Location and characterisation of a new replication origin in the E. coli K12 chromosome

Replication of the Escherichia coli chromosome in RNase HI-deficient cells: multiple initiation regions and fork dynamics

DNA replication in Escherichia coli is normally initiated at a single origin, oriC, dependent on initiation protein DnaA. However, replication can be initiated elsewhere on the chromosome at multiple ectopic oriK sites. Genetic evidence indicates that initiation from oriK depends on RNA-DNA hybrids (R-loops), which are normally removed by enzymes such as RNase HI to prevent oriK from misfiring during normal growth. Initiation from oriK sites occurs in RNase HI-deficient mutants, and possibly in wild-type cells under certain unusual conditions. Despite previous work, the locations of oriK and their impact on genome stability remain unclear. We combined 2D gel electrophoresis and whole genome approaches to map genome-wide oriK locations. The DNA copy number profiles of various RNase HI-deficient strains contained multiple peaks, often in consistent locations, identifying candidate oriK sites. Removal of RNase HI protein also leads to global alterations of replication fork migration patterns, often opposite to normal replication directions, and presumably eukaryote-like replication fork merging. Our results have implications for genome stability, offering a new understanding of how RNase HI deficiency results in R-loop-mediated transcription-replication conflict, as well as inappropriate replication stalling or blockage at Ter sites outside of the terminus trap region and at ribosomal operons.

Patterns of chromosomal fragmentation due to uracil-DNA incorporation reveal a novel mechanism of replication-dependent double-stranded breaks

There is growing evidence that spontaneous chromosomal fragmentation, one of the main contributors to genetic instability, is intimately linked to DNA replication. In particular, we proposed before that uracil incorporation in DNA triggers chromosomal fragmentation due to replication fork collapse at uracil-excision intermediates. We tested predictions of this model at the chromosomal level in the dut mutants of Escherichia coli, by determining the relationship between DNA replication and patterns of fragmentation in defined chromosomal segments. Here we show that the uracil-DNA-triggered chromosomal fragmentation: (i) has a gradient that parallels the replication gradient, (ii) shows polarity within defined segments pointing towards replication origins and (iii) reorganizes to match induced replication gradients, confirming its dynamic pattern. Unexpectedly, these fragmentation patterns not only support the replication fork collapse model, but also reveal another mechanism of the replication-dependent chromosomal fragmentation triggered by uracil excision.

The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse

Escherichia coli DH10B was designed for the propagation of large insert DNA library clones. It is used extensively, taking advantage of properties such as high DNA transformation efficiency and maintenance of large plasmids. The strain was constructed by serial genetic recombination steps, but the underlying sequence changes remained unverified. We report the complete genomic sequence of DH10B by using reads accumulated from the bovine sequencing project at Baylor College of Medicine and assembled with DNAStar's SeqMan genome assembler. The DH10B genome is largely colinear with that of the wild-type K-12 strain MG1655, although it is substantially more complex than previously appreciated, allowing DH10B biology to be further explored. The 226 mutated genes in DH10B relative to MG1655 are mostly attributable to the extensive genetic manipulations the strain has undergone. However, we demonstrate that DH10B has a 13.5-fold higher mutation rate than MG1655, resulting from a dramatic increase in insertion sequence (IS) transposition, especially IS150. IS elements appear to have remodeled genome architecture, providing homologous recombination sites for a 113,260-bp tandem duplication and an inversion. DH10B requires leucine for growth on minimal medium due to the deletion of leuLABCD and harbors both the relA1 and spoT1 alleles causing both sensitivity to nutritional downshifts and slightly lower growth rates relative to the wild type. Finally, while the sequence confirms most of the reported alleles, the sequence of deoR is wild type, necessitating reexamination of the assumed basis for the high transformability of DH10B.

Is modification sufficient to protect a bacterial chromosome from a resident restriction endonuclease?

It has been generally accepted that DNA modification protects the chromosome of a bacterium encoding a restriction and modification system. But, when target sequences within the chromosome of one such bacterium (Escherichia coli K-12) are unmodified, the cell does not destroy its own DNA; instead, ClpXP inactivates the nuclease, and restriction is said to be alleviated. Thus, the resident chromosome is recognized as 'self' rather than 'foreign' even in the absence of modification. We now provide evidence that restriction alleviation may be a characteristic of Type I restriction-modification systems, and that it can be achieved by different mechanisms. Our experiments support disassembly of active endonuclease complexes as a potential mechanism. We identify amino acid substitutions in a restriction endonuclease, which impair restriction alleviation in response to treatment with a mutagen, and demonstrate that restriction alleviation serves to protect the chromosome even in the absence of mutagenic treatment. In the absence of efficient restriction alleviation, a Type I restriction enzyme cleaves host DNA and, under these conditions, homologous recombination maintains the integrity of the bacterial chromosome.

Evolution of lambdoid replication modules

Comparison of the putative iteron-binding proteins of lambdoid phages allows us to propose that in the case of lambdoid replication modules, the units on which natural selection acts do not coincide with the open reading frames. Rather, the first replication gene is split into two segments, and its 3' part (corresponding to the C-terminal domain of the iteron-binding protein) forms one unit with the second gene. We also propose from the phylogenetic analysis of phage-encoded homologs of E. coli DnaB and DnaC, that the recombination with the host sequences is not frequent. Accessory ATP-ases for helicase loading (E. coli DnaC homologs) may not be universal replication proteins. Our analysis may suggest that the bacterial helicase loaders might be of phage origin. The comparison of DnaC homologs of enterobacteria and enterobacterial phages supports the experimental data on residues important in interaction with DnaB. We propose that construction of plasmids carrying the replication origins of lambdoid prophages could be useful not only in further research on DNA replication but also on the role of these prophages in shuttling genes for bacterial virulence. The phage replication sequences could be also useful for identification of clinical enterobacterial isolates.

Replication of oriJ-based plasmid DNA during the stringent and relaxed responses of Escherichia coli

The oriJ-based plasmids contain the origin of DNA replication from the cryptic Rac prophage, present in the chromosomes of most Escherichia coli K-12 strains. The organization of the oriJ replication region resembles that of the bacteriophage lambda, although sequence similarity is small. Here we investigated the regulation of replication of the oriJ-based plasmid in E. coli relA(+) and relA(-) hosts during amino acid starvation and limitation, i.e., during the stringent and relaxed responses. We found that, contrary to plasmids derived from phage lambda, replication of the oriJ-based plasmid proceeds efficiently during both stringent and relaxed responses. On the other hand, density shift experiments and measurement of the stability of a putative replication initiator protein (the lambda O protein homologue) suggest that this replication may be carried out by the heritable replication complex, as previously demonstrated for lambda plasmids. We demonstrate that contrary to bacteriophage lambda p(R) promoter, an analogous promoter from the oriJ region is activated rather than inhibited at increased ppGpp levels. We propose that various responses of these promoters (p(R) and p(R-Rac), which are necessary for transcriptional activation of orilambda and perhaps oriJ, respectively) to ppGpp are responsible for differences in the replication regulation between orilambda- and oriJ-based plasmids during the stringent response.

Regulation of endonuclease activity by proteolysis prevents breakage of unmodified bacterial chromosomes by type I restriction enzymes

ClpXP-dependent proteolysis has been implicated in the delayed detection of restriction activity after the acquisition of the genes (hsdR, hsdM, and hsdS) that specify EcoKI and EcoAI, representatives of two families of type I restriction and modification (R-M) systems. Modification, once established, has been assumed to provide adequate protection against a resident restriction system. However, unmodified targets may be generated in the DNA of an hsd(+) bacterium as the result of replication errors or recombination-dependent repair. We show that ClpXP-dependent regulation of the endonuclease activity enables bacteria that acquire unmodified chromosomal target sequences to survive. In such bacteria, HsdR, the polypeptide of the R-M complex essential for restriction but not modification, is degraded in the presence of ClpXP. A mutation that blocks only the modification activity of EcoKI, leaving the cell with approximately 600 unmodified targets, is not lethal provided that ClpXP is present. Our data support a model in which the HsdR component of a type I restriction endonuclease becomes a substrate for proteolysis after the endonuclease has bound to unmodified target sequences, but before completion of the pathway that would result in DNA breakage.

Linkage map of Escherichia coli K-12, edition 10: the traditional map

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.

Genetic manipulation of Bacillus methanolicus, a gram-positive, thermotolerant methylotroph

We report the fist genetic transformation system, shuttle vectors, and integrative vectors for the thermotolerant, methylotrophic bacterium Bacillus methanolicus. By using a polyethylene glycol-mediated transformation procedure, we have successfully transformed B. methanolicus with both integrative and multicopy plasmids. For plasmids with a single BmeTI recognition site, dam methylation of plasmid DNA (in vivo or in vitro) was found to enhance transformation efficiency from 7- to 11-fold. Two low-copy-number Escherichia coli-B, methanolicus shuttle plasmids, pDQ507 and pDQ508, are described. pDQ508 caries the replication origin cloned from a 17-kb endogenous B. methanolicus plasmid, pBM1. pDQ507 carries a cloned B. methanolicus DNA fragment, pmr-1, possibly of chromosomal origin, that supports maintenance of pDQ507 as a circular, extrachromosomal DNA molecule. Deletion analysis of pDQ507 indicated two regions required for replication, i.e., a 90-bp AT-rich segment containing a 46-bp imperfect, inverted repeat sequence and a second region 65% homologous to the B. subtilis dpp operon. We also evaluated two E. coli-B. subtilis vectors, pEN1 and pHP13, for use as E. coli-B. methanolicus shuttle vectors. The plasmids pHP13, pDQ507, and pDQ508 were segregationally and structurally stable in B. methanolicus for greater than 60 generations of growth under nonselective conditions; pEN1 was segregationally unstable. Single-stranded plasmid DNA was detected in B. methanolicus transformants carrying either pEN1, pHP13, or pDQ508, suggesting that pDQ508, like the B. subtilis plasmids, is replicated by a rolling-circle mechanism. These studies provide the basic tools for the genetic manipulation of B. methanolicus.

Restriction alleviation and modification enhancement by the Rac prophage of Escherichia coli K-12

Bacteriophage lambda encodes an antirestriction function, RaI, which is able to modulate the activity of the Escherichia coli K-12 restriction and modification system, EcoKI. Here we report the characterization of an analogous function, Lar, expressed by E. coli sbcA mutants and the hybrid phage lambda reverse. E. coli sbcA mutants and lambda reverse both express genes of the Rac prophage, and we have located the lar gene immediately downstream of recT in this element. The lar gene has been cloned in an expression plasmid, and a combination of site-directed mutagenesis and labelling of plasmid-encoded proteins has enabled us to identify a number of translational products of lar, the smallest of which is sufficient for restriction alleviation. Lar, like RaI, is able both to alleviate restriction and to enhance modification by EcoKI. Lar, therefore, is functionally similar to RaI and the nucleotide sequences of their genes share 47% identity, indicating a common origin. A comparison of the predicted amino acid sequences of Lar and RaI shows only a 25% identity, but a few short regions do align and may indicate residues important for structure and/or function.

Integration of bacteriophage lambda into the cryptic lambdoid prophages of Escherichia coli

Bacteriophage lambda missing its chromosomal attachment site will integrate into recA+ Escherichia coli K-12 and C at the sites of cryptic prophages. The specific regions in which these recombination events occur were identified in both lambda and the bacterial chromosomes. A NotI restriction site on the prophage allowed its physical mapping. This allowed us to identify the locations of Rac, Qin, and Qsr' cryptic prophages on the NotI map of E. coli K-12 and, by analogy, to identify the cryptic prophage in E. coli C as Qin. No new cryptic prophages were detected in E. coli K-12.

Structure of cryptic lambda prophages

When Escherichia coli cells lysogenic for bacteriophage lambda are induced with ultraviolet light, cells carrying cryptic lambda prophages are occasionally found among the apparently cured survivors. The lambda variant crypticogen (lambda crg) carries an insertion of the transposable element IS2, which increases the frequency of cryptic lysogens to about 50% of cured cells: 43 of these cryptic prophages have been characterized. They all contain substitutions that replace the early segment of the prophage genome (from the IS2 to near the cos site) with a duplicate copy of a large segment of the host chromosome. The right end of the substitution always results from recombination between the nin-QSR-cos region of the prophage and the homologous incomplete lambdoid prophage Qsr' at 12.5 minutes in the E. coli chromosome. The left end of the substitution is usually a crossover that recombines the IS2 element in the prophage with an E. coli IS2 at 8.5 minutes, near the lac gene, or with a second IS2 located counterclockwise from leu at 2 minutes, generating duplications of at least 200,000 bases. Five cryptic lysogens derived from cells lysogenic for a reference strain of lambda (which lacks the IS2 present in lambda crg) have been characterized. They contain substitutions whose right termini are generated by a crossover with the Qsr' prophage. The left termini of these substitutions are formed either by a crossover between the lambda exo gene and a short exo-homologous segment of Qsr' (2/5), or by a crossover between sequences to the left of attL and an unmapped distant region of the host chromosome (3/5). The large duplications carried by these cryptic lysogens are stable, unlike tandem duplications, and so may significantly influence the cell's evolutionary potential.

The terminus region of the Escherichia coli chromosome contains two separate loci that exhibit polar inhibition of replication

The terminus region of the chromosome of Escherichia coli contains two separate sites, called T1 and T2, that inhibit replication forks. T1 is located near 28.5 min, which is adjacent to trp, and T2 is located at 34.5-35.7 min on the opposite side of the terminus region, near manA. The sites act in a polar fashion, and replication forks traveling in a clockwise direction with respect to the genetic map are not inhibited as they pass through T1 but are inhibited at T2. Similarly, counterclockwise forks are not inhibited at T2 but are inhibited at T1. Consequently, forks are not inhibited until they have passed through the terminus region and are about to leave it. Studies with deletion strains have located T2 within a 58-kilobase interval, which corresponds to kilobase coordinates 387-445 on the physical map of the terminus region.

Functioning of the F-plasmid origin of replication in an Escherichia coli K12 Hfr strain during exponential growth

The pattern of chromosome replication in the Escherichia coli K12 Hfr strain KL99 was investigated during exponential growth by DNA-DNA hybridization. The levels of chromosomal markers close to the point of insertion of F (near pyrC) were raised in relation to other markers by comparison with the situation in an isogenic F- strain. The data are shown to be consistent with the proposal that the integrated F plasmid was regulating its copy number by a mass-titration mechanism.

Multiple origin usage for DNA replication in sdrA(rnh) mutants of Escherichia coli K-12. Initiation in the absence of oriC

In stable DNA replication (sdrA/rnh) mutants of Escherichia coli, initiation of rounds of DNA replication occurs in the absence of the normal origin of replication, oriC. To determine whether or not the initiation occurs at a fixed site(s) on the chromosome in sdrA mutants, the DNA from exponentially growing sdrA mutant cells with or without the oriC site (delta oriC) was analyzed for the relative copy numbers of various genes along the chromosome. The results suggest that there are at least four fixed sites or regions of the sdrA delta oriC chromosome from which DNA replication can be initiated in the absence of the oriC sequence.

A third defective lambdoid prophage of Escherichia coli K12 defined by the lambda derivative, lambdaqin111

We describe the isolation and characterization of a new Q-independent substitution mutant of lambda, lambdaqin111, which differs from other characterized Q-independent lambda phages. This mutant defines a new lambda-like prophage in the bacterial chromosome, as seen by homologous recombination between lambdaqin111 and the host DNA and by DNA/DNA hybridization methods. Genetic and electron microscopy data show that this new prophage carries, at least, genes analogous to Q-S-R of lambda and also a cos site functionally identical to lambda cos. It is located near 34 min on the Escherichia coli K12 map, i.e. in the same region but at a different site from the defective Rac prophage.

Zygotic induction of the rac locus can cause cell death in E. coli

Conjugational transfer of the rac locus of E. coli K-12 into a Rac- recipient strain (i.e. rac+ X rac-) results in the killing of a majority of the recipient cells. The efficiency of killing depends somewhat on the plating medium, and can be as high as 98%. The killing is not observed in the rac+ X rac+, rac- X rac- or rac- X rac+ configurations. The rac locus, which has the properties of a cryptic prophage, may carry a function analogous to the kil function of bacteriophage lambda, or may instead cause killing by some replication related process.

Isolation of an autonomously replicating DNA fragment from the region of defective bacteriophage PBSX of Bacillus subtilis

We have isolated a 5.4-kilobase fragment of Bacillus subtilis DNA that confers the ability to replicate upon a nonreplicative plasmid. The B. subtilis 168 EcoRI fragment was ligated into the chimeric plasmid pCs540, which contains a chloramphenicol resistance determinant from the Staphylococcus aureus plasmid pC194 and an HpaII fragment from the Escherichia coli plasmid, pSC101. A recE B. subtilis derivative, strain BD224, is capable of maintaining this DNA as an autonomously replicating plasmid. In rec+ recipients, chloramphenicol-resistant transformants do not contain free plasmid. The plasmid is integrated as demonstrated by alterations in the pattern of chromosomal restriction enzyme fragments to which the plasmid hybridizes. The site of plasmid integration was mapped by PBS1-mediated transduction to the metC-PBSX region. A strain was a deletion in the region of defective bacteriophage PBSX differs in the hybridization profile obtained by probing EcoRI digests with this cloned fragment. This same deletion mutant, though proficient in normal recombinational pathways, permits autonomous replication of the plasmid apparently owing to the lack of an homologous chromosomal region with which to recombine. We believe that, like E. coli. B. subtilis contains at least one DNA fragment capable of autonomous replication when liberated from its normally integrated chromosomal site and that this cloned DNA fragment comes from the region of defective bacteriophage PBSX.

UV-mutable hybrids of Salmonella incorporating Escherichia coli region adjacent to tryptophan operon

Salmonella typhimurium recombinants have been constructed which have acquired UV-induced mutability. Such recombinants were obtained after transfer of plasmid F'126 from E. coli. UV-mutability was acquired by UV-stable Salmonella as a nonselective marker after selection of trp+ marker in 2.5% of the cases. Possible deficiency in UV-stable Salmonella of the umuC gene is discussed.

Rac-E. coli K12 strains carry a preferential attachment site for lambda rev

Lambda rev is a hybrid lambdoid phage formed by recombination between lambda and a defective lambdoid prophage (Rac) present in most E. coli K12 derivatives. We show here that three independently derived Rac-E. coli K12 strains are specifically deleted for the entire Rac prophage consistent with loss of Rac by excisive recombination between hybrid attachment sites that flank the prophage (c.f. excision of a lambda prophage). lambda rev, in which int and PP' of lambda have been replaced by integrative recombination genes and an attachment site derived from Rac (Gottesman et al. 1974), integrates site-specifically and in the correct orientation at the preferential attachment site generated by Rac excision.

Isolation and properties of Tn10 insertions in the rac locus of Escherichia coli

Two Tn10 insertions that are in the rac locus of the chromosome of Escherichia coli have been isolated and characterized. The insertions are located at min 29.7 and min 30.0. The insertions are stable when an F123 rac::Tn10 episome is transferred to an F- rac+ recipient, but they are lost at a high frequency when transferred to an F- rac- recipient. This latter condition has been previously demonstrated to cause the excision of the rac locus. The Tn10 insertions are also lost at a high frequency when strains containing them are lysogenized with lambda reverse. If the lysogens that have lost the Tn10 insertion are subsequently cured of lambda reverse, the cells no longer contain sequences homologous with rac locus DNA. These strains were rac- when tested for recombination activation (Low 1973), and this procedure consequently provides a simple means to make isogenic rac+ and rac- strains.

Identification of a second cryptic lambdoid prophage locus in the E. coli K12 chromosome

In addition to the cryptic lambdoid prophage genes that are known to reside at the rac locus in Escherichia coli K12 strains, a second cryptic lambdoid prophage has been located near the gal operon. This prophage was shown to contain DNA that is homologous to the QSR genes of lambda phage.

The origin of Q-independent derivatives of phage lambda

lambda qsr' (Q-independent) phages are characterised by the replacement of the region of the lambda genome that contains Q, S, R, and the late gene promoter, P'R, with host-derived DNA that codes for functions analogous to those deleted. Restriction endonuclease analysis and DNA/DNA hybridisation methods have been used to show that lambda p4 and lambda qin A3, two such Q-independent phages, are the product of recombination between lambda and a defective lambdoid prophage (the qsr' prophage) located at an as yet unidentified site in the E. coli K 12 chromosome. The qsr' prophage is distinct from the defective lambdoid prophage Rac (Kaiser and Murray 1979). In the E. coli K12 strain AB1157 from which lambda qsr' phages cannot be generated, the qsr' prophage has suffered an internal deletion. That the qsr' prophage appears not to carry a full complement of essential late genes suggests one explanation for its apparently defective nature.

On the nature of sbcA mutations in E. coli K 12

We have recently shown (Kaiser and Murray 1979) that many E. coli K 12 strains carry a defective prophage (Rac) located a few minutes clockwise of the trp operon on the genetic map. The Rac genome contains recE, the determinant for the ATP-independent exonuclease, ExoVIII. E. coli K 12 strains which carry sbcA mutations express recE constitutively. This paper describes an investigation of several such strains. We show that the SbcA phenotype may arise from more than one type of mutational change. The most readily explained SbcA phenotype is that of sbcA8 strains in which a large section of the Rac genome (including one hybrid attachment site and probably the prophage repressor gene) is deleted. Three sbcA- strains carry multiple (and probably tandemly repeated) copies of the Rac genome while two others carry a single Rac prophage that is indistinguishable in its hybridisation behaviour from that carried by sbcA+ strains.

Molecular cloning of the gene for the beta-lactamase of Bacillus licheniformis and its expression in Escherichia coli

The structural gene, pen, for the beta-lactamase of B. licheniformis has been cloned into a lambda vector and shown to be expressed at a low rate in E. coli. The cloned pen gene appears to be expressed from a promoter within the fragment of B. licheniformia DNA, since its rate of expression is not affected by the presence of the phage repressor, the absence of the phage's positive-control functions, or the position or orientation of the gene within the phage genome.

Physical characterisation of the "Rac prophage" in E. coli K12

We confirm the hypothesis of Low (1973) that many E. coli K12 strains contain a prophage (the Rac prophage) located a few minutes clockwise of the trp operon on the genetic map. We have used restriction endonucleases and 32P-labelled probes to construct a physical map of this prophage. Some E. coli K12 strains, including AB1157, have lost the entire prophage, apparently by a specific deletion. This is consistent with prophage excision by site-specific recombination. lambda reverse (lambda rev) phages (Zissler et al., 1971) are recombination proficient derivatives of phage lambda in which the phage recombination functions have been replaced by analogous functions (RecE) derived from the host chromosome (Gottesman et al., 1974; Gillen et al., 1977). Our data support the origin of lambda rev plages by recombination between lambda and the Rac prophage following excision of the Rac prophage from the E. coli chromosome. Important experimental data are included in the Figure legends.