A transducing lambda phage carrying grpE, a bacterial gene necessary for lambda DNA replication, and two ribosomal protein genes, rpsP (S16) and rplS (L19)

The Hsp70 chaperone machines of Escherichia coli: a paradigm for the repartition of chaperone functions

Molecular chaperones are highly conserved in all free-living organisms. There are many types of chaperones, and most are conveniently grouped into families. Genome sequencing has revealed that many organisms contain multiple members of both the DnaK (Hsp70) family and their partner J-domain protein (JDP) cochaperone, belonging to the DnaJ (Hsp40) family. Escherichia coli K-12 encodes three Hsp70 genes and six JDP genes. The coexistence of these chaperones in the same cytosol suggests that certain chaperone-cochaperone interactions are permitted, and that chaperone tasks and their regulation have become specialized over the course of evolution. Extensive genetic and biochemical analyses have greatly expanded knowledge of chaperone tasking in this organism. In particular, recent advances in structure determination have led to significant insights of the underlying complexities and functional elegance of the Hsp70 chaperone machine.

Isolation and characterization of point mutations in the Escherichia coli grpE heat shock gene

The Escherichia coli grpE gene (along with dnaK, dnaJ, groEL, and groES) was originally identified as one of the host factors required for phage lambda growth. The classical grpE280 mutation was the only grpE mutation that resulted from the initial screen and shown to specifically block the initiation of lambda DNA replication. Here we report the isolation of several new grpE missense mutations, again using phage lambda resistance as a selection. All mutants fall into two groups based on their temperature-dependent phenotype for lambda growth. Members of the first group (I), including grpE17 and grpE280, which was obtained again, are resistant to lambda growth at both 30 and 42 degrees C. Members of the second group (II), including grpE25, grpE66, grpE103, grpE13a, grpE57b, and grpE61, are sensitive to lambda growth at 30 degrees C but resistant at 42 degrees C. All mutations are recessive, since an E. coli grpE null mutant strain carrying these mutant alleles on low-copy-number plasmids are sensitive to infection by the lambda grpE+ transducing phage. Both group I and group II mutants are temperature sensitive for E. coli growth above 42 degrees C. The nucleotide changes were identified by sequencing analyses and shown to be dispersed throughout the latter 75% of the grpE coding region. Most of the amino acid changes occur at conserved residues, as judged by sequence comparisons between E. coli and other bacterial and yeast GrpE homologs. The isolation of these new mutations is the first step toward a structure-function analysis of the GrpE protein.

The essential Escherichia coli msgB gene, a multicopy suppressor of a temperature-sensitive allele of the heat shock gene grpE, is identical to dapE

The grpE gene product is one of three Escherichia coli heat shock proteins (DnaK, DnaJ, and GrpE) that are essential for both bacteriophage lambda DNA replication and bacterial growth at all temperatures. In an effort to determine the role of GrpE and to identify other factors that it may interact with, we isolated multicopy suppressors of the grpE280 point mutation, as judged by their ability to reverse the temperature-sensitive phenotype of grpE280. Here we report the characterization of one of them, designated msgB. The msgB gene maps at approximately 53 min on the E. coli chromosome. The minimal gene possesses an open reading frame that encodes a protein with a predicted size of 41,269 M(r). This open reading frame was confirmed the correct one by direct amino-terminal sequence analysis of the overproduced msgB gene product. Genetic experiments demonstrated that msgB is essential for E. coli growth in the temperature range of 22 to 37 degrees C. Through a sequence homology search, MsgB was shown to be identical to N-succinyl-L-diaminopimelic acid desuccinylase (the dapE gene product), which participates in the diaminopimelic acid-lysine pathway involved in cell wall biosynthesis. Consistent with this finding, the msgB null allele mutant is viable only when the growth medium is supplemented with diaminopimelic acid. These results suggest that GrpE may have a previously unsuspected function(s) in cell wall biosynthesis in E. coli.

Cloning, sequencing, and molecular analysis of the dnaK locus from Bacillus subtilis

By using an internal part of the dnaK gene from Bacillus megaterium as a probe, a 5.2-kb HindIII fragment of chromosomal DNA of Bacillus subtilis was cloned. Downstream sequences were isolated by in vivo chromosome walking. Sequencing of 5,085 bp revealed four open reading frames in the order orf39-grpE-dnaK-dnaJ. orf39 encodes a 39-kDa polypeptide of unknown biological function with no noticeable homology to any other protein within the data bases. Alignment of the GrpE protein with those of three other bacterial species revealed a low overall homology, but a higher homology restricted to two regions which might be involved in interactions with other proteins. Alignment of the DnaK protein with six bacterial DnaK polypeptides revealed that a contiguous region of 24 amino acids is absent from the DnaK proteins of all known gram-positive species. Primer extension studies revealed three potential transcription start sites, two preceding orf39 (S1 and S2) and a third one in front of grpE (S3). S2 and S3 were activated at a high temperature. Northern (RNA) analysis led to the detection of three mRNA species of 4.9, 2.6, and 1.5 kb. RNA dot blot experiments revealed an at-least-fivefold increase in the amount of specific mRNA from 0 to 5 min postinduction and then a rapid decrease. A transcriptional fusion between dnaK and the amyL reporter gene exhibited a slight increase in alpha-amylase activity after heat induction. A 9-bp inverted repeat was detected in front of the coding region of orf39. This inverted repeat is present in a number of other heat shock operons in other microorganisms ranging from cyanobacteria to mycobacteria. The biological property of this inverted repeat as a putative key element in the induction of heat shock genes is discussed. The dnaK locus was mapped at about 223 degrees on the B. subtilis genetic map.

Alp, a suppressor of lon protease mutants in Escherichia coli

Escherichia coli lon mutants lack a major ATP-dependent protease, are sensitive to UV light and methylmethane sulfonate (MMS), and overproduce capsular polysaccharide. Evidence is presented that an activity (Alp), cloned on a multicopy plasmid, can suppress the phenotypes of lon mutants. The sensitivity to UV and MMS is a reflection of the stabilization of the cell division inhibitor SulA, while the capsule overproduction arises through the stabilization of a transcriptional activator of capsule biosynthetic genes, RcsA. Multicopy alp (pAlp) suppressed capsule formation in delta lon cells, and delta lon cells containing the pAlp plasmid were resistant to MMS treatment. The MMS resistance of delta lon pAlp+ cells correlates with an increase in the degradation of SulA to that found in lon+ cells. Lon-directed degradation of SulA was energy dependent, as was the increase in degradation of SulA in delta lon pAlp+ cells. alp maps close to pheA, at 57 min on the E. coli chromosome. Although pAlp can substitute for Lon, cells lacking alp activity did not have the phenotype on a lon mutant. This study demonstrates that at least one activity, when overproduced in the cell, can substitute for Lon protease.

The heat-shock-regulated grpE gene of Escherichia coli is required for bacterial growth at all temperatures but is dispensable in certain mutant backgrounds

Previous work has established that the grpE+ gene product is a heat shock protein that is essential for bacteriophage lambda growth at all temperatures and for Escherichia coli growth at temperatures above 43 degrees C. Here it is shown that the grpE+ gene product is essential for bacterial viability at all temperatures. The strategy required constructing a grpE deletion derivative carrying a selectable chloramphenicol drug resistance marker provided by an omega insertion and showing that this deletion construct can be crossed into the bacterial chromosome if and only if a functional grpE+ gene is present elsewhere in the same cell. As a control, the same omega insertion could be placed immediately downstream of the grpE+ coding sequence without any observable effects on host growth. This result demonstrates that the inability to construct a grpE-deleted E. coli strain is not simply due to a lethal polar effect on neighboring gene expression. Unexpectedly, it was found that the grpE deletion derivative could be crossed into the bacterial chromosome in a strain that was defective in DnaK function. Further analysis showed that it was not the lack of DnaK function per se that allowed E. coli to tolerate a deletion in the grpE+ gene. Rather, it was the presence of unknown extragenic suppressors of a dnaK mutation that somehow compensated for the deficiency in both DnaK and GrpE function.

Sequence analysis and transcriptional regulation of the Escherichia coli grpE gene, encoding a heat shock protein

We have sequenced the Escherichia coli grpE gene and shown that it encodes a 197-amino acid residue protein of 21,668-Mr. The predicted N-terminal amino acid sequence, as well as the overall amino acid composition agree well with that of the purified protein. From Northern analysis, we have shown that transcription of the grpE gene is under heat shock regulation, i.e., there is a rapid and transient increase in the rate of synthesis of grpE mRNA upon a shift-up in temperature. Forty-six bases upstream of the structural gene is a sequence closely related to the consensus heat shock promoter identified by Cowing et al. [Proc. Natl. Acad. Sci. U.S.A, 82, 2679-2683]. We have shown by S1 mapping and RNA sequencing that this is indeed the promoter for the grpE mRNA. It appears that all discernable transcription initiates only from this promoter, even under non-heat shock conditions.

Induction of the heat shock regulon of Escherichia coli markedly increases production of bacterial viruses at high temperatures

Production of bacteriophages T2, T4, and T6 at 42.8 to 44 degrees C was increased from 8- to 260-fold by adapting the Escherichia coli host (grown at 30 degrees C) to growth at the high temperature for 8 min before infection; this increase was abolished if the host htpR (rpoH) gene was inactive. Others have shown that the htpR protein increases or activates the synthesis of at least 17 E. coli heat shock proteins upon raising the growth temperature above a certain level. At 43.8 to 44 degrees C in T4-infected, unadapted cells, the rates of RNA, DNA, and protein synthesis were about 100, 70, and 70%, respectively, of those in T4-infected, adapted cells. Production of the major processed capsid protein, gp23, was reduced significantly more than that of most other T4 proteins in unadapted cells relative to adapted cells. Only 4.6% of the T4 DNA made in unadapted cells was resistant to micrococcal nuclease, versus 50% in adapted cells. Thus, defective maturation of T4 heads appears to explain the failure of phage production in unadapted cells. Overproduction of the heat shock protein GroEL from plasmids restored T4 production in unadapted cells to about 50% of that seen in adapted cells. T4-infected, adapted E. coli B at around 44 degrees C exhibited a partial tryptophan deficiency; this correlated with reduced uptake of uracil that is probably caused by partial induction of stringency. Production of bacteriophage T7 at 44 degrees C was increased two- to fourfold by adapting the host to 44 degrees C before infection; evidence against involvement of the htpR (rpoH) gene is presented. This work and recent work with bacteriophage lambda (C. Waghorne and C.R. Fuerst, Virology 141:51-64, 1985) appear to represent the first demonstrations for any virus that expression of the heat shock regulon of a host is necessary for virus production at high temperature.

Identification and characterization of mutations in Escherichia coli that selectively influence the growth of hybrid lambda bacteriophages carrying the immunity region of bacteriophage P22

Mutations in two Escherichia coli genes, sipA and sipB, result in a specific inhibition of the growth of certain hybrid lambdoid bacteriophages, lambda immP22, that have the early regulatory regions and adjacent genes from bacteriophage P22. The sipB391 mutation maps near minute 56 and exerts the strongest inhibitory effect on the growth of the hybrid phages. The sipA1 mutation maps near minute 72 and plays an auxiliary role: enhancing the action of sipB391. Such a role is not limited to sipA1, since there is a similar enhancement by the nusA1 and nusE71 mutations. The Sip-imposed restriction on the growth of lambda immP22 phages is not observed if the phage carries a mutation in the c1 gene. Perhaps this reflects the fact that the c1 product regulates phage DNA replication and is a major determinant in the decision governing whether the phage takes the lytic or lysogenic pathway. Consistent with this idea is the observation that lambda immP22 DNA replication is severely inhibited in bacteria carrying the sipB391 mutation. It is suggested that sip mutations exaggerate the normal role of c1 in limiting lytic growth. This causes a failure in the expression of sufficient amounts of some or all of the lytic gene products required for phage growth.

Escherichia coli grpE gene codes for heat shock protein B25.3, essential for both lambda DNA replication at all temperatures and host growth at high temperature

We have identified the grpE gene product as the B25.3 heat shock protein of Escherichia coli on the following evidence: (i) a protein similar in size and isoelectric point to B25.3 was induced after infection of UV-irradiated bacteria by lambda grpE+ transducing phage, (ii) mutant phage lambda grpE40, isolated by its inability to propagate on grpE280 bacteria, failed to induce the synthesis of the B25.3 protein, and (iii) lambda grpE+ revertants, derived from phage grpE40 as able to propagate on grpE280 bacteria, simultaneously recovered the ability to induce synthesis of the B25.3 protein. In addition, we show that E. coli bacteria carrying the grpE280 mutation are temperature sensitive for bacterial growth at 43.5 degrees C. Through transductional analysis and temperature reversion experiments, it was demonstrated that the grpE280 mutation is responsible for both the inability of lambda to replicate at any temperature tested and the lack of colony formation at high temperature. At the nonpermissive temperature the rates of synthesis of DNA and RNA were reduced in grpE280 bacteria.

Suppressors of temperature-sensitive mutations in a ribosomal protein gene, rpsL (S12), of Escherichia coli K12

Temperature-sensitive (ts) mutations were isolated within a ribosomal protein gene (rpsL) of Escherichia coli K12. Mutations were mapped by complementation using various transducing phages and plasmids carrying the rpsL gene, having either a normal or a defective promoter for the rpsL operon. One of these mutations, ts118, resulted in a mutant S12 protein which behaved differently from the wild-type S12 on CM-cellulose column chromatography. Suppressors of these ts mutations were isolated and characterized; one was found to be a mutation of a nonribosomal protein gene which was closely linked to the RNAase III gene on the E. coli chromosome. This suppressor, which was recessive to its wild-type allele, was cloned into a transducing phage and mapped finely. A series of cold-sensitive mutations, affecting the assembly of ribosomes at 20 degrees C, was isolated within the purL to nadB region of the E. coli chromosome and one group, named rbaA, mapped at the same locus as the suppressor mutation, showing close linkage to the RNAase III gene.

Isolation of conditionally lethal amber mutations affecting synthesis of the nusA protein of Escherichia coli

Amber mutants (am3 and am4) of Escherichia coli K12 defective in the synthesis of nusA protein (Friedman 1971) were isolated from a strain harboring an amber suppressor (sup-126) that is active only at low temperatures. These mutants grew at low temperature (30 degrees C) but did not grow at temperatures above 38 degrees C. Complementation experiments with plasmids carrying the nusA+ gene and its derivatives or with plasmids carrying the nusA1 or am4 mutation indicated that the mutations am3, am4 and nusA1 affected the same gene function. Analysis of proteins produced by minicells containing a plasmid demonstrated that the plasmid pYN87, which can complement the nusA1 and amber mutations, codes for three bacterial proteins, a truncated nusA gene product (61 K), argG gene product (48 K) and a 21 K dalton protein, and that the am4 mutation affects the synthesis of only NusA protein. lambda Nam7 (and lambda Nam7Nam53) phages could grow on these amber mutants at 32 degrees C but not on the parental strain. Spontaneous temperature-resistant revertants of the amber mutants simultaneously lost the ability to permit lambda Nam7 phage development, indicating that the two phenotypes are due to a single mutation. These results suggest that the nusA gene function is essential for the growth of E. coli, and that the lambda N function is dispensable for phage development if the nusA gene is defective.

Cloning of the nusA gene of Escherichia coli

The EcoRI restriction fragment of wild-type Escherichia coli DNA that can complement the argG mutation was cloned into the EcoRI site on pBR322. The resulting chimeric plasmid (pYN81) contains a 16.0 kilobase fragment and can complement the nusA1 (Friedman 1971) as well as argG mutations. Examination of several deletion derivatives of pYN81 revealed that the activity that complements nusA1 and argG mutations is localized within the 5.3 kilobase segment defined by SalI and BglII sites. When the nusA gene segment was recloned into lambda vector L512, the resulting transducing phages lambda nusA+-1 and lambda nusA+-2 grew normally in nusA1 cells at 40 degrees C or above, unlike the vector phage L512. Proteins encoded by the cloned DNA fragment were examined with minicells containing the chimeric plasmid or UV-irradiated cells infected by the transducing phages. At least six proteins were apparently encoded by the 16.0 kilobase DNA fragment, and genes coding for each of these proteins were localized on the respective restriction segment. One of them with a molecular weight of 64,000 was identified as the nusA gene product. The nusA gene was found to be transcribed counterclockwise with respect to the E. coli genetic map. Endonulease BglII cleaves the gene in the vicinity of the C-terminus, generating a truncated nusA gene product with a molecular weight of 61,000 that can complement the nusA1 mutation.

Intragenic localization of amber and temperature-sensitive rpoD mutations affecting RNA polymerase sigma factor of Escherichia coli

A set of multi-copy plasmids carrying part or all of the rpoD gene of Escherichia coli have been used to localize several amber and temperature-sensitive mutations affecting RNA polymerase sigma factor. In contrast to the plasmid carrying a complete rpoD sequence, plasmids carrying part of rpoD could not complement any of the rpoD mutations tested. However, the mutants harboring some of the latter plasmids produced wild-type recombinants at high frequency, provided that they carry the recA+ gene. The results permitted us to localize the rpoD mutations into one of the three intragenic segments. Thus, the rpoD285(ts) mutation (Harris et al. 1978) was located on the 0.8 kilobase segment defined by the Bg/II and BamHI sites in the middle segment, and the amber mutation rpoD40 (Osawa and Yura 1980) in the N-terminal 0.8 kilobase segment. Four additional amber mutations were also identified and classified into one of the segments of rpoD. It was further revealed that plasmids carrying certain amber mutations (rpoD47 or rpoD63) in the C-terminal segment of rpoD render all rpoD mutants tested (including rpoD47 and rpoD63 mutants themselves) able to grow at the restrictive condition. It is suggested that the enhanced synthesis of incomplete sigma polypeptides encoded by rpoD47 or rpoD63 phenotypically suppresses the defects in sigma function at least partially.

Processing of mRNA by ribonuclease III regulates expression of gene 1.2 of bacteriophage T7

A bacteriophage T7 mutation, HS9, is phenotypically defective in gene 1.2, although it maps outside the gene. The single nucleotide change responsible for the HS9 mutation lies within the RNAase III recognition site immediately following gene 1.2. This RNAase III recognition site, responsible for the processing of the mRNA encoding genes 1.1 and 1.2, contains two cleavage sites, separated by 29 bases. The HS9 mutation prevents cutting by RNAase III at one site in vitro, yielding a mRNA containing an additional 29 bases at its 3' end. The ten second-site reversion mutations of HS9 are all located in the RNAase III recognition site and either restore or eliminate cutting at both sites. RNAase III mutants of Escherichia coli phenotypically suppress the HS9 mutation. We propose that the extra 29 bases at the 3' end of the mRNA hybridize to the ribosome-binding site of gene 1.1; gene 1.1 immediately precedes gene 1.2 on the same mRNA molecule. Such hybridization prevents the initiation of translation of this mRNA containing gene 1.1. A strong polar effect represses the translation of gene 1.2.

Functional cooperation of the dnaE and dnaN gene products in Escherichia coli

A system was designed to isolate second-site intergenic suppressors of a thermosensitive mutation of the dnaE gene of Escherichia coli. The dnaE gene codes for the alpha subunit of DNA polymerase III [McHenry, C. S. & Crow, W. (1979) J. Biol. Chem. 254, 1748-1753]. One such suppressor, named sueA77, was finely mapped and found to be located at 82 min on the E. coli chromosome, between dnaA and recF, and within the dnaN gene [Sakakibara, Y. & Mizukami, T. (1980) Mol. Gen. Genet. 178, 541-553]. The dnaN gene codes for the beta subunit of DNA polymerase III holoenzyme [Burgers, P. M. J., Kornberg, A. & Sakakibara, Y. (1981) Proc. Natl. Acad. Sci. USA 78, 5391-5395]. The sueA77 mutation was trans-dominant over its wild-type allele, and it suppressed different thermosensitive mutations of dnaE with different maximal permissive temperature. These properties were interpreted as providing genetic evidence for interaction of the dnaE and dnaN gene products in E. coli.

Isolation and characterization of specialized transducing lambda phages carrying ribosomal protein genes of Escherichia coli

Specialized transducing lambda phages have been isolated which carry the regions of the Escherichia coli chromosome containing the gene or gene-clusters for ribosomal proteins (r-proteins) S1, S6-S18-L9, S16-L19, and L28-L33. To investigate whether these phages also carry the genes for r-proteins S9, L13, L20, L31 and L34 whose gene locations are not known, cells irradiated with UV light were infected with these phages and the r-proteins synthesized were analyzed by two-dimensional gel electrophoresis. However, no synthesis of these r-proteins was stimulated, indicating that their genes are not located in the neighborhood of any of the above-mentioned genes or gene clusters. It was found that proteins S6 and S18 synthesized in the cells irradiated with UV light were not modified under these conditions in which no concomitant ribosome assembly took place.

Genetic fine structure of the pyrE region containing the genes for ribosomal proteins L28 and L33 in Escherichia coli

Temperature-sensitive mutants harbouring alterations in ribosomal proteins L28 and L33 have been isolated and used in mapping the genes coding for the two proteins. It was found that they mapped very close to each other and near pyrE at 80.7 min on the E. coli genetic map. The genes affected by the mutations have been concluded to be the structural genes for proteins L28 (rpmB) and L33 (rpmG) by constructing merodiploids heterozygous for pyrE and for the two ribosomal proteins. Various transduction studies with P1kc phages indicate the gene order in this region to be (rpmB, rpmG)-pyrE-spoT-gltC.

Identification of the E. coli dnaJ gene product

We have previously shown that a mutation (groPC259) in the E. coli dnaJ gene renders the cell inviable at high temperatures and arrests bacteriophage lambda DNA replication at all temperatures (Sunshine et al., 1977). We have isolated lambda dnaJ+ transducing phages both by in vitro cloning and by abnormal excision of a lambda dnaK transducing phage integrated near the dnaJ locus. The dnaJ gene product has been identified on SDS polyacrylamide gels after infection of UV-irradiated E. coli cells by lambda dnaJ+ derivative phages. It is a polypeptide chain with an apparent molecular weight of 37,000-daltons. This has been verified by the fact that a transducing phage carrying an amber mutation in the dnaJ gene fails to induce the synthesis of the 37,000-dalton polypeptide chain upon infection of sup+ bacteria, but does so upon infection of supF or supD bacteria.

Identification of the C. coli dnaK (groPC756) gene product

The E. coli dnaK (groPC756) gene product is essential for bacteriophage lambda DNA replication. Bacterial DNA segments carrying this gene have been cloned onto a bacteriophage lambda vector. The product of the dnaK gene has been identified on SDS polyacrylamide gels after infection of UV-irradiated E. coli cells. The dnaK gene codes for a polypeptide with an apparent molecular weight of 93,000-Mr. Transducing phages carrying amber mutations in the dnaK gene fail to induce the synthesis of the 93,000-Mr polypeptide chain upon infection of sup+ bacteria, but do so upon infection of supF bacteria. E coli carrying the dnaK756 mutation are, in addition, temperature sensitive for growth at 43 degrees C. It is shown that the dnaK756 mutation results in an overproduction of the dnaK gene product at that temperature.