Histidyl-transfer ribonucleic acid synthetase in positive control of the histidine operon in Salmonella typhimurium

Histidyl-tRNA synthetase

Histidyl-tRNA synthetase (HisRS) is responsible for the synthesis of histidyl-transfer RNA, which is essential for the incorporation of histidine into proteins. This amino acid has uniquely moderate basic properties and is an important group in many catalytic functions of enzymes. A compilation of currently known primary structures of HisRS shows that the subunits of these homo-dimeric enzymes consist of 420-550 amino acid residues. This represents a relatively short chain length among aminoacyl-tRNA synthetases (aaRS), whose peptide chain sizes range from about 300 to 1100 amino acid residues. The crystal structures of HisRS from two organisms and their complexes with histidine, histidyl-adenylate and histidinol with ATP have been solved. HisRS from Escherichia coli and Thermus thermophilus are very similar dimeric enzymes consisting of three domains: the N-terminal catalytic domain containing the six-stranded antiparallel beta-sheet and the three motifs characteristic of class II aaRS, a HisRS-specific helical domain inserted between motifs 2 and 3 that may contact the acceptor stem of the tRNA, and a C-terminal alpha/beta domain that may be involved in the recognition of the anticodon stem and loop of tRNA(His). The aminoacylation reaction follows the standard two-step mechanism. HisRS also belongs to the group of aaRS that can rapidly synthesize diadenosine tetraphosphate, a compound that is suspected to be involved in several regulatory mechanisms of cell metabolism. Many analogs of histidine have been tested for their properties as substrates or inhibitors of HisRS, leading to the elucidation of structure-activity relationships concerning configuration, importance of the carboxy and amino group, and the nature of the side chain. HisRS has been found to act as a particularly important antigen in autoimmune diseases such as rheumatic arthritis or myositis. Successful attempts have been made to identify epitopes responsible for the complexation with such auto-antibodies.

Defective regulation of the phenylalanine biosynthetic operon in mutants of the phenylalanyl-tRNA synthetase operon

Among mutants of Escherichia coli resistant to p-fluorophenylalanine (PFP) were some with constitutive expression of the phenylalanine biosynthetic operon (the pheA operon). This operon is repressed in the wild type by phenylalanine. The mutation in three of these mutants mapped in the aroH-aroD region of the E. coli chromosome at 37 min. A plasmid bearing wild-type DNA from this region restored p-fluorophenylalanine sensitivity and wild-type repression of the pheA operon. Analysis of subclones of this plasmid and comparison of its restriction map with published maps indicated that the mutations affecting regulation of the pheA operon lie in the structural genes for phenylalanyl-tRNA synthetase, pheST, probably in pheS. Thus, the pheST operon has a role in the regulation of phenylalanine biosynthesis, the most likely being that wild-type phenylalanyl-tRNA synthetase maintains a sufficient intracellular concentration of Phe-tRNA(Phe) for attenuation of the pheA operon in the presence of phenylalanine. A revised gene order for the 37-min region of the chromosome is reported. Read clockwise, the order is aroD, aroH, pheT, and pheS.

Attenuation control of the Escherichia coli phenylalanyl-tRNA synthetase operon

The pheST operon codes for the two subunits of the essential enzyme phenylalanyl-tRNA synthetase. The nucleotide sequence of the regulatory regions of the operon, in vitro transcription data and in vivo experiments indicate that the operon is controlled by attenuation in a way similar to many amino acid biosynthetic operons. In this work the control of the pheST operon was studied in vivo by measuring the effect of deletions in the regulatory regions on downstream expression. The presence of a strong promoter followed by an approximately 90% efficient terminator in front of the structural parts of the operon is demonstrated. An open reading frame coding for a 14 amino acid long leader peptide containing five phenylalanine residues is located between the promoter and the terminator. The presence of the transcription terminator is shown to be essential to the operon's regulation. The localization of the promoter and the terminator agrees with the results of previous in vitro experiments. It is also shown that about 30% of the transcripts covering the pheST operon come from the upstream gene, rplT, which codes for the ribosomal protein L20. Although cotranscription exists between rplT and pheST, these genes are not systematically coregulated since reducing the translation of rplT about tenfold, does not change pheST expression. The pheST operon is also shown to be derepressed by a cellular excess of phenylalanyl-tRNA synthetase. This derepression is shown to be due to the pheST attenuator.

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.

The leader mRNA of the histidine attenuator region resembles tRNAHis: possible general regulatory implications

The leader region of the mRNA of the his operon is involved in regulating the frequency of transcription termination through attenuation and therefore expression of the his structural genes. We now report that the his leader mRNA has a remarkable sequence homology with the tRNAHis molecule. Of the 75 nucleotides forming tRNAHis (not counting the -CCA tail), 45 are homologous to nucleotide sequences found in the his leader mRNA. This homology extends to secondary structures which can form in the leader mRNA. The stems and loops of tRNAHis are thus related to those of the his leader mRNA which play a critical role in regulating expression of the his operon through attenuation. Many proteins that bind tRNAHis thus might bind to the similar structures found in the his leader mRNA and influence regulation by favoring the attenuator or anti-attenuator configuration. These include tRNA-modifying enzymes, the histidyl-tRNA synthetase, and the hisG enzyme. The significance of similar structures in other regulatory systems is discussed, particularly in relation to the role of tRNA-modifying enzymes as important regulatory molecules in both prokaryotes and eukaryotes.

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.

Factors modulating transcription and translation in vitro of ribosomal protein S20 and isoleucyl-tRNA synthetase from Escherichia coli

The DNA-dependent protein-synthesizing system developed by Zubay [Zubay, G. (1973) Annu. Rev. Genet. 7, 267--287] was optimized for the transcription and translation of genes from the 0.5-min region of the Escherichia coli chromosome carried by transducing lambda phages. The E. coli gene products synthesized were isoleucyl tRNA synthetase, ribosomal protein S20, dihydrodipicolinic acid reductase and (possibly) the two subunits carbamoyl-phosphate synthetase. Formation of ribosomal protein S20 is specifically stimulated by the addition of 16-S rRNA and not by 5-S or 23-S rRNA. 16-S rRNA increases the rate of S20 synthesis, the final yield of product depends on the duration of persistence of the RNA added. Addition of 16-S rRNA to the separate transcription and translation systems showed that it is the translation of the S20 mRNA which is enhanced. Furthermore, S20 synthesis is stimulated more than fourfold when concomitant synthesis of rRNA occurs from a plasmid carrying an rrn transcriptional unit. The results described are explained in terms of a model which suggests that ribosomal protein S20 feedback inhibits its synthesis at the translational level and that removal of S20 into ribosomal assembly (i.e. binding to 16-S rRNA) releases inhibition. The model postulates a direct link between synthesis of ribosomal RNA and ribosomal protein and between the rates of ribosomal assembly and ribosomal protein synthesis. The stimulatory effect of guanosine 3'-diphosphate 5'-diphosphate on isoleucyl-tRNA synthetase formation and its inhibition of the synthesis of ribosomal protein S20 in vitro occurs at the level of transcription. Its relevance in vivo, however, remains to be demonstrated. Formation of isoleucyl-tRNA synthetase in vitro is not influenced either by the addition of a surplus of purified enzyme nor by the limitation of protein synthesis by the addition of anti-(isoleucyl-tRNA synthetase) serum. There is no evidence, therefore, that isoleucyl-tRNA synthetase is autogenously regulated.

Genetic mapping of the Salmonella typhimurium pepB locus

Transposon technology has been used to map the pepB locus of Salmonella typhimurium. This locus is cotransducible by phage P22 with glyA and strB at min 56 on the Salmonella genetic map. The gene order is strB pepB glyA.

Purification and characterization of histidyl-transfer RNA synthetase from Neurospora crassa

Histidyl-tRNA synthetase (L-histidine:tRNAHis ligase (AMP-forming), EC 6.1.1.21) has been purified 921-fold from crude extracts of lyophilized mycelia of Neurospora crassa. Sodium dodecyl sulfate gel electrophoresis at pH 8.9 of the purified enzyme yields one band with an apparent Mr of 62 500. The estimated Mr by Sephadex gel filtration is 125 000. Thus the native histidyl-tRNA synthetase of N. crassa is a dimer, composed of two identical subunits. The Km values determined in the enzyme-catalyzed esterification of [14C]-histidine to tRNAHis are: for histidine, 5.8 x 10(-6 M, for ATP, 5.9 x 10(-4) M, and for tRNAHis, 1.2 x 10(-7) M. Effects of various intermediates of the histidine, tryptophan and arginine biosynthetic pathways on histidyl-tRNA synthetase activity were studied. The Ki values for imidazoleglycerol phosphate and histidinol (histidine intermediates and competitive inhibitors of the enzyme) are 1.1 x 10(-2) M, 1.3 x 10(-6) M, respectively. The Ki for indoleglycerol phosphate (a tryptophan intermediate and non-competitive inhibitor) is 1.2 x 10(-3) M.

Specialized lambda transducing bacteriophage which carries hisS, the structural gene for histidyl-transfer ribonucleic acid synthetase

A number of specialized lambda transducing bacteriophages which carry the Escherichia coli gene guaB were isolated from E. coli. One of these bacteriophages, lambda cI857 Sam7 d guaB-2, also carries hisS, the structural gene for histidyl-transfer ribonucleic acid synthetase (EC 6.1.1.21). Histidyl-transfer ribonucleic acid synthetase activities in induced and uninduced lysogens carrying lambda d guaB-2 indicate that the phage carries the entire structural gene and that the gene is under the control of an E. coli promoter. These conclusions were confirmed by the in vivo production of a protein encoded by the phage which comigrates with authentic histidyl-transfer ribonucleic acid synthetase on two-dimensional polyacrylamide gels.

Mapping hisS, the structural gene for histidyl-transfer ribonucleic acid synthetase, in Escherichia coli

The structural gene for histidyl-tRNA synthetase was localized to 53.8 min on the Escherichia coli genome. The gene order in this region was determined to be dapE-purC-upp-purG-(guaA, guaB)-hisS-glyA.

Construction of an M13 histidine-transducing phage: a single-stranded cloning vehicle with one EcoRI site

In order to create a ready source of single-stranded DNA for DNA sequence determination by the dideoxy chain-termination method, the promoter-proximal part of the histidine operon, the hisOGD region of Salmonella typhimurium, was cloned onto the single-stranded phage M13. Both orientations of the his DNA were cloned to supply DNA template for sequencing of each strand. Insertion was achieved at an HaeIII site in the intergenic region (IR) of M13, and a single EcoRI site was purposely regenerated at one boundary of the his DNA insert. Infected colonies, not plaques, were selected using the hisD gene as a selective marker. The single RI site and the hisD marker for auxotrophic selection represent improvements on the wild type M13 as a single-stranded vector for cloning other DNA.

DNA sequence from the histidine operon control region: seven histidine codons in a row

The DNA sequence of 250 base pairs preceding the first structural gene of the histidine operon of Salmonella typhimurium was determined by the dideoxy chain-termination method. Single-stranded DNA template was provided by an M13-histidine transducing phage constructed for the purpose by in vitro recombination. The termination site for the histidine leader RNA is identified by analogy with the trp operon leader termination sequence, and is 47 nucleotides before the start codon of the first structural gene G. Beginning 150 nucleotides before the end of the presumed leader RNA is a possible short protein-coding region with seven histidine codons in a row. It is proposed that the major mechanism of histodine operon control must involve a ribosome arrested at this run of histidine codons when histidine is limiting.

Expression of the histidine operon in rho mutants of Escherichia coli

Expression of the Escherichia coli histidine operon was measured in four independently isolated sets of strains carrying ten different rho mutations. Rho factor does not act as a major regulatory element of histidine operon attenuation.

Promoter- and attenuator-related metabolic regulation of the Salmonella typhimurium histidine operon

Expression of the histidine (his) operon in Salmonella typhimurium was found to be positively correlated with the intracellular level of guanosine tetraphosphate (ppGpp). Limitation for amino acids other than histidine elicited a histidine-independent metabolic regulation of the operon. In bacteria grown at decreased growth rates, his operon expression was metabolically regulated up to a point, after which further decreases in growth rate no longer resulted in further enhancement of operon expression. Studies using strains carrying various regulatory and deletion mutations indicated that metabolic regulation is achieved predominantly by increased RNA chain initiations at the primary (P1) and internal (P2) promoters. Metabolic regulation ordinarly did not involve changes in RNA chain terminations at the attenuator site of the his operon. A model is proposed that involves ppGpp-induced changes in RNA polymerase initiation specificity at particular promoters. A second, special form of metabolic regulation may operate which also is histidine independent, but does involve relief of attenuation.

Role of lysyl-tRNA in the regulation of lysine biosynthesis in Escherichia coli K12

A mutant of lysyl-tRNA synthetase has been isolated in Escherichia coli K12. With this strain the Kmapp for lysine is 25 fold higher than with the parental strain. The percentage of charged tRNAlys in vivo is only 7 per cent (as against 65 per cent with HFR H). Under these conditions no derepression of synthesis is observed for three lysine biosynthetic enzymes (AK III, ASA-dehydrogenase, DAP-decarboxylase) ; a partial derepression is obtained in the case of the dhdp-reductase. Thus lysyl-tRNA does not act as the only corepressor molecule in the lysine regulon.

Significance of autogenously regulated and constitutive synthesis of regulatory proteins in repressible biosynthetic systems

The functional implications of the different modes of regulation have been examined systematically. The results lead to certain predictions. The regulatory protein in repressor-controlled systems is constitutively synthesised. In activator-controlled systems synthesis of the regulatory protein is autogenously regulated. There is favourable agreement between these predictions and published experimental evidence.

Histidine regulation in Salmonella typhimurium: an activator attenuator model of gene regulation

An activator-attenuator model of positive control, a s opposed to the classic repressor-operator model of negative control, is proposed for the major operon-specific mechanism governing expression of the histidine gene cluster of Salmonella typhimurium. Evidence for this mechanism is derived from experiments performed with a coupled in vitro transcription-translation system, as well as with a minimal in vitro transcription system [Kasai, T. (1974) Nature 249, 523--527]. The product (G enzyme, or N-1-[5'-phosphoribosyl]adenosine triphosphate:pyrophosphate phosphoribosyltransferase; EC 2.4.2.17) of the first structural gene (hisG) of the histidine operon is not involved in the positive control mechanism. However, a possible role for G enzyme as an accessory negative control element interacting at the attenuator can be accommodated in our model. The operon-specific mechanism works in conjunction with an independent mechanism involving guanosine 5'-diphosphate 3'-diphosphate (ppGpp) which appears to be a positive effector involved in regulating amino-acid-producing systems, in general [Stephens, J.C., Artz, S.W. & Ames, B.N. (1975) Proc. Nat. Acad. Sci. USA, in press].

Interaction between phosphoribosyltransferase and purified histidine tRNA from wild type Salmonella typhimurium and a derepressed hisT mutant strain

We have examined the interaction between phosphoribosyltransferase and purified tRNA-His from the wild type strain of Salmonella typhimurium, LT-2, and the histidine regulatory mutant hisTl504. Histidyl-tRNA from the mutant strain functions normally in protein synthesis but is defective in its role in the repression mechanism of the histidine operon. Phosphoribosyltransferase has been suggested as a possible aporegulator for this operon and as such might be expected to interact abnormally with tRNA-His from hisT1504. In these studies we have been unable to detect any difference between the affinities of phosphoribosyltransferase for tRNA-His from LT-2 or hisT1504, and thus we conclude that if the complex between phosphoribosyltransferase and histidyl-tRNA does function in regulation, the defect in the hisT1504 mutant must influence the interaction of the complex with some other regulatory element.

Round-cell mutant of Salmonella typhimurium

A mutation at the divD locus in Salmonella typhimurium confers a round-cell morphology and enhances cell division under certain growth conditions.

Physiological studies of salmonella histidine operator-promoter mutants

S. typhimurium hisO mutations are cis dominant and trans recessive and occur in a regulatory segment separate from but adjacent to the first structural gene of the histidine operon, hisG. Strains containing hisO mutations singly and in combination with other regulatory mutations were examined for their content of L-histidinol phosphate phosphatase when grown on limiting and on excess L-histidine. HisO mutations classed as "constitutive" (high enzyme levels) or as "promoter-like" (low enzyme levels) cause a variety of sub-phenotypes. A model is proposed that accounts for the phenotypes found as well as for the interspersion of constitutive and promoter-like mutations on the genetic map (Ely, Fankhauser and Hartman 1974). In this model we suggest that the his operator-promoter DNA is a functional unit that assumes alternate conformations including: (a) the classic linear duplex, active in transcription, and (b) a looped structure that is transcriptionally closed and susceptible to the binding of repressor.