Genetic suppression of a dnaG mutation in Escherichia coli

Characterization of mutations affecting the Escherichia coli essential GTPase era that suppress two temperature-sensitive dnaG alleles

Two suppressor mutations of the temperature-sensitive DNA primase mutant dnaG2903 have been characterized. The gene responsible for suppression, era, encodes an essential GTPase of Escherichia coli. One mutation, rnc-15, is an insertion of an IS1 element within the leader region of the rnc operon and causes a polar defect on the downstream genes of the operon. A previously described polar mutation, rnc-40, was also able to suppress dnaG2903. The other mutation, era-1, causes a single amino acid substitution (P17R) in the G1 region of the GTP-binding domain of Era. Analysis of the GTPase activity of the Era-1 mutant protein showed a four- to five-fold decrease in the ability to convert GTP to GDP. Thus, lowered expression of wild-type Era caused by the polar mutations and reduced GTPase activity caused by the era-1 mutation suppresses dnaG2903 as well as a second dnaG allele, parB. Phenotypic analysis of the era-1 mutant at 25 degrees C showed that 10% of the cells contain four segregated nucleoids, indicative of a delay in cell division. Possible mechanisms of suppression of dnaG and roles for Era are discussed.

Isolation and characterization of suppressors of two Escherichia coli dnaG mutations, dnaG2903 and parB

The dnaG gene of Escherichia coli encodes the primase protein, which synthesizes a short pRNA that is essential for the initiation of both leading and lagging strand DNA synthesis. Two temperature-sensitive mutations in the 3' end of the dnaG gene, dnaG2903 and parB, cause a defect in chromosome partitioning at the nonpermissive temperature 42 degrees. We have characterized 24 cold-sensitive suppressor mutations of these two dnaG alleles. By genetic mapping and complementation, five different classes of suppressors have been assigned; sdgC, sdgD, sdgE, sdgG and sdgH. The genes responsible for suppression in four of the five classes have been determined. Four of the sdgC suppressor alleles are complemented by the dnaE gene, which encodes the enzymatic subunit of DNA polymerase III. The sdgE class are mutations in era, an essential GTPase of unknown function. The sdgG suppressor is likely a mutation in one of three genes: ubiC, ubiA or yjbI. The sdgH class affects rpsF, which encodes the ribosomal protein S6. Possible mechanisms of suppression by these different classes are discussed.

Missense mutations in the 3' end of the Escherichia coli dnaG gene do not abolish primase activity but do confer the chromosome-segregation-defective (par) phenotype

Isogenic dnaG strains of Escherichia coli with the parB and dnaG2903 alleles in the MG1655 chromosomal background displayed the classic par phenotype at the nonpermissive temperature of 42 degrees C. These strains synthesized DNA at 42 degrees C, but remained chromosome segregation defective as determined by cytology. A strain with the dnaG2903 allele was tested for its ability to support DNA replication of a primase-dependent G4ori(c)-containing M13 phage derivative by quantitative competitive PCR (QC-PCR). The dnaG2903 strain converted the single-stranded DNA into double-stranded replicative form DNA at 42 degrees C. These results indicate that DnaG2903 retains primase activity at the restrictive temperature. Nucleoids remained unsegregated in the central region of cell filaments at 42 degrees C. The observed suppression of cell filamentation in dnaG sfiA or dnaG lexA double mutants suggests that the SOS response is induced at the restrictive temperature in parB and dnaG2903 strains but fails to account entirely for the cell filamentation phenotype. ParB and DnaG2903 presumably can synthesize primer RNA for DNA replication, but may be defective in their interactions with DNA replication proteins, cell cycle regulatory factors, or the chromosome segregation apparatus itself.

Functional analysis of mutations in the transcription terminator T1 that suppress two dnaG alleles in Escherichia coli

The mutations dnaG2903 and parB are both temperature-sensitive conditional lethal alleles of the Escherichia coli dnaG gene, which encodes the protein primase. The lesions are located in the 3' end of the gene, 9 basepairs apart, and both cause Glu-to-Lys substitutions in the carboxy terminus of primase. Previously, it was shown that dnaG2903 can be suppressed by point mutations in the rho-independent transcription terminator T1, which is located just upstream of dnaG in the rpsU-dnaG-rpoD macromolecular synthesis operon. We report here that parB can also be suppressed by point mutations in T1, demonstrating that parB can be suppressed in the same manner as dnaG2903. We also identified additional suppressors of dnaG2903 that are point mutations in T1, suggesting that defective transcription termination leading to overexpression of dnaG2903 and parB suppresses the temperature-sensitive phenotype of strains harboring these mutations. Utilizing two mutant rpoB alleles whose transcription termination phenotypes at rho-independent terminators have been previously characterized, we demonstrate that defective transcription termination leading to the overexpression of dnaG does indeed suppress dnaG2903 and parB. The point mutations in T1 identified in this study were analyzed for their effects on termination efficiency at T1. Our results indicate that the thermodynamic stability of the hairpin structures may not be the sole determinant of termination efficiency in vivo.

Conservation and evolution of the rpsU-dnaG-rpoD macromolecular synthesis operon in bacteria

The macromolecular synthesis (MMS) operon contains three essential genes (rpsU, dnaG, rpoD) whose products (S21, primase, sigma-70) are necessary for the initiation of protein, DNA, and RNA synthesis respectively. PCR amplifications with primers complementary to conserved regions within these three genes, and subsequent DNA sequencing of rpsU-dnaG PCR products, demonstrate that the three genes appear to be contiguous in 11 different Gram-negative species. Within the Gram-negative enteric bacterial lineage, the S21 amino acid sequence is absolutely conserved in 10 species examined. The putative nuteq antiterminator sequence in rpsU consists of two motifs, boxA and boxB, conserved in primary sequence and secondary structure. The terminator sequence, T1, located between rpsU and dnaG is conserved at 31 positions in nine enterobacterial species, suggesting the importance of primary sequence in addition to secondary structure for transcription termination. The intergenic region between rpsU and dnaG varies in size owing to the presence or absence of the Enterobacterial Repetitive Intergenic Consensus (ERIC) DNA element. The rpoD gene contains rearrangements involving a divergent sequence, although two carboxy-terminal regions which encode functional domains are conserved in primary sequence and spacing. Our data suggest that primary sequence divergence and DNA rearrangements in both coding and non-coding sequences account for the interspecies variation in operon structure. However, MMS operon gene organization and cis-acting regulatory sequences appear to be conserved in diverse bacteria.

Initiation of chromosomal DNA replication which is stimulated without oversupply of DnaA protein in Escherichia coli

The temperature-sensitive dnaA46 mutation in Escherichia coli can be phenotypically suppressed at 42 degrees C by oversupply of GroELS proteins, and the suppressed cells grow extremely slowly at 30 degrees C. We found that the phenotype of dnaA46 showing this cold sensitivity was dominant over the phenotype of dnaA+, and could not be rescued by introduction of oriC-independent replication systems. These results suggest that the cold sensitivity was not caused by a simple defect in replication. When a growing culture of a dnaA46 strain with a GroELS-overproducing plasmid was shifted from 42 degrees to 30 degrees C in the presence of chloramphenicol, the chromosomal DNA replicated excessively. Initiation of replication occurred at the site of oriC repeatedly four or five times during a 4 h incubation period without concomitant protein synthesis, indicating an excessive capacity for initiation. Such overreplication did not take place at 42 degrees C in the suppressed dnaA46 strain, or at either temperature in GroELS-oversupplied dnaA+ cells. No significant difference was detected between the cellular content of DnaA protein in suppressed cells where the initiation capacity was abnormally high, and that in wild-type cells in which the initiation capacity was normal. Thus, DnaA protein might function in vivo through some phase control mechanism for initiation, apart from a simple regulation by its total amount. A possible mechanism is proposed based on the participation of GroELS proteins in protein folding.

Mutations in the Escherichia coli dnaG gene suggest coupling between DNA replication and chromosome partitioning

Eleven conditional lethal dnaG(Ts) mutations were located by chemical cleavage of heteroduplexes formed between polymerase chain reaction-amplified DNAs from wild-type and mutant dnaG genes. This entailed end labeling one DNA strand of the heteroduplex, chemically modifying the strands with hydroxylamine or osmium tetroxide (OsO4) at the site of mismatch, and cleaving them with piperidine. The cleavage products were electrophoresed, and the size corresponded to the position of the mutation with respect to the labeled primer. Exact base pair changes were then determined by DNA sequence analysis. The dnaG3, dnaG308, and dnaG399 mutations map within 135 nucleotides of one another near the middle of dnaG. The "parB" allele of dnaG is 36 bp from the 3' end of dnaG and 9 bp downstream of dnaG2903; both appear to result in abnormal chromosome partitioning and diffuse nucleoid staining. A suppressor of the dnaG2903 allele (sdgA5) maps within the terminator T1 just 5' to the dnaG gene. Isogenic strains that carried dnaG2903 and did or did not carry the sdgA5 suppressor were analyzed by a combination of phase-contrast and fluorescence microscopy with 4',6-diamidino-2-phenylindole to stain DNA and visualize the partitioning chromosome. Overexpression of the mutant dnaG allele corrected the abnormal diffuse-nucleoid-staining phenotype associated with normally expressed dnaG2903. The mutations within the dnaG gene appear to cluster into two regions which may represent distinct functional domains within the primase protein.

Inhibition of cell growth and stable DNA replication by overexpression of the bla gene of plasmid pBR322 in Escherichia coli

A composite plasmid comprising the mini-F and pBR322 replicons was found to inhibit cell growth of a host with conditional mutations in dnaA and rnh under restrictive conditions, where the normal initiation of replication from oriC was inactivated, but the alternative replication initiation from oriK was active. It was further shown that the composite plasmid inhibited stable DNA replication (SDR) which occurs constitutively in cells mutant for rnh. Neither pBR322 nor mini-F alone produced these inhibitory effects. Deletion analyses revealed that the mini-F segment responsible for the inhibition of both processes was the promoter region of the sopA gene which had been cloned into a site upstream of the bla gene on pBR322 in such an orientation as to cause overexpression of bla. Inserting the promoter of the Escherichia coli lac gene into the same site had the same effect. Introduction of a deletion and a frameshift mutation into bla abolished the inhibition. Thus, the inhibition of growth and SDR appear to be due to overproduction of the bla gene product, beta-lactamase.