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R Devoret

Publications and source records attributed to R Devoret.

At least 37 records · Page 2Linked to original sources

The bI4 RNA mitochondrial maturase of Saccharomyces cerevisiae can stimulate intra-chromosomal recombination in Escherichia coli.

When the bI4 RNA maturase, encoded by the fourth intron of the mitochondrial cytochrome b gene of Saccharomyces cerevisiae, was expressed in Escherichia coli, formation of intra-chromosomal Lac+ recombinants was stimulated threefold. This "hyper-rec" phenotype was recA as well as recBCD dependent. The most active form of the bI4 maturase stimulated homologous recombination whereas splicing deficient mutants of bI4 maturase were either deficient in or unable to stimulate homologous recombination.

DNA Nucleotidyltransferases

KIN, a mammalian nuclear protein immunologically related to E. coli RecA protein.

A polypeptide of about 120 kDa, called KIN, has been identified in rat FR 3T3 cells by immunoblotting using affinity-purified antibodies against the RecA protein of Escherichia coli (38 kDa). The KIN protein as shown by fluorescent light microscopy and electron microscopy is essentially concentrated in the nucleus. Its level is higher in proliferating than in quiescent cells. Cell treatment with mitomycin C increases the level of the KIN protein. We sought similar proteins in other mammalian cells. Proteins with the same electrophoretic mobility were detected in mouse, monkey and human cell lines as well as in rat and mouse embryos.

Animals

New recA mutations that dissociate the various RecA protein activities in Escherichia coli provide evidence for an additional role for RecA protein in UV mutagenesis.

To isolate strains with new recA mutations that differentially affect RecA protein functions, we mutagenized in vitro the recA gene carried by plasmid mini-F and then introduced the mini-F-recA plasmid into a delta recA host that was lysogenic for prophage phi 80 and carried a lac duplication. By scoring prophage induction and recombination of the lac duplication, we isolated new recA mutations. A strain carrying mutation recA1734 (Arg-243 changed to Leu) was found to be deficient in phi 80 induction but proficient in recombination. The mutation rendered the host not mutable by UV, even in a lexA(Def) background. Yet, the recA1734 host became mutable upon introduction of a plasmid encoding UmuD*, the active carboxyl-terminal fragment of UmuD. Although the recA1734 mutation permits cleavage of lambda and LexA repressors, it renders the host deficient in the cleavage of phi 80 repressor and UmuD protein. Another strain carrying mutation recA1730 (Ser-117 changed to Phe) was found to be proficient in phi 80 induction but deficient in recombination. The recombination defect conferred by the mutation was partly alleviated in a cell devoid of LexA repressor, suggesting that, when amplified, RecA1730 protein is active in recombination. Since LexA protein was poorly cleaved in the recA1730 strain while phage lambda was induced, we conclude that RecA1730 protein cannot specifically mediate LexA protein cleavage. Our results show that the recA1734 and recA1730 mutations differentially affect cleavage of various substrates. The recA1730 mutation prevented UV mutagenesis, even upon introduction into the host of a plasmid encoding UmuD* and was dominant over recA+. With respect to other RecA functions, recA1730 was recessive to recA+. This demonstrates that RecA protein has an additional role in mutagenesis beside mediating the cleavage of LexA and UmuD proteins.

Bacterial Proteins

Identification of psiB genes of plasmids F and R6-5. Molecular basis for psiB enhanced expression in plasmid R6-5.

PsiB protein of plasmid R6-5 inhibits the induction of the SOS pathway. The F sex factor also carries a psiB gene homologous to that of R6-5. Yet, it fails to inhibit SOS induction. In order to solve this difference, we characterized the psiB genes of R6-5 and F. We found that (i) the sequences of the two psiB genes share extensive homology the predicted amino acid sequences of the two proteins differing by 5 residues, (ii) the expression of R6-5 psiB is 4 times higher than F psiB gene, (iii) in plasmid R6-5, a Tn10 transposon upstream from the psiB gene enhances psiB expression. Hence, the F sex factor may be unable to prevent SOS induction for two non-exclusive reasons: (i) F PsiB protein, being slightly different from R6-5, may be less active, (ii) the level of synthesis of F PsiB protein may be insufficient to prevent SOS induction.

Amino Acid Sequence

PsiB polypeptide prevents activation of RecA protein in Escherichia coli.

We further characterize a novel plasmid function preventing SOS induction called Psi (Plasmid SOS Inhibition). We show that Psi function is expressed by psiB, a gene located at coordinate 54.9 of plasmid R6-5 and near oriT, the origin of conjugal transfer. Deletions and amber mutations of the psiB gene permitted us to demonstrate that PsiB polypeptide (apparent molecular weight, 12 kDa) is responsible for Psi function. PsiB protein prevents recA730-promoted mutagenesis and intra-chromosomal recombination but not recombination following conjugation. Overproduction of PsiB protein sensitizes the host cell to UV irradiation. We propose that PsiB polypeptide has an anti-SOS action by inhibiting activation of RecA protein, thus preventing the occurrence of LexA-controlled functions.

Bacterial Proteins

An inhibitor of SOS induction, specified by a plasmid locus in Escherichia coli.

Plasmid R6-5 contains a locus whose product inhibits induction of sfiA and prophage lambda in a recA441 mutant at 42 degrees C and in a recA+ host after treatment with nalidixic acid. This plasmidic SOS-inhibition locus (psi) is situated on an 8.1-kilobase DNA fragment near oriT, the origin of plasmid R6-5 conjugational transfer. Loss of the Psi function, resulting from the insertion of Tn3 into psi+, greatly reduced the synthesis of two proteins, designated PsiA (Mr 24,500) and PsiB (Mr 12,500). Using host cells in which there was an inactive LexA repressor, we found that Psi function does not act by interfering with the expression of the SOS pathway. The Psi function may affect the generation of an SOS signal. We postulate that during the course of evolution, the Psi function has been selected in some conjugative plasmids so as to permit them to transfer single-stranded DNA without generating an SOS signal.

Biological Evolution

SOS induction by thermosensitive replication mutants of miniF plasmid.

MiniF, a 9.3 kb fragment of the dispensable F plasmid, carries genes necessary for its replication and partition as well as for the expression of an SOS signal. The arrest of replication of a thermo-sensitive miniFts at 42 degrees C induced SOS functions such as prophage lambda, sfiA expression, W-reactivation of UV-irradiated phage lambda. Two miniF ts9 and ts17 mutations were located within the KpnI fragment (43.6-46.9) in the minimal oriS replicon. Blocking miniF replication by incBC+ incompatibility genes situated in trans on a second plasmid also induced SOS functions. In contrast, if miniFts17 plasmid escaped the replication block at 42 degrees C by being inserted into pR325, there was no SOS induction. SOS induction by the arrest of miniF replication required the miniF lynA+ locus in cis, the host recA+ and lexA+ genes. We found that SOS induction was increased greatly near the stationary phase and that cell viability declined. During host cell exponential growth, miniFts9 and miniFts17 plasmids were lost rapidly, although SOS induction persisted for several cell generations. We postulate that lynA expresses a persistent product that may lead to the unwinding of chromosomal DNA.

Bacterial Proteins

A yeast protein analogous to Escherichia coli RecA protein whose cellular level is enhanced after UV irradiation.

In Saccharomyces cerevisiae, a protein was recognized by polyclonal antibodies raised against homogeneous Escherichia coli K 12 RecA protein. The cellular level of the yeast protein called RecAsc (molecular weight 44 kDa, pI 6.3), was transiently enhanced after UV irradiation. Protease inhibitors were required to minimize degradation of the RecAsc protein during cell lysis. The RecAsc protein exhibited similar basal levels and similar kinetics of increase after UV irradiation in DNA-repair proficient (RAD+) strains carrying mitochondrial DNA or not (rho0). This was also true for the following DNA-repair deficient (rad-) strains: rad2-6 rad6-1 rad52-1, a triple mutant blocked in three major repair pathways; rad6-delta, a mutant containing an integrative deletion in a gene playing a central role in mutagenesis; pso2-1, a mutant that exhibits a reduced rate of mutagenesis and recombination after exposure to DNA cross-linking agents.

Antibodies

Mini-F plasmid-induced SOS signal in Escherichia coli is RecBC dependent.

Dispensable replicons such as F plasmid [95 kilobases (kb)] or its mini-derivatives such as mini-F (9.3 kb) or lambda mini-F efficiently induced cellular SOS genes such as sfiA (sulA) when they were damaged by UV irradiation and then introduced into a recipient bacterium. To generate an SOS signal, UV light-damaged mini-F or mini-F conditional mutants deficient in replication required that the bacterial RecBC enzyme retained some activity different from the nuclease activity that was dispensable. In contrast, UV light-damaged F plasmid produced an SOS signal independently of the activity of the RecBC enzyme and of the expression of the mini-F, -H, and -G proteins. Our findings are consistent with a picture in which the SOS signal is constituted by stretches of single-stranded DNA on a replicon. Moreover, our present data combined with other data previously published lead to the hypothesis that the SOS signal induced by mini-F plasmid is located in trans on the host chromosome, whereas the one generated by UV light-damaged F plasmid is in cis on the transferred DNA.

Chromosomes, Bacterial

Efficiency of induction of prophage lambda mutants as a function of recA alleles.

Mutants of the cI gene of prophage lambda have been defined phenotypically in a recA+ host as noninducible (Ind-), inducible (Ind+), or induction sensitive (Inds). We showed that a phage lambda cI+ carrying operator mutations v2 and v3 displays an Inds phenotype, as does lambda cI inds-1. We characterized a fourth induction phenotype called induction resistant (Indr). Using these four prophage types, we tested the influence of bacterial recA mutations on prophage induction. Indr prophages were fully induced in recA441 bacteria whose RecA441 protein is activated constitutively. Indr prophages were not induced in a mutant overproducing RecA+ protein, confirming that RecA+ protein must be activated to promote prophage induction. Inds prophages were induced in recA142 and recA453-441 lysogens, previously described as deficient in prophage induction.

Bacteriophage lambda

Indirect SOS induction is promoted by ultraviolet light-damaged miniF and requires the miniF lynA locus.

Indirect prophage induction is produced by transfer to recipients of u.v.-damaged F plasmid (95 kb). We tested whether the SOS signal can be produced by miniF, a 9.3 kb restriction fragment, coding for the replication and segregation functions of plasmid F. We used lambda miniF, a hybrid phage-plasmid. u.v.-irradiated lambda miniF induced prophages phi 80 or lambda and sfiA, a chromosomal SOS gene, in more than 50% of the infected cells. The maximal inducing dose produced about 0.5 pyrimidine dimers per kb and left 1% of lambda miniF survivors. Thus, the SOS signal produced by u.v.-damaged lambda miniF was almost as potent as that resulting from direct u.v.-irradiation of the lysogens. The u.v.-damaged vector lambda, devoid of miniF, failed to promote SOS induction. In contrast, efficient induction was observed when u.v.-damaged lambda miniF infected a lambda immune host, in which replication and expression of the phage genome were repressed. When replication and expression of the miniF genome was repressed by Hfr incompatibility, SOS induction was largely prevented. All these facts indicate that, in the hybrid lambda-miniF, it is the u.v.-damaged miniF that generates an SOS signal. To locate on the miniF genome the loci that are involved in the production of the SOS signal, we isolated deletions spanning all the miniF restriction fragments. We characterized six mutant phenotypes (Par+, Rep-, Fid-, Par-2, Par-1 and SOS-) related to four functions; partition, copy number, replication and SOS induction. A locus, we call lynA, 800 bp long, located by deletion mapping between the two origins of replication oriP and oriS is required for the production of an inducing signal. We postulate that indirect SOS induction by u.v.-damaged miniF results from the disturbance of the lynA function that may be involved in the co-segregation of F plasmid with the host chromosome.

Bacteriophage lambda

Gratuitous induction.

We describe a novel mode of SOS induction, called gratuitous indirect induction, which is elicited when the maintenance of an intact lambda miniF introduced into a recipient was inhibited by a resident plasmid or by mutations in miniF that impaired partition or replication. Gratuitous induction required the presence of the lynA locus on miniF and was dependent on the host recA and lexA alleles. To account for gratuitous induction, we postulate that impairment of the normal co-regulation between partition and replication of miniF affects lynA functions whose disturbance leads to the production of an SOS signal.

Bacteriophage lambda

Restoration of RecA protein activity by genetic complementation.

Bacteria carrying either recA430 or recA453-441 mutations are sensitive to UV-irradiation since they amplify the synthesis of RecA protein either poorly or not at all. We show here that, in a recA453-441 (recA430) heterodiploid, UV-resistance and amplification of RecA430 protein were restored, indicating that the cellular level of RecA-associated protease activity was high enough to inactivate LexA repressor. Prophage 434 repressor was also extensively inactivated, whereas RecA430 protein alone cannot cleave this substrate. On the other hand, during growth of the recA453-441(recA430) heterodiploid at 42 degrees C in the presence of adenine, a treatment activating only RecA441 protein, RecA441 protease activity was as high as in a recA441 haploid. In contrast, following this inducing treatment, there was no complementation between RecA441 and RecA+ proteins in a recA453-441(recA+) heterodiploid. These results indicate that multimerization of RecA protein molecules results in a functional interaction that, in some combination between RecA protein subunits, may enhance RecA-associated protease activity.

Alleles

Prophage phi 80 is induced in Escherichia coli K12 recA430.

In contrast to prophage lambda, wild-type prophage phi 80 was induced by UV-irradiation or thymine deprivation in recA430 mutants of E. coli K12. There was no induction of prophage phi 80 in two recombination-deficient mutants recA13 and recA99. Phage phi 80ind3, a non-inducible derivative in a rec+ was not induced in a recA430 lysogen. Two other lambdoid prophages were tested for UV-induction in recA430 lysogens: in common with lambda prophage, 434 was not induced whereas prophage 21 was induced in 1% of the cells. Induction of RecA430 protein synthesis was 30% of that observed in recA+ bacteria at 30 min of post-irradiation incubation, indicating that LexA repressor had been cleaved by RecA430 protease. In lexA1 recA430 and lexA1 recA+ bacteria, RecA protein synthesis was not amplified, yet, prophage phi 80 was fully induced. If phi 80cI repressor is inactivated by cleavage by RecA430 protease as is LexA repressor, RecA430 protease can inactivate all the molecules of phi 80cI repressor, its basal level being high enough in a recA430 lysogen. In such a lysogen, a fraction only of 21cI and LexA repressors are cleaved but no molecules of either lambda cI or 434cI repressor. We postulate that RecA430 protein has an altered pattern of recognition of repressor molecules and a cleavage efficiency which is more efficient the more remote is the repressor conformation from that of lambda repressor.

Bacterial Proteins

Cleavage of lambda repressor and synthesis of RecA protein induced by transferred UV-damaged F sex factor.

Transfer of a UV-damaged F sex factor to a recipient lambda lysogen induces prophage lambda development. Under these conditions RecA protein synthesis was induced and lambda repressor cleaved, as observed upon direct induction, that is, when the recipient lambda lysogen was directly exposed to UV-light. The efficiency of induction of RecA protein synthesis in recipient bacteria which had received an irradiated F-lac factor was about 80% of that measured upon direct induction. We observed the simultaneous disappearance of lambda repressor and a slight production of cleavage fragments; quantitation by densitometric scanning of the autoradiogram after correction for the efficiency of transfer indicated that 55% of lambda repressor was cleaved. Transfer of UV-damaged Hfr DNA failed to induce RecA protein synthesis. A lambda phage vector carrying oriF, the cloned origin of F plasmid replication, after exposure to UV-light and infection of a recipient lysogen, induced RecA protein synthesis and a moderate but significant cleavage of lambda repressor. Indirect induction by UV-damaged F sex factor or phage lambda oriF resulted in biochemical cellular reactions similar to those observed upon direct induction. LexA repressor that negatively controls RecA protein synthesis appeared more susceptible to cleavage than did lambda repressor.

Bacterial Proteins

Cell survival, UV-reactivation and induction of prophage lambda in Escherichia coli K12 overproducing RecA protein.

The effect of the cellular level of RecA protein on the ability of E. coli K12 bacteria to (i) survive UV-irradiation (ii) promote UV-reactivation of UV-damaged phage lambda (iii) induce prophage lambda was determined in bacterial mutants with discrete increasing levels of RecA protein. The various levels of RecA protein were obtained by combining lexA and recA alleles. Except for the double mutant lexA3 recAo98, whose repair ability was 25% less than that observed in wild type bacteria, bacterial survival was proportional to the level of RecA protein measured after 90 min of incubation. In lexA3 recAo98 bacteria, RecA protein, at a constitutive high basal level, failed to compensate totally for the lack of LexA repressor cleavage; UV-reactivation of UV-damaged phage lambda was not restored; yet, prophage lambda was induced with 35% efficiency. Efficient UV-induction of prophage lambda is linked to the induction of lexA-controlled host processes that repair the UV-damaged prophage.

Bacterial Proteins