Indirect selection of bacterial plasmids lacking identifiable phenotypic properties

New yeast recombineering tools for bacteria

Recombineering with Saccharomyces cerevisiae is a powerful methodology that can be used to clone multiple unmarked pieces of DNA to generate complex constructs with high efficiency. Here, we introduce two new tools that utilize the native recombination enzymes of S. cerevisiae to facilitate the manipulation of DNA. First, yeast recombineering was used to make directed nested deletions in a bacteria-yeast shuttle plasmid using only one or two single stranded oligomers, thus obviating the need for a PCR step. Second, we have generated several new shuttle vectors for yeast recombineering capable of replication in a wide variety of bacterial genera. As a demonstration of utility, some of the approaches and vectors generated in this study were used to make a pigP deletion mutation in the opportunistic pathogen Serratia marcescens.

Improvements to gene deletion in the fungal pathogen Cryptococcus neoformans: absence of Ku proteins increases homologous recombination, and co-transformation of independent DNA molecules allows rapid complementation of deletion phenotypes

Cryptococcus neoformans is a pathogenic fungus that is relatively amenable to molecular genetic analysis, including gene deletion. However, rates of homologous recombination can be low, so obtaining specific gene deletion transformants is challenging. We have utilized two new technologies, cku deletion strains to improve the efficiency of gene deletions in this organism, and co-transformations. The Ku70-Ku80 heterodimer is predicted to be an essential part of the non-homologous end-joining process in C. neoformans. Here we show that a deletion in one or both of these proteins results in an increase in the rates of homologous recombination. Importantly, we demonstrate that after generation of a strain with a particular deletion of interest, the cku deletion can be removed by mating and segregation. We also utilize co-transformation of wild-type genes and selectable markers on separate linear DNA molecules to complement a deletion event. We show that co-transformation results in the successful restoration of wild-type phenotype, though variations in this phenotype often occur.

Co-transformation with autonomous replicating and integrative plasmids in Penicillium chrysogenum is highly efficient and leads in some cases to rescue of the intact integrative plasmid

The efficiency of co-transformation in Penicillium chrysogenum Wisconsin 54-1255 pyrG(-) and the fate of the transforming DNA were studied using an integrative (pEF43) and an autonomous replicating plasmid (pAM9L). The results showed a co-transformation frequency of nearly 70% of all transformants tested. The total efficiency of transformation was shown to be dependent on the plasmid marker used as transformant selection (i.e., markers in the integrative or autonomous replicating vector). Analysis of the plasmids re-isolated from several co-transformants showed that different populations of plasmids co-exist in the fungal host. Interestingly, in all co-transformants studied, the integrative plasmid was found to be replicating autonomously without integrating into the host genome. In some cases, co-integrates were formed by recombination between autonomous replicating (pAM9L) and integrative (pEF43) plasmids. However, unexpectedly in some cases, the non-reorganised pEF43 integrative plasmid used in the co-transformation assays was rescued from some co-transformants.

Genetic characterization of a Streptococcus mutans LraI family operon and role in virulence

Proteins belonging to the LraI (for "lipoprotein receptor antigen") family function as adhesins in several streptococci, as a virulence factor for endocarditis in at least one of these species, and potentially as metal transporters in many bacteria. We have identified and characterized the chromosomal locus containing the LraI family gene (designated sloC) from Streptococcus mutans, an agent of dental caries and endocarditis in humans. Northern blot analysis indicated that sloC is cotranscribed with three other genes. As with other LraI operons, the sloA and sloB genes apparently encode components of an ATP-binding cassette transport system. The product of the fourth gene, sloR, has homology to the metal-dependent regulator from Corynebacterium diphtheriae, DtxR. A potential binding site for SloR was identified upstream from the sloABCR operon and was conserved upstream from LraI operons in several other streptococci. Potential SloR homologs were identified in the unfinished genomic sequences from two of these, S. pneumoniae and S. pyogenes. Mutagenesis of sloC in S. mutans resulted in apparent loss of expression of the entire operon as assessed by Northern blot analysis. The sloC mutant was indistinguishable from its wild-type parent in a gnotobiotic rat model of caries but was significantly less virulent in a rat model of endocarditis. Virulence for endocarditis was restored by correction of the sloC mutation but not by provision of the sloC gene in trans, suggesting that virulence requires the expression of other genes in the sloC operon.

New cloning vectors with temperature-sensitive replication

A series of cloning vectors with conditional, temperature-sensitive replication that are selectable with ampicillin, chloramphenicol, and kanamycin has been constructed. These vectors are derivatives of a pSC101 mutant that can replicate only at low temperatures. The cloning vectors carry a number of unique restriction sites and provide for screening of recombinant plasmids by alpha complementation. These vectors have proven useful for a variety of applications where conditional replication of a recombinant plasmid is desired.

Isolation and characterization of plasmid pSW200 from Erwinia stewartii

The nucleotide sequence of pSW200 of Erwinia stewartii SW2 was determined. This plasmid is 4367 bp long, consisting of four mobilization genes, mobCABD, and an origin of replication homologous to those of ColE1-type plasmids. The plasmid also contains a region of forty-one 15-bp repeats. Deleting this region does not affect the stability or the copy number when maintained as sole plasmid in the cell. However, the plasmid is rapidly lost when a homoplasmid with the intact repeat region is introduced into the cell. The function of this region may provide pSW200 an advantage in competing with an incompatible plasmid in the cell.

Cotransformation and Targeted Gene Inactivation in the Maize Anthracnose Fungus, Glomerella graminicola

Cotransformation of Glomerella graminicola was achieved with the G. graminicola genes TUB1 R1 (encoding a β-tubulin which confers resistance to the fungicide benomyl) and PYR1 (encoding orotate phosphoribosyl transferase, which confers pyrimidine prototrophy). The cotransformation frequency was about 30% when selection was for pyrimidine prototrophy (Pyr + ) and 87% when selection was for benomyl-resistant (Bml r ) transformants. Southern blots confirmed that both transforming DNAs had integrated into the genomes of transformants which were expressing both Pyr + and Bml r phenotypes. A plasmid, p23, which contained a truncated 500-bp segment representing the central region of the PYR1 gene was constructed. The plasmid was introduced with pCG7, containing TUB1 R1, into G. graminicola M1.001 (Pyr + Bml s ), and Bml r transformants were selected. The Bml r transformants were screened on medium which did not contain uridine in order to identify Pyr - mutants created by integration of p23 at the PYR1 locus. None of the primary transformants were Pyr - , but 0.2% of uninucleate conidia collected from the pooled primary transformants gave rise to Pyr - auxotrophs. Southern blots representing two of these Pyr - mutants confirmed that they had the expected homologous integration of p23 at the PYR1 locus. This suggested that integration resulted in production of two nonfunctional copies of the gene, one lacking the 5′ sequences and the other lacking the 3′ sequences. This study demonstrates the feasibility of using cotransformation to perform targeted gene disruptions in G. graminicola .

Cointegration of transforming DNAs in Aspergillus nidulans: a model using autonomously-replicating plasmids

Transforming DNAs form cointegrates in Aspergillus nidulans by homologous and non-homologous recombination as well as by end-to-end ligation of linear fragments. This process has been studied by means of a model in which the linkage of a marker gene to the origin of autonomous replication AMA1 was selected for. Recombinant plasmids were rescued into Escherichia coli and subjected to restriction mapping and sequence analysis. It was shown that circular DNA molecules recombined predominantly within homologous fragments. Linear DNA fragments integrated into circular plasmids by invasion of their ends into random non-homologous sites, but exhibited some bias in choice of a target sequence. Cointegrates of multiple plasmid copies were often observed. In some of the plasmids analysed, short duplications of the target sequence flanking an inserted linear DNA fragment have been revealed.

An 'instant gene bank' method for gene cloning by mutant complementation

We describe a new method of gene cloning by complementation of mutant alleles which obviates the need for construction of a gene library in a plasmid vector in vitro and its amplification in Escherichia coli. The method involves simultaneous transformation of mutant strains of the fungus Aspergillus nidulans with (i) fragmented chromosomal DNA from a donor species and (ii) DNA of a plasmid without a selectable marker gene, but with a fungal origin of DNA replication ('helper plasmid'). Transformant colonies appear as the result of the joining of chromosomal DNA fragments carrying the wild-type copies of the mutant allele with the helper plasmid. Joining may occur either by ligation (if the helper plasmid is in linear form) or recombination (if it is cccDNA). This event occurs with high efficiency in vivo, and generates an autonomously replicating plasmid cointegrate. Transformants containing Penicillium chrysogenum genomic DNA complementing A. nidulans niaD, nirA and argB mutations have been obtained. While some of these cointegrates were evidently rearranged or consisted only of unaltered replicating plasmid, in other cases plasmids could be recovered into E. coli and were subsequently shown to contain the selected gene. The utility of this "instant gene bank" technique is demonstrated here by the molecular cloning of the P. canescens trpC gene.

Bacterial plasmids: their extraordinary contribution to molecular genetics

Reviewed here are certain of the extraordinary contributions to molecular genetics that have resulted from the study of bacterial plasmids. Work with plasmids has led to both the 'operon' and 'replicon' concepts, and has provided seminal information about bacterial conjugation and fertility, recombination, transposable genetic elements, genome evolution and antisense RNA. Studies of plasmid functions have yielded important findings about the regulation of DNA replication, DNA topology and partitioning, gene control signals and restriction/modification enzymes. Plasmids have had a central role in the development of DNA cloning (recombinant DNA) methods; additionally, they have provided a paradigm for both the co-transformation of non-selected DNA into eukaryotic cells and the creation of the artificial chromosomes.

Co-transformation with autonomously-replicating helper plasmids facilitates gene cloning from an Aspergillus nidulans gene library

Autonomously-replicating, marker-less "helper" plasmids were added to transformations of Aspergillus nidulans with plasmids which normally transform by chromosomal integration. This resulted in as much as a 200-fold increase in transformation efficiency. Recovery of autonomously-replicating plasmid co-integrates indicated that co-transformation involves recombination between integrating and helper plasmids, which occurs at a high frequency. Increasing DNA sequence-homology between pairs of plasmids used in simultaneous transformations enhanced co-transformation efficiency. Using helper plasmids and an A. nidulans gene library in a normally-integrating vector, the genes adC and adD were cloned as part of such a co-integrate. In effect, the addition of helper plasmid converts an integrating into an autonomously-replicating gene library in vivo.

High efficiency transformation of Escherichia coli with plasmids

We have re-evaluated the conditions for preparing competent Escherichia coli cells and established a simple and efficient method (SEM) for plasmid transfection. Cells (DH5, JM109 and HB101) prepared by SEM are extremely competent for transformation (1-3 x 10(9) cfu/microgram of pBR322 DNA), and can be stored in liquid nitrogen for at least 40 days without loss of competence. Unlike electroporation, transformation using these competent cells is affected minimally by salts in DNA preparation. These competent cells are particularly useful for construction of high-complexity cDNA libraries with a minimum expenditure of mRNA.

Type 3 fimbriae among enterobacteria and the ability of spermidine to inhibit MR/K hemagglutination

The distribution of the gene cluster encoding type 3 fimbriae among various isolates of the family Enterobacteriaceae was investigated by using 112 clinical and nonclinical isolates. Closely related DNA sequences were detected in all Klebsiella strains, in most Enterobacter isolates, in a smaller number of Escherichia coli and Salmonella spp., and in a single isolate each of Yersinia enterocolitica and Serratia liquefaciens but not in isolates of Morganella or Providencia species or Serratia marcescens. Except for E. coli and Salmonella strains, the presence of gene sequences was correlated with the phenotypic expression of either the MR/K hemagglutinin or fimbriae that reacted with specific antibodies. In one isolate of Y. enterocolitica the expression of type 3 fimbriae was plasmid determined. The polyamine spermidine was identified as an inhibitor of MR/K hemagglutinating activity, exhibiting an MIC of 1.2 mM. Spermidine inhibited the hemagglutination of 37 MR/K-positive clinical isolates from various genera. However, one clinical isolate of Enterobacter cloacae and most (four of five) nonclinical Klebsiella isolates were not completely inhibited.

Controllable alteration of cell genotype in bacterial cultures using an excision vector

We have used recombinant DNA techniques to construct a derivative of phage lambda, called an excision vector, which retains only those functions necessary for conditional maintenance of lysogeny and integration/excision. The tyrA+ gene was cloned on this excision vector, integrated into the Escherichia coli chromosome, and stably maintained and expressed under permissive conditions. Upon shift to non-permissive conditions, the excision vector and its passenger gene were very efficiently excised from the chromosome and lost, leaving a culture of Tyr- bacteria. This illustrates a new class of conditional mutations in which the genotype changes in response to external stimuli.

Cotransformation of Aspergillus nidulans: a tool for replacing fungal genes

When a non-selected DNA sequence was added during the transformation of amdS320 deletion strains of Aspergillus nidulans with a vector containing the wild-type amdS gene the AmdS+ transformants were cotransformed at a high frequency. Cotransformation of an amdS320, trpC801 double mutant strain showed that both the molar ratio of the two vectors and the concentration of the cotransforming vector affected the cotransformation frequency. The maximum frequency obtained was defined by the gene chosen as selection marker for transformation. Cotransformation was used to induce a gene replacement in A. nidulans. An amdS320 strain was transformed to AmdS+ and cotransformed with a DNA fragment containing a fusion between a non-functional A. nidulans trpC gene and the Escherichia coli lacZ gene. Ten AmdS+, LacZ+ transformants with a Trp- mutant phenotype were selected. All of these strains could be transformed with a functional copy of the A. nidulans trpC gene, but only two strains yielded TrpC+ transformants which, with a low frequency, had a LacZ- phenotype. These latter transformants had also lost the AmdS+ phenotype. Southern blotting analysis of DNA from these transformants confirmed the inactivation of the wild-type trpC gene, but revealed that amdS vector sequences were also involved in the gene replacement events.

A common plasmid of Chlamydia trachomatis

A 7.4-kb plasmid is a common and perhaps essential component of the Chlamydia trachomatis genome. This plasmid occurs as 10 copies per chlamydial chromosomal equivalent. It is unable to replicate in Escherichia coli. Complete plasmid genomes from eight serovars of C. trachomatis have been isolated in E. coli as cloned sequences ligated to pBR322. Restriction enzyme cleavage site mapping indicates that these plasmids are closely related. Homologous plasmid sequences have also been detected by DNA hybridization in all of the 200 clinically isolated strains of C. trachomatis which have been examined. DNA sequences homologous to the C. trachomatis plasmid were not found in eucaryotic DNA nor in a plasmid of similar size isolated from C. psittaci. C. trachomatis plasmid genes are expressed in vivo and the plasmid encoded gene products may play a role in the intracellular growth of this organism. Plasmid encoded genes were also expressed from the cloned C. trachomatis plasmid in E. coli minicells and using an E. coli S-30 in vitro transcription translation extract.

Spontaneous deletion mutants resulting from a frameshift insertion in the simian virus 40 agnogene

The 61-amino-acid agnoprotein is a nonessential polypeptide encoded by the late leader region of simian virus 40 which appears to play a role in viral assembly. A 2-base-pair (bp) insertion mutant (in2379) was created by altering the coding region of this protein. This mutation prevents the synthesis of the agnoprotein and, in contrast to the more extensive deletion mutations previously described in this region, might be expected to have a lesser effect on the template for late viral transcription. In fact, the 2-bp insertion mutant grew significantly less well than most mutants containing larger deletions in the agnoprotein region and frequently gave rise to stock containing second-site alterations in the same region. These observations suggested that the defect in mutant in2379 extends beyond the loss of the agnoprotein. Characterization of a number of second-site mutants indicated that all of them grew more efficiently than the original 2-bp insertion mutant. Based on the nucleotide sequence of these mutants, we suggest possibilities for the deleterious effect induced by the insertion in mutant in2379.

Repair of cis-platinum-DNA adducts by ABC excinuclease in vivo and in vitro

cis-Platinum compounds, which are used in cancer chemotherapy, are thought to exert their effect by damaging DNA. It is known that this damage is partially repaired in Escherichia coli. Using cis-Pt-treated pBR322 DNA as a probe, we investigated the role of nucleotide excision repair in the removal of Pt-DNA adducts. We found that the nucleotide excision pathway was the major mechanism for repairing Pt adducts in transforming plasmid DNA but that a recA-dependent pathway also contributed to plasmid survival. When cis-Pt-damaged pBR322 was treated with the purified nucleotide excision enzyme ABC excinuclease in vitro, a fraction of the adducts was removed by the enzyme; this removal resulted in a corresponding increase in transformation efficiency.

Expression of antigenic factor O:54 is associated with the presence of a plasmid in Salmonella

Salmonella serovar Tonev (antigenic formula, 21,54:b:e,n,x) is classified in the Salmonella group O:54, and contains a 7.5-kilobase plasmid, designated pIP1340. Tonev NV, a variant lacking pIP1340, failed to express O:54 (antigenic formula identical with that of serovar Minnesota, 21:b:e,n,x). Phenotypic tagging of plasmid pIP1340 by transposon Tn5 produced plasmid pIP1341. Factor O:54 expression in Tonev NV was restored after transformation by pIP1341 NDA or after co-transformation by a mixture of pBR322 and pIP1340 DNA. Similarly, the twelve other serovars presently classified in Salmonella group O:54 harboured a small plasmid which was not detectable in isogenic O:54-negative variants isolated from the parent strain. Transfer of plasmid pIP1341 into these O:54-negative variants and also into reference strains of serovars of Salmonella group O:4 (Banana and Typhimurium), group O:7 (Thompson and Mbandaka), group O:8 (Ferruch, Hadar and Kentucky), group O:3,10 (Orion) and group O:21 (Minnesota) supported the conclusion that plasmid pIP1340 encodes or regulates some functions required for factor O:54 expression by various serovars of Salmonella.

Cointegration and resolution mediated by IS101 present in plasmid pSC101

A certain class of cointegrate plasmids was found to occur between a pSC101 derivative and a second plasmid pBV320 in E. coli F- cells. Cleavage analysis and DNA sequencing showed that the cointegrate plasmid contained direct repeats of an insertion sequence IS101 at the recombination junctions, indicating that formation of cointegrates was mediated by IS101, which is a natural constituent of pSC101. These cointegrates were formed only in cells which contained the transposon gamma-delta, suggesting that the gamma-delta sequence, which provides transposase, is responsible for cointegration. Whenever the cointegrate plasmids were present in cells containing gamma-delta or its related transposon Tn3, the cointegrates were dissolved to give pBV320::IS101 due to recombination at duplicated IS101 sequences in the cointegrates, suggesting that both gamma-delta and Tn3, which provide a resolvase, are responsible for the resolution of the cointegrates. Comparison between the nucleotide sequence of IS101 and those of gamma-delta and Tn3 shows a high degree of homology in the regions that have been shown to be the binding sites of resolvases, as well as in the terminal inverted repeats. However, there is no homology between IS101 and the other element, gamma-delta or Tn3, in the internal resolution site, at which the resolution event may occur.

Plasmid-mediated factors conferring diffuse and localized adherence of enteropathogenic Escherichia coli

Histopathological evidence suggests that the adherence of enteropathogenic Escherichia coli (EPEC) to the mucosa of the small bowel is an important step in pathogenesis. Several reports have shown that many EPEC isolates adhere to HEp-2 and HeLa cells in tissue cultures. In the HeLa cell assay, there are at least two distinct patterns of adherence: localized adherence, which is characterized by the formation of bacterial microcolonies, and diffuse adherence, in which bacteria cover the cell uniformly. We have found that these two patterns can be demonstrated in HEp-2 cells as well as in HeLa cells and that the results of the two assays are closely correlated. Using a DNA probe which is sensitive and specific for localized adherence to HEp-2 cells, we provide evidence that localized adherence and diffuse adherence by EPEC are due to at least two genetically distinct adhesions which confer phenotypic differences in both the morphology of HEp-2 cell adherence and in surface hydrophobicity. The two factors are each encoded on plasmids which vary in size from 55 to 70 megadaltons; one strain exhibiting localized adherence carried these genes on the chromosome.

Identification of an Rts1 DNA fragment conferring temperature-dependent instability to vector plasmids

The multiphenotypic drug resistance factor Rts1 expresses a temperature-dependent instability characteristic. This plasmid was digested with the restriction enzyme BamHI. A DNA fragment with a molecular weight of 5.6 MDa (the H fragment) was inserted into plasmid pBR322 (pFK896) or into pSC105 (pYH156) at the BamHI site. These plasmids were unstable at 42 degrees C but stable at 32 degrees C. A restriction-enzyme map of the H fragment was constructed and the instability phenotype (Tdi) was localized to a DNA fragment with 0.5 MDa molecular weight. The temperature-dependent loss of the unstable plasmid pFK896 is abrupt and no gradual plasmid loss of this multicopy recombinant plasmid is observed. The possibility that the Tdi phenotype is due to overgrowth of R- cells was eliminated.

Cointegrates carrying two copies of a Tn3 derivative in an inverted orientation

We constructed a mutant of Tn3, Tn3 #2, that contains a 55-bp direct repeat of sequences near the amino-terminal coding region of the transposase, and an 8-bp EcoRI linker. This mutant transposase is functional. The plasmid carrying Tn3 #2, pMB8::Tn3 #2, recombines with the plasmid pHS1 at a frequency of 2.8 X 10(-7) recombinants per division cycle. This is similar to the recombination frequency of pHS1 and pMB8::Tn3+ (wild-type) which is 4.5 X 10(-6) recombinants per division cycle. One-third of the recombinants between pMB8::Tn3 #2 and pHS1 were approx. 22 kb in length. Restriction analysis and nucleotide sequencing showed that these large plasmids were Tn3 #2-mediated cointegrates formed by integration of pMB8::Tn3 #2 into pHS1. However, unlike Tn3 tnpR- -mediated cointegrates that contain direct repeats of the incoming element, Tn3 #2-mediated cointegrates carry two copies of Tn3 #2 in the form of inverted repeats. Like the tnpR- repeats, the Tn3 #2 repeats occur at both junctions between the parental plasmids, and are associated with a 5-bp direct duplication of the pHS1 target site. Furthermore, these recombinants contain a small deletion starting precisely at the end of Tn3 #2 and extending into pMB8 sequences. We propose a model for the generation of Tn3 #2-mediated cointegrates.

Aerobactin iron transport genes commonly encoded by certain ColV plasmids occur in the chromosome of a human invasive strain of Escherichia coli K1

The aerobactin-mediated iron uptake system encoded by pColV-K30 and other ColV plasmids has been associated with the ability of Escherichia coli strains to cause disease. We investigated whether the pColV-K30 aerobactin system is present in E. coli K1 VW187 isolated from a human neonate with meningitis. This strain exhibited a functional aerobactin-mediated iron uptake system, as assessed by a cross-feeding bioassay and by its sensitivity to cloacin, a bacteriocin that recognizes the outer membrane receptor for iron-aerobactin complexes. By using a variety of techniques, we could not find any plasmid harboring the aerobactin genes. Hybridization of restriction endonuclease-cleaved chromosomal DNA from strain VW187 with various clones containing subsets of the pColV-K30 aerobactin region showed that the aerobactin genes were located on a 10.5-kilobase-pair chromosomal HindIII restriction fragment which also contained IS1-like insertion sequences. The chromosomal aerobactin region showed a high degree of conservation when compared with the homologous region in plasmid pColV-K30, although it was located on a different restriction endonuclease site environment.

Insertion element IS1 encodes two structural genes required for its transposition

The nucleotide sequence analysis of insertion element IS1 has shown that IS1 could have as many as six translational reading frames encoding possible proteins. In order to determine which reading frames are actual structural genes responsible for IS1-mediated recombination, we introduced base substitution mutations including nonsense mutations into all of the potential reading frames and examined the ability of these IS1 mutants to mediate cointegration between two plasmids. The results reveal that IS1 has two structural genes (termed insA and insB), which are required for plasmid cointegration mediated by IS1.

The replication origin of pSC101: the nucleotide sequence and replication functions of the ori region

The nucleotide sequence of a 770-bp ori region of plasmid pSC101 is presented. The sequence shows homologies to some parts of Escherichia coli oriC and phage G4 ori. Several other features are an 80-bp A + T-rich region overlapping a part of the region homologous to oriC, three direct repeats of an 18-bp sequence adjacent to the A + T-rich region, a typical promoter sequence just upstream of the longest open reading frame (ORF) and a long inverted repeat sequence overlapping the putative promoter region. Analysis of successive deletions by BAL31 exonuclease demonstrated that one of the regions homologous to oriC along with the A + T-rich region are essential for autonomous replication of the plasmid. The three 18-bp repeats are responsible for incompatibility phenotype. The region containing the promoter-like sequence is required for expression of a trans-acting function.

Exonucleases I, III, and V are required for stability of ColE1-related plasmids in Escherichia coli

The stability of two ColE1-related plasmids (pRSF2124 and pMB9) was examined in strains of Escherichia coli multiply deficient in exonucleases I (sbcB), III (xthA), or V (recB recC). Any combination of exonuclease I, III, and V deficiency resulted in dramatically decreased stability of both pRSF2124 and pMB9. Inactivation of the RecF pathway by introducing either recF or recJ mutations to the recB recC subcB background resulted in nearly wild-type levels of stability for both plasmids. In contrast, the introduction of uvrD3 uvr-257, uvrE100, or recL152 into the recB21 recC22 sbcB15 strain did not affect plasmid stability. Furthermore, the amount of plasmid DNA recovered from pRSF2124 or pMB9 transformants of a xthA1 sbcB15 strain was strikingly reduced relative to that of a wild-type control. Taken together, these results suggest that some aspect of DNA repair is required for stable maintenance of ColE1-related plasmids in E. coli.

Effects of point mutations on formation and structure of the RNA primer for ColE1 DNA replication

We report mutations affecting several steps of CoIE1 primer formation. Primer precursor forms the hybrid with the template DNA and is cleaved by RNAase H to form the primer. Point mutations at positions -264, -265, -268, and -308 (base pairs upstream of the replication origin) reduce efficiency of hybrid formation. A suppressor mutation at -18 increases the efficiency for a mutant transcript and reduces that for a wild-type transcript. Therefore, hybrid formation probably starts after transcription passes this position. A mutation at -10 affects the site of cleavage by RNAase H. The site appears to be determined by the distance from a stem-loop structure immediately upstream. A double mutation at -186 and -188 results in formation of an RNA secondary structure that prevents use of an RNAase H-cleaved transcript as primer.

Characterization of common virulence plasmids in Yersinia species and their role in the expression of outer membrane proteins

The virulence plasmids pYV019, pYV8081, and pIB1 from Yersinia pestis, Yersinia enterocolitica, and Yersinia pseudotuberculosis, respectively, were characterized by restriction endonuclease analysis. The three plasmids exhibited a region of common DNA previously shown to encode determinants which confer Ca2+ dependence. The plasmids from Y. pestis and Y. pseudotuberculosis were similar throughout their genomes. In contrast, a region of the plasmid from Y. enterocolitica which contained an origin of replication differed from the other two plasmids as determined by DNA homology and replication properties. Plasmid-associated outer membrane proteins from all three species of Yersinia were characterized by polyacrylamide gel electrophoresis. There were no differences in the outer membrane protein profiles between plasmid-containing and homogenic strains lacking the plasmid after growth at 28 degrees C. After growth at 37 degrees C, both Y. enterocolitica and Y. pseudotuberculosis showed at least four major plasmid-associated outer membrane proteins. Y. pestis did not show any discernible changes after growth at 37 degrees C. It was shown by using E. coli minicell analysis that the plasmid DNA from all three species of Yersinia contained the coding capacity for production of the novel outer membrane proteins.

Studies on transformation of Escherichia coli with plasmids

Factors that affect the probability of genetic transformation of Escherichia coli by plasmids have been evaluated. A set of conditions is described under which about one in every 400 plasmid molecules produces a transformed cell. These conditions include cell growth in medium containing elevated levels of Mg2+, and incubation of the cells at 0 degrees C in a solution of Mn2+, Ca2+, Rb+ or K+, dimethyl sulfoxide, dithiothreitol, and hexamine cobalt (III). Transformation efficiency declines linearly with increasing plasmid size. Relaxed and supercoiled plasmids transform with similar probabilities. Non-transforming DNAs compete consistent with mass. No significant variation is observed between competing DNAs of different source, complexity, length or form. Competition with both transforming and non-transforming plasmids indicates that each cell is capable of taking up many DNA molecules, and that the establishment of a transformation event is neither helped nor hindered significantly by the presence of multiple plasmids.

Construction and propagation of deletion derivatives of staphylococcal tetracycline-resistance plasmid pTP-5 in Bacillus subtilis

Tetracycline-resistance (TCr) plasmid pTP-5 (4.46 kb) from Staphylococcus aureus was cleaved with HindIII into three fragments: A (2.35 kb), B (1.57 kb) and C (0.54 kb). A deletion plasmid (3.92 kb) lacking HindIII-C fragment was obtained, and was designated pNS1. This plasmid retained the TCr phenotype and the ability to replicate autonomously in Bacillus subtilis. A restriction endonuclease cleavage map of pNS1 was constructed. Attempts to construct smaller plasmids by digesting pNS1 with BAL31 nuclease led to production of a set of deletion derivatives whose molecular sizes range from 3.75 to 2.77 kb. Through analyses of these derivatives, the regions essential for autonomous replication and expression of TCr were deduced.

Insertion of nonhomologous DNA into the yeast genome mediated by homologous recombination with a cotransforming plasmid

Bacterial plasmids containing no detectable homology with yeast DNA sequences were inserted into the yeast genome by cotransforming with a plasmid containing a yeast gene. Analysis of the yeast transformants confirmed that recombination events occurred between the prokaryotic sequences shared by the two plasmids and between the yeast sequences common to the cotransforming plasmid and to the genome. Multiple copies of the two plasmids, in both tandem and interspersed arrays, are inserted by this method. Populations of cells grown from individual transformants are heterogeneous for the number of integrated sequences. The number of integrated bacterial sequences is greatly reduced after 100 generations of growth in the populations that initially contained large numbers of sequences, while it is stable in those populations that initially contained either a single or a small number of copies.

Broad-host-range IncP-4 plasmid R1162: effects of deletions and insertions on plasmid maintenance and host range

R1162 is an 8.7-kilobase (kb) broad-host-range replicon encoding resistance to streptomycin and sulfa drugs. In vitro deletion of 1.8-kb DNA between coordinates 3.0 and 5.3 kb did not affect plasmid maintenance, but a Tn1 insertion at coordinate 6.3 kb led to a recessive defect in plasmid maintenance. The only cis-acting region necessary for plasmid replication appears to lie between the Tn1 insertion at coordinate 6.3 kb and a second Tn1 insertion at coordinate 6.5 kb. All R1162 sequences between position 6.5 kb and the EcoRI site at coordinate 8.7/0 kb were dispensible for replication in Escherichia coli and Pseudomonas putida. Plasmids carrying insertions in a variety of restriction sites in an R1162::Tn1 derivative were unstable in P. putida but stable in E. coli. Tn5 insertions in R1162 showed a hot spot at coordinate 7.5 kb. A Tn5 insertion at coordinate 8.2 kb appeared to mark the 3' end of the streptomycin phosphotransferase coding sequence. All R1162::Tn5 derivatives showed specific instability in Pseudomonas strains but not in E. coli. The instability could be relieved by internal deletions of Tn5 sequences. In the haloaromatic-degrading Pseudomonas sp. strain B13, introduction of an unstable R1162::Tn5 plasmid led to loss of ability to utilize m-chlorobenzoate as a growth substrate. Our results showed that alteration of plasmid sequence organization in nonessential regions can result in restriction of plasmid host range.

Plasmids, drug resistance, and gene transfer in the genus Streptococcus

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Stable chromosomal integration of the entire nitrogen fixation gene cluster from Klebsiella pneumoniae in yeast

A bacterial plasmid containing the entire nitrogen fixation (nif) gene cluster (consisting of at least 15 genes) from Klebsiella pneumoniae was used in conjunction with an Escherichia coli-yeast shuttle plasmid containing the yeast his4 gene cluster to cotransform a his4- recipient strain of Saccharomyces cerevisiae. Of 87 histidine-independent clones screened, 2 contained nif DNA. Restriction and hybridization analyses showed that two copies of the nif plasmid (46 kilobases each) are integrated in tandem in the recipient chromosome by recombination between homologous regions in the transforming plasmids. Chromosomal integration was also verified by tetrad analysis, showing that the nif DNA behaved in meiosis like a Mendelian element. During mitotic growth, one of the two copies of the nif region is frequently lost. The remaining copy of nif is stable, even after 40 generations in nonselective medium.

Insertion element IS102 resides in plasmid pSC101

In vivo recombination was found to occur between plasmid pHS1, a temperature-sensitive replication mutant of pSC101 carrying tetracycline resistance, and plasmid ColE1 after selection for tetracycline resistance at the restrictive temperature, 42 degrees C. Extensive analysis of the physical structures of three of these recombinant plasmids, using restriction endonucleases and the electron microscope heteroduplex method, revealed that the plasmid pHS1 was integrated into different sites on ColE1. The recombinant plasmids contained a duplication of a unique 1-kilobase (kb) sequence of pHS1 in a direct orientation at the junctions between the two parental plasmid sequences. This was confirmed by comparing the nucleotide sequence of the recombinants and their parental plasmids. Nucleotide sequence analysis further revealed that nine nucleotides at the site of recombination of ColE1 were duplicated at the junction of each of the 1-kb sequences. The formation of recombinants was independent of RecA function. Based on our previous finding that a plasmid containing a deoxyribonucleic acid insertion (IS) element can recombine with a second plasmid to generate a duplication of the IS element, we conclude that the 1-kb sequence is an insertion sequence, which we named IS102. For convenience, we have also denoted the IS102 sequence as eta theta to assign the orientation of the sequence. Eighteen nucleotides at one end (eta end) were found to be repeated in an inverted orientation at the other end (theta end) of IS102. The nucleotide sequence of the eta end of the sequence was found to be identical to the sequence at the ends of the transposon Tn903, which is responsible for transposition of the kanamycin resistance gene.

Altering genotype and phenotype by DNA-mediated gene transfer

Transformation, or DNA-mediated gene transfer, permits the introduction of new genetic information into a cell and frequently results in a change in phenotype. The transforming DNA is ultimately integrated into a recipient cell chromosome. No unique chromosomal locations are apparent, different lines contain the transforming DNA on different chromosomes. Expression of transformed genes frequently results in the synthesis of new polypeptide products which restore appropriate mutant cells to the wild-type phenotype. Thus transformation provides an in vivo assay for the functional role of DNA sequence organization about specific genes. Transforming genes coding for selectable functions, such as adenine phosphoribosyltransferase or thymidine kinase, have now been isolated by utilizing transformation in concert with molecular cloning. Finally, transformation may provide a general approach to the analysis of complex heritable phenotypes by permitting the distinction between phenotypic changes without concomitant changes in DNA and functional genetic rearrangements.

Involvement of plasmid deoxyribonucleic acid in indoleacetic acid synthesis in Pseudomonas savastanoi

Olive (or oleander) knot is a plant disease incited by Pseudomonas savastanoi. Disease symptoms consist of tumorous outgrowths induced in the plant by bacterial production of indole-3-acetic acid (IAA). Synthesis of IAA occurs by the following reactions: L-tryptophan leads to indoleacetamide leads to indoleacetic acid, catalyzed by tryptophan 2-monooxygenase and indoleacetamide hydrolase, respectively. Whereas the enzymology of IAA synthesis is well characterized, nothing is known about the genetics of the system. We devised a positive selection for the presence of tryptophan 2-monooxygenase based on its capacity to use as a substrate the toxic tryptophan analogue 5-methyltryptophan. Efficient curing of the bacterium of tryptophan 2-monoxygenase, indoleacetamide hydrolase, and IAA production was obtained by acridine orange treatment. Further, loss of capacity to produce IAA by curing was correlated with loss of a plasmid of 34 X 10(6) molecular weight. This plasmid, here called pIAA1, when reintroduced into Iaa- mutants by transformation, restored tryptophan 2-monooxygenase and indoleacetamide hydrolase activities and production of IAA.