Regulation of ilvEDA expression occurs upstream of ilvG in Escherichia coli: additional evidence for an ilvGEDA operon

Small stress response proteins in Escherichia coli: proteins missed by classical proteomic studies

Proteins of 50 or fewer amino acids are poorly characterized in all organisms. The corresponding genes are challenging to reliably annotate, and it is difficult to purify and characterize the small protein products. Due to these technical limitations, little is known about the abundance of small proteins, not to mention their biological functions. To begin to characterize these small proteins in Escherichia coli, we assayed their accumulation under a variety of growth conditions and after exposure to stress. We found that many small proteins accumulate under specific growth conditions or are stress induced. For some genes, the observed changes in protein levels were consistent with known transcriptional regulation, such as ArcA activation of the operons encoding yccB and ybgT. However, we also identified novel regulation, such as Zur repression of ykgMO, cyclic AMP response protein (CRP) repression of azuC, and CRP activation of ykgR. The levels of 11 small proteins increase after heat shock, and induction of at least 1 of these, YobF, occurs at a posttranscriptional level. These results show that small proteins are an overlooked subset of stress response proteins in E. coli and provide information that will be valuable for determining the functions of these proteins.

Linkage map of Escherichia coli K-12, edition 10: the traditional map

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.

The absence of branched-chain amino acid and growth rate control at the internal ilvEp promoter of the ilvGMEDA operon

The question of whether the promoter ilvEp, located in the coding region of ilvM, the second structural gene in the ilvGMEDA operon, is subject to either amino acid- or growth rate-mediated regulation is examined. The experiments described here were performed with ilvEp-cat and ilvEp-lac fusions carried as single copies on the chromosome. The activity of the ilvEp promoter was found to respond neither to the availability of branched-chain amino acids nor to a wide range of growth rates between 35 to 390 min. In the absence of any known role for the products of the ilvGMEDA operon when repressing levels of branched-chain amino acids are present, there appears to be only a gratuitous role for the transcription at ilvEp.

Specificity of attenuation control in the ilvGMEDA operon of Escherichia coli K-12

Three different approaches were used to examine the regulatory effects of the amino acids specified by the peptide-coding region of the leader transcript of the ilvGMEDA operon of Escherichia coli K-12. Gene expression was examined in strains carrying an ilvGMED'-lac operon fusion. In one approach, auxotrophic derivatives were starved of single amino acids for brief periods, and the burst of beta-galactosidase synthesis upon adding the missing amino acid was determined. Auxotrophic derivatives were also grown for brief periods with a limited supply of one amino acid (derepression experiments). Finally, prototrophic strains were grown in minimal medium supplemented with single and multiple supplements of the chosen amino acids. Although codons for arginine, serine, and proline are interspersed among the codons for the three branched-chain (regulatory) amino acids, they appeared to have no effect when added in excess to prototrophs or when supplied in restricted amounts to auxotrophs. Deletions removing the terminator stem from the leader removed all ilv-specific control, indicating that the attenuation mechanism is the sole mechanism for ilv-specific control.

Physical identification of an internal promoter, ilvAp, in the distal portion of the ilvGMEDA operon

It has been previously demonstrated that the ilvGMEDA operon is expressed in vivo from the promoters ilvGp2 and ilvEp. An additional internal promoter is identified and designated ilvAp. This internal promoter, which allows independent expression of ilvA, has been analyzed both in vivo and in vitro. Our results indicate that: (1) ilvAp exists in both Escherichia coli K-12 and Salmonella typhimurium, as demonstrated by fusion to the galK reporter gene; (2) ilvAp is located in the distal coding sequence of ilvD; (3) the ilvAp sequences are not identical for these two bacterial species; (4) transcription from ilvAp of E. coli K-12 was demonstrated; (5) expression from ilvAp responds to the availability of oxygen; (6) potential 3' 5'-cyclic AMP receptor protein binding sites exist adjacent to ilvAp.

Translational coupling between the ilvD and ilvA genes of Escherichia coli

The hypothesis that translation of the ilvD and ilvA genes of Escherichia coli may be linked has been examined in strains in which lacZ-ilvD protein fusions are translated in all three reading frames with respect to ilvD. In these strains, the nucleotide sequence was altered to obtain premature termination of ilvD translation, and in one strain translation termination of ilvD DNA occurred two bases downstream of the ilvA initiation codon. In the wild-type strain, the ilvD translation termination site was located two bases upstream of the ilvA start codon. In each of the mutant strains, expression of ilvA, as determined by the level of threonine deaminase activity, was strikingly lower than in the wild-type strain. The data suggest that expression of ilvD and ilvA is translationally coupled. By inserting a promoterless cat gene downstream of ilvA, it was shown that the differences in enzyme activity were not the result of differences in the amount of ilvA mRNA produced.

DNA replication termination in Escherichia coli parB (a dnaG allele), parA, and gyrB mutants affected in DNA distribution

We investigated the Escherichia coli mutants carrying the parB, parA, and gyrB mutations, all of which display faulty chromosome partitioning at the nonpermissive temperature, to see whether their phenotype reflected a defect in the termination of DNA replication. In the parB strain DNA synthesis slowed down at 42 degrees C and the SOS response was induced, whereas in the parA strain DNA synthesis continued normally for 120 min and there was no SOS induction. To see whether replication forks accumulated in the vicinity of terC at the nonpermissive temperature, the mutants were incubated for 60 min at 42 degrees C and then returned to low temperature and pulse-labeled with [3H]thymidine. In all cases the restriction pattern of the labeled DNA was incompatible with that of the terC region, suggesting that replication termination was normal. In the parA mutant no DNA sequences were preferentially labeled, whereas in the parB and gyrB strains there was specific labeling of sequences whose restriction pattern resembled that of oriC. In the case of parB this was confirmed by DNA-DNA hybridization with appropriate probes. This test further revealed that the parB mutant over initiates at oriC after the return to the permissive temperature. Like dna(Ts) strains, the parB mutant formed filaments at 42 degrees C in the absence of SOS-associated division inhibition, accompanied by the appearance of anucleate cells of nearly normal size (28% of the population after 3 h), as revealed by autoradiography. The DNA in the filaments was either centrally located or distributed throughout. The parB mutation lies at 67 min, and the ParB- phenotype is corrected by a cloned dnaG gene or by a plasmid primase, strongly suggesting that parB is an allele of dnaG, the structural gene of the E. coli primase. It is thus likely that the parB mutant possesses an altered primase which does not affect replication termination but causes a partial defect in replication initiation and elongation and in chromosome distribution.

Examination of the internal promoter, PE, in the ilvGMEDA operon of E. coli K-12

The ilvGMEDA operon of Escherichia coli K-12 contains an internal promoter, PE, in the distal portion of the ilvM gene immediately upstream from the ilvE gene. The location of this promoter was determined using S1 nuclease protection analyses of in vivo and in vitro transcripts. The transcriptional activity of the internal promoter was compared to the transcriptional activity of the operon-proximal promoter P1P2 using transcriptional fusion vectors and plasmid copy number determinations. These measurements showed that the P1P2 promoter is 52-fold stronger than the internal PE promoter. Estimates of the transcriptional role of the internal promoter on ilvE gene expression during growth conditions in excess and limiting branch chain amino acids is presented.

Analysis and comparison of the internal promoter, pE, of the ilvGMEDA operons from Escherichia coli K-12 and Salmonella typhimurium

It was previously determined that the distal portion of the ilvGMEDA operon was expressed despite the insertion of transposons into ilvG and ilvE. This observation suggested the existence of internal promoters upstream of ilvE (pE) and ilvD (pD). The internal promoter pE, responsible for part of ilvEDA expression, has been analyzed both in vivo and in vitro. Our results indicate that: pE exists in both E. coli K-12 and S. typhimurium; pE is located in the distal end of the ilvM coding sequence; the pE sequence is highly conserved in the two bacteria; the amino acid sequence of the ilvM gene product is 93% homologous between the two bacteria; transcription from pE can be demonstrated both in vivo and in vitro; the efficiency of pE is essentially equivalent in the two bacteria.

Comparison of the regulatory regions of ilvGEDA operons from several enteric organisms

The nucleotide sequence preceding the ilvGEDA operon has been examined and compared in five enteric organisms. The sequence in Escherichia coli B was identical to the earlier-described strain K-12 sequence. The sequences of Salmonella typhimurium and Klebsiella aerogenes were remarkably similar to that of E. coli and identical in that part of the leader region that specified the putative 32-amino-acid peptide. Thus, identical secondary structures could be postulated for the leaders of all three organisms, and regulation of operon expression could be like that postulated earlier for E. coli. Different secondary structures had to be postulated for the leader transcripts of Edwardsiella tarda and Serratia marcescens. Control of attenuation of the operon in these organisms by the level of leucyl tRNA could be explained only if ribosome stalling occurred at a single leucine codon. In both organisms, that single leucine codon is the rarely used CUA rather than the CUG that is in E. coli, S. typhimurium, and K. aerogenes.

Internal promoter in the ilvGEDA transcription unit of Escherichia coli K-12

Segments of the ilvGEDA transcription unit have been cloned into the promoter tester plasmid pMC81. This vector contains cloning sites situated upstream of the lacZ gene coding for beta-galactosidase. Using this method we have quantitatively evaluated in vivo (i) the activity of previously described promoter, pG, preceding ilvG; (ii) the relative activity of pE promoter, previously postulated to be located between ilvG and ilvE; and (iii) the effect of the frameshift site present in the wild-type ilvG gene by comparison with mutant derivatives lacking this frameshift site. Isogenic derivatives of strain MC1000 were constructed by transduction with phage P1 grown on rho-120, delta(ilvGEDA), delta(ilvED), and ilvA538 hosts. The potential effects of these alleles that were previously postulated to affect ilvGEDA expression were assessed in vivo by monitoring beta-galactosidase production directed by ilv DNA fragments. Cloned ilv segments were also tested for activity in vitro with a DNA-directed coupled transcription and translation system. The production in vitro of ilv-directed ilv gene expression and beta-galactosidase expression with ara-ilv-lac fusions paralleled the in vivo activity.

Isolation and analysis of two Escherichia coli K-12 ilv attenuator deletion mutants with high-level constitutive expression of an ilv-lac fusion operon

A lysogenizing lambda phage, lambda dilv-lac11, was constructed to carry an ilvD-lac operon fusion. Expression from the phage of the ilvE and lacZ genes is controlled by an intact ilv control region also carried by this phage. Two spontaneous mutants of lambda dilv-lac11 that have high-level constitutive expression of the ilv-lac fusion operon were isolated by growth on a beta-chloroalanine selective medium. The mutants were shown by nucleotide sequence determination to contain large deletions (delta 2216, approximately 1.6 kilobases; delta 2219, approximately 1.9 kilobases), which in both cases remove the proposed ilv attenuator terminator. The rest of the ilv leader and promoter region DNA remains intact in these mutants. Deletion 2216 also removed part of the downstream ilvG gene, whereas delta 2219 extended through the entire ilvG gene into the ilvGE intercistronic region. A possible mechanism of deletion formation is discussed.

Absence of significant membrane localization of the proteins coded by the ilvGEDAC genes of Escherichia coli K-12

We previously characterized a set of lambda dilv phages by genetic, restriction enzyme, and heteroduplex analyses and tentatively correlated isoleucine-valine gene products with specific ilv DNA segments by using cloned ilv segments in maxicells and lambda dilv phage infection of UV-irradiated cells. In this work, the identity of the ilvC gene product, alpha-acetohydroxy acid isomeroreductase, was confirmed by demonstrating its induction by the physiological inducers alpha-acetolactate and alpha-acetohydroxybutyrate. The identity of the ilvE gene product, transaminase, B, was confirmed by antibody precipitation of the purified enzyme. Phage derivatives with ilv regulatory mutations were found to have the predicted effect upon the ilvGEDA and ilvC protein products. The distribution of the ilvGEDA and ilvC gene products in the soluble, periplasmic, inner membrane, and outer membrane fractions was examined, and no significant membrane association was observed. The expression of the ilv genes in the lambda dilv phage from ilv and phage lambda promoters was compared in order to determine the fractional contribution of each to ilv gene expression. An additional protein of 54,000 daltons that was not detected in the previous analysis was observed to be coded by a bacterial gene but was produced only by readthrough from phage promoters.

DNA sequence fine-structure analysis of ilvG (IlvG+) mutations of Escherichia coli K-12

Six ilvG (IlvG+) mutations of Escherichia coli K-12 were transferred to recombinant plasmids, and the DNA sequence of each mutation was determined. This analysis confirmed that expression of the ilvG gene product (acetohydroxy acid synthase II) requires the deletion of a single base pair or the addition of two base pairs within ilvG to displace a frameshift site present in wild-type E. coli K-12. This system should be useful in the analysis of potential frameshift mutagens.

Genetical and structural analysis of a group of lambda ilv and lambda rho transducing phages

Eight lambda ilv C transducing phages generated from E. coli K12 secondary site lysogens have been analysed genetically and physically. Two of them carry, in addition, the rho gene and its promotor region, but not the cya gene. The ilv O 603 mutation has been located between ilv G and ilv E. Electrophoretic analysis of the proteins synthesized by these phages in a system of UV irradiated cells allowed us to assign molecular weights of 55000 and 66000 daltons to the ilv C and the ilv D gene products, respectively, and to show that an ilv G-encoded polypeptide of 60000 daltons is made from an ilv O- but not from an ilv O+ phage. The expression of the ilv G gene is discussed in the light of the recent finding of a promoter-attenuator region lying upstream to ilv G. Finally, we have found that one of the lambda ilv phages does not have the classical structure of a transducing phage.

Mutations in the ilvY gene of Escherichia coli K-12 that cause constitutive expression of ilvC

A derivative of Escherichia coli K-12 bearing an ilvC-lac fusion has been studied. beta-Galactosidase formation in this strain is under the control of the ilvC promoter and is therefore induced by the acetohydroxy acids. Derivatives of this fusion strain were isolated that constitutively expressed beta-galactosidase. When an ilvC-containing episome was introduced into these strains, acetohydroxy acid isomeroreductase was also constitutively expressed. The lesions are trans dominant and lie in ilvY, the structural gene specifying a positive control element, v, needed for induction of the isomeroreductase. It was concluded from measurements of beta-galactosidase levels in various diploid strains that, although wild-type v requires inducer to act as a positive control element, it does not act as a repressor in the absence of inducer.

Organization and regulation of the ilvGEDA operon in Salmonella typhimurium LT2

A total of 102 isoleucine- and isoleucine-valine-requiring (ilv) mutants induced by insertion of the transposable element Tn10 have been classified to cistron by growth requirement, cross-feeding behavior, and enzyme assays. The mutations are in a polycistronic operon transcribed in the order ilvGEDA and in a monocistronic operon ilvC. Analysis of distal gene expression in these polar insertion mutants revealed the existence of two constitutive interval promoters, one preceding ilvE and the other preceding ilvD.

In vitro formation of beta-galactosidase with a template containing the lac genes fused to gene ilvD

An in vitro coupled transcription-translation system was used to synthesize transaminase B and beta-galactosidase in the presence of a deoxyribonucleic acid template containing lac deoxyribonucleic acid under normal lac-specific control and in the presence of several deoxyribonucleic acid templates containing lac deoxyribonucleic acid fused to the ilvD gene. Time course experiments revealed that transcription of the lacZ gene from the fusion template required a longer time than did that initiated at the lac promoter. With a phage template containing an intact ilvE gene but lacking the normal ilv-specific promoter, synthesis of ilvE message was completed before synthesis of lacZ message. A phage template that contained the normal ilv-specific promoter but from which part of ilvE had been deleted also allowed formation of beta-galactosidase. Three plasmids containing the ilv-lac fusion were also used as templates. Two plasmids that contained both an intact ilvE gene and the normal ilv-specific promoter required longer times for lacZ transcription but were more efficient templates than was a plasmid in which the ilv-lac fusion, the ilvE gene, and the contiguous non-specific ilvE promoter were inverted with respect to the normal ilv-specific promoter. beta-Galactosidase synthesis was stimulated by guanosine 3'-pyrophosphate-5'-pyrophosphate with all templates tested except that in which the ilv-lac fusion had been inverted. Presumptive evidence was obtained for the generation of a limiting isoleucine signal by incorporating inhibitors of isoleucyl transfer ribonucleic acid synthetase into the coupled transcription-translation system.