Genetic studies of an Escherichia coli K-12 temperature-sensitive mutant defective in membrane protein synthesis

A little gene with big effects: a serT mutant is defective in flgM gene translation

A conditional-lethal mutant was isolated as having a flagellar regulatory phenotype at 30 degrees C and being unable to grow at 42 degrees C. Chromosomal mapping localized the mutation to the serT gene, which encodes an essential serine tRNA species (tRNA((cmo)5UGA)(Ser)). DNA sequence analysis revealed the mutation to be a single base change in G:A at position 10 of the serT gene that lies within the D-stem of the essential tRNA((cmo)5)UGA(Ser) species. tRNA((cmo)5)UGA(Ser) recognizes UCA, UCG, and UCU codons, but UCU is also recognized by tRNA(GGA)(Ser) and UCG by tRNA(CGA)(Ser). No other tRNAs are known to read the UCA codon. Thus, the UCA codon is specifically recognized by tRNA((cmo)5)UGA(Ser). We show that the anti-sigma(28) activity of FlgM is defective in the serT mutant strain. The serT allele causes a 10-fold increase in sigma(28)-dependent fliC promoter transcription, indicating a defect in FlgM anti-sigma(28) activity in the presence of the serT mutation. The flgM gene contains only one UCA codon. Changing the UCA of flgM to ACG reversed the effect of the serT allele. Implications for context effects in regulation of gene expression are discussed.

Eight UCA codons differentially affect the expression of the lacZ gene in the divE42 mutant of Escherichia coli

In the divE mutant, which has a temperature-sensitive mutation in the tRNA1Ser gene, the synthesis of beta-galactosidase is dramatically decreased at the non-permissive temperature. In Escherichia coli, the UCA codon is only recognized by tRNA1Ser. Several genes containing UCA codons are normally expressed at 42°C in the divE mutant. Therefore, it is unlikely that the defect is due to the general translational deficiency of the mutant tRNA1Ser. In this study, we constructed mutant lacZ genes, in which one or several UCA codons at eight positions were replaced with other serine codons such as UCU or UCC, and we examined the expression of these mutant genes in the divE mutant. We found that a single UCA codon at position 6 or 462 was sufficient to cause the same level of reduced beta-galactosidase synthesis as that of the wild-type lacZ gene, and that the defect in beta-galactosidase synthesis was accompanied by a low level of lacZ mRNA. It was also found that introduction of an rne-1 pnp-7 double mutation restored the expression of mutant lacZ genes with only UCA codons at position 6 or 462. A polarity suppressor mutation in the rho gene had no effect on the defect in lacZ gene expression in the divE mutant. We propose a model to explain these results.Key words: divE gene, tRNA1Ser, lacZ gene expression, UCA codon.

An rne-1 pnp-7 double mutation suppresses the temperature-sensitive defect of lacZ gene expression in a divE mutant

A divE mutant, which has a temperature-sensitive mutation in the tRNA1Ser gene, exhibits differential loss of the synthesis of certain proteins, such as beta-galactosidase and succinate dehydrogenase, at nonpermissive temperatures. In Escherichia coli, the UCA codon is recognized only by tRNA1Ser. Several genes containing UCA codons are normally expressed after a temperature shift to 42 degrees C in the divE mutant. Therefore, it is unlikely that the defect in protein synthesis at 42 degrees C is simply caused by a defect in the decoding function of the mutant tRNA1Ser. In this study, we sought to determine the cause of the defect in lacZ gene expression in the divE mutant. It has also been shown that the defect in lacZ gene expression is accompanied by a decrease in the amount of lacZ mRNA. To examine whether inactivation of mRNA degradation pathways restores the defect in lacZ gene expression, we constructed divE mutants containing rne-1, rnb-500, and pnp-7 mutations in various combinations. We found that the defect was almost completely restored by introducing an rne-1 pnp-7 double mutation into the divE mutant. Northern hybridization analysis showed that the rne-1 mutation stabilized lacZ mRNA, whereas the pnp-7 mutation stabilized mutant tRNA1Ser, at 44 degrees C. We present a mechanism that may explain these results.

Suppression of the serT42 mutation with modified tRNA(1Ser) and tRNA(5Ser) genes

Serine tRNA gene derivatives with altered anticodons were introduced to the temperature-sensitive serT42 mutant, whose tRNA(1Ser) shows a base substitution of A10 for wild type G10. When a low copy number vector-system was used, the growth and beta-galactosidase synthetic activity of the serT42 mutant were restored by complementation with the tRNA(5Ser) (T34) gene or the tRNA(1Ser) (G34) gene as well as the tRNA(1Ser) (wt) gene, but not with tRNA(5Ser) (wt), tRNA(1Ser) (A34) or tRNA(1Ser) (C34) genes at 42 degrees C. When multicopy vectors were used, the transformation even with tRNA(1Ser) (A10) gene restored the growth and beta-galactosidase synthetic activity at 42 degrees C. The tRNA(1Ser) (A10) showed no thermosensitivity in serine acceptor activity by in vitro assay. At 42 degrees C, the amount of tRNA(1Ser) (A10) in the serT42 mutant was almost the same as those in the wild type. The nucleotides in the tRNA(1Ser) (A10) were found to be fully modified like those in the wild type tRNA(1Ser). Both of the tRNAs transcribed from tRNA(5Ser) (T34) and tRNA(1Ser) (G34) genes showed serine acceptor activity. Modified nucleosides of these tRNAs were also analyzed.

Functions of the gene products of Escherichia coli

A list of currently identified gene products of Escherichia coli is given, together with a bibliography that provides pointers to the literature on each gene product. A scheme to categorize cellular functions is used to classify the gene products of E. coli so far identified. A count shows that the numbers of genes concerned with small-molecule metabolism are on the same order as the numbers concerned with macromolecule biosynthesis and degradation. One large category is the category of tRNAs and their synthetases. Another is the category of transport elements. The categories of cell structure and cellular processes other than metabolism are smaller. Other subjects discussed are the occurrence in the E. coli genome of redundant pairs and groups of genes of identical or closely similar function, as well as variation in the degree of density of genetic information in different parts of the genome.

A minor arginine tRNA mutant limits translation preferentially of a protein dependent on the cognate codon

The Escherichia coli argU gene encodes a rare arginine tRNA (anticodon UCU) that translates the similarly rare AGA codon. The argU10(Ts) mutation is a transition that changes the first nucleotide of the mature tRNA from G to A, presumably destabilizing the acceptor stem. This mutation, when present in haploid condition in the chromosome, reduces the growth rate at 30 degrees C and results in cessation of growth after 60 to 90 min at 43 degrees C. The mutation also preferentially limits (compared with total protein synthesis) translation of an induced gene that depends on five AGA codons, i.e., the lambda cI repressor gene. Translation of another inducible protein, beta-galactosidase, which does not involve AGA codons, was inhibited to a much lesser extent. The chromosomal argU(Ts) mutation also confers the Pin phenotype, that is, loss of ability of the host, as a P2 lysogen, to inhibit growth of bacteriophage lambda, probably the result of reduced translation of the P2 old gene, which contains five AGA codons (E. Haggård-Ljungquist, V. Barreiro, R. Calendar, D. M. Kurnit, and H. Cheng, Gene 85:25-33, 1989).

Tracking bacterial DNA replication forks in vivo by pulsed field gel electrophoresis

The location of chromosomal DNA replication forks was identified in synchronously replicating E. coli cultures by pulse labeling DNA at specific times with 14C-thymidine and following incorporation of radionucleotide into genomic Not I restriction fragments. This technique could be used to characterize chromosomal DNA replication, to characterize mutations which affect this process, to identify the location of DNA replication origins and termini as well as aid in the construction of macrorestriction maps. Here, we further characterize the DNA replication mutations divE and dnaK and preliminary characterize the genomic organization of E. coli isolate 15.

A cell division regulatory mechanism controls the flagellar regulon in Escherichia coli

The formation of flagella in various thermosensitive (Ts) cell division mutants of Escherichia coli was examined at the nonpermissive temperature. The number of flagella per unit cell length decreased sharply after shifting the culture temperature from 30 degrees to 40 degrees C in the following Ts mutants: ftsC108, ftsD1033, ftsE1181, ftsF1141, ftsG29, ftsZ84, parA110, dnaB42, nrdB, and dnaG. It was found that transcription of genes responsible for the formation and/or function of flagella (hag, fla, mot, che) decreased significantly at 40 degrees C. However, in the ftsI730 mutant at the nonpermissive temperature, or in penicillin G treated wild-type cells, cell division was blocked but formation of flagella continued. Moreover, when the cfcA1 mutation, of a gene involved in coordinating DNA replication and cell division, was introduced into the dnaB42 mutant strain, inhibition of cell division and also of formation of flagella at 40 degrees C was relaxed. These results indicate that the flagellar regulon is under the control of a cell division regulatory mechanism.

Selection for mutants altered in the expression or export of outer membrane porin OmpF

Strains in which the lacZ gene (which specifies beta-galactosidase) is fused to a gene encoding an envelope protein often exhibit a phenotype termed overproduction lethality. In such strains, high-level synthesis of the cognate hybrid protein interferes with the process of protein export, and this leads ultimately to cell death. A variation of this phenomenon has been discovered with lacZ fusions to the gene specifying the major outer membrane porin protein OmpF. In this case, we find that lambda transducing phage carrying an ompF-lacZ fusion will not grow on a host strain that constitutively overexpresses ompF. We have exploited this observation to develop a selection for ompF mutants. Using this protocol, we have isolated mutants altered in ompF expression and have identified mutations that block OmpF export. Our results suggest that it should be possible to adapt this selection for use with other genes specifying exported proteins.

ExpA: a conditional mutation affecting the expression of a group of exported proteins in Escherichia coli K-12

A mutant of Escherichia coli K-12 was isolated as conditionally deficient in the expression of two exported proteins simultaneously (i.e. two acid phosphatases). The mutant was found to be thermosensitive on minimal medium at 37 degrees C and above, but grew normally on rich media at these temperatures. The mutation, named expA and located at 22 min on the recalibrated linkage map, depressed the levels of six periplasmic enzymatic activities in bacteria grown at 37 degrees C. At least ten proteins were greatly reduced in the periplasm under these conditions. The mutation also affected some outer membrane proteins, among which were the ompF protein and a protein which may be protein III, but had little effect on cytoplasmic membrane proteins. The gel patterns of the soluble cytoplasmic proteins were not modified except for one major protein of MW 47,000. The activities of beta-galactosidase and of aspartate transcarbamylase were unmodified. After growth at 30 degrees C no difference was observed between expA and expA+ isogenic strains. The results are discussed with respect to the mechanism of protein export.

Regulatory mutations conferring constitutive synthesis of major outer membrane proteins (OmpC and OmpF) in Escherichia coli

An ompB strain of Escherichia coli K-12 lacking major outer membrane proteins OmpC and OmpF was used to isolate a pair of mutants that have restored the ability to synthesize either OmpC or OmpF protein. These mutants were found to produce the respective proteins constitutively under the several conditions where the synthesis in the wild-type strain was markedly repressed; namely, in the absence of the ompB gene function, under restrictive medium conditions, or upon lysogenization with phage PA-2. The mutations ompCp1 and ompFp9 responsible for such synthesis were shown to be located in the close vicinity of the corresponding structural genes, ompC and ompF. Moreover, the mutations affect the expression of these genes in a cis-dominant fashion. Taken together with other evidence, it was suggested that ompCp1 and ompFp9 represent regulatory site mutations occurring at the promoter regions of ompC and ompF respectively. Relevance of these findings to the genetic control of outer membrane protein synthesis is discussed.

Temperature-induced synthesis of specific proteins in Escherichia coli: evidence for transcriptional control

Synthesis of several protein chains of Escherichia coli is markedly, though transiently, induced upon shift-up of a log-phase culture to or above the critical temperature (about 34 degrees C). Such induction occurs coordinately for at least three protein chains (76K, 73K, and 64K) examined. Studies of initial kinetics of induction using a specific inhibitor of transcription (rifampin) revealed that induction occurs at the level of transcription with very little lag, though actual synthesis of messenger ribonucleic acids and proteins requires about 1 min when temperature is shifted up from 30 to 42 degrees C. Evidence suggests that E. coli cells somehow "recognize" the temperature change and activate transcription of several distinct operons, one of which contains the mop (morphogenesis of phages; groE) gene.

Chromosomal location and expression of the structural gene for major outer membrane protein Ia of Escherichia coli K-12 and of the homologous gene of Salmonella typhimurium

The gene determining the structure of a major outer membrane protein of Escherichia coli, protein Ia, has been located between serC and pyrD, at the min 21 region of the linkage map. This is based on the isolation and characterization of E. coli-Salmonella typhimurium intergeneric hybrids as well as analyses of a mutation (ompF2) affecting the formation of protein Ia. When the serC region of the S. typhimurium chromosome was transduced by phage P1 into E. coli, two classes of transductants were obtained; one produced protein Ia like the parental strain of E. coli, whereas the other produced not protein Ia but a pair of outer membrane proteins structurally related to 35K protein, one of the major outer membrane proteins of S. typhimurium. Furthermore, a strain of S. typhimurium harboring an F' plasmid which carries the ompF region of the E. coli chromosome was found to produce a protein indistinguishable from protein Ia, beside the outer membrane proteins characteristic to the parental Salmonella strain. These results suggest that the structural genes for protein Ia (E. coli) and for 35K protein (S. typhimurium) are homologous to each other and are located at the ompF region of the respective chromosome. The bearing of these findings on the genetic control of protein Ia formation is discussed.