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van Putten AJ, de Lang R, Süter CPPM, Nijkamp HJJ. Escherichia coli host G668 stabilizes plasmids that are unstable in otherEscherichia coli strains. Curr Microbiol 1987. [DOI: 10.1007/bf01577530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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2
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van Putten AJ, de Lang R, Veltkamp E, Nijkamp HJ, Van Solingen P, van den Berg JA. Methylation-dependent transcription controls plasmid replication of the CloDF13 cop-1(Ts) mutant. J Bacteriol 1986; 168:728-33. [PMID: 2430942 PMCID: PMC213542 DOI: 10.1128/jb.168.2.728-733.1986] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The CloDF13 cop-1(Ts) mutant expresses a temperature-dependent plasmid copy number. At 42 degrees C the mutant shows a "runaway" behavior, and cells harboring this plasmid are killed. The cop-1(Ts) mutation is a G-to-A transition that disturbs one of the two methylation sites which are located opposite in the stem-loop structure within a region involved in both the initiation of primer synthesis for DNA replication and the termination of the cloacin operon transcript. We demonstrate that the mutation results in an increased primer (RNA II) synthesis resulting from nonconditional enhanced RNA II promoter activity, which at 42 degrees C causes a decrease in the amount of active replication repressor molecules (RNA I) synthesized from the opposite strand. We found that the absence of Dam methylation abolishes the mutant phenotype and that under this condition the high mutant level of RNA II synthesis is reduced, which is accompanied by a restoration of the regulation by RNA I. The role of methylation in the regulation of plasmid replication is discussed.
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Nijkamp HJ, de Lang R, Stuitje AR, van den Elzen PJ, Veltkamp E, van Putten AJ. The complete nucleotide sequence of the bacteriocinogenic plasmid CloDF13. Plasmid 1986; 16:135-60. [PMID: 3749334 DOI: 10.1016/0147-619x(86)90072-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The complete nucleotide sequence of the bacteriocinogenic plasmid CloDF13 has been determined. The plasmid consists of 9957 base pairs (molecular weight 6.64 X 10(6] with a GC content of 54.4%. At this moment 16 identified biological functions can be assigned to the primary structure of the CloDF13 DNA. The functions include those of eight protein encoding genes, two untranslated RNA species, and six DNA sites. We discuss these functions in relation to the structure of CloDF13 DNA. For convenience we have divided the CloDF13 genome into five defined regions: region I (origin of vegetative replication, priming and control of replication, type I incompatibility), region II (cloacin DF13, cloacin immunity, cloacin release, cloacin operon control), region III (double-stranded DNA-phage interaction, type II incompatibility, multimer resolution), region IV (inhibition of male specific RNA phages and transfer of Flac), and region V (mobility proteins, basis of mobility).
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Andreoli PM. Versatile Escherichia coli-Bacillus shuttle vectors derived from runaway replication plasmids related to CloDF13. MOLECULAR & GENERAL GENETICS : MGG 1985; 199:372-80. [PMID: 2993788 DOI: 10.1007/bf00330745] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Versatile cloning vectors were constructed employing a runaway replication mutant of the bacteriocinogenic plasmid CloDF13. These vectors can, under conditions where protein synthesis is not inhibited, be amplified in Escherichia coli to high levels by elevating the temperature and are therefore useful for the production of large quantities of DNA and protein. Since the constructed shuttle vectors, which harbour at least six unique restriction endonucleases sites, replicate in E. coli, Enterobacter cloacae, Staphylococcus aureus and a variety of Bacilli, they are applicable for the genetic engineering of both gram-negative and gram-positive bacteria.
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Nijkamp HJ, van Gemen B, Hakkaart MJ, van Putten AJ, Veltkamp E. Stable maintenance of plasmid Clo DF13: structural and functional relationships between replication control, partitioning, and incompatibility. BASIC LIFE SCIENCES 1985; 30:283-98. [PMID: 3893410 DOI: 10.1007/978-1-4613-2447-8_23] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Lee SB, Bailey JE. A mathematical model for lambda dv plasmid replication: analysis of copy number mutants. Plasmid 1984; 11:166-77. [PMID: 6728936 DOI: 10.1016/0147-619x(84)90021-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A mathematical model based on the molecular control mechanisms for lambda dv plasmid replication in a single Escherichia coli cell has been applied to simulate replication of mutant lambda dv plasmids. Model simulations of changes in repressor level and copy number resulting from mutations in the promoter-operator PROR region are consistent with experimental data. Calculated effects on lambda dv plasmid copy number of oligomer formation and of alternations in termination efficiency at tR1 also agree with experiment. The model has been employed to simulate the influence of cro mutants and of cro and tR1 double mutants on copy number and stable maintenance of lambda dv plasmid copy number. The genetic structure included in formulation of the replicon model provides a framework for relating changes in specific genetic loci on the plasmid with resulting alterations in host-plasmid system function.
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van den Elzen PJ, Hakkaart MJ, van Putten AJ, Walters HH, Veltkamp E, Nijkamp HJ. Structure and regulation of gene expression of a Clo DF13 plasmid DNA region involved in plasmid segregation and incompatibility. Nucleic Acids Res 1983; 11:8791-808. [PMID: 6324101 PMCID: PMC326624 DOI: 10.1093/nar/11.24.8791] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The bacteriocinogenic plasmid Clo DF13 contains genetic information involved in the accurate partitioning of the plasmid (parA and parB) as well as in incompatibility phenomena (incA, B, C and D). In this paper we report on the primary structure and regulation of gene expression of the 29% - 50% part of Clo DF13, containing the DNA regions incA, incB and parB as well as genes K and L. According to the results of our DNA sequence analysis, mapping of transposon insertions, RNA blotting and S1 mapping experiments, we conclude that: a) genes K and L are transcribed as one operon; transcription of this operon is initiated at a promoter (P2) located at 32.5% and proceeds in a clockwise direction. b) treatment of cells with mitomycin-C, significantly enhances transcription from P2, although this promoter is probably not directly repressed by lexA protein. c) Termination of transcription of this operon occurs between genes K and L, as well as distal to gene L. The possible role of gene products and/or sites, located within the 29-50% DNA region, in plasmid incompatibility and segregation is discussed.
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Snijders A, van Putten AJ, Veltkamp E, Nijkamp HJ. Localization and nucleotide sequence of the bom region of Clo DF13. MOLECULAR & GENERAL GENETICS : MGG 1983; 192:444-51. [PMID: 6336327 DOI: 10.1007/bf00392189] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Mobilization of the non-conjugative plasmid Clo DF13 requires both gene products of a conjugative plasmid and Clo DF13 encoded proteins as well as a cis-acting Clo DF13 DNA region, termed bom (basis of mobility). The bom region was located within a 264 bp fragment around the unique HpaI site. Comparison with the corresponding ColE1 and pBR322 sequences showed similarities with respect to the secondary structure. With respect to a possible relationship between the origin of vegetative replication (oriV) and the origin of transfer (oriT), we found that neither distance nor orientation of the Clo DF13 bom region with respect to oriV had any significant influence on the mobilization frequency. Surprisingly, after cloning of the 264 bp HpaII fragment in a bom- vector, restoration of the bom+ phenotype was only observed in one orientation. From these observations and from the sequence analysis of the bom region we suggest that transcription into this cloned bom fragment is essential for effective mobilization of the plasmid.
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Hakkaart MJ, Veltkamp E, Nijkamp HJ. Maintenance of the bacteriocinogenic plasmid Clo DF13 in Escherichia coli cells. II. Specific recombination functions involved in plasmid maintenance. MOLECULAR & GENERAL GENETICS : MGG 1982; 188:338-44. [PMID: 6296634 DOI: 10.1007/bf00332698] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Hakkaart MJ, Wesseling JG, Veltkamp E, Nijkamp HJ. Maintenance of the bacteriocinogenic plasmid Clo DF13 in Escherichia coli cells. I. Localisation and mutual interactions of four Clo DF13 incompatibility regions. MOLECULAR & GENERAL GENETICS : MGG 1982; 186:531-9. [PMID: 6752661 DOI: 10.1007/bf00337961] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The incompatibility properties of the bacteriocinogenic plasmid Clo DF13 have been examined. By using Clo DF13, Clo DF13 deletion, and transposon insertion mutants as well as compatible R plasmids into which Clo DF13 fragments have been cloned, we could identify and localise four different incompatibility regions on the Clo DF13 genome. These regions, designated incA, incB, incC, and incD are located in the following positions: incA about 32%, incB between 45% and 50%; incC about 97% and incD between 1.8% and 9% of the Clo DF13 genome. We studied the contribution of each of the four inc regions, separately and/or in combination with each other, to the incompatibility between two plasmid replicons. Two types of incompatibility can be distinguished: Type I evoked by incD, that overlaps the replication control area of Clo DF13 and type II, caused by incA, B and C. From our observations we present a model for plasmid incompatibility based on a combination of the existing repressor dilution and membrane attachment models.
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van Tiel-Menkveld GJ, Veltkamp E, De Graaf FK. Mitomycin C-induced synthesis of cloacin DF13 and lethality in cloacinogenic Escherichia coli cells. J Bacteriol 1981; 146:41-8. [PMID: 7012123 PMCID: PMC217049 DOI: 10.1128/jb.146.1.41-48.1981] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Treatment of cloacinogenic cultures with increasing concentrations of mitomycin C induced an increasing synthesis of cloacin DF13 accompanied by a decreasing number of colony-forming cells. Cells grown in the presence of glucose required a 10-fold-higher concentration of mitomycin C for optimal induction of cloacin production than did cells grown with lactate. Release of the cloacin was hampered in glucose-grown cells. Experiments with various CloDF13 insertion and deletion mutants revealed that the transcription of CloDF13 deoxyribonucleic acid sequences adjacent to the cloacin structural gene was essential for mitomycin C-induced lethality.
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Stuitje AR, Spelt CE, Veltkamp E, Nijkamp HJ. Identification of mutations affecting replication control of plasmid Clo DF13. Nature 1981; 290:264-7. [PMID: 6163089 DOI: 10.1038/290264a0] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The bacteriocinogenic plasmid Clo DF13, originally isolated from Escherichia cloacae, is stably maintained in Escherichia coli to the extent of about 10 copies per cell. Its replication resembles that of many other small, multicopy plasmids; plasmid-encoded protein is not required but plasmid-specific genetic information is involved in regulation of replication as both conditional and nonconditional copy-number mutants of Clo DF13, and transcomplementable copy-number mutants of plasmid Col E1 have been described. The sequences essential for replication of Col E1 (refs 16, 17) and Clo DF13 (refs 18, 19) have been identified within a region surrounding the replication origin. Initiation of Col E1 replication is preceded by transcription of the origin region, providing the RNA primer at the origin. However, transcription in the opposite direction results in a small transcript of approximately 100 nucleotides (RNA-100) for both Col E1 (refs 21, 22) and Clo DF13 (ref. 23). Data suggest that Col E1 RNA-100 acts as a negative control element for the initiation of replication. We show here that single base transitions in the RNA-100 cistron of Clo DF13 can result in a nonconditional increase in plasmid copy-number. Also, sequence analysis has revealed that a specific base transition in a DNA region, apparently involved in both termination and initiation of transcription towards the replication origin, results in a thermosensitive plasmid copy-number.
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Veltkamp E, Stuitje AR. Replication and structure of the bacteriocinogenic plasmids Clo DF13 and CoI E1. Plasmid 1981; 5:76-99. [PMID: 6164067 DOI: 10.1016/0147-619x(81)90078-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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van den Elzen PJ, Konings RN, Veltkamp E, Nijkamp HJ. Transcription of bacteriocinogenic plasmid CloDF13 in vivo and in vitro: structure of the cloacin immunity operon. J Bacteriol 1980; 144:579-91. [PMID: 6159346 PMCID: PMC294705 DOI: 10.1128/jb.144.2.579-591.1980] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Escherichia coli minicells harboring plasmid CloDF13 synthesized at least 25 messenger ribonucleic acid (RNA) species; three of these RNAs, a 2,400-, a 2,200-, and a 100-nucleotide RNA, were synthesized in relatively large amounts. Using insertion and deletion mutants of CloDF13 as well as an RNA blotting technique, we could demonstrate that these three RNAs are transcripts from the CloDF13 DNA region from 0 to 40%. This region contains the cloacin and immunity genes and the genetic information involved in plasmid DNA replication. A transcription map of this region is presented and discussed. The data indicate that the cloacin and immunity genes were coordinately transcribed into messenger RNAs of about 2,400 and 2,200 nucleotides, which differ in length at their 3' terminus. RNA polymerase binding studies and in vitro transcription assays indicated that transcription of these genes initiates at a promoter located around 32% on the CloDF13 map. Furthermore, it is shown that a 100-nucleotide RNA is encoded by the CloDF13 DNA region between 7.7 and 8.8% on the plasmid genome; the synthesis of this RNA proceeds in a direction opposite to the transcription of the cloacin and immunity genes.
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vd Pol H, Veltkamp E, Nijkamp HJ. Genetic information of the bacteriocinogenic plasmid Clo DF13 involved in the inhibition of the multiplication of double stranded DNA phages. MOLECULAR & GENERAL GENETICS : MGG 1980; 178:535-40. [PMID: 6993852 DOI: 10.1007/bf00337858] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The presence of plasmid Clo DF13 in Escherichia coli cells alters the response of these cells to infection with the double stranded DNA phages P1vir, lambda vir or T1. The multiplication of these phages is reduced in Clo DF13 harbouring cells, resulting in an altered burstsize and plaque morphology. The degree of reduction is correlated to the amount of particular Clo DF13 gene product(s) in the cell. The genetic information of Clo DF13 involved in this plasmid-phage interaction could be located, using insertion and deletion mutants of Clo DF13, between 29 an 62% on the Clo DF13 physical map. The genetic analysis of this region shows that at least two different genes, K and L, coding for polypeptides with a molecular weight of respectively 21 KD and 10.5 KD, are located in this region. The results presented, indicate that gene L and not gene K is involved in the interaction of Clo DF13 with the propagation of double stranded DNA phages.
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16
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Stuitje AR, Veltkamp E, Maat J, Heyneker HL. The nucleotide sequence surrounding the replication origin of the cop3 mutant of the bacteriocinogenic plasmid Clo DF13. Nucleic Acids Res 1980; 8:1459-73. [PMID: 6253936 PMCID: PMC324009 DOI: 10.1093/nar/8.7.1459] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The nucleotide sequence from about 100 base-pairs downstream to about 600 base pairs upstream the CloDF13 replication origin has been determined. A comparison of this sequence with the corresponding ColE1 origin sequence reveals that: The sequence at the origin of replication is conserved. There are large differences in the nucleotide sequence downstream the replication origin, whereas there is a large homology in the region of about 410 base-pairs upstream the replication origin. This conserved region might code for a largely homologous basic, arginine rich polypeptide of about 45 amino-acids, for both ColE1 and CloDF13. Although there are large differences in the primary structure of the region coding for the 100 nucleotide RNA, the secondary structure of this region seems to be conserved.
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van de Pol H, Veltkamp E, Nijkamp HJ. Clo DF13 plasmid genes affecting Flac transfer and propagation of male specific RNA phages. MOLECULAR & GENERAL GENETICS : MGG 1979; 168:309-17. [PMID: 374991 DOI: 10.1007/bf00271501] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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18
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Stuitje AR, Veltkamp E, Weijers PJ, Nijkamp HJ. Origin and direction of replication of the bacteriocinogenic plasmid Clo DF13. Nucleic Acids Res 1979; 6:71-80. [PMID: 370788 PMCID: PMC327674 DOI: 10.1093/nar/6.1.71] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Cairn's type replicative intermediates of both the wildtype Clo DF13 plasmid and the copy mutant CLO DF13 cop3 were isolated by dye-buoyant density centrifugation. Replicative intermediates were linearized at the HpaI or Sa1I cleavage site, and examined with the electron-microscope. The data show that replication of both the Clo DF13 wild type plasmid and the Clo DF13 cop3 plasmid, initiates at about 2.8% on the physical map. Replication proceeds unindirectionally and counterclockwise on this map.
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Andreoli PM, Brandsma RA, Veltkamp E, Nijkamp HJ. Isolation and characterization of a Clo DF13::Tn901 plasmid mutant with thermosensitive control of DNA replication. J Bacteriol 1978; 135:612-21. [PMID: 355238 PMCID: PMC222422 DOI: 10.1128/jb.135.2.612-621.1978] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
After nitrosoguanidine mutagenesis, a mutant Escherichia coli strain harboring the Clo DF13::Tn901 plasmid pJN03 was isolated that is thermosensitive (Ts) for growth at 43 degrees C. The mutation responsible for this thermosensitive phenotype resides on the pJN03 plasmid genome. Cells harboring the pJN03 cop-1(Ts) plasmid mutant showed a large increase in plasmid copy number at 43 degrees C accompanied by an increase in the synthesis of plasmid-specified gene products like cloacin DF13 and beta-lactamase. The pJN03 cop-1(Ts) mutant showed uncontrolled plasmid DNA replication at the nonpermissive temperature. Analysis of plasmid deletions showed that the mutation is located in the Clo DF13 map interval from 0 to 12% or 29 to 45%. This implies that native cloacin DF13 and the Clo DF13-specified polypeptides B, C, D, E, and G are not involved in the pleiotropic phenotype of the plasmid mutant pJN03 cop-1(Ts).
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