Identification of E. coli uvrC protein

The Helicobacter pylori UvrC Nuclease Is Essential for Chromosomal Microimports after Natural Transformation

Helicobacter pylori is a Gram-negative bacterial carcinogenic pathogen that infects the stomachs of half of the human population. It is a natural mutator due to a deficient DNA mismatch repair pathway and is naturally competent for transformation. As a result, it is one of the most genetically diverse human bacterial pathogens. The length of chromosomal imports in H. pylori follows an unusual bimodal distribution consisting of macroimports with a mean length of 1,645 bp and microimports with a mean length of 28 bp. The mechanisms responsible for this import pattern were unknown. Here, we used a high-throughput whole-genome transformation assay to elucidate the role of nucleotide excision repair pathway (NER) components on import length distribution. The data show that the integration of microimports depended on the activity of the UvrC endonuclease, while none of the other components of the NER pathway was required. Using H. pylori site-directed mutants, we showed that the widely conserved UvrC nuclease active sites, while essential for protection from UV light, one of the canonical NER functions, are not required for generation of microimports. A quantitative analysis of recombination patterns based on over 1,000 imports from over 200 sequenced recombinant genomes showed that microimports occur frequently within clusters of multiple imports, strongly suggesting they derive from a single strand invasion event. We propose a hypothetical model of homologous recombination in H. pylori, involving a novel function of UvrC, that reconciles the available experimental data about recombination patterns in H. pylori. IMPORTANCE Helicobacter pylori is one of the most common and genetically diverse human bacterial pathogens. It is responsible for chronic gastritis and represents the main risk factor for gastric cancer. In H. pylori, DNA fragments can be imported by recombination during natural transformation. The length of those fragments determines how many potentially beneficial or deleterious alleles are acquired and thus influences adaptation to the gastric niche. Here, we used a transformation assay to examine imported fragments across the chromosome. We show that UvrC, an endonuclease involved in DNA repair, is responsible for the specific integration of short DNA fragments. This suggests that short and long fragments are imported through distinct recombination pathways. We also show that short fragments are frequently clustered with longer fragments, suggesting that both pathways may be mechanistically linked. These findings provide a novel basis to explain how H. pylori can fine-tune the genetic diversity acquired by transformation.

UvrC Coordinates an O2-Sensitive [4Fe4S] Cofactor

Recent advances have led to numerous landmark discoveries of [4Fe4S] clusters coordinated by essential enzymes in repair, replication, and transcription across all domains of life. The cofactor has notably been challenging to observe for many nucleic acid processing enzymes due to several factors, including a weak bioinformatic signature of the coordinating cysteines and lability of the metal cofactor. To overcome these challenges, we have used sequence alignments, an anaerobic purification method, iron quantification, and UV-visible and electron paramagnetic resonance spectroscopies to investigate UvrC, the dual-incision endonuclease in the bacterial nucleotide excision repair (NER) pathway. The characteristics of UvrC are consistent with [4Fe4S] coordination with 60-70% cofactor incorporation, and additionally, we show that, bound to UvrC, the [4Fe4S] cofactor is susceptible to oxidative degradation with aggregation of apo species. Importantly, in its holo form with the cofactor bound, UvrC forms high affinity complexes with duplexed DNA substrates; the apparent dissociation constants to well-matched and damaged duplex substrates are 100 ± 20 nM and 80 ± 30 nM, respectively. This high affinity DNA binding contrasts reports made for isolated protein lacking the cofactor. Moreover, using DNA electrochemistry, we find that the cluster coordinated by UvrC is redox-active and participates in DNA-mediated charge transport chemistry with a DNA-bound midpoint potential of 90 mV vs NHE. This work highlights that the [4Fe4S] center is critical to UvrC.

Recruitment of UvrBC complexes to UV-induced damage in the absence of UvrA increases cell survival

Nucleotide excision repair (NER) is the primary mechanism for removal of ultraviolet light (UV)-induced DNA photoproducts and is mechanistically conserved across all kingdoms of life. Bacterial NER involves damage recognition by UvrA₂ and UvrB, followed by UvrC-mediated incision either side of the lesion. Here, using a combination of in vitro and in vivo single-molecule studies we show that a UvrBC complex is capable of lesion identification in the absence of UvrA. Single-molecule analysis of eGFP-labelled UvrB and UvrC in living cells showed that UV damage caused these proteins to switch from cytoplasmic diffusion to stable complexes on DNA. Surprisingly, ectopic expression of UvrC in a uvrA deleted strain increased UV survival. These data provide evidence for a previously unrealized mechanism of survival that can occur through direct lesion recognition by a UvrBC complex.

The complex choreography of transcription-coupled repair

A quarter of a century has elapsed since the discovery of transcription-coupled repair (TCR), and yet our fascination with this process has not diminished. Nucleotide excision repair (NER) is a versatile pathway that removes helix-distorting DNA lesions from the genomes of organisms across the evolutionary scale, from bacteria to humans. TCR, defined as a subpathway of NER, is dedicated to the repair of lesions that, by virtue of their location on the transcribed strands of active genes, encumber elongation by RNA polymerases. In this review, we will report on newly identified proteins, protein modifications, and protein complexes that participate in TCR in Escherichia coli and in human cells. We will discuss general models for the biochemical pathways and how and when cells might choose to utilize TCR or other pathways for repair or bypass of transcription-blocking DNA alterations.

Real-time single-molecule imaging reveals a direct interaction between UvrC and UvrB on DNA tightropes

Nucleotide excision DNA repair is mechanistically conserved across all kingdoms of life. In prokaryotes, this multi-enzyme process requires six proteins: UvrA–D, DNA polymerase I and DNA ligase. To examine how UvrC locates the UvrB–DNA pre-incision complex at a site of damage, we have labeled UvrB and UvrC with different colored quantum dots and quantitatively observed their interactions with DNA tightropes under a variety of solution conditions using oblique angle fluorescence imaging. Alone, UvrC predominantly interacts statically with DNA at low salt. Surprisingly, however, UvrC and UvrB together in solution bind to form the previously unseen UvrBC complex on duplex DNA. This UvrBC complex is highly motile and engages in unbiased one-dimensional diffusion. To test whether UvrB makes direct contact with the DNA in the UvrBC–DNA complex, we investigated three UvrB mutants: Y96A, a β-hairpin deletion and D338N. These mutants affected the motile properties of the UvrBC complex, indicating that UvrB is in intimate contact with the DNA when bound to UvrC. Given the in vivo excess of UvrB and the abundance of UvrBC in our experiments, this newly identified complex is likely to be the predominant form of UvrC in the cell.

The endonuclease Ankle1 requires its LEM and GIY-YIG motifs for DNA cleavage in vivo

The LEM domain (for lamina-associated polypeptide, emerin, MAN1 domain) defines a group of nuclear proteins that bind chromatin through interaction of the LEM motif with the conserved DNA crosslinking protein, barrier-to-autointegration factor (BAF). Here, we describe a LEM protein annotated in databases as 'Ankyrin repeat and LEM domain-containing protein 1' (Ankle1). We show that Ankle1 is conserved in metazoans and contains a unique C-terminal GIY-YIG motif that confers endonuclease activity in vitro and in vivo. In mammals, Ankle1 is predominantly expressed in hematopoietic tissues. Although most characterized LEM proteins are components of the inner nuclear membrane, ectopic Ankle1 shuttles between cytoplasm and nucleus. Ankle1 enriched in the nucleoplasm induces DNA cleavage and DNA damage response. This activity requires both the catalytic C-terminal GIY-YIG domain and the LEM motif, which binds chromatin via BAF. Hence, Ankle1 is an unusual LEM protein with a GIY-YIG-type endonuclease activity in higher eukaryotes.

Isolation and characterization of the RAD3 gene of Saccharomyces cerevisiae and inviability of rad3 deletion mutants

The RAD3 gene of Saccharomyces cerevisiae is required for nicking of DNA containing pyrimidine dimers or interstrand crosslinks. We have cloned the RAD3 gene and physically mapped it to 2.6 kilobase of DNA. A DNA segment of the cloned RAD3 insert was ligated into plasmid YIp5, which transforms yeast by homologous integration, and shown to integrate at the RAD3 site in chromosome V, thus verifying the cloned DNA segment to be the RAD3 gene and not a suppressor. The RAD3 gene encodes a 2.5-kilobase mRNA, extending between the Kpn I site and the Sau3A1/BamHI fusion junction in plasmid pSP10, and the direction of transcription has been determined. The 2.5-kilobase transcript could encode a protein of about 90,000 daltons. We also show the deletions of the RAD3 gene to be recessive lethals, indicating that the RAD3 gene plays an important role in other cellular processes in addition to incision of damaged DNA.

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.

The UvrABC endonuclease system of Escherichia coli--a view from Baltimore

Nucleotide excision is initiated by the UvrABC endonuclease system in which the initial DNA interaction is with UvrA which was dimerized in the presence of ATP. Nucleoprotein formation most likely takes place on undamaged regions of DNA by (UvrA)2 which has been dimerized in the presence of ATP. Topological unwinding of DNA, driven by ATP binding, is increased by the presence of UvrB to approximately a single helical turn. The Uvr(A)2B complex translocates to a damaged site by the combined Uvr(A)2B helicase in which the driving force is provided by the UvrB-associated ATPase. The dual incision reaction is initiated by the binding of the UvrC protein to the Uvr(A)2B-nucleoprotein complex. The proteins in this post-incision nucleoprotein complex do not turn over and require the presence of the UvrD protein and DNA polymerase I under polymerizing conditions. The final integrity of the DNA strands is restored with polynucleotide ligase.

Excision-repair capacity in Streptococcus pneumoniae: cloning and expression of a uvr-like gene

Although deficient in photoreactivation and some SOS-like functions, Streptococcus pneumoniae has the capacity to carry out excision repair when exposed to UV light. The repair ability and sensitivity to UV irradiation or treatment with chemical agents in the wild type and a UV-sensitive mutant strain indicate that UV-induced pyrimidine dimers might be repaired in pneumococcus by a system similar to the uvr-dependent system in Escherichia coli. A gene complementing the mutation conferring UV sensitivity of the mutant strain has been cloned. The coding region directs the synthesis of a polypeptide with a molecular weight of 78 kDa. The relationship with uvr-like protein in E. coli is discussed.

Nucleotide excision repair in Escherichia coli

One of the best-studied DNA repair pathways is nucleotide excision repair, a process consisting of DNA damage recognition, incision, excision, repair resynthesis, and DNA ligation. Escherichia coli has served as a model organism for the study of this process. Recently, many of the proteins that mediate E. coli nucleotide excision have been purified to homogeneity; this had led to a molecular description of this repair pathway. One of the key repair enzymes of this pathway is the UvrABC nuclease complex. The individual subunits of this enzyme cooperate in a complex series of partial reactions to bind to and incise the DNA near a damaged nucleotide. The UvrABC complex displays a remarkable substrate diversity. Defining the structural features of DNA lesions that provide the specificity for damage recognition by the UvrABC complex is of great importance, since it represents a unique form of protein-DNA interaction. Using a number of in vitro assays, researchers have been able to elucidate the action mechanism of the UvrABC nuclease complex. Current research is devoted to understanding how these complex events are mediated within the living cell.

The molecular genetics of the incision step in the DNA excision repair process

This review describes the evolution of research into the genetic basis of how different organisms use the process of excision repair to recognize and remove lesions from their cellular DNA. One particular aspect of excision repair, DNA incision, and how it is controlled at the genetic level in bacteriophage, bacteria, S. cerevisae, D. melanogaster, rodent cells and humans is examined. In phage T4, DNA is incised by a DNA glycosylase-AP endonuclease that is coded for by the denV gene. In E. coli, the products of three genes, uvrA, uvrB and uvrC, are required to form the UVRABC excinuclease that cleaves DNA and releases a fragment 12-13 nucleotides long containing the site of damage. In S. cerevisiae, genes complementing five mutants of the RAD3 epistasis group, rad1, rad2, rad3, rad4 and rad10 have been cloned and analyzed. Rodent cells sensitive to a variety of mutagenic agents and deficient in excision repair are being used in molecular studies to identify and clone human repair genes (e.g. ERCC1) capable of complementing mammalian repair defects. Most studies of the human system, however, have been done with cells isolated from patients suffering from the repair defective, cancer-prone disorder, xeroderma pigmentosum, and these cells are now beginning to be characterized at the molecular level. Studies such as these that provide a greater understanding of the genetic basis of DNA repair should also offer new insights into other cellular processes, including genetic recombination, differentiation, mutagenesis, carcinogenesis and aging.

Analysis of the regulatory elements of the Escherichia coli uvrC gene by construction of operon fusions

The regulatory region of the Escherichia coli uvrC gene has been analysed by the subcloning of appropriate restriction fragments into the promoter probe vector pPV502. A series of plasmids carrying operon fusions to the gene for chloramphenicol acetyltransferase (cat) has been constructed. Three promoters capable of controlling uvrC have been identified (P1, P2 and P3), the majority of transcription being derived from the most distal of these promoters (P1). Transcription termination apparently plays some role in the control of the gene through premature termination of the P1-, but not the P2- or P3-derived transcripts. In addition, a promoter acting in the opposite direction to uvrC transcription has been detected. The activity of each of the promoters has been assayed under normal and SOS-inducing conditions. The uvrC gene is not apparently under the control of the recA-lexA regulatory circuit, unlike uvrA and uvrB. A series of recombinant plasmids carrying a 1.9 kb Bg/II fragment encoding most of the uvrC gene has been constructed. The properties of these plasmids suggest that the six amino acids at the carboxy-terminus of the uvrC gene product are not critical for DNA repair activity.

The expression of the Escherichia coli uvrA gene in human cells

Cells cultured from xeroderma pigmentosum (XP) patients are defective in excision repair of damaged DNA specifically at the incision step. In Escherichia coli this step is mediated by the UvrA, UvrB and UvrC gene products. Our goal is to express each of these genes in XP cells, singly or in combination, and to determine the most suitable conditions for generating faithful E. coli Uvr protein copies in functional concentrations and properly localized for the eventual repair of damaged chromosomal DNA or DNA which is introduced exogenously. The E. coli gpt gene in pSV2gpt is used as a selection marker for uvr gene transfection into XP cells. The uvr genes were cloned into composite pBR322, SV40 and gpt vectors in which each E. coli gene is flanked by individual SV40 regulatory elements. SV40-transformed XP-A cells were transfected with pSV2uvrASV2gpt, gpt+ colonies were selected, and cell lines established. Several lines were examined in detail. Cell lines 714 and 1511 contain uvrA together with flanking SV40 regulatory elements integrated intact in genomic DNA and express UvrA protein as well as a 95,000-dalton UvrA-related protein. The expression of uvrA was found to be 50-100-fold lower than the expression of gpt. Attempts were made to assay the mammalian UvrA protein for functionality, but endogenous activities interfered with assays for each of the UvrA protein's three activities. The peptide maps derived from partial proteolysis of the "mammalian" UvrA protein are identical to the E. coli UvrA protein. The sub-cellular location of UvrA protein in uvrA+ XP cells was investigated by fractionation of cell extracts in which an indirect immunofluorescence method revealed its location as being largely extra-nuclear. Two uvrA+ cell lines were examined for their UV-resistant phenotype and not unexpectedly were found not to be reverted to a state of repair proficiency.

Regulation of the Escherichia coli excision repair gene uvrC. Overlap between the uvrC structural gene and the region coding for a 24 kD protein

The UvrA, UvrB and UvrC proteins of E. coli are subunits of a DNA repair enzyme, the ABC exonuclease. In this paper we study the uvrC regulatory region. The uvrC structural gene is preceded by an open reading frame encoding a 24 kD protein. A uvrC promoter has been mapped within this gene. The transcription start of a second promoter located 5' of the 24 kD gene is mapped in vivo. We show that transcription from both promoters on the chromosome is not inducible by UV damage. The possible translation start codons of the UvrC and of the 24 kD protein are determined. Sequences encoding the N-terminal part of the UvrC protein overlap with sequences encoding the C-terminal part of the 24 kD protein. To examine a possible function of the 24 kD gene in repair, a 24 kD insertion mutant was created in the chromosome. The mutant however only slightly affects the UV sensitivity of the cell. Transcription of P3 alone provides sufficient UvrC protein for the normal repair of UV lesions.

The purification of the Escherichia coli UvrABC incision system

The UvrA, UvrB and UvrC proteins of Escherichia coli have been purified in good yields to homogeneity with rapid three- or four-step purification procedures. The cloned uvrA and uvrB genes were placed under control of the E. coli bacteriophage lambda PL promoter for amplification of expression. Expression of the uvrC gene could not be amplified by this strategy, however, subcloning of this gene into the replication-defective plasmid pRLM24 led to significant overproduction of the UvrC protein. The purified UvrA protein, with its associated ATPase activity, has a molecular weight of 114,000, the purified UvrB is an 84,000 molecular weight protein and the UvrC protein has a molecular weight of 67,000.

Protein complexes formed during the incision reaction catalyzed by the Escherichia coli UvrABC endonuclease

An examination has been made into the nature of the nucleoprotein complexes formed during the incision reaction catalyzed by the Escherichia coli UvrABC endonuclease when acting on a pyrimidine dimer-containing fd RF-I DNA species. The complexes of proteins and DNA form in unique stages. The first stage of binding involves an ATP-stimulated interaction of the UvrA protein with duplex DNA containing pyrimidine dimer sites. The UvrB protein significantly stabilizes the UvrA-pyrimidine dimer containing DNA complex which, in turn, provides a foundation for the binding of UvrC to activate the UvrABC endonuclease. The binding of one molecule of UvrC to each UvrAB-damaged DNA complex is needed to catalyze incision in the vicinity of pyrimidine dimer sites. The UvrABC-DNA complex persists after the incision event suggesting that the lack of UvrABC turnover may be linked to other activities in the excision-repair pathway beyond the initial incision reaction.

Sequences of the E. coli uvrB gene and protein

The UvrB protein is one of the three subunits of the E. coli ABC excinuclease. We have reported the sequences of the other two subunits, the UvrA and UvrC proteins. In this paper the sequence of the UvrB protein is presented. The protein sequence was determined from the DNA sequence of the uvrB gene and was confirmed by sequencing the NH2-terminus of the UvrB protein and analyzing its overall amino acid composition. The coding region of uvrB is 2019 basepairs, specifying a protein of 672 amino acids and Mr of 76,118. The sequence of the UvrB protein shows a moderate level of homology to that of the UvrC protein and to the ATP binding site of the UvrA protein. During purification of UvrB protein a proteolytic product, UvrB, is produced in high quantities. We find that UvrB results from removal of about 40 amino acids from the COOH-terminus of the UvrB protein. The uvrB gene has complex regulatory features. On the 5' side, the coding region is preceded by 3 promoters, a DnaA box and an SOS box. On the 3' side the gene is followed by an REP (Repetitive Extragenic Palindrome) sequence which has been implicated in gene regulation by an unknown mechanism.

In vitro study of the interaction of the LexA repressor and the UvrC protein with a uvrC regulatory region

The in vitro interaction of the LexA repressor with a regulatory region of the uvrC gene has been studied by polyacrylamide gel electrophoresis. Although the uvrC promoter region shows some homology with the canonic LexA binding site, no specific binding of the repressor to this DNA sequence could be observed, but only a cooperative nonspecific binding. By the same technique we show that the UvrC protein does not bind specifically to this regulatory DNA sequence either, although the protein is able to bind nonspecifically and cooperatively to the double-stranded DNA fragment.

Multiple control elements for the uvrC gene unit of Escherichia coli

We have sequenced the control region of the uvrC protein including two open reading frames (ORF) encoding polypeptides of 28 kd and 23 kd molecular weight. The uvrC gene is preceded by five promoters. The P1, P2a and P2b promoter sequences are 5' to the 28 kd and the 23 kd proteins respectively. The P3 and P4 promoters are located within the structural gene for the 23 kd protein. The P3 promoter is required for adequate in vivo expression. There are three putative lexA protein binding sites, detected at the 3' end of the 28 kd protein (lexA1), within the coding sequences for the 23 kd protein (lexA2) and within the P3 promoter (lexA3). Promoter P2 is responsible for transcription of the uvrC gene, producing transcripts of 2.8 and 1.6 kb. The upstream region including the 28 kd protein is required for enhanced expression under non-induced conditions. These results show that the uvrC gene is controlled by multiple promoters and is transcribed as part of a multigene unit.

Effect of DNA polymerase I and DNA helicase II on the turnover rate of UvrABC excision nuclease

UvrABC excision nuclease (UvrA, UvrB, and UvrC proteins) of Escherichia coli removes nucleotide mono- and diadducts from DNA in the form of oligonucleotides 12 or 13 bases long. We find that the purified enzyme dissociates from DNA very slowly, if at all, in the absence of other proteins implicated in excision repair. Addition of DNA polymerase I and helicase II (UvrD protein) to the reaction mixture stimulates the turnover rate of the excision nuclease to a level comparable to that observed in vivo.

Organisation and control of the Escherichia coli uvrC gene

The Escherichia coli uvrC gene has been cloned into multicopy plasmids from the transducing phage lambda uvrC+ and the structural gene assigned to a 1.9-kb BglII fragment. Deletion of upstream sequences shows the presence of an in vivo uvrC promoter close to the start of the structural gene, as confirmed by subcloning the uvrC fragment into actively transcribed or 'promoter-free' restriction sites in various plasmid vectors. The control of uvrC transcription has been investigated using hybrid uvrC-cat operons. There are at least two promoters upstream of uvrC. Only the proximal promoter, some two orders of magnitude less effective than the cat promoter, is required for in vivo expression of the uvrC gene. We can find no evidence that expression of the uvrC gene on multicopy plasmids is either autogenously controlled or controlled by the product of the lexA gene.

Distal regulatory functions for the uvrC gene of E. coli

We find that the uvrC gene is preceded by three promoters (P1, P2 and P3), identified by heparin-resistant RNA polymerase-DNA complex formation, P2 and P3 promoters are located proximal to the 5' end of the uvrC gene, while the P1 promoter is separated from the uvrC structural gene by an interposed DNA region of more than 1 kb. We have reported that P2 and P3 are not sufficient to promote uvrC complementation. However, plasmids containing the direct fusion of the P1 promoter to the uvrC gene complements the uvrC defect. Insertion of IS1 downstream from the P1 promoter leads to efficient synthesis of the uvrC protein as measured in maxicells. Fusion of the lac promoter to the uvrC structural gene can substitute for in vivo regulatory functions. We conclude that uvrC protein synthesis is controlled in a complex manner and that a distal promoter, P1, is required.

Sequences of the E. coli uvrC gene and protein

We have determined the sequence of a 2400 bp region of E. coli chromosomal DNA containing the uvrC gene. The coding region of uvrc is 2267 bp in length, encodes a polypeptide with a calculated molecular weight of 66,038 daltons, and is preceded by a typical E. coli ribosome binding site. By constructing deletion derivatives we have established that a uvrC promoter lies within the 113 bp region preceding the translational start of uvrC. The codon usage in uvrC is strongly biased in favor of codons used infrequently in E. coli, which may contribute to the relatively low intracellular concentration of uvrC protein.

Use of an Escherichia coli mutant strain permits measurement of single-stranded apurinic-apyrimidinic endonuclease in crude extracts: studies with untransformed cells and cells transformed with plasmids containing the uvrC gene

We have constructed a strain of Escherichia coli that is defective in exonuclease VII and uracil-DNA glycosylase activities. This strain (xse ung) facilitates the quantitation of single-stranded apurinic-apyrimidinic endonuclease activity in crude extracts. Quantitative comparisons of single-stranded apurinic-apyrimidinic endonuclease activity under conditions in which uvrC protein is overexpressed showed no differences, suggesting that single-stranded apurinic-apyrimidinic endonuclease and uvrC protein are probably distinct.

Molecular cloning of pheR in Escherichia coli K-12

The regulator gene pheR, which in Escherichia coli controls the expression of pheA, the structural gene for chorismate mutase P-prephenate dehydratase, was cloned on to multicopy plasmids directly from the E. coli chromosome; this was achieved with the aid of the tetracycline resistance transposon, Tn10, that had been inserted very close to the pheR gene. Subsequently, pheR was subcloned on a 1.1-kilobase-pair fragment on the plasmid vector pBR322; its position on the plasmid was localized by the method of gamma delta-mediated transpositional inactivation. The pheR gene product was identified in maxicells and found to be a protein of subunit molecular weight 19,000, suggesting that the coding segment of the gene is about 500 nucleotide pairs long.

Molecular cloning of eucaryotic genes required for excision repair of UV-irradiated DNA: isolation and partial characterization of the RAD3 gene of Saccharomyces cerevisiae

We describe the molecular cloning of a 6-kilobase (kb) fragment of yeast chromosomal DNA containing the RAD3 gene of Saccharomyces cerevisiae. When present in the autonomously replicating yeast cloning vector YEp24, this fragment transformed two different UV-sensitive, excision repair-defective rad3 mutants of S. cerevisiae to UV resistance. The same result was obtained with a variety of other plasmids containing a 4.5-kb subclone of the 6-kb fragment. The UV sensitivity of mutants defective in the RAD1, RAD2, RAD4, and RAD14 loci was not affected by transformation with these plasmids. The 4.5-kb fragment was subcloned into the integrating yeast vector YIp5, and the resultant plasmid was used to transform the rad3-1 mutant to UV resistance. Both genetic and physical studies showed that this plasmid integrated by homologous recombination into the rad3 site uniquely. We conclude from these studies that the cloned DNA that transforms the rad3-1 mutant to UV resistance contains the yeast chromosomal RAD3 gene. The 4.5-kb fragment was mapped by restriction analysis, and studies on some of the subclones generated from this fragment indicate that the RAD3 gene is at least 1.5 kb in size.

Molecular structure of uvrC gene of Escherichia coli: identification of DNA sequences required for transcription of the uvrC gene

We have carried out experiments to identify the regulatory regions of the uvrC gene of Escherichia coli. A uvrC+ plasmid, pUV7, containing the intact transcriptional unit for the uvrC gene, was used to subclone either the structural gene or combinations of the structural gene and 5'-flanking sequences. The plasmids so constructed were tested for ability to restore UV-resistant phenotype to uvrC- cells as an indication of expression of the uvrC gene. The chromosomal DNA in plasmid pUV7 was probed for strong binding with E. coli RNA polymerase in an attempt to identify a restriction fragment which bears the regulatory sequences for the uvrC transcriptional unit. The results indicate that DNA sequences at least 0.9 Kb upstream from the structural gene, but not the 5'-proximal sequences, regulate expression of the uvrC gene. Analysis of protein synthesis encoded by plasmid pUV7 and its derivatives suggest that there may be another gene that lies between the promoter and the uvrC gene and codes for a 27,000-Mr protein. The relation of this gene to uvrC function is not clear.

Two separable protein species which both restore uvrABC endonuclease activity in extracts from uvrC mutated cells

Two different protein species which both complement the detective repair endonuclease (uvrABC endonuclease) in uvrC mutated cells have been detected. These proteins have quite different chromatographic properties and were easily separated by ion exchange chromatography. One has affinity for DEAE cellulose and co-cromatographs with the uvrB protein. The other has strong affinity for phosphocellulose and appears to be the uvrC protein itself. The uvrB associated uvrC+ activity is absent from both uvrC and uvrB mutated cells, indicating that this species result from an interaction between uvrB+ and uvrC+ functions at the protein level.

Properties and regulation of the UVRABC endonuclease

This report summarizes the cloning of the uvrA, uvrB and uvrC genes of E. coli, the identification and isolation of the gene products, the regulation of the genes, and reconstitution of active UVRABC endonuclease from the individually isolated components.

Isolation of UV-sensitive mutants of mouse L5178Y cells by a cell suspension spotting method

We have isolated 56 UV-sensitive mutant clones from a mouse L51 T/t line of L5178Y cells by a cell suspension spotting method. Five mutants have also been isolated from L51 T/t and L5178Y cells by the method reported by Thompson and coworkers (22). We divided the mutants into two groups, "highly sensitive" and "moderately sensitive" mutants, according to their sensitivity to UV irradiation. Fifty-eight mutants were highly sensitive and three were moderately sensitive to UV. The reconstruction experiments indicate that more than 90% of highly sensitive mutants were recovered by the cell suspension spotting method. Frequencies of recovered mutants highly sensitive to UV increased with increasing dose of mutagens. Recovered mutant frequency reached 10(-2) after treatment with 1.5 micrograms/ml of N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) (survival 0.2%). Eight UV-sensitive mutants were divided into four complementation groups. These mutants were 2-6 times more sensitive to UV than parental L51 T/t cells in terms of D37 (dose required to reduce survival to 37%). Four representative UV-sensitive mutants which are classified into different complementation groups were examined for their sensitivity to killing by UV, 4-nitroquinoline-1-oxide (4NQO), mitomycin C (MMC), X-rays, and MNNG. All four classes of mutants were found to be cross-sensitive to UV, 4NQO, and MMC, but not sensitive to X-rays and MNNG.

Amplification of the uvrA gene product of Escherichia coli to 7% of cellular protein by linkage to the pL promoter of pKC30

We have constructed a hybrid pKC30-uvrA plasmid (pGHY5003) in which transcription of the uvrA gene can be induced under pL control to amplify the uvrA gene product to 7% of cellular protein. To construct pGHY5003, we developed a genetic selection using the basal level of expression (30 degrees C) from pL in thermosensitive cI857 lysogens to isolate appropriately tailored repair genes inserted at the Hpa I site of pKC30 from recombinant DNA mixtures with a variety of products. In addition, a post-UV-irradiation radiolabeling method was adapted to screen inserts for temperature-inducible polypeptide synthesis directed by transcription under pL control rapidly. This should prove generally useful for isolating genes inserted at the Hpa I site of plasmid pKC30 with the following characteristics: (i) genetically functional hybrid plasmids selected from a large population of exonucleolytically tailored fragments ligated into Hpa I of pKC30 and (ii) production of high-level amplification for the gene product of interest by screening for post-UV-irradiation temperature inducibility of polypeptides synthesized from hybrid plasmids. The level of amplification obtained for the uvrA gene product from pGHY5003 is approximately 10,000-fold higher than estimates of the level of uvrA protein in logarithmic phase Escherichia coli.

Cloning of the uvrC gene of Escherichia coli: expression of a DNA repair gene

We have cloned the uvrC gene of Escherichia coli, using an F' plasmid carrying the uvrC region as a source of DNA. Two plasmids, pSC101 and pBR322, were used as cloning vectors. The recombinant plasmids were selected for their ability to complement the uvrC defect of E. coli strains AB1884 and N177. We conclude that the uvrC structural gene is contained in a 1.9-kilobase DNA fragment. The protein encoded by the uvrC gene appears to have a monomer molecular weight of 64,500 as analyzed by denaturing polyacrylamide gel electrophoresis. Strains containing multicopy uvrC+ plasmids overproduce a factor that is missing in lysates of uvrC- mutants and required for an in vitro model repair reaction. The expression of uvrC+ hybrid plasmids suggests that the structural gene is separated by at least 0.8 kilobase from the regulatory region.

Identification of the uvrC gene product

We have constructed a multicopy plasmid that carries the uvrC gene of Escherichia coli. By inserting the transposon Tn1000 (previously designated gamma delta) into this plasmid, we obtained many derivatives that fail to complement uvrC34. The proteins synthesized by the original plasmid and the uvrC::Tn1000 derivatives were labeled in maxicells and analyzed on gels, demonstrating that a protein of Mr 70,000 encoded by the original uvrC+ plasmid was absent from the mutated noncomplementing derivatives; this protein is presumed to be the uvrC gene product. We found that this protein of Mr 70,000 binds to DNA and have partially purified the uvrC protein by DNA-cellulose chromatography. Because some of the uvrC::Tn1000 derivatives produce truncated polypeptides, the orientation of expression and the location of the promoter were determined by correlating the sizes of the truncated polypeptides with the sites of insertion of Tn1000.