Compartmentalization of prokaryotic DNA replication

FEMS Microbiology Reviews - Tập 29 - Trang 25-47 - 2005
Alicia Bravo1, Gemma Serrano-Heras1, Margarita Salas1
1Instituto de Biología Molecular “Eladio Viñuela” (CSIC), Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain

Tài liệu tham khảo

10.1101/SQB.1963.028.01.048 Nordström K. (2003) The replicon theory 40 years: an EMBO workshop held in Villefranche sur Mer, France, January 18–23, 2003. Plasmid 49, 269–280. 10.1146/annurev.mi.27.100173.001401 Liebowitz P.J. Schaechter M. (1975) The attachment of the bacterial chromosome to the cell membrane. Int. Rev. Cytol. 41, 1–28. 10.1146/annurev.mi.43.100189.000513 10.1046/j.1365-2958.1997.2061569.x Sueoka N. (1998) Cell membrane and chromosome replication in Bacillus subtilis . Prog. Nucl. Acid Res. Mol. Biol. 59, 35–53. Crooke E. (2001) Escherichia coli DnaA protein–phospholipid interactions: in vitro and in vivo. Biochimie 83, 19–23. 10.1016/0092-8674(88)90186-9 10.1016/0092-8674(90)90508-C Herrick J. Kern R. Guha S. Landoulsi A. Fayet O. Malki A. Kohiyama M. (1994) Parental strand recognition of the DNA replication origin by the outer membrane in Escherichia coli . EMBO J. 13, 4695–4703. 10.1016/0092-8674(95)90272-4 10.1046/j.1365-2958.1996.00106.x 10.1073/pnas.95.19.11117 D'Alencon E. Taghbalout A. Kern R. Kohiyama M. (1999) Replication cycle dependent association of SeqA to the outer membrane fraction of E. coli . Biochimie 81, 841–846. Losick R. Shapiro L. (1999) Changing views on the nature of the bacterial cell: from biochemistry to cytology. J. Bacteriol. 181, 4143–4145. 10.1016/S0962-8924(00)01840-7 Phillips G.J. (2001) Green fluorescent protein: a bright idea for the study of bacterial protein localization. FEMS Microbiol. Lett. 204, 9–18. 10.1126/science.282.5393.1516 10.1046/j.1365-2958.2000.01928.x 10.1146/annurev.genet.34.1.21 10.1146/annurev.micro.54.1.681 10.1146/annurev.micro.56.012302.160729 10.1016/j.mib.2003.10.015 10.1016/S1369-5274(02)00370-3 Skarstad K. Boye E. Steen H.B. (1986) Timing of initiation of chromosome replication in individual Escherichia coli cells. EMBO J. 5, 1711–1717. 10.1093/embo-reports/kvd116 10.1111/j.1574-6976.2002.tb00620.x 10.1016/0092-8674(89)90802-7 10.1016/0092-8674(87)90221-2 Yung B.Y. Crooke E. Kornberg A. (1990) Fate of the DnaA initiator protein in replication at the origin of the Escherichia coli chromosome in vitro. J. Biol. Chem. 265, 1282–1285. 10.1093/emboj/18.23.6642 10.1074/jbc.M108303200 Sekimizu K. Yung B.Y. Kornberg A. (1988) The DnaA protein of Escherichia coli. Abundance, improved purification, and membrane binding. J. Biol. Chem. 263, 7136–7140. Sekimizu K. Kornberg A. (1988) Cardiolipin activation of DnaA protein, the initiation protein of replication in Escherichia coli . J. Biol. Chem. 263, 7131–7135. Crooke E. Castuma C.E. Kornberg A. (1992) The chromosome origin of Escherichia coli stabilizes DnaA protein during rejuvenation by phospholipids. J. Biol. Chem. 267, 16779–16782. 10.1073/pnas.85.19.7202 Castuma C.E. Crooke E. Kornberg A. (1993) Fluid membranes with acidic domains activate DnaA, the initiator protein of replication in Escherichia coli . J. Biol. Chem. 268, 24665–24668. 10.1074/jbc.273.9.5167 Garner J. Crooke E. (1996) Membrane regulation of the chromosomal replication activity of E. coli DnaA requires a discrete site on the protein. EMBO J. 15, 3477–3485. 10.1074/jbc.275.6.4513 10.1074/jbc.M009643200 10.1128/JB.182.9.2604-2610.2000 Hwang D.S. Crooke E. Kornberg A. (1990) Aggregated DnaA protein is dissociated and activated for DNA replication by phospholipase or DnaK protein. J. Biol. Chem. 265, 19244–19248. 10.1016/0022-2836(73)90416-6 10.1073/pnas.92.3.783 10.1093/emboj/20.5.1164 10.1128/JB.182.2.371-376.2000 10.1007/s004380050019 10.1046/j.1365-2958.2002.03161.x 10.1016/0092-8674(90)90271-F 10.1016/0092-8674(87)90173-5 10.1093/emboj/19.22.6240 Boye E. (1991) The hemimethylated replication origin of Escherichia coli can be initiated in vitro. J. Bacteriol. 173, 4537–4539. 10.1016/0092-8674(94)90156-2 10.1093/emboj/cdg020 10.1073/pnas.93.22.12206 10.1093/emboj/18.8.2304 10.1046/j.1365-2958.2000.01943.x 10.1074/jbc.274.17.11463 10.1093/emboj/17.14.4158 10.1093/emboj/18.17.4882 10.1046/j.1365-2443.2000.00380.x 10.1111/j.1574-6968.1997.tb10192.x 10.1046/j.1365-2958.1999.01156.x 10.1101/gad.12.7.1036 10.1016/S0092-8674(00)80377-3 10.1101/gad.14.2.212 10.1046/j.1365-2443.2000.00334.x 10.1016/S0300-9084(99)00217-5 10.1016/S0300-9084(99)00218-7 10.1046/j.1365-2958.2003.03640.x 10.1046/j.1365-2958.2002.02901.x 10.1093/emboj/cdg504 10.1016/j.cub.2003.08.043 10.1046/j.1365-2958.2003.03607.x 10.1016/S0959-440X(03)00027-7 10.1016/S1097-2765(00)80038-6 10.1046/j.1365-2958.1999.01313.x 10.1128/JB.184.3.867-870.2002 Withers H.L. Bernander R. (1998) Characterization of dnaC2 and dnaC28 mutants by flow cytometry. J. Bacteriol. 180, 1624–1631. 10.1111/j.1365-2958.2004.04097.x 10.1006/jmbi.1993.1134 10.1074/jbc.271.12.7072 Kornacki J.A. Firshein W. (1986) Replication of plasmid RK2 in vitro by a DNA–membrane complex: evidence for initiation of replication and its coupling to transcription and translation. J. Bacteriol. 167, 319–326. 10.1016/0147-619X(89)90046-2 10.1006/plas.1994.1040 Mei J. Benashski S. Firshein W. (1995) Interactions of the origin of replication (oriV) and initiation proteins (TrfA) of plasmid RK2 with submembrane domains of Escherichia coli . J. Bacteriol. 177, 6766–6772. 10.1128/JB.182.6.1757-1760.2000 10.1128/JB.182.16.4380-4383.2000 10.1006/plas.2000.1467 10.1016/S0092-8674(00)80359-1 10.1128/JB.184.11.3142-3145.2002 10.1046/j.1365-2958.1999.01611.x 10.1093/emboj/18.14.4076 10.1093/emboj/cdf320 10.1093/emboj/cdf672 10.1016/S1097-2765(03)00451-9 10.1073/pnas.081075798 10.1093/emboj/21.7.1864 10.1006/plas.1999.1457 10.1111/j.1365-2958.1992.tb01997.x 10.1126/science.8197460 Yoshikawa, H., Wake, R.G. (1993) Initiation and termination of chromosome replication. In: Bacillus subtilis and Other Gram-Positive Bacteria: Biochemistry, Physiology, and Molecular Genetics (Sonenshein, A.L., Hoch, J.A., Losick, R., Eds.), pp.507–528 American Society for Microbiology, Washington, DC. 10.1006/plas.1998.1381 10.1016/S0092-8674(00)81909-1 10.1046/j.1365-2958.1998.00808.x 10.1099/00221287-138-1-1 Ireton K. Gunther N.W. IV Grossman A.D. (1994) Spo0J is required for normal chromosome segregation as well as the initiation of sporulation in Bacillus subtilis . J. Bacteriol. 176, 5320–5329. 10.1111/j.1365-2958.1996.tb02559.x 10.1016/S0092-8674(00)81135-6 10.1073/pnas.94.9.4721 10.1101/gad.11.9.1160 10.1111/j.1365-2958.1997.mmi530.x 10.1046/j.1365-2958.1998.00857.x 10.1128/JB.185.4.1326-1337.2003 10.1016/j.cub.2003.10.024 10.1016/S0092-8674(01)00287-2 10.1016/S1534-5807(02)00403-3 10.1016/S0092-8674(03)00421-5 10.1126/science.1072163 10.1093/emboj/cdf393 10.1126/science.1079914 10.1101/gad.197501 10.1046/j.1365-2958.2003.03643.x 10.1016/S1097-2765(00)00130-1 10.1101/gad.913301 10.1046/j.1365-2958.2001.02350.x 10.1126/science.1066351 10.1016/S1097-2765(03)00130-8 10.1073/pnas.122040799 10.1126/science.8456299 10.1046/j.1365-2958.2000.01676.x 10.1073/pnas.77.5.2834 10.1073/pnas.84.3.653 10.1016/0022-2836(86)90395-5 Mosig G. Macdonald P. Powell D. Trupin M. Gary T. (1987) A membrane protein involved in initiation of DNA replication from the oriA region of phage T4. DNA replication and recombination. UCLA Symp. Mol. Cell. Biol. 47, 403–414. 10.1128/MMBR.65.2.261-287.2001 10.1006/viro.1995.1048 10.1016/0042-6822(86)90202-3 Barthelemy I. Mellado R.P. Salas M. (1989) In vitro transcription of bacteriophage φ29 DNA: inhibition of early promoters by the viral replication protein p6. J. Virol. 63, 460–462. 10.1074/jbc.M103738200 10.1016/S0378-1119(98)00167-X 10.1074/jbc.M210289200 10.1111/j.1365-2958.2004.03993.x Salas M. (1998) Control mechanisms of bacteriophage φ29 DNA expression. Int. Microbiol. 1, 307–310. 10.1016/S0079-6603(08)60888-0 10.1093/nar/12.4.1943 Barthelemy I. Salas M. Mellado R.P. (1986) In vivo transcription of bacteriophage φ29 DNA: transcription initiation sites. J. Virol. 60, 874–879. 10.1093/emboj/19.20.5575 Barthelemy I. Salas M. Mellado R.P. (1987) In vivo transcription of bacteriophage φ29 DNA: transcription termination. J. Virol. 61, 1751–1755. 10.1146/annurev.bi.60.070191.000351 Salas, M., Rojo, F. (1993) Replication and transcription of bacteriophage φ29 DNA. In: Bacillus subtilis and other Gram-positive Bacteria: Biochemistry, Physiology, and Molecular Genetics (Sonenshein, A.L., Hoch, J.A., Losick, R., Eds.), pp.843–857 American Society for Microbiology, Washington, DC. Salas, M., Miller, J.T., Leis, J., DePamphilis, M.L. (1996) Mechanisms for priming DNA synthesis. In: DNA Replication in Eukaryotic Cells (DePamphilis, M.L., Ed.), pp.131–176 Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. 10.1016/1047-8477(90)90059-L 10.1101/gad.13.19.2502 10.1093/emboj/20.21.6060 10.1093/emboj/cdf623 10.1016/j.jmb.2003.12.039 Salas, M. Mechanisms of initiation of linear DNA replication in prokaryotes Setlow, J.K., Ed., Genetic Engineering. Vol. 21, 1999. Kluwer Academic/Plenum Publishers, New York. 159–171 Inciarte M.R. Salas M. Sogo J.M. (1980) Structure of replicating DNA molecules of Bacillus subtilis bacteriophage φ29. J. Virol. 34, 187–199. Sogo J.M. García J.A. Peñalva M.A. Salas M. (1982) Structure of protein-containing replicative intermediates of Bacillus subtilis phage φ29 DNA. Virology 116, 1–18. 10.1093/nar/14.12.4923 Serrano M. Gutiérrez J. Prieto I. Hermoso J.M. Salas M. (1989) Signals at the bacteriophage φ29 DNA replication origins required for protein p6 binding and activity. EMBO J. 8, 1879–1885. 10.1126/science.2111580 10.1006/jmbi.1993.1140 10.1074/jbc.271.48.31000 10.1073/pnas.81.17.5325 10.1073/pnas.77.11.6425 10.1093/nar/13.21.7715 10.1073/pnas.78.3.1446 10.1073/pnas.78.3.1336 10.1073/pnas.89.20.9579 10.1093/emboj/16.9.2519 10.1073/pnas.82.19.6404 Blanco L. Bernad A. Lázaro J.M. Martín G. Garmendia C. Salas M. (1989) Highly efficient DNA synthesis by the phage φ29 DNA polymerase. Symmetrical mode of DNA replication. J. Biol. Chem. 264, 8935–8940. 10.1093/nar/17.10.3663 10.1016/0042-6822(73)90330-9 McGuire J.C. Pène J.J. Barrow-Carraway J. (1974) Gene expression during the development of bacteriophage φ29. Analysis of viral-specific protein synthesis with suppressible mutants. J. Virol. 13, 690–698. Mellado R.P. Moreno F. Viñuela E. Salas M. Reilly B.E. Anderson D.L. (1976) Genetic analysis of bacteriophage φ29 of Bacillus subtilis: integration and mapping of reference mutants of two collections. J. Virol. 19, 495–500. 10.1006/jmbi.1997.1032 Konings W.N. Bisschop A. Veenhuis M. Vermeulen C.A. (1973) New procedure for the isolation of membrane vesicles of Bacillus subtilis and an electron microscopy study of their ultrastructure. J. Bacteriol. 116, 1456–1465. 10.1093/emboj/17.20.6096 Reilly B.E. Zeece V.M. Anderson D.L. (1973) Genetic study of suppressor-sensitive mutants of the Bacillus subtilis bacteriophage φ29. J. Virol. 11, 756–760. 10.1016/0378-1119(89)90067-X 10.1074/jbc.M306935200 Bordier C. (1981) Phase separation of integral membrane proteins in Triton X-114 solution. J. Biol. Chem. 256, 1604–1607. 10.1016/0076-6879(94)28019-3 10.1074/jbc.M011296200 10.1073/pnas.93.1.519 10.1146/annurev.genet.33.1.423 10.1016/S0378-1119(99)00249-8 Younghusband H.B. Maundrell K. (1982) Adenovirus DNA is associated with the nuclear matrix of infected cells. J. Virol. 43, 705–713. Bodnar J.W. Hanson P.I. Polvino-Bodnar M. Zempsky W. Ward D.C. (1989) The terminal regions of adenovirus and minute virus of mice DNAs are preferentially associated with the nuclear matrix in infected cells. J. Virol. 63, 4344–4353. 10.1101/gad.4.7.1197 Fredman J.N. Engler J.A. (1993) Adenovirus precursor to terminal protein interacts with the nuclear matrix in vivo and in vitro. J. Virol. 67, 3384–3395. 10.1046/j.1365-2958.2001.02260.x 10.1093/emboj/19.15.4182 10.1074/jbc.M109312200 10.1093/emboj/cdg221 10.1016/S0955-0674(96)80011-1 10.1016/0092-8674(93)90235-I 10.1126/science.284.5421.1790 Verheijen R. Van Venrooij W. Ramaekers F. (1988) The nuclear matrix: structure and composition. J. Cell Sci. 90, 11–36. Bridge E. Pettersson U. (1995) Nuclear organization of replication and gene expression in adenovirus-infected cells. Curr. Top. Microbiol. Immunol. 199, 99–117. 10.1126/science.280.5363.547 Pombo A. Ferreira J. Bridge E. Carmo-Fonseca M. (1994) Adenovirus replication and transcription sites are spatially separated in the nucleus of infected cells. EMBO J. 13, 5075–5085. Angeletti P.C. Engler J.A. (1998) Adenovirus preterminal protein binds to the CAD enzyme at active sites of viral DNA replication on the nuclear matrix. J. Virol. 72, 2896–2904. 10.1016/S0065-3527(08)60736-8 10.1093/emboj/16.13.4049 10.1093/emboj/18.11.3164 10.1074/jbc.M004865200 10.1073/pnas.170295097 10.1093/emboj/cdg034 10.1093/emboj/cdg033 10.1128/JVI.75.3.1252-1264.2001 10.1006/viro.2001.1229 10.1074/jbc.M103358200 10.1128/JVI.76.24.13088-13093.2002 10.1034/j.1600-0854.2001.20108.x 10.1128/JVI.74.19.8953-8965.2000 10.1128/JVI.75.20.9808-9818.2001 Egger D. Pasamontes L. Bolten R. Boyko V. Bienz K. (1996) Reversible dissociation of the poliovirus replication complex: functions and interactions of its components in viral RNA synthesis. J. Virol. 70, 8675–8683. Lama J. Paul A.V. Harris K.S. Wimmer E. (1994) Properties of purified recombinant poliovirus protein 3AB as substrate for viral proteinases and as co-factor for RNA polymerase 3Dpol. J. Biol. Chem. 269, 66–70. Hope D.A. Diamond S.E. Kirkegaard K. (1997) Genetic dissection of interaction between poliovirus 3D polymerase and viral protein 3AB. J. Virol. 71, 9490–9498. 10.1074/jbc.M112429200 10.1016/S0969-2126(97)00261-X 10.1126/science.1070585