Nucleotide sequence of the attenuator region of the histidine operon of Escherichia coli K-12

A DMSO-assisted iridium(III) complex as a luminescent "turn-on" sensor for selective detection of L-histidine and bacterial imaging

Histidine (His) is a semi-essential amino acid and a unique key neurotransmitter involved in numerous physiological processes. An excessive or deficient amount of His in the body can lead to various related diseases. However, since the chemical structures of L-His and its metabolites (such as histamine (Ha), imidazole-4-acetate (ImA), etc.) are very similar, simple and efficient selective detection of L-His and its related metabolites is of great importance but remains a great challenge. Herein, we successfully designed and synthesized a DMSO-assisted iridium(III) complex (Ir1-DMSO), which can be applied as a "turn-on" photoluminescence (PL) probe for the selective detection and quantification of L-His/Ha. More importantly, Ir1-DMSO exhibited good sensitivity, high selectivity, and anti-interference capability for L-His/Ha/His-containing proteins, which is advantageous due to its simple fabrication and low technical demands. This was attributed to the reaction of Ir1-DMSO with imidazole and amino groups of L-His/Ha. Furthermore, we show the utility of Ir1-DMSO as a PL imaging agent in cultures of E. coli and S. aureus. Considering its diversity of composition and structural flexibility, it can be extended to other solvents and Ir-ligand complexes for various analyses based on specific molecular recognition sensing platforms.

A DnaA-dependent riboswitch for transcription attenuation of the his operon

Transcription attenuation in response to the availability of a specific amino acid is believed to be controlled by alternative configurations of RNA secondary structures that lead to the arrest of translation or the release of the arrested ribosome from the leader mRNA molecule. In this study, we first report a possible example of the DnaA-dependent riboswitch for transcription attenuation in Escherichia coli. We show that (i) DnaA regulates the transcription of the structural genes but not that of the leader hisL gene; (ii) DnaA might bind to rDnaA boxes present in the HisL-SL RNA, and subsequently attenuate the transcription of the operon; (iii) the HisL-SL RNA and rDnaA boxes are phylogenetically conserved and evolutionarily important; and (iv) the translating ribosome is required for deattenuation of the his operon, whereas tRNAHis strengthens attenuation. This mechanism seems to be phylogenetically conserved in Gram-negative bacteria and evolutionarily important.

Riboregulation in bacteria: From general principles to novel mechanisms of the trp attenuator and its sRNA and peptide products

Gene expression strategies ensuring bacterial survival and competitiveness rely on cis- and trans-acting RNA-regulators (riboregulators). Among the cis-acting riboregulators are transcriptional and translational attenuators, and antisense RNAs (asRNAs). The trans-acting riboregulators are small RNAs (sRNAs) that bind proteins or base pairs with other RNAs. This classification is artificial since some regulatory RNAs act both in cis and in trans, or function in addition as small mRNAs. A prominent example is the archetypical, ribosome-dependent attenuator of tryptophan (Trp) biosynthesis genes. It responds by transcription attenuation to two signals, Trp availability and inhibition of translation, and gives rise to two trans-acting products, the attenuator sRNA rnTrpL and the leader peptide peTrpL. In Escherichia coli, rnTrpL links Trp availability to initiation of chromosome replication and in Sinorhizobium meliloti, it coordinates regulation of split tryptophan biosynthesis operons. Furthermore, in S. meliloti, peTrpL is involved in mRNA destabilization in response to antibiotic exposure. It forms two types of asRNA-containing, antibiotic-dependent ribonucleoprotein complexes (ARNPs), one of them changing the target specificity of rnTrpL. The posttranscriptional role of peTrpL indicates two emerging paradigms: (1) sRNA reprograming by small molecules and (2) direct involvement of antibiotics in regulatory RNPs. They broaden our view on RNA-based mechanisms and may inspire new approaches for studying, detecting, and using antibacterial compounds. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.

Reframing gene essentiality in terms of adaptive flexibility

BACKGROUND

Essentiality assays are important tools commonly utilized for the discovery of gene functions. Growth/no growth screens of single gene knockout strain collections are also often utilized to test the predictive power of genome-scale models. False positive predictions occur when computational analysis predicts a gene to be non-essential, however experimental screens deem the gene to be essential. One explanation for this inconsistency is that the model contains the wrong information, possibly an incorrectly annotated alternative pathway or isozyme reaction. Inconsistencies could also be attributed to experimental limitations, such as growth tests with arbitrary time cut-offs. The focus of this study was to resolve such inconsistencies to better understand isozyme activities and gene essentiality.

RESULTS

In this study, we explored the definition of conditional essentiality from a phenotypic and genomic perspective. Gene-deletion strains associated with false positive predictions of gene essentiality on defined minimal medium for Escherichia coli were targeted for extended growth tests followed by population sequencing and transcriptome analysis. Of the twenty false positive strains available and confirmed from the Keio single gene knock-out collection, 11 strains were shown to grow with longer incubation periods making these actual true positives. These strains grew reproducibly with a diverse range of growth phenotypes. The lag phase observed for these strains ranged from less than one day to more than 7 days. It was found that 9 out of 11 of the false positive strains that grew acquired mutations in at least one replicate experiment and the types of mutations ranged from SNPs and small indels associated with regulatory or metabolic elements to large regions of genome duplication. Comparison of the detected adaptive mutations, modeling predictions of alternate pathways and isozymes, and transcriptome analysis of KO strains suggested agreement for the observed growth phenotype for 6 out of the 9 cases where mutations were observed.

CONCLUSIONS

Longer-term growth experiments followed by whole genome sequencing and transcriptome analysis can provide a better understanding of conditional gene essentiality and mechanisms of adaptation to such perturbations. Compensatory mutations are largely reproducible mechanisms and are in agreement with genome-scale modeling predictions to loss of function gene deletion events.

Transcriptional Interference in Convergent Promoters as a Means for Tunable Gene Expression

An important goal of synthetic biology involves the extension and standardization of novel biological elements for applications in medicine and biotechnology. Transcriptional interference, occurring in sets of convergent promoters, offers a promising mechanism for building elements for the design of tunable gene regulation. Here, we investigate the transcriptional interference mechanisms of antisense roadblock and RNA polymerase traffic in a set of convergent promoters as novel modules for synthetic biology. We show examples of elements, including antisense roadblock, relative promoter strengths, interpromoter distance, and sequence content that can be tuned to give rise to repressive as well as cooperative behaviors, therefore resulting in distinct gene expression patterns. Our approach will be useful toward engineering new biological devices and will bring new insights to naturally occurring cis-antisense systems. Therefore, we are reporting a new biological tool that can be used for synthetic biology.

Biosynthesis of Histidine

The biosynthesis of histidine in Escherichia coli and Salmonella typhimurium has been an important model system for the study of relationships between the flow of intermediates through a biosynthetic pathway and the control of the genes encoding the enzymes that catalyze the steps in a pathway. This article provides a comprehensive review of the histidine biosynthetic pathway and enzymes, including regulation of the flow of intermediates through the pathway and mechanisms that regulate the amounts of the histidine biosynthetic enzymes. In addition, this article reviews the structure and regulation of the histidine (his) biosynthetic operon, including transcript processing, Rho-factor-dependent "classical" polarity, and the current model of his operon attenuation control. Emphasis is placed on areas of recent progress. Notably, most of the enzymes that catalyze histidine biosynthesis have recently been crystallized, and their structures have been determined. Many of the histidine biosynthetic intermediates are unstable, and the histidine biosynthetic enzymes catalyze some chemically unusual reactions. Therefore, these studies have led to considerable mechanistic insight into the pathway itself and have provided deep biochemical understanding of several fundamental processes, such as feedback control, allosteric interactions, and metabolite channeling. Considerable recent progress has also been made on aspects of his operon regulation, including the mechanism of pp(p)Gpp stimulation of his operon transcription, the molecular basis for transcriptional pausing by RNA polymerase, and pathway evolution. The progress in these areas will continue as sophisticated new genomic, metabolomic, proteomic, and structural approaches converge in studies of the histidine biosynthetic pathway and mechanisms of control of his biosynthetic genes in other bacterial species.

Histidine biosynthesis, its regulation and biotechnological application in Corynebacterium glutamicum

l-Histidine biosynthesis is an ancient metabolic pathway present in bacteria, archaea, lower eukaryotes, and plants. For decades l-histidine biosynthesis has been studied mainly in Escherichia coli and Salmonella typhimurium, revealing fundamental regulatory processes in bacteria. Furthermore, in the last 15 years this pathway has been also investigated intensively in the industrial amino acid-producing bacterium Corynebacterium glutamicum, revealing similarities to E. coli and S. typhimurium, as well as differences. This review summarizes the current knowledge of l-histidine biosynthesis in C. glutamicum. The genes involved and corresponding enzymes are described, in particular focusing on the imidazoleglycerol-phosphate synthase (HisFH) and the histidinol-phosphate phosphatase (HisN). The transcriptional organization of his genes in C. glutamicum is also reported, including the four histidine operons and their promoters. Knowledge of transcriptional regulation during stringent response and by histidine itself is summarized and a translational regulation mechanism is discussed, as well as clues about a histidine transport system. Finally, we discuss the potential of using this knowledge to create or improve C. glutamicum strains for the industrial l-histidine production.

Two ATP phosphoribosyltransferase isozymes of Geobacter sulfurreducens contribute to growth in the presence or absence of histidine and under nitrogen fixation conditions

Bacteria of the Geobacter clade possess two distinct ATP phosphoribosyltransferases encoded by hisG(L) and hisG(S)+hisZ to catalyze the first reaction of histidine biosynthesis. This very unusual redundancy was investigated by mutational analysis. The hisG(L), hisG(S), and hisZ genes of Geobacter sulfurreducens were deleted, effects on growth and histidine biosynthesis gene expression were evaluated, and deficiencies were complemented with plasmid-borne genes. Both hisG(L) and hisG(S)+hisZ encode functional ATP phosphoribosyltransferases. However, deletion of hisG(L) resulted in no growth defect, whereas deletion of hisG(S) delayed growth when histidine was not provided. Both deletions increased hisZ transcript abundance, and both ΔhisG(S) and ΔhisZ mutations increased hisG(L) transcript abundance. Growth with HisG(L) alone (due to deletion of either hisG(S) or hisZ) was better under nitrogen fixation conditions than when ammonium was provided. Deletion of hisZ caused growth defects under all conditions tested, with or without exogenous sources of histidine, with different patterns of histidine biosynthesis gene expression under each condition. Taken together, the data indicate that G. sulfurreducens depends primarily on the HisG(S)Z isozyme as an ATP phosphoribosyltransferase in histidine biosynthesis, and for other functions when histidine is available; however, HisG(L) also functions as ATP phosphoribosyltransferase, particularly during nitrogen fixation.

Biosynthesis of Histidine

The biosynthesis of histidine in Escherichia coli and Salmonella typhimurium has been an important model system for the study of relationships between the flow of intermediates through a biosynthetic pathway and the control of the genes encoding the enzymes that catalyze the steps in a pathway. This article provides a comprehensive review of the histidine biosynthetic pathway and enzymes, including regulation of the flow of intermediates through the pathway and mechanisms that regulate the amounts of the histidine biosynthetic enzymes. In addition, this article reviews the structure and regulation of the histidine (his) biosynthetic operon, including transcript processing, Rho-factor-dependent "classical" polarity, and the current model of his operon attenuation control. Emphasis is placed on areas of recent progress. Notably, most of the enzymes that catalyze histidine biosynthesis have recently been crystallized, and their structures have been determined. Many of the histidine biosynthetic intermediates are unstable, and the histidine biosynthetic enzymes catalyze some chemically unusual reactions. Therefore, these studies have led to considerable mechanistic insight into the pathway itself and have provided deep biochemical understanding of several fundamental processes, such as feedback control, allosteric interactions, and metabolite channeling. Considerable recent progress has also been made on aspects of his operon regulation, including the mechanism of pp(p)Gpp stimulation of his operon transcription, the molecular basis for transcriptional pausing by RNA polymerase, and pathway evolution. The progress in these areas will continue as sophisticated new genomic, metabolomic, proteomic, and structural approaches converge in studies of the histidine biosynthetic pathway and mechanisms of control of his biosynthetic genes in other bacterial species.

Dominant lethality by expression of a catalytically inactive class I tRNA synthetase

Alignment-guided mutagenesis was used to create an inactive, but toxic, aminoacyl-tRNA synthetase. An Asp-96-->Ala (D96A) replacement in the nucleotide binding fold of the class I Escherichia coli isoleucyl-tRNA synthetase inactivates the enzyme without disrupting its competence for binding isoleucine tRNA. Expression of plasmid-encoded mutant enzyme in a cell with a wild-type ileS chromosomal allele resulted in cell death. Introduction of a second K732T substitution previously shown to weaken tRNA binding gives an inactive D96A/K732T double mutant. Expression of the double mutant is not lethal to E. coli. D96A but not the double mutant significantly inhibited in vitro charging of isoleucine tRNA by the wild-type enzyme. The results suggest a dominant tRNA binding-dependent arrest of cell growth caused by a reduction in the pool of a specific tRNA. Specific tRNA binding drugs may have therapeutic applications for treatment of microbial pathogens.

Nucleotide sequence, organisation and structural analysis of the products of genes in the nirB-cysG region of the Escherichia coli K-12 chromosome

The DNA sequence and derived amino-acid sequence of a 5618-base region in the 74-min area of the Escherichia coli chromosome has been determined in order to locate the structural gene, nirB, for the NADH-dependent nitrite reductase and a gene, cysG, required for the synthesis of the sirohaem prosthetic group. Three additional open reading frames, nirD, nirE and nirC, were found between nirB and cysG. Potential binding sites on the NirB protein for NADH and FAD, as well as conserved central core and interface domains, were deduced by comparing the derived amino-acid sequence with those of database proteins. A directly repeated sequence, which includes the motif -Cys-Xaa-Xaa-Cys-, is suggested as the binding site for either one [4Fe-4S] or two [2Fe-2S] clusters. The nirD gene potentially encodes a soluble, cytoplasmic protein of unknown function. No significant similarities were found between the derived amino-acid sequence of NirD and either NirB or any other protein in the database. If the nirE open reading frame is translated, it would encode a 33-amino-acid peptide of unknown function which includes 8 phenylalanyl residues. The product of the nirC gene is a highly hydrophobic protein with regions of amino-acid sequence similar to cytochrome oxidase polypeptide 1.

Escherichia coli B/r leuK mutant lacking pseudouridine synthase I activity

Escherichia coli B/r strain EB146 containing mutation leuK16 has elevated levels of enzymes involved in the synthesis of leucine, valine, isoleucine, histidine, and tryptophan (Brown et al., J. Bacteriol. 135:542-550, 1978). We show here that strain EB146 (leuK16) has properties that are similar to those of E. coli and Salmonella typhimurium hisT strains. In tRNA1Leu from both hisT and leuK strains, positions 39 and 41 are uridine residues rather than pseudouridine residues. Furthermore, in tRNA3Leu and tRNA4Leu from a leuK strain, uridine residues at positions 39 and 40, respectively, are unmodified. Pseudouridine synthase I activity is missing in extracts of strain EB146 (leuK16), and extracts of strain EB146 (leuK16) and of a hisT strain do not complement one another in vitro. Four phenotypes of strain EB146 (leuK16), leucine excretion, wrinkled colony morphology, and elevated levels of leu and his enzymes, are complemented by a plasmid having a 1.65-kilobase DNA fragment containing the E. coli K-12 hisT locus. These results indicate that either leuK codes for pseudouridine synthase I (and is thus a hisT locus in reality) or, less likely, it codes for a product that affects the synthesis or activity of pseudouridine synthase I.

Escherichia coli tryptophan operon directs the in vivo synthesis of a leader peptide

Here we report the identification of the Escherichia coli trp leader peptide synthesized in vivo. We identified the peptide in UV-irradiated maxicells by selective labeling with radioactive amino acids which are included in the predicted sequence of this peptide. Our results support the hypothesis that translation of the peptide-coding region of the leader RNA has a role in the mechanism of attenuation of biosynthetic operons in general and in the E. coli trp operon in particular.

Cloning, structure, and expression of the Escherichia coli K-12 hisC gene

We used an expression vector plasmid containing the Escherichia coli K-12 histidine operon regulatory region to subclone the E. coli hisC gene. Analysis of plasmid-coded proteins showed that hisC was expressed in minicells. A protein with an apparent molecular weight of 38,500 was identified as the primary product of the hisC gene. Expression was under control of the hisGp promoter and resulted in very efficient synthesis (over 100-fold above the wild-type levels) of imidazolylacetolphosphate:L-glutamate aminotransferase, the hisC gene product. The complete nucleotide sequence of the hisC gene has been determined. The gene is 1,071 nucleotides long and codes for a protein of 356 amino acids with only one histidine residue.

Regulation of single and multicopy his operons in Escherichia coli

We fused segments of the Escherichia coli his regulatory region to galK in single-copy and multicopy vectors. These fusions demonstrated that (i) derepression of his by histidine starvation is due exclusively to attenuation; (ii) the his promoter is metabolically regulated; and (iii) both regulatory systems operate when the his regulatory region is present on a multicopy plasmid. Thus, there is no evidence for titration of his regulatory elements. Deletions of the his anti-attenuator region, carried on multicopy plasmids, cause low-level galK expression. This expression is not stimulated by histidine starvation, but is growth rate dependent. We replaced the his attenuator with the efficient lambda terminator, to. In the context of the his regulatory region, however, lambda to only partially terminates transcription.

Overproduction of tryptophanyl-tRNA synthetase relieves transcription termination at the Escherichia coli tryptophan operon attenuator

Overproduction of tryptophanyl-tRNA synthetase increased trp operon expression by reducing transcription termination at the trp attenuator. The total cellular level of charged tRNATrp was not affected by increased levels of the synthetase. We propose that excess synthetase binds charged tRNATrp and reduces the concentration available for translation.

Repression is relieved before attenuation in the trp operon of Escherichia coli as tryptophan starvation becomes increasingly severe

Expression of the tryptophan operon of Escherichia coli is regulated over about a 500- to 600-fold range by the combined action of repression and attenuation. Repression regulates transcription initiation in response to variation in the intracellular concentration of tryptophan. Attenuation regulates transcription termination at a site in the leader region of the operon in response to changes in the extent of charging of tRNATrp. We measured repression independently of attenuation to ascertain whether these regulatory mechanisms were used differentially by the bacterium as the severity of tryptophan starvation was increased. We found that repression regulated transcription of the operon over the range from growth with excess tryptophan to growth under moderate tryptophan starvation. By contrast, attenuation (termination control) was not relaxed until tryptophan starvation was in the moderate-to-severe range. Thus, attenuation and repression were used to regulate transcription in response to different degrees of tryptophan deprivation. Consistent with this conclusion is the observation that when tryptophan starvation was sufficient to relieve repression 50 to 60%, 65% of the tRNATrp of the bacterium was charged. These findings provide a possible explanation for the existence of only two tryptophan codons in the coding region for the trp leader peptide of Enterobacteriaceae.

Use of complementary DNA oligomers to probe trp leader transcript secondary structures involved in transcription pausing and termination

DNA oligomers were synthesized that are perfectly complementary to different segments of the tryptophan (trp) operon leader transcript. These 15 nucleotide long oligomers were used as probes of the involvement of transcript secondary structures in two processes: transcription pausing at the pause site located near base pair 90 in the leader region, and transcription termination at the attenuator. The 15-mers were complementary to the four segments of the trp leader transcript which have been shown to form the alternative secondary structures that are believed to be responsible for pausing, termination, and antitermination. Oligomers complementary to RNA segments 1 and 3 relieved termination while the 15-mer complementary to RNA segment 1 relieved pausing. 15-mers complementary to segment 2 had no effect on pausing and the oligomer complementary to segment 4 had virtually no effect on termination.

Histidine operon control region of Klebsiella pneumoniae: analysis with an Escherichia coli promoter-probe plasmid vector

The control region for the histidine operon of Klebsiella pneumoniae was cloned and analyzed with the Escherichia coli promoter-probe plasmid pPV33. A restriction fragment which contained the his control region was identified by its ability to activate the tetracycline resistance (Tcr) gene on this vector. Expression of Tcr by bacteria containing the his promoter-active plasmid was found to be under the attenuation control of the his promoter. DNA sequence analysis of the his control region revealed a base sequence homology of approximately 86% of the analogous DNA sequences of E. coli and Salmonella typhimurium. Most of the base alterations in the K. pneumoniae DNA sequence were found to reside in regions flanking the transcriptional and translational regulatory sites.

Effect of dnaA and rpoB mutations on attenuation in the trp operon of Escherichia coli

The rate of synthesis of tryptophan synthetase was found to be increased by heat inactivation of the dnaA protein in three dnaA mutants temperature sensitive for initiation of DNA replication. The effect of the dnaA mutations was dependent upon the presence of an intact attenuator in the tryptophan operon. The activity of the mutated dnaA protein at the tryptophan attenuator and its activity as initiator for chromosome replication decreased gradually with increasing temperature. Two rpoB mutations that suppress the temperature defect of the dnaA46 mutation in initiation of replication were tested for effects on attenuation in the tryptophan operon. One of the rpoB mutations caused increased transcription termination at the attenuator independent of the dnaA allele, whereas the other mutation had no effect. Expression of the histidine and threonine operons, which are also regulated by attenuation, was unaffected by the dnaA mutations.

Structure and function of the internal promoter (hisBp) of the Escherichia coli K-12 histidine operon

The entire histidine operon of Escherichia coli K-12 was cloned in the vector plasmid pBR313, and a complete restriction map of the operon was determined. By using subclones, complementation tests, and enzyme assays, we were able to make a correlation between the physical map and the genetic map of the operon. We determined the sequence of a fragment of DNA 665 base pairs long, comprising the distal portion of the hisC gene, the proximal portion of the hisB gene, and the internal transcription initiation site hisBp. The efficiency of this promoter was assessed under different physiological conditions by cloning the DNA fragment in a recombinant vector system used to study transcriptional regulatory signals. The precise point at which transcription initiates was determined by S1 nuclease mapping.

Evidence that repression mechanisms can exert control over the thr, leu, and ilv operons of Escherichia coli K-12

Mutants of Escherichia coli K-12 resistant to either the threonine analog DL-alpha-amino-beta-hydroxyvaleric acid or the leucine analog 5',5',5'-trifluoro-DL-leucine were isolated. One DL-alpha-amino-beta-hydroxyvaleric acid-resistant mutant strain, designated SP572, constitutively expressed the thr and ilv operons. The mutant allele, avr-16, was localized between trpR and the thr operon at min 0. The wildtype allele of avr-16, designated ileR, is trans dominant. One 5',5',5'-trifluoro-DL-leucine-resistant mutant strain, designated FLR9, expressed the leu and ilv operons constitutively. The mutant allele, flr-9, is linked to entA at min 13. The constitutive expression of the thr, leu, and ilv operons in mutants avr-16 and flr-9 was partly reversed in cells harboring a plasmid, which leads to elevated levels of the trpR gene product, the Trp aporepressor protein. Operator-like sequences situated upstream from the transcription startpoints of the thr, leu, and ilv operons are plausible candidates for targets of systems of repressor-operator control functioning in parallel with attenuation.

In vitro synthesis of the tryptophan operon leader peptides of Escherichia coli, Serratia marcescens, and Salmonella typhimurium

We used an in vitro DNA-dependent protein-synthesizing system to demonstrate de novo synthesis of the leader peptide specified by the tryptophan (trp) operons of several bacterial species. Peptide synthesis was directed by self-ligated short restriction fragments containing the trp promoter and leader regions. Synthesis of leader peptides was established by demonstrating that they were labeled in vitro only by those amino acids predicted to be present in the peptides. Leader peptide synthesis was abolished by the addition of the Escherichia coli trp repressor. The E. coli trp leader peptide was found to be extremely labile in vitro; it had a half-life of 3-4 min. In a highly purified DNA-dependent peptide-synthesizing system, synthesis of the di- and tripeptides predicted from the Salmonella typhimurium trp operon leader sequence, fMet-Ala and fMet-Ala-Ala, also was observed. Using this dipeptide synthesis system, we demonstrated that translation initiation at the ribosome binding site used for trp leader peptide synthesis was reduced 10-fold when the transcript contained a segment complementary to the ribosome binding site.

Transcription termination in vitro at the tryptophan operon attenuator is controlled by secondary structures in the leader transcript

The role of alternative RNA secondary structures in regulating transcription termination at the attenuator of the tryptophan (trp) operon of Serratia marcescens was examined in vitro by transcribing mutant DNA templates having deletions of different segments of the trp leader region. Deletions that removed sequences corresponding to successive segments of postulated RNA secondary structures either increased or decreased transcription termination at the attenuator. The results obtained are consistent with the hypothesis that transcription termination results from RNA polymerase recognition of a particular RNA secondary structure, the terminator. This structure forms only in the absence of an alternative, preceding, RNA secondary structure, the antiterminator.

Effects of the hisT mutation of Salmonella typhimurium on translation elongation rate

The hisT mutation in Salmonella typhimurium which results in loss of pseudouridine base modifications in the anticodon regions of many tRNAs was shown to reduce the rate of protein synthesis in vivo by about 20 to 25% as compared with that measured in hisT strains. Reduced protein synthesis rate occurred predominantly at the level of translation rather than transcription. Increased sensitivity of hisT mutants to growth inhibition by antibiotics that inhibit translation elongation, but not by those that inhibit translation initiation, transcription initiation, or transcription elongation, indicates that the hisT mutation leads to a defect in one or more of the steps in the polypeptide chain elongation mechanism. These results can account for effects of the hisT mutation on regulation of certain amino acid biosynthetic operons, including the his, leu, and ilv operons.

Gene organization in the distal part of the Salmonella typhimurium histidine operon and determination and sequence of the operon transcription terminator

Several transducing phages, carrying different deletions of the Salmonella typhimurium histidine operon were constructed and mapped. These phages were used to obtain fragments of DNA comprising different regions of the operon, which were subcloned in plasmid vectors. The recombinant plasmids allowed the construction of a physical and restriction map of the histidine operon. The presence of the different genes on individual fragments was confirmed by complementation tests. The transcription termination site of the histidine operon has been established by S1 mapping and sequence analysis. The entire operon measures about 7100 base pairs and the last six structural genes are contained in 3450 bases of genetic materials.

Studies on the involvement of the UGA readthrough process in the mechanism of attenuation of the tryptophan operon of Escherichia coli

We asked if UGA suppression by charged tRNATrp, a process called UGA readthrough, is involved in the mechanism of attenuation of the tryptophan (trp) operon in Escherichia coli. For this purpose we used two mutations: strA(LD1) which causes restriction of UGA readthrough, and revA which partially overcomes the restriction of UGA readthrough caused by strA(LD1)(Engelberg-Kulka et al. 1982). trp attenuation was monitored by the regulation of the synthesis of the trp operon enzyme anthranilate synthetase (ASase) in trpR strains. We showed that the strA(LD1) mutation causes a significant increase in the level of synthesis of ASase in the presence of an excess of tryptophan, while the revA mutation reverses this effect, indicating that transcription termination at the trp attenuator site is relieved by restriction of UGA readthrough. Based on our results and the sequence data of the trp leader RNA of E. coli (Oxender et al. 1979), we offer a model for the involvement of the UGA readthrough process in trp attenuation. We suggest that the UGA readthrough process permits trp attenuation to respond to slight changes in the cellular concentration of charged tRNATrp.

Attenuation regulation in the thr operon of Escherichia coli K-12: molecular cloning and transcription of the controlling region

Recombinant plasmids were constructed which carry defined regions of the threonine (thr) operon regulatory region of Escherichia coli. In vitro transcription experiments utilizing plasmid or restriction fragment templates showed that two major RNA transcripts, which differ in length by one to a few bases, are transcribed from this region. The approximate length of the transcripts is 150 to 170 bases, and the site(s) of termination is near or within the thr attenuator. The efficiency of termination at the thr operon attenuator in vitro is approximately 90%. A regulatory mutation, thr79-20, which is a G-C insertion in the attenuator, reduces the frequency of transcription termination to 75%. In addition, in vivo RNA transcripts were identified which hybridize to the thr operon regulatory region. These transcripts appeared to be identical to the two major in vitro transcripts as judged by their mobilities on 8% polyacrylamide-8 M urea gels. This result indicates that the thr operon regulatory region is transcribed in vivo and that termination occurs near or within the thr attenuator.

Cloning and expression of the distal portion of the histidine operon of Escherichia coli K-12

The operator-distal genes hisBHAFI(E) of the Escherichia coli K-12 histidine operon were mapped on a DNA fragment 4,500 base pairs long. This fragment, originally present in a lambda transducing phage, was cloned in the vector plasmid pBR313. A restriction map was determined, allowing identification of the orientation of the genes in the fragment. The cloned genes were expressed in appropriate hosts, independent of the orientation of the DNA fragment, as shown by transformation tests and by enzyme assays of one of the gene products, hisB, histidinol phosphatase. An internal transcription initiation site was identified by isolation of the cellular RNA, hybridization to specific DNA probes, and mapping by S1 nuclease.

Translational attenuation of ermC: a deletion analysis

ermC is a plasmid gene which specifies resistance to macrolide-lincosamide-streptogramin B antibiotics. The product of ermC was previously shown to be an inducible rRNA methylase, which is regulated translationally, and a mechanism for this regulation, termed the translational attenuation model, has been proposed. This model postulates that alternative inactive and active conformational states of the ermC mRNA are modulated by erythromycin-induced ribosome-stalling during translation of a leader peptide. In the present study the translational attenuation model was tested by constructing a series of deletants missing the ermC promoter and portions of the regulatory (leading) region. In these mutants, ermC transcription is dependent on fusion to an upstream promoter. Depending on the terminus of each deletion within the regulatory region, determined by DNA sequencing, ermC expression is observed to be either high level and inducible (like the wild-type), high level and noninducible, or low level and noninducible. The translational attenuation model predicts that as the deletions extend deeper into the leader region, successively masking and unmasking sequences required for translation of the methylase, an alternation of high and low level methylase expression will be observed. These predictions are confirmed. Based on this and other information, the model is refined and extended, and both direct translational activation and kinetic trapping of a metastable active intermediate during transcription are proposed to explain basal synthesis of methylase and to rationalize the effects of certain regulatory mutants.

Characterization of translational initiation sites in E. coli

We characterize the Shine and Dalgarno sequence of 124 known gene beginnings. This information is used to make "rules" which help distinguish gene beginning from other sites in a library of over 78,000 bases of mRNA. Gene beginnings are found to have information besides the initiation codon and Shine and Dalgarno sequence which can be used to make better "rules".

Strains of Escherichia coli carrying the structural gene for histidyl-tRNA synthetase on a high copy-number plasmid

That portion of the Escherichia coli chromosome carried by a number of lambda transducing phages, all of which carry the gua operon, was mapped using restriction endonucleases. The DNA from one of these transducing phages was subcloned onto pBR322. We have identified two recombinant plasmids which carry the Escherichia coli gene hisS, the structural gene for histidyl-tRNA synthetase. The two plasmids, pSE301 and pSE401, have in common a 3,540 bp fragment of E. coli DNA which is bounded by BglII and SalI restriction endonuclease recognition sites. Strains carrying these plasmids overproduce histidyl-tRNA synthetase 20 to 30 fold. The growth rate of these strains is not affected although the histidine biosynthetic enzymes are derepressed. This derepression seems to be in addition to that caused by introduction of a hisT mutation on the chromosome.

The DNA sequence of the promoter-attenuator of the ilvGEDA operon of Salmonella typhimurium

The isolation of a lambda gt . ilvGEDA . S.t. hybrid transducing phage has permitted the characterization of the promoter-attenuator region of the ilvGEDA operon of Salmonella typhimurium. In vitro transcription and Southern hybridization indicate that the promoter-attenuator resides on a 400 nucleotide Rsa I restriction fragment. DNA sequence analysis shows only seven base pair differences exist between the DNA sequence of the ilvGEDA promoter-attenuator of S. typhimurium and that previously published for Escherichia coli K12.

Genetic analysis of a temperature-sensitive Salmonella typhimurium rho mutant with an altered rho-associated polycytidylate-dependent adenosine triphosphatase activity

A conditional-lethal rho mutant of Salmonella typhimurium LT2 has been isolated. The mutation was selected as a suppressor of the polarity of an insertion sequence (IS)2-induced mutation (gal3) carried on an F' plasmid. In addition to suppression of IS2-induced polarity, the rho-111 mutation suppressed nonsense and frameshift polarity. The rho-associated polycytidylic acid-dependent adenosine triphosphatase activity in the mutant strain was elevated 15-fold above that in the parental strain, and the mutant rho protein was thermally unstable. A temperature-resistant revertant of the mutant strain did not suppress polarity and contained normal levels of polycytidylic acid-dependent adenosine triphosphatase, suggesting that the phenotype of the rho-111-bearing strain is the consequence of a single mutation. The rho-111 mutation was located on the S. typhimurium linkage map midway between the ilv and cya loci by phage P22 cotransduction studies. F' plasmid maintenance was not impaired in the mutant strain, and the mutation was recessive to the wild-type allele. The rho-111 mutation did not alter in vivo expression of either the tryptophan or histidine operons.

An aminoacyl tRNA synthetase binds to a specific DNA sequence and regulates its gene transcription

Alanine tRNA synthetase represses transcription of its own gene by binding specifically to a palindromic sequence which flanks the gene's transcription start site. Transcription repression is greatly enhanced by elevated concentrations of the cognate amino acid. The amino acid effect is caused by direct association of the ligand with the synthetase, which in turn mediates tighter binding to the DNA.

Identification, nucleotide sequence and expression of the regulatory region of the histidine operon of Escherichia coli K-12

A restriction fragment has been isolated and its nucleotide sequence determined. This fragment contains sites for RNA polymerase binding, initiation and termination of transcription of the Escherichia coli histidine operon. In vitro transcription of plasmids containing this region generates one single histidine-specific, attenuated, small RNA: the leader RNA. This RNA is more efficiently transcribed when the template DNA is supercoiled. Another promoter was identified on the same fragment of deoxyribonucleic acid by in vitro transcription, DNA sequencing and RNA polymerase binding. Both promoters, transcribing in opposite direction, are very A-T rich and are separated by a G-C rich region containing a palyndromic structure.

In vivo and in vitro detection of the leader RNA of the histidine operon of Escherichia coli K-12

The DNA of the attenuator region of the histidine operon of Escherichia coli has been transcribed in a purified in vitro system and found to synthesize two major RNA transcripts. The first one, 180 nucleotides long, has been identified as the histidine-specific leader RNA. It contains the coding sequence for the leader peptide [Di Nocera, P. P., Blasi, F., Di Lauro, R., Frunzio, R. & Bruni, C. B. (1978) Proc. Natl. Acad. Sci. USA 75, 4276-4280] and is terminated at the attenuator site. Termination of transcription at this site is extremely efficient in the in vitro system. The leader RNA also has been detected in vivo in a minicell producer strain transformed with plasmids harboring the regulatory region of the histidine operon of E. coli. A second RNA molecule is synthesized in the in vitro system. It has a divergent direction of transcription with respect to the histidine leader RNA, but its role, if any, in the regulation of the histidine operon remains to be ascertained. The existence of the histidine leader RNA lends support to the regulatory mechanism which postulates that regulation of the histidine operon is dependent on the alternative secondary structures that the leader RNA may assume, depending on whether or not the histidine-rich leader peptide is translated.

Attenuation in the control of expression of bacterial operons

Bacterial operons concerned with the biosynthesis of amino acids are often controlled by a process of attenuation. The translation product of the initial segment of the transcript of each operon is a peptide rich in the amino acid that the particular operon controls. If the amino acid is in short supply translation is stalled at the relevant codons of the transcript long enough for the succeeding segment of the transcript to form secondary structures that allow the transcribing RNA polymerase molecule to proceed through a site that otherwise dictates termination of transcription. This site is the attenuator; the process is attenuation.

Regulation of aromatic amino acid transport by tRNA: role of 2-methylthio-N6-(delta2-isopentenyl)-adenosine

E. coli growing rapidly in media where ferric iron is not freely available contain a population of specifically undermodified tRNAs. These tRNAs contain isopentenyl adenosine instead of the usual methylthioisopentenyl adenosine adjacent to the 3' end of the anticodon. Iron restricted E. coli also show an enhanced capacity to transport aromatic amino acids into the cell. Our work shows that undermodified tRNAs for phe, tyr and trp can function as positive regulatory elements of the aromatic amino acid transport system in E. coli. This iron related metabolic control, mediated through a specific post-transcriptional modification of the tRNAs, may be an important mechanism for adapting E. coli for growth in an iron restricted environment.