BMC Molecular Biology | |
Insight into the cellular involvement of the two reverse gyrases from the hyperthermophilic archaeon Sulfolobus solfataricus | |
Marc Nadal4  Florence Garnier1  Anna H Bizard2  Mohea Couturier3  | |
[1] Institut de Génétique et Microbiologie, UMR 8621 CNRS, Université Paris-Sud, Bât. 409, Orsay Cedex 91405, France;Present address: Institute of Cellular and Molecular Medicine (ICMM), Center for Healthy Ageing (CEHA), University of Copenhagen, Blegdamsvej 3B, København N DK-2200, Denmark;Present address: Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden;Université Paris Diderot, 5 rue Thomas Mann, Paris 75013, France | |
关键词: Quantification; TopR; Cytometry; Low temperature; Topology; Supercoiling; Topoisomerase; Hyperthermophile; Archaea; | |
Others : 1090301 DOI : 10.1186/1471-2199-15-18 |
|
received in 2014-07-15, accepted in 2014-08-27, 发布年份 2014 | |
【 摘 要 】
Background
Reverse gyrases are DNA topoisomerases characterized by their unique DNA positive-supercoiling activity. Sulfolobus solfataricus, like most Crenarchaeota, contains two genes each encoding a reverse gyrase. We showed previously that the two genes are differently regulated according to temperature and that the corresponding purified recombinant reverse gyrases have different enzymatic characteristics. These observations suggest a specialization of functions of the two reverse gyrases. As no mutants of the TopR genes could be obtained in Sulfolobales, we used immunodetection techniques to study the function(s) of these proteins in S. solfataricus in vivo. In particular, we investigated whether one or both reverse gyrases are required for the hyperthermophilic lifestyle.
Results
For the first time the two reverse gyrases of S. solfataricus have been discriminated at the protein level and their respective amounts have been determined in vivo. Actively dividing S. solfataricus cells contain only small amounts of both reverse gyrases, approximately 50 TopR1 and 125 TopR2 molecules per cell at 80°C. S. solfataricus cells are resistant at 45°C for several weeks, but there is neither cell division nor replication initiation; these processes are fully restored upon a return to 80°C. TopR1 is not found after three weeks at 45°C whereas the amount of TopR2 remains constant. Enzymatic assays in vitro indicate that TopR1 is not active at 45°C but that TopR2 exhibits highly positive DNA supercoiling activity at 45°C.
Conclusions
The two reverse gyrases of S. solfataricus are differently regulated, in terms of protein abundance, in vivo at 80°C and 45°C. TopR2 is present both at high and low temperatures and is therefore presumably required whether cells are dividing or not. By contrast, TopR1 is present only at high temperature where the cell division occurs, suggesting that TopR1 is required for controlling DNA topology associated with cell division activity and/or life at high temperature. Our findings in vitro that TopR1 is able to positively supercoil DNA only at high temperature, and TopR2 is active at both temperatures are consistent with them having different functions within the cells.
【 授权许可】
2014 Couturier et al.; licensee BioMed Central Ltd.
【 预 览 】
Files | Size | Format | View |
---|---|---|---|
20150128155827714.pdf | 1402KB | download | |
Figure 4. | 52KB | Image | download |
Figure 3. | 32KB | Image | download |
Figure 2. | 104KB | Image | download |
Figure 1. | 36KB | Image | download |
【 图 表 】
Figure 1.
Figure 2.
Figure 3.
Figure 4.
【 参考文献 】
- [1]Liu LFL, Wang JCJ: Supercoiling of the DNA template during transcription. Proc Natl Acad Sci U S A 1987, 84:7024-7027.
- [2]Champoux JJ: DNA topoisomerases: structure, function, and mechanism. Annu Rev Biochem 2001, 70:369-413.
- [3]Chen SH, Chan N-L, Hsieh T-S: New Mechanistic and Functional Insights into DNA Topoisomerases. Annu Rev Biochem 2013, 82:139-170.
- [4]Mirambeau G, Duguet M, Forterre P: Atp-Dependent Dna Topoisomerase From the Archaebacterium Sulfolobus-Acidocaldarius - Relaxation of Supercoiled Dna at High-Temperature. J Mol Biol 1984, 179:559-563.
- [5]Kikuchi A, Asai K: Reverse gyrase–a topoisomerase which introduces positive superhelical turns into DNA. Nature 1984, 309:677-681.
- [6]Forterre P, Mirambeau G, Jaxel C, Nadal M, Duguet M: High positive supercoiling in vitro catalyzed by an ATP and polyethylene glycol-stimulated topoisomerase from Sulfolobus acidocaldarius. EMBO J 1985, 4:2123-2128.
- [7]Nakasu S, Kikuchi A: Reverse gyrase; ATP-dependent type I topoisomerase from Sulfolobus. EMBO J 1985, 4:2705-2710.
- [8]Nadal M, Jaxel C, Portemer C, Forterre P, Mirambeau G, Duguet M: Reverse gyrase of Sulfolobus: purification to homogeneity and characterization. Biochemistry 1988, 27:9102-9108.
- [9]Nadal M: Reverse gyrase: an insight into the role of DNA-topoisomerases. Biochimie 2007, 89:447-455.
- [10]Bouthier de la Tour C, Portemer C, Nadal M, Stetter KO, Forterre P, Duguet M: Reverse gyrase, a hallmark of the hyperthermophilic archaebacteria. J Bacteriol 1990, 172:6803-6808.
- [11]Bouthier de la Tour C, Portemer C, Huber R, Forterre P, Duguet M: Reverse gyrase in thermophilic eubacteria. J Bacteriol 1991, 173:3921-3923.
- [12]Forterre P: A hot story from comparative genomics: reverse gyrase is the only hyperthermophile-specific protein. Trends Genet 2002, 18:236-237.
- [13]Brochier-Armanet C, Forterre P: Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers. Archaea 2007, 2:83-93.
- [14]Nadal M, Mirambeau G, Forterre P, Reiter WD, Duguet M: Positively Supercoiled Dna in a Virus-Like Particle of an Archaebacterium. Nature 1986, 321:256-258.
- [15]Lim HM, Lee HJ, Jaxel C, Nadal M: Hin-mediated inversion on positively supercoiled DNA. J Biol Chem 1997, 272:18434-18439.
- [16]Bell SD, Jaxel C, Nadal M, Kosa PF, Jackson SP: Temperature, template topology, and factor requirements of archaeal transcription. Proc Natl Acad Sci U S A 1998, 95:15218-15222.
- [17]Garnier F, Nadal M: Transcriptional analysis of the two reverse gyrase encoding genes of Sulfolobus solfataricus P2 in relation to the growth phases and temperature conditions. Extremophiles 2008, 12:799-809.
- [18]Menzel R, Gellert M: Regulation of the genes for E. coli DNA gyrase: homeostatic control of DNA supercoiling. Cell 1983, 34:105-113.
- [19]Peter BJ, Arsuaga J, Breier AM, Khodursky AB, Brown PO, Cozzarelli NR: Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biol 2004, 5:R87. BioMed Central Full Text
- [20]Kampmann M, Stock D: Reverse gyrase has heat-protective DNA chaperone activity independent of supercoiling. Nucleic Acids Res 2004, 32:3537-3545.
- [21]Confalonieri F, Elie C, Nadal M, Bouthier de La Tour C, Forterre P, Duguet M: Reverse Gyrase: A Helicase-Like Domain and a Type 1 Topoisomerase in the Same Polypeptide. Volume 1993, 90:4753-4757.
- [22]Jaxel C, Bouthier de la Tour C, Duguet M, Nadal M: Reverse gyrase gene from Sulfolobus shibatae B12: gene structure, transcription unit and comparative sequence analysis of the two domains. Nucleic Acids Res 1996, 24:4668-4675.
- [23]Gangloff S, McDonald JP, Bendixen C, Arthur L, Rothstein R: The yeast type I topoisomerase Top3 interacts with Sgs1, a DNA helicase homolog: a potential eukaryotic reverse gyrase. Mol Cell Biol 1994, 14:8391-8398.
- [24]Harmon FG, DiGate RJ, Kowalczykowski SC: RecQ helicase and topoisomerase III comprise a novel DNA strand passage function: a conserved mechanism for control of DNA recombination. Mol Cell 1999, 3:611-620.
- [25]Mankouri HW, Hickson ID: The RecQ helicase-topoisomerase III-Rmi1 complex: a DNA structure-specific ‘dissolvasome’? Trends Biochem Sci 2007, 32:538-546.
- [26]Perugino G, Valenti A, D’amaro A, Rossi M, Ciaramella M: Reverse gyrase and genome stability in hyperthermophilic organisms. Biochem Soc Trans 2009, 37:69-73.
- [27]Slesarev AI, Kozyavkin SA: DNA substrate specificity of reverse gyrase from extremely thermophilic archaebacteria. J Biomol Struct Dyn 1990, 7:935-942.
- [28]Hsieh T-S, Plank JL: Reverse gyrase functions as a DNA renaturase: annealing of complementary single-stranded circles and positive supercoiling of a bubble substrate. J Biol Chem 2006, 281:5640-5647.
- [29]Napoli A, Valenti A, Salerno V, Nadal M, Garnier F, Rossi M, Ciaramella M: Reverse gyrase recruitment to DNA after UV light irradiation in Sulfolobus solfataricus. J Biol Chem 2004, 279:33192-33198.
- [30]Napoli AA, Valenti AA, Salerno VV, Nadal MM, Garnier FF, Rossi MM, Ciaramella MM: Functional interaction of reverse gyrase with single-strand binding protein of the archaeon Sulfolobus. Nucleic Acids Res 2004, 33:564-576.
- [31]Wadsworth RIR, White MFM: Identification and properties of the crenarchaeal single-stranded DNA binding protein from Sulfolobus solfataricus. Nucleic Acids Res 2001, 29:914-920.
- [32]Valenti A, Perugino G, Nohmi T, Rossi M, Ciaramella M: Inhibition of translesion DNA polymerase by archaeal reverse gyrase. Nucleic Acids Res 2009, 37:4287-4295.
- [33]Valenti A, Perugino G, Varriale A, D'Auria S, Rossi M, Ciaramella M: The archaeal topoisomerase reverse gyrase is a helix-destabilizing protein that unwinds four-way DNA junctions. J Biol Chem 2010, 285:36532-36541.
- [34]Campbell BJ, Smith JL, Hanson TE, Klotz MG, Stein LY, Lee CK, Wu D, Robinson JM, Khouri HM, Eisen JA, Cary SC: Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola. PLoS Genet 2009, 5:e1000362.
- [35]Atomi H, Matsumi R, Imanaka T: Reverse gyrase is not a prerequisite for hyperthermophilic life. J Bacteriol 2004, 186:4829-4833.
- [36]Zhang C, Tian B, Li S, Ao X, Dalgaard K, Gökce S, Liang Y, She Q: Genetic manipulation in Sulfolobus islandicus and functional analysis of DNA repair genes. Biochem Soc Trans 2013, 41:405-410.
- [37]Bizard A, Garnier F, Nadal M: TopR2, the Second Reverse Gyrase of Sulfolobus solfataricus, Exhibits Unusual Properties. J Mol Biol 2011, 408:839-849.
- [38]Lübben M, Schäfer G: Chemiosmotic energy conversion of the archaebacterial thermoacidophile Sulfolobus acidocaldarius: oxidative phosphorylation and the presence of an F0-related N, N'-dicyclohexylcarbodiimide-binding proteolipid. J Bacteriol 1989, 171:6106-6116.
- [39]Lin H-KH, Chase SFS, Laue TMT, Jen-Jacobson LL, Trakselis MAM: Differential temperature-dependent multimeric assemblies of replication and repair polymerases on DNA increase processivity. Biochemistry 2012, 51:7367-7382.
- [40]Choi J-Y, Eoff RL, Pence MG, Wang J, Martin MV, Kim E-J, Folkmann LM, Guengerich FP: Roles of the four DNA polymerases of the crenarchaeon Sulfolobus solfataricus and accessory proteins in DNA replication. J Biol Chem 2011, 286:31180-31193.
- [41]Hjort K, Bernander R: Changes in Cell Size and DNA Content in Sulfolobus Cultures during Dilution and Temperature Shift Experiments. J Bacteriol 1999, 181:5669-5675.
- [42]Boulos L, Prévost M, Barbeau B, Coallier J, Desjardins R: LIVE/DEAD® BacLight™: application of a new rapid staining method for direct enumeration of viable and total bacteria in drinking water. J Microbiol Methods 1999, 37:77-86.
- [43]Leuko S, Legat A, Fendrihan S, Stan-Lotter H: Evaluation of the LIVE/DEAD BacLight kit for detection of extremophilic archaea and visualization of microorganisms in environmental hypersaline samples. Appl Environ Microbiol 2004, 70:6884-6886.
- [44]De Rosa M, Gambacorta A, Nicolaus B, Sodano S, Bu'lock JD: Structural regularities in tetraether lipids of Caldariella and their biosynthetic and phyletic implications. Phytochemistry 1980, 19:833-836.
- [45]Bernander RR, Poplawski AA: Cell cycle characteristics of thermophilic archaea. J Bacteriol 1997, 179:4963-4969.
- [46]Esser D, Pham TK, Reimann J, Albers S-V, Siebers B, Wright PC: Change of Carbon Source Causes Dramatic Effects in the Phospho-Proteome of the Archaeon Sulfolobus solfataricus. J Proteome Res 2012, 11:4823-4833.
- [47]Barry RC, Young MJ, Stedman KM, Dratz EA: Proteomic mapping of the hyperthermophilic and acidophilic archaeon Sulfolobus solfataricus P2. Electrophoresis 2006, 27:2970-2983.
- [48]Reimann J, Esser D, Orell A, Amman F, Pham TK, Noirel J, Lindås A-C, Bernander R, Wright PC, Siebers B, Albers S-V: Archaeal Signal Transduction: Impact of Protein Phosphatase Deletions on Cell Size, Motility, and Energy Metabolism in Sulfolobus acidocaldarius. Mol Cell Proteomics 2013, 12:3908-3923.
- [49]Perugino G, Vettone A, Illiano G, Valenti A, Ferrara MC, Rossi M, Ciaramella M: Activity and regulation of an archaeal DNA-alkyltransferase: conserved protein involved in repair of DNA alkylation damage. J Biol Chem 2012, 287:4222-4231.
- [50]Napoli A, Zivanovic Y, Bocs C, Buhler C, Rossi M, Forterre P, Ciaramella M: DNA bending, compaction and negative supercoiling by the architectural protein Sso7d of Sulfolobus solfataricus. Nucleic Acids Res 2002, 30:2656-2662.
- [51]Lundgren M, Bernander R: Genome-wide transcription map of an archaeal cell cycle. Proc Natl Acad Sci U S A 2007, 104:2939-2944.
- [52]Saifi B, Ferat J-L, Marinus MG: Replication Fork Reactivation in a dnaC2 Mutant at Non-Permissive Temperature in Escherichia coli. PLoS One 2012, 7:3613.
- [53]She QQ, Singh RKR, Confalonieri FF, Zivanovic YY, Allard GG, Awayez MJM, Chan-Weiher CCC, Clausen IGI, Curtis BAB, De Moors AA, Erauso GG, Fletcher CC, Gordon PMP, Jong IIH-D, Jeffries ACA, Kozera CJC, Medina NN, Peng XX, Thi-Ngoc HPH, Redder PP, Schenk MEM, Theriault CC, Tolstrup NN, Charlebois RLR, Doolittle WFW, Duguet MM, Gaasterland TT, Garrett RAR, Ragan MAM, Sensen CWC, et al.: The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci U S A 2001, 98:7835-7840.
- [54]Rodríguez AC, Stock D: Crystal structure of reverse gyrase: insights into the positive supercoiling of DNA. EMBO J 2002, 21:418-426.