Potential role of proteolysis in the control of UvrABC incision

Biocompatible artificial DNA linker that is read through by DNA polymerases and is functional in Escherichia coli

A triazole mimic of a DNA phosphodiester linkage has been produced by templated chemical ligation of oligonucleotides functionalized with 5'-azide and 3'-alkyne. The individual azide and alkyne oligonucleotides were synthesized by standard phosphoramidite methods and assembled using a straightforward ligation procedure. This highly efficient chemical equivalent of enzymatic DNA ligation has been used to assemble a 300-mer from three 100-mer oligonucleotides, demonstrating the total chemical synthesis of very long oligonucleotides. The base sequences of the DNA strands containing this artificial linkage were copied during PCR with high fidelity and a gene containing the triazole linker was functional in Escherichia coli.

UvrB domain 4, an autoinhibitory gate for regulation of DNA binding and ATPase activity

UvrB, a central DNA damage recognition protein in bacterial nucleotide excision repair, has weak affinity for DNA, and its ATPase activity is activated by UvrA and damaged DNA. Regulation of DNA binding and ATP hydrolysis by UvrB is poorly understood. Using atomic force microscopy and biochemical assays, we found that truncation of domain 4 of Bacillus caldotenax UvrB (UvrBDelta4) leads to multiple changes in protein function. Protein dimerization decreases with an approximately 8-fold increase of the equilibrium dissociation constant and an increase in DNA binding. Loss of domain 4 causes the DNA binding mode of UvrB to change from dimer to monomer, and affinity increases with the apparent dissociation constants on nondamaged and damaged single-stranded DNA decreasing 22- and 14-fold, respectively. ATPase activity by UvrBDelta4 increases 14- and 9-fold with and without single-stranded DNA, respectively, and UvrBDelta4 supports UvrA-independent damage-specific incision by Cho on a bubble DNA substrate. We propose that other than its previously discovered role in regulating protein-protein interactions, domain 4 is an autoinhibitory domain regulating the DNA binding and ATPase activities of UvrB.

Structural insights into the cryptic DNA-dependent ATPase activity of UvrB

The UvrABC pathway is a ubiquitously occurring mechanism targeted towards the repair of bulky base damage. Key to this process is UvrB, a DNA-dependent limited helicase that acts as a lesion recognition element whilst part of a tracking complex involving UvrA, and as a DNA-binding platform required for the presentation of damage to UvrC for subsequent processing. We have been able to determine the structure of a ternary complex involving UvrB* (a C-terminal truncation of full-length UvrB), a polythymine trinucleotide and ADP. This structure has highlighted the roles of key conserved residues in DNA binding distinct from those of the beta-hairpin, where most of the attention in previous studies has been focussed. We are also the first to report the structural basis underlying conformational re-modelling of the beta-hairpin that is absolutely required for DNA binding and how this event results in an ATPase primed for catalysis. Our data provide the first insights at the molecular level into the transformation of UvrB into an active helicase.

'Close-fitting sleeves': DNA damage recognition by the UvrABC nuclease system

DNA damage recognition represents a long-standing problem in the field of protein-DNA interactions. This article reviews our current knowledge of how damage recognition is achieved in bacterial nucleotide excision repair through the concerted action of the UvrA, UvrB, and UvrC proteins.

Role of DNA polymerase II in the tolerance of thymine dimers remaining unexcised in UV-irradiated Escherichia coli exposed to pre-UV nutritional stress

Nutritional stress applied prior to UV-irradiation to E. coli 15 555-7 reduced thymine dimer excision and inhibited post-UV incorporation of thymidine in polB(+) as well as in polB(-) cells. However, the pre-UV-stressed polB(+) cells were significantly more UV-resistant and after UV synthesized larger DNA molecules than the pre-UV-stressed polB(-) cells. The data suggest that DNA polymerase II is involved in the tolerance of unremoved thymine dimers.

Inducible stable DNA replication (iSDR) and the uvr-dependent tolerance of pyrimidine dimers in UV-irradiated Escherichia coli are two uncoupled processes

Inducible stable DNA replication (iSDR) is dependent on recombination and is supposed to play a role in DNA repair of Escherichia coli. Our previous data suggested that iSDR may be involved in the tolerance of UV lesions, which remain unexcised in excision-proficient E. coli exposed to some UV pretreatments. Now, the tolerance of unexcised lesions has been followed in E. coli recB21 and in E. coli priA1 sup mutants, incapable of iSDR. The obtained data do not confirm the previous hypothesis about the involvement of iSDR in the putative uvr-dependent lesion tolerance. They rather suggest that iSDR and the uvr-dependent lesion tolerance are two uncoupled processes.

A non-excision uvr-dependent DNA repair pathway of Escherichia coli (involvement of stress proteins)

In UV-irradiated excision-proficient (uvr+) Escherichia coli, pre-induced by simultaneous pre-starvation for thymine (T) and amino acids (AAs), and/or a low UV pre-dose applied after prestarvation for AAs, pyrimidine dimer excision (PDE) is reduced without an adequate increase of UV sensitivity and UV mutagenesis. The unexcised lesions are tolerated by a putative repair pathway that is uvr dependent but does not involve excision. The process consists of PDE inhibition, which requires outer membrane protease OmpT, and subsequent pyrimidine dimer (PD) toleration, which may be mediated by interaction with a sister duplex using a number of SOS and stress-inducible proteins.

The effect of the OmpT protease on excision repair in UV-irradiated Escherichia coli

The extent of pyrimidine dimer excision (PDE) was inhibited in UV-irradiated E. coli KS272 (ompT+) cells when they were preinduced by a low UV predose preceded by a nutrition stress but not in the preinduced E.coli SF100 (ompT-) mutants. The preinduction, however, markedly inhibited PDE in the ompT- cells transformed with a multicopy plasmid carrying ompT gene. The data are consistent with the hypothesis that the inducible OmpT protease (controlled by rpoH) might terminate the SOS period of excision repair so that when cells are preinduced PDE might be inhibited prematurely.

The pre-UV nutritional stresses increase UV resistance, decrease UV mutagenesis and inhibit excision repair

Nutritional stresses applied to E. coli prior to UV irradiation increase UV resistance and decrease UV mutagenesis. This effect is uvrA-dependent and might reflect a more efficient excision of pyrimidine dimers [1]. The data presented here, however, indicate that after prestarvation for glucose or amino acids pyrimidine dimer excision (PDE) was partly inhibited. It appears that the stress conditions stimulate a mode of uvr-dependent tolerance of lesions, efficient and precise. Possible modes of PDE inhibition and lesion tolerance are discussed.

Domain structure of Thermus thermophilus UvrB protein. Similarity in domain structure to a helicase

UvrB protein plays an essential role in the prokaryotic excision repair system. UvrB protein shows cryptic ATPase activity, DNA binding, helicase-like activity, and incision activity by interacting with UvrA or UvrC proteins. To reveal the structure-function relationship of this multifunctional protein, the domain structure of Thermus thermophilus UvrB protein (ttUvrB) was studied by limited proteolysis and denaturation experiments. Proteolytic profiles indicated that ttUvrB consists of four domains: the N domain (residues 2-105), M domain (106-455), C1 domain (456-590), and C2 domain (591-665). The properties of the proteolytic fragments indicated the involvement of the respective domains in the functions of the protein as follows: the N and C1 domains are necessary for ATPase activity, the C1 domain is indispensable for DNA binding, and the N and/or M domains are involved in UvrA binding. The structural stability of the C1 and C2 domains was higher than that of the N and M domains, which supports the proposed domain nature of ttUvrB. Based on these results and the crystal structure of PcrA helicase (Subramanya, H. S., Bird, L. E., Brannigan, J. A., and Wigley, D. B. (1996) Nature 384, 379-383), the domain organization of ttUvrB was proposed.

Substrate spectrum of human excinuclease: repair of abasic sites, methylated bases, mismatches, and bulky adducts

Nucleotide-excision repair is the repair system for removing bulky lesions from DNA. Humans deficient in this repair pathway suffer from xeroderma pigmentosum (XP), a disease characterized by photodermatoses, including skin cancers. At the cellular level, XP patients fail to remove cyclobutane pyrimidine dimers and pyrimidine(6-4)pyrimidone photoproducts induced by UV light, as well as other bulky DNA lesions caused by various genotoxic agents. XP cells are not particularly sensitive to ionizing radiation or to alkylating agents that cause mostly nonbulky DNA lesions. Therefore, it has generally been assumed that the human nucleotide-excision repair enzyme (excinuclease) is specific for bulky adducts. To determine the substrate range of human excinuclease we used the highly sensitive excision assay and tested bulky adducts, synthetic apurinic/apyrimidinic sites, N6-methyladenine, O6-methylguanine, and mismatches as potential substrates. We found that all of these "lesions" were removed by human excinuclease, although with vastly different efficiencies.

Proteases and protein degradation in Escherichia coli

In E. coli, protein degradation plays important roles in regulating the levels of specific proteins and in eliminating damaged or abnormal proteins. E. coli possess a very large number of proteolytic enzymes distributed in the cytoplasm, the inner membrane, and the periplasm, but, with few exceptions, the physiological functions of these proteases are not known. More than 90% of the protein degradation occurring in the cytoplasm is energy-dependent, but the activities of most E. coli proteases in vitro are not energy-dependent. Two ATP-dependent proteases, Lon and Clp, are responsible for 70-80% of the energy-dependent degradation of proteins in vivo. In vitro studies with Lon and Clp indicate that both proteases directly interact with substrates for degradation. ATP functions as an allosteric effector promoting an active conformation of the proteases, and ATP hydrolysis is required for rapid catalytic turnover of peptide bond cleavage in proteins. Lon and Clp show virtually no homology at the amino acid level, and thus it appears that at least two families of ATP-dependent proteases have evolved independently.

Heat-inducible reactivation of UV-damaged bacteriophage lambda

Induction of the SOS response in UV-irradiated bacteria leads to an increase in the survival of an infecting irradiated bacteriophage lambda (Weigle 1953). We report that a similar reactivation of irradiated phage lambda was induced by shifting the culture of recipient bacteria from 30 degrees to 47 degrees C. However, this repair process was nonmutagenic. The amplitude of the phenomenon was increased with the quantity of UV lesions in the phage DNA. It was present despite mutations affecting the SOS response or the heat shock response in the infected strains (recA, lexA, umuC or rpoH mutations respectively). In contrast, the heat-inducible repair process was abolished in uvrA derivatives. Also, pretreatment with chloramphenicol largely enhanced phage reactivation after heat shock. Therefore, it appears that the excision repair mechanism of UV lesions was stimulated both by temperature shift-up and blockage of protein synthesis.

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.

Processing of Ada protein by two serine endoproteases Do and So from Escherichia coli

Two soluble serine proteases Do and So from Escherichia coli were found to distinctively cleave the purified, 39 kDa Ada protein into fragments with sizes of 12-31 kDa. Protease So appears to generate a C-terminal 19 kDa polypeptide, similarly to OmpT protease. In addition, the purified 19 kDa C-terminal half of Ada protein can be further processed mainly to an 18 kDa fragment by protease So and to a 12 kDa by protease Do. These results suggest that proteases Do and So are involved in endogenous cleavage of Ada protein, which may play a role in down-regulating the adaptive response to alkylating agents.