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Near-continuously synthesized leading strands in Escherichia coli are broken by ribonucleotide excision. Proc Natl Acad Sci U S A 2019; 116:1251-1260. [PMID: 30617079 DOI: 10.1073/pnas.1814512116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
In vitro, purified replisomes drive model replication forks to synthesize continuous leading strands, even without ligase, supporting the semidiscontinuous model of DNA replication. However, nascent replication intermediates isolated from ligase-deficient Escherichia coli comprise only short (on average 1.2-kb) Okazaki fragments. It was long suspected that cells replicate their chromosomal DNA by the semidiscontinuous mode observed in vitro but that, in vivo, the nascent leading strand was artifactually fragmented postsynthesis by excision repair. Here, using high-resolution separation of pulse-labeled replication intermediates coupled with strand-specific hybridization, we show that excision-proficient E. coli generates leading-strand intermediates >10-fold longer than lagging-strand Okazaki fragments. Inactivation of DNA-repair activities, including ribonucleotide excision, further increased nascent leading-strand size to ∼80 kb, while lagging-strand Okazaki fragments remained unaffected. We conclude that in vivo, repriming occurs ∼70× less frequently on the leading versus lagging strands, and that DNA replication in E. coli is effectively semidiscontinuous.
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Jun S, Si F, Pugatch R, Scott M. Fundamental principles in bacterial physiology-history, recent progress, and the future with focus on cell size control: a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:056601. [PMID: 29313526 PMCID: PMC5897229 DOI: 10.1088/1361-6633/aaa628] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Bacterial physiology is a branch of biology that aims to understand overarching principles of cellular reproduction. Many important issues in bacterial physiology are inherently quantitative, and major contributors to the field have often brought together tools and ways of thinking from multiple disciplines. This article presents a comprehensive overview of major ideas and approaches developed since the early 20th century for anyone who is interested in the fundamental problems in bacterial physiology. This article is divided into two parts. In the first part (sections 1-3), we review the first 'golden era' of bacterial physiology from the 1940s to early 1970s and provide a complete list of major references from that period. In the second part (sections 4-7), we explain how the pioneering work from the first golden era has influenced various rediscoveries of general quantitative principles and significant further development in modern bacterial physiology. Specifically, section 4 presents the history and current progress of the 'adder' principle of cell size homeostasis. Section 5 discusses the implications of coarse-graining the cellular protein composition, and how the coarse-grained proteome 'sectors' re-balance under different growth conditions. Section 6 focuses on physiological invariants, and explains how they are the key to understanding the coordination between growth and the cell cycle underlying cell size control in steady-state growth. Section 7 overviews how the temporal organization of all the internal processes enables balanced growth. In the final section 8, we conclude by discussing the remaining challenges for the future in the field.
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Affiliation(s)
- Suckjoon Jun
- Department of Physics, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, United States of America. Section of Molecular Biology, Division of Biology, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, United States of America
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Amado L, Kuzminov A. The replication intermediates in Escherichia coli are not the product of DNA processing or uracil excision. J Biol Chem 2006; 281:22635-46. [PMID: 16772291 DOI: 10.1074/jbc.m602320200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The current model of DNA replication in Escherichia coli postulates continuous synthesis of the leading strand, based on in vitro experiments with purified enzymes. In contrast, in vivo experiments in E. coli and its bacteriophages, in which maturation of replication intermediates was blocked, report discontinuous DNA synthesis of both the lagging and the leading strands. To address this discrepancy, we analyzed nascent DNA species from ThyA+ E. coli cells replicating their DNA in ligase-deficient conditions to block maturation of replication intermediates. We report here that the bulk of the newly synthesized DNA isolated from ligase-deficient cells have a length between 0.3 and 3 kb, with a minor fraction being longer that 11 kb but shorter than the chromosome. The low molecular weight of the replication intermediates is unchanged by blocking linear DNA processing with a recBCD mutation or by blocking uracil excision with an ung mutation. These results are consistent with the previously proposed discontinuous replication of the leading strand in E. coli.
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Affiliation(s)
- Luciana Amado
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3709, USA
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Crisona NJ, Strick TR, Bensimon D, Croquette V, Cozzarelli NR. Preferential relaxation of positively supercoiled DNA by E. coli topoisomerase IV in single-molecule and ensemble measurements. Genes Dev 2000; 14:2881-92. [PMID: 11090135 PMCID: PMC317058 DOI: 10.1101/gad.838900] [Citation(s) in RCA: 165] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We show that positively supercoiled [(+) SC] DNA is the preferred substrate for Escherichia coli topoisomerase IV (topo IV). We measured topo IV relaxation of (-) and (+) supercoils in real time on single, tethered DNA molecules to complement ensemble experiments. We find that the preference for (+) SC DNA is complete at low enzyme concentration. Otherwise, topo IV relaxed (+) supercoils at a 20-fold faster rate than (-) supercoils, due primarily to about a 10-fold increase in processivity with (+) SC DNA. The preferential cleavage of (+) SC DNA in a competition experiment showed that substrate discrimination can take place prior to strand passage in the presence or absence of ATP. We propose that topo IV discriminates between (-) and (+) supercoiled DNA by recognition of the geometry of (+) SC DNA. Our results explain how topo IV can rapidly remove (+) supercoils to support DNA replication without relaxing the essential (-) supercoils of the chromosome. They also show that the rate of supercoil relaxation by topo IV is several orders of magnitude faster than hitherto appreciated, so that a single enzyme may suffice at each replication fork.
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Affiliation(s)
- N J Crisona
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
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Ullsperger C, Cozzarelli NR. Contrasting enzymatic activities of topoisomerase IV and DNA gyrase from Escherichia coli. J Biol Chem 1996; 271:31549-55. [PMID: 8940171 DOI: 10.1074/jbc.271.49.31549] [Citation(s) in RCA: 119] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
DNA gyrase and topoisomerase IV (Topo IV) have distinct roles as unlinking enzymes during DNA replication despite 40% sequence identity between them. DNA gyrase unlinks replicating DNA by introducing negative supercoils while Topo IV decatenates the two daughter molecules. For this study, we measured the rates of unlinking of various topoisomers of DNA by DNA gyrase and Topo IV. Each enzyme has marked preferences for certain strand-passage reactions. DNA gyrase is a relatively poor decatenase, catalyzing strand-passage events that result in supercoiling at rates several orders of magnitude faster than those causing decatenation. Topo IV, in contrast, decatenates linked circles 10-40 times more quickly than it removes the intramolecular crossings from supercoiled DNA. Supercoiled catenanes are unlinked at an even more increased rate by Topo IV. Thus, the supercoils augment decatenation rather than compete with catenane crossings for their removal. Knot crossings and the crossings of multiply interlinked catenanes are also preferentially removed by Topo IV. This ability of Topo IV to selectively unlink catenated molecules mirrors its key role in decatenation of replicating chromosomes in vivo.
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Affiliation(s)
- C Ullsperger
- Department of Molecular and Cellular Biology, Division of Biochemistry and Molecular Biology, University of California, Berkeley, California 94720, USA
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Ullsperger CJ, Vologodskii AV, Cozzarelli NR. Unlinking of DNA by Topoisomerases During DNA Replication. NUCLEIC ACIDS AND MOLECULAR BIOLOGY 1995. [DOI: 10.1007/978-3-642-79488-9_6] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Dwek R, Or-Gad S, Rozenhak S, Ron EZ. Two new cell division mutants in Escherichia coli map near the terminus of chromosome replication. MOLECULAR & GENERAL GENETICS : MGG 1984; 193:379-81. [PMID: 6363883 DOI: 10.1007/bf00330697] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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8
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9
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Yaffe E, Grossman N, Ron EZ. Membrane-bound deoxyribonucleic acid from Escherichia coli: effects of replication, protein synthesis, and ribonucleic acid synthesis. J Bacteriol 1979; 137:790-4. [PMID: 370100 PMCID: PMC218358 DOI: 10.1128/jb.137.2.790-794.1979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The experiments presented in this paper suggest that the shift observed in sedimentation of deoxyribonucleic acid from cells of Escherichia coli subjected to amino acid starvation is related to inhibition of ribonucleic acid synthesis rather than to its release from the membrane at the termination of replication.
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Fralick JA. Studies on the regulation of initiation of chromosome replication in Escherichia coli. J Mol Biol 1978; 122:271-86. [PMID: 357730 DOI: 10.1016/0022-2836(78)90190-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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11
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Ron E, Grossman N, Helmstetter CE. Control of cell division in Escherichia coli: effect of amino acid starvation. J Bacteriol 1977; 129:569-73. [PMID: 320184 PMCID: PMC234977 DOI: 10.1128/jb.129.2.569-573.1977] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The effect of amino acid starvation on cell division was studied in cells of Escherichia coli B. In this bacterial strain, deprivation of a required amino acid resulted in synchronous cell division upon restoration of the amino acid. This synchronization was apparently due to a shift forward in the cell cycle during the starvation. As a consequence, the cells divided at a size that was smaller than normal.
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Sloan JB, Urban JE. Growth response of Escherichia coli to nutritional shift-up: immediate division stimulation in slow-growing cells. J Bacteriol 1976; 128:302-8. [PMID: 789337 PMCID: PMC232856 DOI: 10.1128/jb.128.1.302-308.1976] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
When Escherichia coli 15T- cells growing exponentially at 70- to 80-min doubling times are subjected to a nutritional shift-up via glucose addition, cell division continues at the preshift rate for about 70 min (rate maintenance). The same cells growing at doubling times of 120 min or longer, however, begin to divide at a new faster rate immediately upon glucose addition. In both the rate maintenance and immediate division situations, cell mass, as measured by optical density (OD), begins to increase immediately upon shift-up. Consequently, the OD/cell pattern differs in the two growth-rate transitions. During rate maintenance, the OD/cell ratio increases dramatically for 60 to 70 min, and then slows appreciably and approaches the OD/cell characteristic of the new medium. During immediate division situations, the OD/cell increases only slightly for the first 180 +/- min; then the rate of increase accelerates but does not stop at the OD/cell characteristic of the new medium. Immediate division upon nutritional shift-up apparently depends upon initial doubling times in excess of 115 to 120 min and provision of a readily metabolized carbon source supporting doubling times of about 40 min. Similar immediate division occurs in E. coli B/r and K-12.
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Helmstetter CE, Pierucci O. DNA synthesis during the division cycle of three substrains of Escherichia coli B/r. J Mol Biol 1976; 102:477-86. [PMID: 775109 DOI: 10.1016/0022-2836(76)90329-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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14
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Rodriguez RL, Davern CI. Direction of deoxyribonucleic acid replication in Escherichia coli under various conditions of cell growth. J Bacteriol 1976; 125:346-52. [PMID: 1107310 PMCID: PMC233369 DOI: 10.1128/jb.125.1.346-352.1976] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The direction of chromosome replication in a temperature-sensitive initiation mutant of Escherichia coli (CT28) is shown autoradiographically to be bidirectional. This mode of replication persists even when the rate of replication is reduced by slow growth in succinate minimal medium or in the presence of chloramphenicol. Therefore, although the rate of replication can be affected by certain physiological stimuli, the topology of replication need not be.
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Paetkau V, Langman L, Miller RC. The origin of nascent single-stranded fragments in replicating TM DNA. J Mol Biol 1975; 98:719-37. [PMID: 1104877 DOI: 10.1016/s0022-2836(75)80006-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Abstract
DNA ligase of E. coli is a polypeptide of molecular weight 75,000. The comparable T4-induced enzyme is somewhat smaller (63,000 to 68,000). Both enzymes catalyze the synthesis of phosphodiester bonds between adjacent 5'-phosphoryl and 3'-hydroxyl groups in nicked duplex DNA, coupled to the cleavage of the pyrophosphate bond of DPN (E. coli) or ATP (T4). Phosphodiester bond synthesis catalyzed by both enzymes occurs in a series of these discrete steps and involves the participation of two covalent intermediates (Fig. 1). A steady state kinetic analysis of the reaction-catalyzed E. coli ligase supports this mechanism, and further demonstrates that enzyme-adenylate and DNA-adenylate are kinetically significant intermediates on the direct path of phosphodiester bond synthesis. A strain of E. coli with a mutation in the structural gene for DNA ligase which results in the synthesis of an abnormally thermolabile enzyme is inviable at 42 degrees C. Although able to grow at 30 degrees C, the mutant is still defective at this temperature in its ability to repair damage to its DNA caused by ultraviolet irradiation and by alkylating agents. At 42 degrees C, all the newly replicated DNA is in the form of short 10S "Okazaki fragments," an indication that the reason for the mutant's failure to survive under these conditions is its inability to sustain the ligation step that is essential for the discontinuous synthesis of the E. coli chromosome. DNA ligase is therefore an essential enzyme required for normal DNA replication and repair in E. coli. Purified DNA ligases have proved to be useful reagents in the construction in vitro of recombinant DNA molecules.
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Konrad EB, Modrich P, Lehman IR. DNA synthesis in strains of Escherichia coli K12 with temperature-sensitive DNA ligase and DNA polymerase I. J Mol Biol 1974; 90:115-26. [PMID: 4616094 DOI: 10.1016/0022-2836(74)90260-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Dingman CW, Fisher MP, Ishizawa M. DNA replication in Escherichia coli: physical and kinetic studies of the replication point. J Mol Biol 1974; 84:275-95. [PMID: 4598369 DOI: 10.1016/0022-2836(74)90585-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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8. DNA Joining Enzymes (Ligases). ACTA ACUST UNITED AC 1974. [DOI: 10.1016/s1874-6047(08)60140-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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Fralick JA, Lark KG. Evidence for the involvement of unsaturated fatty acids in initiating chromosome replication in Escherichia coli. J Mol Biol 1973; 80:459-75. [PMID: 4586983 DOI: 10.1016/0022-2836(73)90416-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Marunouchi T, Messer W. Replication of a specific terminal chromosome segment in Escherichia coli which is required for cell division. J Mol Biol 1973; 78:211-28. [PMID: 4581292 DOI: 10.1016/0022-2836(73)90439-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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24
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Doolittle CH, Mandel HG, Hahn GA. Use of fluorouracil-uracil combinations to study growth accompanied by insufficient deoxyribonucleic acid synthesis in Bacillus cereus. J Bacteriol 1973; 113:1311-9. [PMID: 4632399 PMCID: PMC251699 DOI: 10.1128/jb.113.3.1311-1319.1973] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
5-Fluorouracil (FU) at a concentration of 16 muM almost totally inhibited deoxyribonucleic acid (DNA) synthesis and cell division by Bacillus cereus, whereas growth continued at an exponential rate (25% of control for at least 3 h). In cultures simultaneously given 160 muM uracil (U) along with the FU, DNA synthesis still stopped, but cell division continued for one generation at the control rate and at a much slower rate beyond that; in the meantime, cell mass continued to increase at an essentially normal rate. The cells in cultures treated with FU or FU plus U were elongated and contained about half of the control content of DNA, with one nuclear area per cell instead of two. Loss of cloning ability, unlike mass increase, was always correlated with the continuing inhibition of DNA synthesis, in either FU- or U plus FU-treated cultures.
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Jacobson MK, Lark KG. DNA replication in Escherichia coli: evidence for two classes of small deoxyribonucleotide chains. J Mol Biol 1973; 73:371-96. [PMID: 4577039 DOI: 10.1016/0022-2836(73)90088-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Lark KG. Initiation and termination of bacterial deoxyribonucleic acid replication in low concentrations of chloramphenicol. J Bacteriol 1973; 113:1066-9. [PMID: 4570592 PMCID: PMC285329 DOI: 10.1128/jb.113.2.1066-1069.1973] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Escherichia coli 15T(-) can initiate a cycle of deoxyribonucleic acid replication with equal efficiency in the presence of 25 or 50 mug of chloramphenicol/ml. However, these replication cycles are not completed in the presence of these drug concentrations, and the amount of replication decreases with increasing drug concentration.
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Smith DW. DNA synthesis in prokaryotes: replication. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1973; 26:321-408. [PMID: 4122629 DOI: 10.1016/0079-6107(73)90022-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Olivera BM, Bonhoeffer F. Discontinuous DNA replication in vitro. I. Two distinct size classes of intermediates. NATURE: NEW BIOLOGY 1972; 240:233-5. [PMID: 4345241 DOI: 10.1038/newbio240233a0] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Lark KG. Evidence for the direct involvement of RNA in the initiation of DNA replication in Escherichia coli 15T. J Mol Biol 1972; 64:47-60. [PMID: 4552485 DOI: 10.1016/0022-2836(72)90320-8] [Citation(s) in RCA: 290] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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31
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Pierucci O. Chromosome replication and cell division in Escherichia coli at various temperatures of growth. J Bacteriol 1972; 109:848-54. [PMID: 4550822 PMCID: PMC285215 DOI: 10.1128/jb.109.2.848-854.1972] [Citation(s) in RCA: 44] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The effect of temperature on the growth rate and the pattern of chromosome replication during the division cycle of Escherichia coli B/r growing in various media was investigated. The time between divisions, the time for a round of replication (C), and the time between completion of a round and cell division (D) were threefold longer at 21 C than at 37 C. At all temperatures and in all media, D equalled one-half C, suggesting that a common mechanism controls chromosome replication and the progression of the cell toward division after completion of a round of replication.
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Tessler PM, Loos LJ, Salivar WO. On the replication of Escherichia coli DNA. ARCHIV FUR MIKROBIOLOGIE 1972; 84:161-90. [PMID: 4559399 DOI: 10.1007/bf00412436] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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33
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Lehnert S, Moroson H. Dependence of single-stranded DNA length on stage of growth cycle in Escherichia coli B-r and effect of irradiation. Biophys J 1971; 11:798-809. [PMID: 4943726 PMCID: PMC1484044 DOI: 10.1016/s0006-3495(71)86255-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Alkaline sucrose density gradient profiles of DNA from log phase Escherichia coli B/r (CSH) show a main peak with sedimentation coefficient at approximately 130S and a shoulder or second peak at approximately 90S. Incorporation of radioactive precursors into the 90S peak precedes their appearance in the main peak. The size of the second peak appears to be directly related to the rate of replication and it is not present in profiles of nondividing stationary phase cultures. The decrease in weight average molecular weight (Mw) of DNA produced by X-rays is also directly related to the rate of replication. It is greatest in log phase E. coli B/r and least in stationary phase cells, because of the efficiency of rejoining of radiation-induced single strand breaks in DNA of the latter cells.
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35
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Ephrati-Elizur E, Borenstein S. Velocity of chromosome replication in thymine-requiring and independent strains of Bacillus subtilis. J Bacteriol 1971; 106:58-64. [PMID: 4994603 PMCID: PMC248644 DOI: 10.1128/jb.106.1.58-64.1971] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Chromosomes in spores of a thymineless mutant of Bacillus subtilis strain 168 were shown to have a replication fork, unlike chromosomes in spores of the thy(+) strain which are in a complete form. As a consequence the number of replication forks in germinating cultures is higher in the thy(-) strain than in the thy(+) one. Chromosome replication time (C) in the thy(+) strain was found to be about 53 min for growth rates from 20 to 60 min. In the thy(-) strain, C was about 75 min at high growth rates and increased with decreasing growth rate when the thymine concentration was not limiting. With limiting thymine concentrations in the medium replication velocity decreased independently of growth rate.
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39
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40
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Chai NC, Lark KG. Cytological studies of deoxyribonucleic acid replication in Escherichia coli 15T-: replication at slow growth rates and after a shift-up into rich medium. J Bacteriol 1970; 104:401-9. [PMID: 4919753 PMCID: PMC248226 DOI: 10.1128/jb.104.1.401-409.1970] [Citation(s) in RCA: 49] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
We examined the gross nuclear morphology of Escherichia coli 15T(-) grown in different media with doubling times ranging from 22 to 270 min. In slowly growing cells, deoxyribonucleic acid synthesis was measured by autoradiography and shown to occur with greatest probability during the first two-thirds of the division cycle. In such cells, segregation occurred later, at the end of the division cycle rather than at the end of deoxyribonucleic acid replication. Nuclear regions in L-broth cells (22-min doubling time) cannot correspond to separate chromosomes but probably represent regions of replication activity. Segregation of template nucleotide strands was measured after a shift-up from proline M9 or glucose M9 media into L broth. A model is presented to account for the pattern of segregation observed.
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DNA replication in Escherichia coli: location of recently incorporated thymidine within molecules of high molecular weight DNA. Proc Natl Acad Sci U S A 1970; 67:629-36. [PMID: 4943176 PMCID: PMC283252 DOI: 10.1073/pnas.67.2.629] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
More than 50% of the [(3)H]thymidine incorporated during short pulses into the DNA of Escherichia coli 15T(-) can be extracted by alkali as high molecular weight DNA. Density gradient centrifugation and digestion with exonuclease I suggest that these large pieces of DNA are composed of newly synthesized DNA attached to pre-existing material at the 3' end of the molecule.
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