Elimination of lethal and pre-mutational DNA lesions during the photoreactivation of UV-irradiatedEscherichia coli

The comparison of the frequency oftrp ⁺ revertants ofEscherichia coli B/r Hcr⁺ thy trp after UV-irradiation on the one hand and after UV-irradiation plus photoreactivation on the other showed that both photoreversible pyrimidine dimers of the cyclobutane type and the non-photoreversible DNA lesions cause, at equal lethal effects, alsotrp ⁺ reversions with the same efficiency. If lethal, the pyrimidine dimers may thus be conceived as primary pre-mutational lesions.     

Transposition of Tn7 in Pseudomonas aeruginosa and Isolation of alk::Tn7 Mutations

Conjugal crosses with Pseudomonas aeruginosa donors carrying the CAM-OCT and RP4::Tn7 plasmids result in transfer of the Tn7 trimethoprim resistance (Tp(r)) determinant independently of RP4 markers. All Tp(r) exconjugants which lack RP4 markers have CAM-OCT genes and therefore must have received CAM-OCT::Tn7 plasmids formed by transposition of Tn7 from RP4::Tn7 to CAM-OCT. Most crosses yield exconjugants carrying mutant CAM-OCT plasmids which no longer determine either camphor or alkane utilization and thus appear to carry Tn7 inserts in the cam or alk loci, respectively. Transduction and reversion experiments indicated that at least 13 alkane-negative, camphor-positive, Tp(r) CAM-OCT::Tn7 plasmids carry an alk::Tn7 mutation. Determination of linkage between the alk mutation and the Tp(r) determinant of Tn7 on these plasmids is complicated by the presence of multiple copies of the Tn7 element in the genome. Generalized transduction will remove Tn7 from a CAM-OCT alk::Tn7 plasmid to yield alk(+) cells which carry no Tp(r) determinant on the CAM-OCT plasmid (as shown by transfer of the plasmid to a second strain). But the transduction to alk(+) does not remove all Tp(r) determinants from the genome of the recipient cell because the alkane-positive transductants remain trimethoprim resistant. Thus, it appears that copies of Tn7 can accumulate in the genome of P. aeruginosa (CAM-OCT alk::Tn7) strains without leaving their original site. This result is consistent with transposition models that involve replication of the transposable element without excision from the original site.     

Cytochrome b of cob revertants in yeast. 1. Isolation and characterization of revertants derived from cob exon mutants of Saccharomyces cerevisiae

Summary About 300 revertants were derived from 44 cob ^- mutants, mapping in the structure coding regions (exon 1, 3, 4, 5, or 6) of the mitochondrial apocytochrome b gene in Saccharomyces cerevisiae, strain 777-3A. Most of the revertants could not be distinguished from the wild-type by means of physiological properties. Twenty-two revertants different in phenotype are described here in more detail.The suppressor mutations (sup ^a) that compensate the primary cob ^- mutations (i.e., restore growth on glycerol) are mitochondrially inherited. They were localized in the same cob exon regions as the respective primary mutations, except for one revertant with a primary mutation in exon 6 and a suppressor, 4.2 map units distant, which may be located either in intron 5 or downstream in exon 6.Of 21 suppressors 17 are closely coupled to the primary mutation with recombination frequencies of 0.1%–0.3%. An estimate predicts that in more than 80% of these revertants only one amino acid is altered at that point of the polypeptide corresponding to the cob ^- site in the gene.The most interesting revertant phenotypes are: (1) reduced growth rate on glycerol. The respective cob ^-/sup^a mutations are scattered over the whole cob region and cannot be correlated exclusively with special gene regions. (2) decreased cytochrome b content. The most extreme reductions (28% and 30% of wild-type level) were observed to be due to mutations located in the 5 proximal part of exon 1. The highest percentage of revertants with decreased cytochrome b content was predominantly found mapping in exon 3. Complications in protoporphyrin attachment or the chelatase reaction were assumed to be the basic lesion causing reduced cytochrome b content, since in 10 out of 11 revertants examined the polypeptide is produced at wild-type level. (3) shifted maximum absorption wavelength of cytochrome b. The double mutations of the respective revertants map in the middle part of exon 1, in exon 4 and exom 5. The corresponding regions in the polypeptide presumably surround the heme group.     

Genetic and physical studies of restriction-deficient mutants of the Inc FIV plasmids R124 and R124/3

Summary R124 and R124/3 are R plasmids that carry the genes for two different restriction and modification systems. The phenotype of strains carrying either of these plasmids along with the F'lac ⁺ plasmid, is restriction-deficient (Res^-). The Res^- phenotype is not due to selection of preexisting mutants but rather to a complex mutational event caused by the F plasmid. Restriction-deficient mutants carry extensive deletions and other DNA rearrangements. Tn7 insertion is used to locate the restriction gene. Many of the Res^- mutants are genetically unstable and revert at exceptionally high frequencies. Reversion is accompanied by DNA rearrangements which result in a net gain of 9 kb of DNA. F derivates of F⁺ which do not cause restriction-deficiency but do cause deletion were used to distinguish between the DNA rearrangements associated with restriction-deficiency and those associated with deletion. From Res⁺ revertants of strains carrying F'lac ⁺ and R124 or R124/3 we have isolated F plasmids that now carry the genes for the R124 or R124/3 restriction and modification systems. It is suggested that interaction between part of the F plasmid and that segment of the R plasmid which controls the switch in Res-Mod specificity which has been observed (Glover et al. 1983) is responsible for the production of restriction-deficiency.     

Insertion element analysis and mapping of the Pseudomonas plasmid alk regulon.

We characterized and mapped new mutations of the alk (alkane utilization) genes found on Pseudomonas plasmids of the Inc P-2 group. These mutations were isolated after (i) nitrosoguanidine mutagenesis, (ii) transposition of the Tn7 trimethoprim and streptomycin resistance determinant, and (iii) reversion of polarity effects of alk::Tn7 insertion mutations. Our results indicate the existence of two alk loci not previously described--alkD, whose product is required for synthesis of membrane alkane-oxidizing activities, and alkE, whose product is required for synthesis of inducible membrane alcohol dehydrogenase activity. Polarity of alk::Tn7 insertion mutations indicates the existence of an alkBAE operon. Mapping of alk loci by transduction in P. aeruginosa shows that there are at least three alk clusters in the CAM-OCT plasmid--alkRD, containing regulatory genes; alkBAE, containing genes for specific biochemical activities; and alkC, containing one or more genes needed for normal synthesis of membrane alcohol dehydrogenase. The alkRD and alkBAE clusters are linked but separated by about 42 kilobases. The alkC cluster is not linked to either of the other two alk regions. Altogether, these results indicate a complex genetic control of the alkane utilization phenotype in P. putida and P. aeruginosa involving at least six separate genes.     

Revertants from RNase III negative strains of Escherichia coli

Summary E. coli strains carrying the rnc-105 allele do not show any level of RNase III in extracts, grow slower than rnc ⁺ strains at temperatures up to 45°C and fail to grow at 45°C. Revertants which can grow at 45°C were isolated. The vast majority of them still do not grow as fast as rnc ⁺ strains and did not regain RNase III activity. The mutation(s) which caused them are suppressor mutations (physiological suppressors) which do not map in the immediate vicinity of the rnc gene. A few of the revertants regain normal growth, and contain normal levels of RNase III. They do not harbor the rnc-105 allele and therefore are considered to be true revertants. By using purines other than adenine it was possible to isolate rnc ⁺ pur ^- revertants from an rnc ^- pur ^- strain with relative ease. They behaved exactly like the true rnc ⁺ revertants isolated from rnc ^- strains at 45°C.A merodiploid strain which contains the rnc ⁺ gene on an episome behaves exactly like an rnc ⁺ strain with respect to growth and RNA metabolism, eventhough its specific RNase III activity is about 60% of that of an rnc ⁺ strain; thus the level of RNase III is not limiting in the cell.The rnc ^- strains show a characteristic pattern of transitory molecules, related to rRNA, 30S, 25S, p23 and 18S, which are not observed in rnc ⁺ strains. This pattern is unchanged in rnc ^- strains and in the revertants which are still lacking RNase III, regardless of the temperature in which RNA synthesis was examined (30° to 45°C). On the other hand, in the rnc ⁺ strains as well as in the true revertants and the rnc ⁺/rnc ^- merodiploid, the normal pattern of p16 and p23 is observed at all temperatures. These findings suggest that all the effects observed in RNase III^- strains are due to pleiotropic effects of the rnc-105 allele, and that the enzyme RNase III is not essential for the viability of the E. coli cell.     

Revertants of a streptomycin-resistant, oligosporogenous mutant ofBacillus subtilis

Summary Revertants of a streptomycin-resistant (Str^R), oligosporogenous (Spo^-) mutant ofBacillus subtilis were selected for the ability to sporulate. The revertants obtained fell into two phenotypic classes: Str^S Spo⁺ (streptomycin-sensitive, sporeforming), which arose by reversion of the streptomycin resistance mutations of the parent strain; and Str^R Spo⁺, which arose by the acquisition of additional mutations, some of which were shown to affect ribosomal proteins. Alterations of ribosomal proteins S4 and S16 in the 30S subunit and L18 in the 50S subunit were detected in Str^R Spo⁺ revertants by polyacrylamide gel electrophoresis. Streptomycin resistance of the parental strain and the Str^R revertants was demonstrated to reside in the 30S ribosomal subunit. The second site mutations of the revertants depressed the level of streptomycin resistance in vivo and in the in vitro translation of phage SP01 messenger ribonucleic acid (mRNA) relative to the resistance exhibited by the Str^R parental strain. The Str^R parent grew slowly and sporulated at approximately 1% of the wild type level. The Str^S revertants closely resembled the wild type strain with regard to growth and sporulation. The Str^R revertants grew at rates intermediate between those of the Str^R parent and wild type, and sporulated at wild type levels.     

Role of post-replication and excision repair mechanism in the induction ofTrp + revenants of UV-irradiatedEscherichia coli

Both the post-replication and the excision repair mechanism participate in the induction ofTrp ⁺ revertants inEscherichia coli B/rHer ⁺ thy trp after a UV-irradiation. At low radiation doses (surviving cell fraction > 10^?) mostTrp ⁺ reversions are due to post-replication repair mechanism while at high doses (surviving cell fraction « 10^?1) theTrp ⁺ reversions arise probably as the result of an inaccurate excision repair. The absolute accuracy of repair processes decreases with increasing radiation dose.     

Analysis of a genetically unstable region inStreptomyces lividans 66-TK64

Genetic and molecular analyses of an unstable region encompassing the gene loci cml arg and a 5.7 kb amplifiable unit of DNA were done. Spontaneous mutants from Cm1^R →Cml^S and the revertants from Cml^S →Cml^R were analysed for mutations at arg locus and amplification of amplifiable unit of DNA. Twenty-one revertants were analysed. Two of these had large-scale amplification and one of these was also Arg^-. Nine of the revertants which were Arg⁺ had low-level or intermediate-level amplification of the 5.7 kb DNA sequence but no deletions of the flanking sequences were detected. Five of the CmI^R’ revertants, which were also Arg⁺, had lost one of the two copies from the doublet of amplifiable unit of DNA. The remaining five revertants did not show any other change. The amplifiable unit of DNA, therefore, not only undergoes amplification but can also suffer specific deletion of one copy. Thus, this region as a whole is characterized by instability and the events appear to take place at more than one locus concomitantly with a high frequency.     

T-DNA rearrangements due to tissue culture: somaclonal variation in crown gall tissues

After three years of apparent stability in tissue culture, the single cell derived shooty crown gall line sNT1.013 produced a revertant shoot which had switched from non-rooting (Rod⁺) and octopine synthesizing (Ocs⁺) to Rod^- Ocs^-, indicating that in this revertant TL-DNA genes 4 (causing the Rod⁺ trait) and gene 3 (causing the Ocs⁺ trait) had been inactivated. Southern blots revealed that the inactivation of these T-DNA genes was the result of a considerable rearrangement of DNA sequences, accompanied by deletions and possibly also by DNA amplifications. This study for the first time unambiguously proves that foreign genes which have been introduced via Agrobacterium tumefaciens can, at a low frequency, be inactivated after T-DNA integration because of reorganization of T-DNA sequences during tissue culture. This can be considered as an event of somaclonal variation.     

Mutational and dark-repair specificities in U.V.-irradiated di-auxotrophs of E. coli B/r

Summary U.V. irradiation experiments have been performed with three tyr^-leu^- diauxotrophs of E. coli B/r; 36-10, 36-18 and 36-32. These have in common the tyr^- marker WU-36. Three types of mutations were scored; tyr⁺leu^-, tyr^-leu⁺, and tyr⁺leu⁺. The percentages of total mutants scored which are of the tyr⁺leu⁺ type depend, firstly, on the strain. The tyr⁺leu⁺ revertants are rare in 36-10 and common in 36-18 and 36-32. Secondly, the percentages of tyr⁺leu⁺ among total revertants are determined by the nature of the plating medium, being altered by supplementation with a low level of the required amino acids, a low level of nutrient broth, or by caffeine. These differential effects upon tyr⁺leu⁺ and tyr⁺leu^- or tyr^-leu⁺ reversions can be interpreted at the levels of dark-repair and the later stages in the process leading to phenotypic expression. It is suggested that states of repression and derepression may be implicated in determining susceptibility of lesions in suppressor loci to repair processes. Phenotypically different classes of mutations have different pathways leading to final expression.This work was initiated in Dr. Ruth F. Hill's laboratory, Department of Radiology, Columbia University, New York.     

W-mutagenesis in competent cells of Bacillus subtilis

Summary The relative yield (N _m/N) of fluorescent mutants Ind^- after the transformation of Bacillus subtilis cells by means of UV-irradiated DNA is much higher in an uvr ^- recipient than in an uvr ⁺ strain, when compared at equal fluence, but practically identical at equal survival. Ind^- mutations are induced by UV-irradiation of separated single strands of transforming DNA. The H-strand is much more sensitive to the mutagenic action of UV light. Preliminary irradiation of competent recipient cells by moderate UV fluences increases the survival of UV-or -irradiated transforming DNA (W-reactivation) and the frequency of Ind^- mutations (W-mutagenesis). During transfection of B. subtilis cells by UV-irradiated prophage DNA isolated from lysogenic cells B. subtilis (Ø105 c ⁺) c-mutants of the phage are obtained in high yield only in conditions of W-mutagenesis, i.e. in UV-irradiated recipient cells. These data show that there is no substantial spontaneous induction of error-prone SOS-repair system in the competent cells of B. subtilis.     

Integration of IS3 into IS2 generates a short sequence duplication.

Summary The Gal⁺ allele IS2-43 is known to segregate Gal^- clones. Among 11 Gal^- segregants, one was shown to be due to the integration of IS3 into IS2-43. Precise excision of the integrated IS3 element occured at a rate of 5x10^-9/cell/generation. DNA sequence analysis revealed that the termini of the IS3 element have the relation of imperfect inverted repeats and it is now flanked by a 3bp or 4bp duplication, a size which has not been seen before with other elements.     

Properties of strains of Escherichia coli K12 carrying mutant lex-1 and uvrA6 alleles

Summary Strains with both uvrA6 and the lex-1 mutations are more sensitive to ultraviolet light (UV) than isogenic strains with only one of the mutations. The lex ^- uvrA^-double mutant has the same sensitivity to methyl-methane-sulfonate as the lex ^- uvrA⁺single mutant. UV-irradiated cultures of lex ^- uvrA⁺and lex ^- uvrA^-strains do not produce more streptomycinresistant mutants per survivor than unirradiated cultures. UV-irradiated cultures of a lex ⁺ uvrA^-strain produce large yields of mutants at both low (4 ergs/mm²) and high (25 ergs/mm²) doses of UV compared with the lex ⁺ uvrA⁺ strain which produce an intermediate yield of mutants at 25 ergs/mm², and a small yield at 4 ergs/mm², not significantly greater than unirradiated cultures. A dose of UV which does not induce mutations in strains with the lex-1 mutation produces only a small decrease in DNA synthesis in the lex ^- uvrA⁺strain. The results are interpreted to mean that the lex-1 mutation probably does not affect the same pathway of DNA repair as the uvrA ⁺product (i.e. excision of thymine dimers), and that the absence of UV-induced mutations in irradiated cultures of lex ^-strains is probably not due to a cessation of DNA replication.     

Isolation and characterization of cold-sensitive mutations at the benA, beta-tubulin, locus of Aspergillus nidulans

Summary We have isolated large numbers of conditionally lethal -tubulin mutations to provide raw material for analyzing the structure and function of tubulin and of microtubules. We have isolated such mutations as intragenic suppressors of benA33, a heat-sensitive (hs^-) -tubulin mutation of Aspergillus nidulans. Among over 2,600 revertants isolated, 126 were cold-sensitive (cs^-). In 41 of 78 cs^- revertants analyzed, cold sensitivity and reversion from hs^- to hs⁺ were due to mutations linked to benA33. In three cases reversion was due to mutations closely linked to benA33 but cold sensitivity was due to a coincidental mutation unlinked to benA33. In the remaining 34 cases reversion was due to mutations unlinked to benA33. Thirty-three of the revertants in which cold sensitivity and reversion were linked to benA33 were sufficiently cold-sensitive to allow us to select for rare recombinants between benA33 and putative suppressors in a revertant x wild-type (wt) cross. We found only one recombinant among 1,000 or more viable progeny from crosses of each of these revertants with a wt strain. Reversion is thus due to a back mutation or very closely linked suppressor in each case. We have analyzed 17 of these 33 revertants with greater precision and have found that, in each case, reversion is due to a suppressor mutation that maps to the right of benA33. The recombination frequencies between benA33 and the suppressors are very low (less than 1.2×10^-4) in all cases. Five of these 33 revertants have been examined microscopically and in each of them nuclear division and nuclear migration are inhibited at a restrictive temperature. We conclude that at least some and perhaps all of these revertants carry intragenic suppressors of benA33 that, in combination with benA33, cause cold sensitivity by inhibiting the functioning of microtubules at low temperatures. Of the 17 suppressors mapped, 11 map to two clusters. These clusters are likely to define regions particularly important to the functioning of the -tubulin molecule.     

Genetic determination of the donor properties in Escherichia coli K-12. Phenomena of chromosome mobilization and integrative suppression.

Summary The chromosome mobilization is the ability of F⁺ donors to introduce part of the chromosome besides F-plasmids into the recipient cells during conjugation. We studied the genetic determination of this phenomenon. Most efficient almost like true Hfr's are F⁺-cells of the genotype recBC ^- sbcB ^- belonging to the RecF-recombination type. Their ability to chromosome mobilization is 50 fold higher comparing with wild type F⁺ (of the RecBC-recombination type). This property is fully dependent on the recF gene but does not depend on recL. The donors recBC ^-F⁺ but without the mutation sbcB ^- act in mobilization about 4 times weaker than wild type. Hence we see two main levels of mobilization, quantitatively very different: a recF-dependent and recBC-dependent. Both reveal an absolute requirment of the product of recA gene.The efficiency of mobilization of different markers along the chromosome was studied and mapped. The maps were identical, in spite of great difference in absolute frequencies for the RecF- and Rec BC-pathways. They are not at all random. The sites of mobilization are coinsident with the points of interaction of the F-factor leading to stable Hfr's. Therefore it is suggested that these sites of predominant mobilization are IS-sequences and that during chromosome mobilization single-strand integration of the F-factor via a semichiasmus is effected. It gives a pulse to initiate DNA transfer into the recipient but is unstable and transient and does not yield true Hfr's.The suppression of the Dna^ts phenotype in F⁺ cells due to the integration of an F-plasmid into the chromosome (integrative suppression) is increased manyfold on the RecF-pathway of recombination. Probably it is a manifestation of mentioned hot spots of recombination.The regions fre described earlier (Bresler et al., 1978) and confirmed in this paper are regarded as substrates of some recF-dependent endonuclease of recombination. Probably they coinside with clusters of IS-sequences.     

DNA degradation in minicells of Escherichia coli K-12

Summary The properties of minicell producing mutants of Escherichia coli deficient in gentic recombination were examined. Experiments were designed to test recombinant formation in conjugal crosses, survival following UV-irradiation in cells, and the state of DNA metabolism in minicells. The REC^- phenotypes are unaffected by min ⁺/^- genotypes in whole cells. In contrast to minicells produced by rec ⁺ parental cells, minicells from a recB21 strain have limited capacity to degrade linear, Hfr transferred DNA. The lack of a functional recA gene product, presumably involved in inhibiting the recBC nuclease action(s), permits unrestricted Hfr DNA breakdown in minicells produced by a recA1 strain. This results in an increase in TCA soluble products and in the formation of small DNA molecules that sediment near the top of an alkaline sucrose gradient. Unlike the linear DNA, circular duplex DNA from plasmids R64-11 or dv, segregated into the minicells, is resistant to breakdown. By using in vitro criteria, and [³²P]-labelled linear DNA from bacteriophage T₇ for substrate, we found that the ATP-dependent exonuclease of the recBC complex (exo V) is present in rec ⁺ and recA^- minicells, and is lacking in the recB21 mutant. In fact, the absence of a functional exo V in recBC^- minicells results in isolation of larger than average Hfr DNA from minicells. We suggest that recombination (REC) enzymes segregate into the polar minicells at the time of minicell biogenesis. This system should be useful for studies on DNA metabolism and functions of the recBC and recA gene products.Paper 1 in series, see Khachatourians et al., 1974.     

Suppression of temperature sensitive mutants of bacteriophage T4 by bacterial opal suppressors

Summary Some of the partial revertants from opal (UGA) mutants of bacteriophage T4 are temperature sensitive in su ^– host cells but are still temperature resistant in su ⁺ cells. Hence these revertants are missense mutants suppressible by bacterial opal suppressors. Such a suppression may be explained in terms of codon-anticodon interactions by the wobble hypothesis.     

Induced mutagenesis in Ustilago maydis

Summary A UV-revertible mutant of the nar1 structural gene for nitrate reductase was isolated in wildtype (nar ⁺ nir ⁺) Ustilago maydis. It proved to be vigorously revertible by gamma rays as well. Genetic analysis revealed that the strain carried a single, nonleaky, recessive allele (nar1-m) with an unusually high spontaneous reversion rate (3×10^-5/div.). Reliable reversion frequencies were determined with a special agar medium that reduced the normally high level of residual growth observed on nitrate minimal agar. Radiation-induced reversion frequencies in the homozygous diploid were approximately twice those in the hapliod. Following crosses to wild type, two revertants (one spontaneous and one UV-induced) were found to map at nar1. Although the molecular basis of nar1-m reversion is not known, available data suggest that some form of point mutation is involved.     

Double Infection,Recombination, and Segregation of Two R Factors,R 100 and Rts1, and Their Possible Bearing on the Genetic Structure of R 100

Applying the observation by Yokota et al (1969) that a cell doubly harboring an R factor (R100) and a temperature sensitive R factor (Rts1) produces segregant R factors with various resistance patterns, a total of 271 segregant R factors were obtained. There were 163 resistant to (sul, str, kan), 39 resistant to (sul, str, cml, kan), 62 resistant to (sul, str, tet, kan) and finally 7 resistant to (tet, kan). More than 90% of the former 3 segregants were fi⁺ and the remainder, including all of the (tet, kan) segregants, were fi^?. Some fi^? segregants with the former 3 resistance patterns and all of the (tet, kan) segregants were nontransmissible. All of these segregants were still temperature sensitive. Based upon the results of three experiments; (a) the growth at 43 C to observe linked loss of the kan gene and the genes derived from R 100, (b) a conjugal analysis of the relevant resistant markers, and (c) a transductional analysis of these same markers, several conclusions were made. The 2 R factors both consisting of a circle were supposed to have recombined to form a larger circle which then further resulted in the final formation of smaller circles. The possible bearing of these observations and conclusions on the genetic structure of R 100 was discussed.