solidified substrate cultures. World Journal of Microbiology and Biotechnology 17: 229-234. doi:10.1023/A:1016675924997.
6. She Q, Singh RK, Confalonieri F, Zivanovic Y, Allard G et al. (2001) The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci U S A 98: 7835-7840. doi:10.1073/pnas.141222098. PubMed: 11427726.
7. Berkner S, Grogan D, Albers S-V, Lipps G (2007) Small multicopy, non-integrative shuttle vectors based on the plasmid pRN1 for Sulfolobus acidocaldarius and Sulfolobus solfataricus, model organisms of the (cren-).Archaea - Nucleic Acids Research 35: e88-. doi:10.1093/nar/gkl822.
8. Deng L, Zhu H, Chen Z, Liang YX, She Q (2009) Unmarked gene deletion and host-vector system for the hyperthermophilic crenarchaeon Sulfolobus islandicus. Extremophiles 13: 735-746. doi:10.1007/s00792-009-0254-2. PubMed: 19513584.
9. Wagner M, Berkner S, Ajon M, Driessen AJM, Lipps G et al. (2009) Expanding and understanding the genetic toolbox of the hyperthermophilic genus Sulfolobus. Biochem Soc Trans 37: 97-101. doi:10.1042/BST0370097. PubMed: 19143610.
10. Wagner M, van Wolferen M, Wagner A, Lassak K, Meyer B et al. (2012) Versatile Genetic Tool Box for the Crenarchaeote Sulfolobus acidocaldarius. Frontiers - Int Microbiology 3.
11. Berkner S, Lipps G (2008) Genetic tools for Sulfolobus spp.: vectors and first applications. Arch Microbiol 190: 217-230. doi:10.1007/s00203-008-0392-4. PubMed: 18542925.
12. Leigh JA, Albers SV, Atomi H, Allers T (2011) Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales. FEMS Microbiol Rev 35: 577-608. doi:10.1111/j.1574-6976.2011. 00265.x. PubMed: 21265868.
13. Schelert J, Dixit V, Hoang V, Simbahan J, Drozda M et al. (2004) Occurrence and Characterization of Mercury Resistance in the Hyperthermophilic Archaeon Sulfolobus solfataricus by Use of Gene Disruption. J Bacteriol 186: 427-437. doi:10.1128/JB.186.2.427-437.2004. PubMed: 14702312.
14. Jonuscheit M, Martusewitsch E, Stedman KM, Schleper C (2003) A reporter gene system for the hyperthermophilic archaeon Sulfolobus solfataricus based on a selectable and integrative shuttle vector. Mol Microbiol 48: 1241-1252. doi:10.1046/j.1365-2958.2003.03509.x. PubMed: 12787352.
15. Kurosawa N, Grogan DW (2005) Homologous recombination of exogenous DNA with the Sulfolobus acidocaldarius genome: Properties and uses. FEMS Microbiol Lett 253: 141-149. doi:10.1016/j.femsle.2005.09.031. PubMed: 16243457.
16. Reilly MS, Grogan DW (2001) Characterization of Intragenic Recombination in a Hyperthermophilic Archaeon via Conjugational DNA. Exchange - J Bacteriol 183: 2943-2946. doi:10.1128/JB.183.9.2943-2946.2001.
17. Cannio R, Contursi P, Rossi M, Bartolucci S (1998) An Autonomously Replicating Transforming Vector for Sulfolobus solfataricus. J Bacteriol 180: 3237-3240. PubMed: 9620978.
18. Aagaard C, Phan H, Trevisanato S, Garrett RA (1994) A spontaneous point mutation in the single 23S rRNA gene of the thermophilic arachaeon Sulfolobus acidocaldarius confers multiple drug resistance. J Bacteriol 176: 7744-7747. PubMed: 8002603.
19. Cammarano P, Teichner A, Londei P, Acca M, Nicolaus B et al. (1985) Insensitivity of archaebacterial ribosomes to protein synthesis inhibitors. Evolutionary implications. EMBO J 4: 811-816. PubMed: 3924597.
20. Berkner S, Wlodkowski A, Albers S-V, Lipps G (2010) Inducible and constitutive promoters for genetic systems in Sulfolobus acidocaldarius. Extremophiles 14: 249-259. doi:10.1007/s00792-010-0304-9. PubMed: 20221889.
21. Zillig W, Kletzin A, Schleper C, Holtz I, Janekovic D, Hain J, Lanzendorfer M, Kristiansson JK (1994) Screening for Sulfolobales, their plasmids, and their viruses in Islandic solfataras Syst Appl Microbiol 16: 606-628.
22. Keeling PJ, Klenk H-P, Singh RK, Feeley O, Schleper C et al. (1996) Complete nucleotide sequence of the Sulfolobus islandicus multicopy plasmid pRN1. Plasmid 35: 141-144. doi:10.1006/plas.1996.0016. PubMed: 8700967.
23. Peng X, Holz I, Zillig W, Garrett RA, She Q (2000) Evolution of the family of pRN plasmids and their integrase-mediated insertion into the chromosome of the crenarchaeon Sulfolobus solfataricus. J Mol Biol 303: 449-454. doi:10.1006/jmbi.2000.4160. PubMed: 11054282.
24. Beck K, Vannini A, Cramer P, Lipps G (2010) The archaeo-eukaryotic primase of plasmid pRN1 requires a helix bundle domain for faithful primer synthesis. Nucleic Acids Res 38: 6707-6718. doi:10.1093/nar/gkq447. PubMed: 20511586.
25. Lipps G (2009) Molecular biology of the pRN1 plasmid from Sulfolobus islandicus. Biochem Soc Trans 37: 42-45. doi:10.1042/BST0370042. PubMed: 19143599.
26. Sanchez M, Drechsler M, Stark H, Lipps G (2009) DNA translocation activity of the multifunctional replication protein ORF904 from the archaeal plasmid pRN1. Nucleic Acids Res 37: 6831-6848. doi:10.1093/nar/gkp742. PubMed: 19762479.
27. Kletzin A, Lieke A, Urich T, Charlebois RL, Sensen CW (1999) Molecular Analysis of pDL10 From Acidianus ambivalens Reveals a Family of Related Plasmids From Extremely Thermophilic and Acidophilic Archaea. Genetics 152: 1307-1314. PubMed: 10430561.
28. Khan SA (1997) Rolling-circle replication of bacterial plasmids. Microbiol Mol Biol Rev 61: 442-455. PubMed: 9409148.
29. Khan SA (2005) Plasmid rolling-circle replication: highlights of two decades of research. Plasmid 53: 126-136. doi:10.1016/j.plasmid.2004.12.008. PubMed: 15737400.
30. Gennaro ML, Iordanescu S, Novick RP, Murray RW, Steck TR et al. (1989) Functional organization of the plasmid pT181 replication origin. J Mol Biol 205: 355-362. doi:10.1016/0022-2836(89)90346-X. PubMed: 2926812.
31. Zhao AC, Khan SA (1996) An 18-base-pair sequence is sufficient for termination of rolling-circle replication of plasmid pT181. J Bacteriol 178: 5222-5228. PubMed: 8752341.
32. Zhao AC, Khan SA (1997) Sequence requirements for the termination of rolling-circle replication of plasmid pT181. Mol Microbiol 24: 535-544. doi:10.1046/j.1365-2958.1997.3641730.x. PubMed: 9179847.
33. Berkner S, Lipps G (2007) Characterization of the Transcriptional Activity of the Cryptic Plasmid pRN1 from Sulfolobus islandicus REN1H1 and Regulation of Its Replication Operon. J Bacteriol 189: 1711-1721. doi:10.1128/JB.01586-06. PubMed: 17172324.
34. Lipps G, Stegert M, Krauss G (2001) Thermostable and site-specific DNA binding of the gene product ORF56 from the Sulfolobus islandicus plasmid pRN1, a putative archael plasmid copy control protein. Nucleic Acids Res 29: 904-913. doi:10.1093/nar/29.4.904. PubMed: 11160922.
35. Beck K, Lipps G (2007) Properties of an unusual DNA primase from an archaeal plasmid. Nucleic Acids Res 35: 5635-5645. doi:10.1093/nar/gkm625. PubMed: 17709343.
36. Mamie ZL, Stephen JE (2007) SLIC sub-cloning using T4 DNA polymerase treated inserts with RecA.
37. Gibson DG, Young L, Chuang R-Y, Venter JC, Hutchison CA et al. (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6: 343-345. doi:10.1038/nmeth.1318. PubMed: 19363495.
38. Grogan DW (2003) Cytosine methylation by the SuaI restriction- modification system: implications for genetic fidelity in a hyperthermophilic archaeon. J Bacteriol 185: 4657-4661. doi:10.1128/JB.185.15.4657-4661.2003. PubMed: 12867480.
39. Kumar R, Singh S, Singh OV (2008) Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol 35: 377-391. doi:10.1007/s10295-008-0327-8. PubMed: 18338189.
40. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415. doi:10.1093/nar/ gkg595. PubMed: 12824337.
41. del Solar G, Giraldo R, Ruiz-Echevarría MJ, Espinosa M, Díaz-Orejas R (1998) Replication and Control of Circular Bacterial Plasmids. Microbiol Mol Biol Rev 62: 434-464. PubMed: 9618448.
42. Gruss AD, Ross HF, Novick RP (1987) Functional analysis of a palindromic sequence required for normal replication of several staphylococcal plasmids. Proc Natl Acad Sci U S A 84: 2165-2169. doi:10.1073/pnas.84.8.2165. PubMed: 3104910.
43. Solar G, Kramer G, Ballester S, Espinosa M (1993) Replication of the promiscuous plasmid pLSI: a region encompassing the minus origin of replication is associated with stable plasmid inheritance. Molecular and General Genetics MGG 241: 97-105. PubMed: 8232217.