Gene for heat-inducible lysyl-tRNA synthetase (lysU) maps near cadA in Escherichia coli

Identification of Major Enzymes Involved in the Synthesis of Diadenosine Tetraphosphate and/or Adenosine Tetraphosphate in Myxococcus xanthus

Myxococcus xanthus generates diadenosine tetraphosphates (Ap₄A) and diadenosine pentaphosphates (Ap₅A) under various stress conditions. M. xanthus lysyl-tRNA synthetase (LysS) efficiently synthesizes Ap₄A from ATP, Ap₅A from ATP and adenosine tetraphosphate (Ap₄), and Ap₄ from ATP and triphosphate. To identify other M. xanthus enzymes that can catalyze Ap₄A and Ap₄ synthesis, 15 M. xanthus aminoacyl-tRNA synthetases (aaRSs), four acyl-CoA synthetases (Acys), three acetyl-CoA synthetases (Aces), phosphoglycerate kinase (Pgk), and adenylate kinase (Adk) were expressed in Escherichia coli and examined for Ap₄A or Ap₄ synthetase activity using ATP or ATP and triphosphate as substrates. Among the tested enzymes, LysS had the highest Ap₄A synthetase activity. AlaRS, SerRS, and LeuRS1 showed high ADP synthetase activity with ATP as a substrate in the presence of pyrophosphatase, and also demonstrated the ability to produce Ap₄ from ATP and triphosphate in the absence of pyrophosphatase. Ap₄ formation by AlaRS, SerRS, and LeuRS1 was approximately 4- to 13-fold higher compared with that of Ap₄A, suggesting that these enzymes prefer triphosphate over ATP as a substrate in the second reaction. Some of the recombinant M. xanthus Acys and Aces also synthesized Ap₄ from ATP and triphosphate. However, Pgk was capable of catalyzing the production of Ap₄ from ATP and 3-phosphoglycerate in the presence of Mg²⁺ and did not require triphosphate, suggesting that this enzyme is mainly responsible for Ap₄ synthesis in M. xanthus.

Biosynthesis of Arginine and Polyamines

Early investigations on arginine biosynthesis brought to light basic features of metabolic regulation. The most significant advances of the last 10 to 15 years concern the arginine repressor, its structure and mode of action in both E. coli and Salmonella typhimurium, the sequence analysis of all arg structural genes in E. coli and Salmonella typhimurium, the resulting evolutionary inferences, and the dual regulation of the carAB operon. This review provides an overall picture of the pathways, their interconnections, the regulatory circuits involved, and the resulting interferences between arginine and polyamine biosynthesis. Carbamoylphosphate is a precursor common to arginine and the pyrimidines. In both Escherichia coli and Salmonella enterica serovar Typhimurium, it is produced by a single synthetase, carbamoylphosphate synthetase (CPSase), with glutamine as the physiological amino group donor. This situation contrasts with the existence of separate enzymes specific for arginine and pyrimidine biosynthesis in Bacillus subtilis and fungi. Polyamine biosynthesis has been particularly well studied in E. coli, and the cognate genes have been identified in the Salmonella genome as well, including those involved in transport functions. The review summarizes what is known about the enzymes involved in the arginine pathway of E. coli and S. enterica serovar Typhimurium; homologous genes were identified in both organisms, except argF (encoding a supplementary OTCase), which is lacking in Salmonella. Several examples of putative enzyme recruitment (homologous enzymes performing analogous functions) are also presented.

Metabolic Regulation of a Bacterial Cell System with Emphasis on Escherichia coli Metabolism

It is quite important to understand the overall metabolic regulation mechanism of bacterial cells such as Escherichia coli from both science (such as biochemistry) and engineering (such as metabolic engineering) points of view. Here, an attempt was made to clarify the overall metabolic regulation mechanism by focusing on the roles of global regulators which detect the culture or growth condition and manipulate a set of metabolic pathways by modulating the related gene expressions. For this, it was considered how the cell responds to a variety of culture environments such as carbon (catabolite regulation), nitrogen, and phosphate limitations, as well as the effects of oxygen level, pH (acid shock), temperature (heat shock), and nutrient starvation.

Effects of temperature stress on bean-nodulating Rhizobium strains

High soil temperatures in tropical areas limit nodulation and dinitrogen fixation by strains of Rhizobium. Several heat-tolerant bean-nodulating Rhizobium strains have been isolated previously. However, the basis of their resistance to heat remains unknown. In this study, we compared the effects of heat on symbiotic nitrogen fixation, cell survival, amino acid uptake, and protein synthesis in a heat-tolerant (CIAT899) and a heat-sensitive (CNPAF512) bean-nodulating Rhizobium strain. Acetylene reduction activity of nodulated roots excised from unstressed plants was strongly diminished at 35 or 40 degrees C when plants were nodulated either by CIAT899 or by CNPAF512. When these strains were tested under free-living conditions, survival at 40 degrees C as well as the kinetics of l-[S]methionine uptake and protein synthesis at 35 and 40 degrees C indicated the higher tolerance of CIAT899 than of CNPAF512 to thermal stress. The synthesis of heat shock proteins was detected in both strains, although at different temperatures. Increased synthesis of 14 heat shock proteins in CNPAF512 and of 6 heat shock proteins in CIAT899 was observed at 40 and 45 degrees C, respectively. A heat shock protein of approximately 21 kDa, of which the synthesis was strongest in both Rhizobium strains upon a temperature shift up, was also conserved in several other bean-nodulating rhizobia. Acquired thermotolerance in CIAT899 was shown to depend on protein synthesis.

Effect of temperature up-shift on fermentation and metabolic characteristics in view of gene expressions in Escherichia coli

Background

Escherichia coli induces heat shock genes to the temperature up-shift, and changes the metabolism by complicated mechanism. The heat shock response is of practical importance for the variety of applications such as temperature-induced heterologous protein production, simultaneous saccharification and fermentation (SSF) etc. However, the effect of heat shock on the metabolic regulation is not well investigated. It is strongly desired to understand the metabolic changes and its mechanism upon heat shock in practice for the efficient metabolite production by temperature up-shift. In the present research, therefore, we investigated the effect of temperature up-shift from 37°C to 42°C on the metabolism in view of gene expressions.

Results

The results of aerobic batch and continuous cultivations of E. coli BW25113 indicate that more acetate was accumulated with lower biomass yield and less glucose consumption rate at 42°C as compared to the case at 37°C. The down- regulation of the glucose uptake rate corresponds to the down-regulation of ptsG gene expression caused by the up-regulation of mlc gene expression. In accordance with up-regulation of arcA, which may be caused by the lower oxygen solubility at 42°C, the expressions of the TCA cycle-related genes and the respiratory chain gene cyoA were down-regulated. The decreased activity of TCA cycle caused more acetate formation at higher temperature, which is not preferred in heterologous protein production etc. This can be overcome by the arcA gene knockout to some extent. The time courses of gene expressions revealed that the heat shock genes such as groEL, dnaK, htpG and ibpB as well as mlc were expressed in much the same way as that of rpoH during the first 10–20 minutes after temperature up-shift. Under microaerobic condition, the fermentation changed in such a way that formate and lactate were more produced due to up-regulation of pflA and ldhA genes while ethanol was less produced due to down-regulation of adhE gene at higher temperature as compared to the case at 37°C.

Conclusion

The present result clarified the mechanism of metabolic changes upon heat shock from 37°C to 42°C based on gene expressions of heat shock genes, global regulators, and the metabolic pathway genes. It is recommended to use arcA gene knockout mutant to prevent higher acetate production upon heat shock, where it must be noted that the cell yield may be decreased due to TCA cycle activation by arcA gene knockout.

Titration and conditional knockdown of the prfB gene in Escherichia coli: effects on growth and overproduction of the recombinant mammalian selenoprotein thioredoxin reductase

Release factor 2 (RF2), encoded by the prfB gene in Escherichia coli, catalyzes translational termination at UGA and UAA codons. Termination at UGA competes with selenocysteine (Sec) incorporation at Sec-dedicated UGA codons, and RF2 thereby counteracts expression of selenoproteins. prfB is an essential gene in E. coli and can therefore not be removed in order to increase yield of recombinant selenoproteins. We therefore constructed an E. coli strain with the endogenous chromosomal promoter of prfB replaced with the titratable P(BAD) promoter. Knockdown of prfB expression gave a bacteriostatic effect, while two- to sevenfold overexpression of RF2 resulted in a slightly lowered growth rate in late exponential phase. In a turbidostatic fermentor system the simultaneous impact of prfB knockdown on growth and recombinant selenoprotein expression was subsequently studied, using production of mammalian thioredoxin reductase as model system. This showed that lowering the levels of RF2 correlated directly with increasing Sec incorporation specificity, while also affecting total selenoprotein yield concomitant with a lower growth rate. This study thus demonstrates that expression of prfB can be titrated through targeted exchange of the native promoter with a P(BAD)-promoter and that knockdown of RF2 can result in almost full efficiency of Sec incorporation at the cost of lower total selenoprotein yield.

Sequencing, characterization and transcriptional analysis of the histidine decarboxylase operon of Lactobacillus buchneri

The amplification of an internal fragment of the hdcA gene for histidine decarboxylase in Lactobacillus buchneri showed the gene to be located on the bacterial chromosome. Reverse PCR was then used to amplify both it and its adjacent genes. The histidine decarboxylase cluster was found to be composed of four genes: hdcC (expressed in Lactococcus lactis, the product of which is located in the membrane, suggesting it to be a histidine/histamine antiporter), hdcA (which encodes histidine decarboxylase), hdcB (of unknown function but co-transcribed as bicistronic mRNA together with hdcA) and hisS (the only copy of a gene encoding a histidyl-tRNA synthetase in Lb. buchneri). The expression of hisS depends on the histidine concentration of the growth medium, and it can be transcribed as monocistronic or hdcA-hdcB-hisS polycistronic mRNA.

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.

Application of two-dimensional protein gels in biotechnology

The optimal use of biological systems for technologically developed products will not be achieved until biological systems are completely defined in biochemical terms. Two-dimensional polyacrylamide gel electrophoresis, 2-D gels, are contributing to this goal. These gels separate complex mixtures of proteins into individual polypeptide species. The ultimate use of 2-D gels is the construction of cellular 2-D gel databases which identify the proteins on the gels and catalog their responses to different environmental conditions. In addition to these global analyses, many applications for 2-D gels in basic, applied and clinical research have been shown.

Lysyl-tRNA synthetase

Lysyl-tRNA synthetase catalyses the formation of lysyl-transfer RNA, Lys-tRNA(Lys), which then is ready to insert lysine into proteins. Lysine is important for proteins since it is one of only two proteinogenic amino acids carrying an alkaline functional group. Seven genes of lysyl-tRNA synthetases have been localized in five organisms, and the nucleotide and the amino acid sequences have been established. The lysyl-tRNA synthetase molecules are of average chain lengths among the aminoacyl-tRNA synthetases, which range from about 300 to 1100 amino acids. Lysyl-tRNA synthetases act as dimers; in eukaryotes they can be localized in multienzyme complexes and can contain carbohydrates or lipids. Lysine tRNA is recognized by lysyl-tRNA synthetase via standard identity elements, namely anticodon region and acceptor stem. The aminoacylation follows the standard two-step mechanism. However the accuracy of selecting lysine against the other amino acids is less than average. The first threedimensional structure of a lysyl-tRNA synthetase worked out very recently, using the enzyme from the Escherichia coli lysU gene which binds one molecule of lysine, is similar to those of other class II synthetases. However, none of the reaction steps catalyzed by the enzyme is clarified to atomic resolution. Thus surprising findings might be possible. Lysyl-tRNA synthetase and its precursors as well as its substrates and products are targets and starting points of many regulation circuits, e.g. in multienzyme complex formation and function, dinucleoside polyphosphate synthesis, heat shock regulation, activation or deactivation by phosphorylation/dephosphorylation, inhibition by amino acid analogs, and generation of antibodies against lysyl-tRNA synthetase. None of these pathways is clarified completely.

The occurrence of duplicate lysyl-tRNA synthetase gene homologs in Escherichia coli and other procaryotes

The lysyl-tRNA synthetase (LysRS) system of Escherichia coli K-12 consists of two genes, lysS, which is constitutive, and lysU, which is inducible. It is of importance to know how extensively the two-gene LysRS system is distributed in procaryotes, in particular, among members of the family Enterobacteriaceae. To this end, the enterics E. coli K-12 and B; E. coli reference collection (ECOR) isolates EC2, EC49, EC65, and EC68; Shigella flexneri; Salmonella typhimurium; Klebsiella pneumoniae; Enterobacter aerogenes; Serratia marcescens; and Proteus vulgaris and the nonenterics Pseudomonas aeruginosa and Bacillus megaterium were grown in AC broth to a pH of 5.5 or less or cultured in SABO medium at pH 5.0. These growth conditions are known to induce LysRS activity (LysU synthesis) in E. coli K-12. Significant induction of LysRS activity (twofold or better) was observed in the E. coli strains, the ECOR isolates, S. flexneri, K. pneumoniae, and E. aerogenes. To demonstrate an association between LysRS induction and two distinct LysRS genes, Southern blotting was performed with a probe representing an 871-bp fragment amplified from an internal portion of the coding region of the lysU gene. In initial experiments, chromosomal DNA from E. coli K-12 strain MC4100 (lysS+ lysU+) was double digested with either BamHI and HindIII or BamHI and SalI, producing hybridizable fragments of 12.4 and 4.2 kb and 6.6 and 5.2 kb, respectively. Subjecting the chromosomal DNA of E. coli K-12 strain GNB10181 (lysS+ delta lysU) to the same regimen established that the larger fragment from each digestion contained the lysU gene. The results of Southern blot analysis of the other bacterial strains revealed that two hybridizable fragments were obtained from all of the E. coli and ECOR collection strains examined and S. flexneri, K. pneumoniae, and E. aerogenes. Only one lysU homolog was found with S. typhimurium and S. marcescens, and none was obtained with P. vulgaris. A single hybridizable band was found with both P. aeruginose and B, megaterium. These results show that the dual-gene LysRS system is not confined to E. coli K-12 and indicate that it may have first appeared in the genus Enterobacter.

Regulation of lysyl-tRNA synthetase expression by histone-like protein H-NS of Escherichia coli

The lysU gene encoding lysyl-tRNA synthetase of Escherichia coli is normally silent at low temperatures and is expressed by certain metabolites and stimuli. A novel class of lysU-constitutive mutations were isolated by random insertion mutagenesis. These mutations nullified the hns gene encoding a histone-like protein, H-NS, and affected thermoregulation of lysU.

Characterization of a Mycoplasma hominis gene encoding lysyl-tRNA synthetase (LysRS)

The gene encoding lysyl-tRNA synthetase (lysS) in Mycoplasma hominis was cloned and sequenced. The gene was found to have an open reading frame of 1466 bp encoding a polypeptide with a predicted molecular mass of 57 kDa. The amino acid sequence showed 44.3% and 43.7% identity to the Escherichia coli lysyl-tRNA synthetases, encoded by lysS and lysU. Only one lysyl-tRNA synthetase encoding gene was found in M. hominis. The G + C content of the gene was found to be 28.6%, which is significantly lower than in other prokaryotes. The gene was located 4 kb upstream of the M. hominis PG21 rRNA B operon.

Control and function of lysyl-tRNA synthetases: diversity and co-ordination

Lysyl-tRNA synthetases are synthesized from two distinct genes in Escherichia coli, lysS (constitutively) and lysU (inducibly); however, the physiological significance and the differential control mechanism of these two genes have been a long-standing puzzle. Recent studies have successfully uncovered a significant control mechanism of lysU expression, which involves the leucine-responsive regulatory protein (Lrp) and a translational enhancer element called 'downstream box'. Moreover, it is likely that there is a mechanism underlying co-ordinate expression of lysU with other genes outside the leucine-Lrp regulon under harsh conditions such as low pH and anaerobiosis. A possible mechanism of lysyl-tRNA synthetase expression and function is reviewed.

The Escherichia coli heat shock gene htpY: mutational analysis, cloning, sequencing, and transcriptional regulation

We have identified a new heat shock gene, designated htpY, located 700 bp upstream of the dnaK dnaJ operon. We cloned it and showed that it is transcribed clockwise vis-à-vis the Escherichia coli genetic map, in the same direction as the dnaK dnaJ operon. The htpY gene encodes a 21,193-Da polypeptide. Promoter mapping experiments and Northern (RNA) analysis showed that the htpY gene belongs to the classical heat shock gene family, because the transcription from its major promoter is under the positive control of the rpoH gene product (sigma 32) and resembles canonical E sigma 32-transcribed consensus promoter sequences. This conclusion has been strengthened by the construction and analysis of a phtpY-lacZ promoter fusion. Despite the fact that htpY null bacteria are viable, the expression of various E sigma 32 heat shock promoters is significantly decreased, suggesting that HtpY plays an important role in the regulation of the heat shock response. Consistent with this interpretation, overproduction of the HtpY protein results in a generalized increase of the heat shock response in E. coli.

Influence of pH on bacterial gene expression

Bacteria respond to changes in internal and external pH by adjusting the activity and synthesis of proteins associated with many different processes, including proton translocation, amino acid degradation, adaptation to acidic or basic conditions and virulence. While, for many of these examples, the physiological and biological consequence of the pH-induced response is clear, the mechanism by which the transcription/translation machinery is signalled is not. These examples are discussed along with several others in which the function of the gene or protein remains a mystery.

Multiple control of Escherichia coli lysyl-tRNA synthetase expression involves a transcriptional repressor and a translational enhancer element

Lysyl-tRNA synthetases [L-lysine:tRNA(Lys) ligase (AMP-forming), EC 6.1.1.6] are synthesized from two distinct genes in Escherichia coli, lysS (constitutively) and lysU (inducibly), but neither the physiological significance nor the mechanism of differential regulation of these two genes is understood. We have constructed a null mutation of lysS that causes cold-sensitive lethality and then used this mutant to acquire and characterize several bypass mutations called als (abandonment of lysS). Cold-resistant survivors were isolated either spontaneously or by transposon-mediated disruption, and all caused derepression of lysU transcription. One class of als mutations is linked to lysU and presumably affects the cis regulatory element. Mutations of the other class map within the lrp gene, which encodes the leucine-responsive regulatory protein (Lrp). A lysU-lacZ gene fusion study revealed that lysU is susceptible to thermal regulation in the absence of lrp and that a small mRNA region immediately downstream of the initiation codon is required for potentially high-level expression. These results suggest that lysU is part of the leucine regulon and is both negatively controlled by Lrp and positively regulated by a potential translational enhancer sequence. This sequence is similar to that of the "downstream box" complementary to nucleotides 1469-1483 of 16S rRNA, which can be universally found in tRNA synthetase genes of E. coli.

Differential regulation of two genes encoding lysyl-tRNA synthetases in Escherichia coli: lysU-constitutive mutations compensate for a lysS null mutation

Lysyl-tRNA synthetases are synthesized in Escherichia coli from two distinct genes, lysS and lysU, which are regulated differentially. A strain which is null for lysS, the constitutive gene, was created by gene disruption (lysS1) and exhibited cold-sensitive lethality. Hence, lysS is dispensable at high temperatures. This cold sensitivity was suppressed by a multi-copy plasmid carrying lysU, the inducible gene. These data are interpreted as indicating that lysS is functionally replaceable by lysU for cell growth, and that the cold sensitivity of lysS1 is caused by insufficient expression of lysU at low temperatures. To investigate the mechanism of lysU expression, cold-resistant bypass mutations were isolated from lysS1, and named als (for abandonment of lysS). Two als mutations which were linked to lysU contain IS2 insertions upstream of the lysU promoter. They caused a 16-19-fold increase in the lysU-mRNA level. Furthermore, deletion mutations created immediately upstream of the lysU promoter restored growth of lysS1. These results suggest that transcription of lysU is negatively controlled by a cis-element located upstream of the promoter.

Overproduction and purification of lysyl-tRNA synthetase encoded by the herC gene of E coli

Lysyl-tRNA synthetases are synthesized from two distinct genes in E coli, lysS and lysU, but neither gene product has been purified distinctively by using overproducing systems. The lysS gene has been identified by a herC mutation which restores maintenance of the mutant ColE1 replicon. The herC gene product was overproduced by using a tac promoter fusion and purified to homogeneity. The purified HerC protein possesses a lysyl-tRNA synthetase activity as predicted by the sequence identity of herC to lysS. The procedure is useful for rapid mass-scale purification of lysyl-tRNA synthetase.

Nucleotide sequence of the Escherichia coli cad operon: a system for neutralization of low extracellular pH

Lysine decarboxylase of Escherichia coli has been the subject of enzymological studies, and the gene encoding lysine decarboxylase (cadA) and a regulatory gene (cadR) have been mapped. This enzyme is induced at low pH in the presence of lysine and achieves maximal level under anaerobic conditions. The induction of lysine decarboxylase increases the pH of the extracellular medium and provides a distinctive marker in tests of clinical strains. We report the sequence of the cad operon encoding lysine decarboxylase, a protein of 715 amino acids, and another protein, CadB, of 444 amino acids. The amino acid sequence of lysine decarboxylase showed high homology to that of the lysine decarboxylase of Hafnia alvei with less homology to the sequence of speC, which encodes the biosynthetic ornithine decarboxylase of E. coli. The cadA and cadB genes were separately cloned and placed under the control of lac and tac promoters, respectively, to facilitate independent study of their physiological effects. The cadB gene product had a mobility characteristic of a smaller protein on protein gels, analogous to that found for some other membrane proteins. The CadB sequence showed homology to that of ArcD of Pseudomonas aeruginosa, encoding an arginine/ornithine antiporter. Excretion studies of various strains, the coinduction of cadB and cadA, and the attractive physiological role for an antiport system led to a model for the coupled action of cadA and cadB in uptake of lysine, the reduction of H+ concentration, and excretion of cadaverine.

Identification of elements involved in transcriptional regulation of the Escherichia coli cad operon by external pH

Expression of the lysine decarboxylase gene (cadA) of Escherichia coli is induced upon external acidification. To dissect the molecular mechanisms responsible for this regulation, we analyzed a 4.2-kbp region upstream from cadA. DNA sequencing revealed two long open reading frames upstream of and on the same strand as cadA. One of these, cadB, is 444 codons long and is situated immediately upstream of cadA. Transcriptional fusions between fragments upstream of cadA and lacZ, Northern (RNA) hybridization, primer extension, and site-directed mutagenesis experiments defined a promoter, Pcad, upstream of cadB that was responsible for pH-regulated expression of cadA. Upstream of Pcad is an open reading frame, cadC, consisting of 512 codons. The predicted amino terminal region of the cadC gene product (CadC) resembles the carboxy-terminal domain of prokaryotic transcriptional activators involved in environmental sensing. Tn10 insertions within or immediately upstream of cadC abolished Pcad activity, suggesting that cadC encodes a positive transcription factor. Expression of plasmid-borne cadC in the Tn10 mutants restored Pcad activity, while introduction of a plasmid expressing truncated CadC resulted in the inability to complement. The presence of Pcad on a multicopy plasmid was found to lower expression arising from chromosomal Pcad, suggesting that a positive-acting factor is limiting. Our data suggests that cadA, cadB, and the acid-inducible Pcad comprise, at least in part, the cad operon which is under control of the cadC product.

Lysyl-tRNA synthetase gene of Campylobacter jejuni

We report the cloning and complete nucleotide sequence of the Campylobacter jejuni lysyl-tRNA synthetase gene (lysS). The C. jejuni lysS gene sequence shows high homology to the two Escherichia coli lysyl-tRNA synthetase genes, lysS and lysU. The Campylobacter lysyl-tRNA synthetase protein (LysRS) shows 47.9 and 46.6% sequence identity to the E. coli enzymes encoded by the lysS and lysU genes, respectively. The LysRS encoded by the C. jejuni gene is a polypeptide of 501 amino acids with a deduced molecular weight of 57,867. The enzyme is active in E. coli. The gene is expressed from its own promoter, and the transcription start site has been mapped. The carboxyl-terminal codon of the C. jejuni lysS gene overlaps by 1 bp with the Met initiation codon of the glyA gene, which has been shown to have a promoter which is functional in E. coli (V.L. Chan and H.L. Bingham, Gene 101:51-58, 1991). C. jejuni, unlike E. coli, has only one lysyl-tRNA synthetase gene.

Induction of a heat-shock-type response in Saccharomyces cerevisiae following glucose limitation

The protein pattern of yeast cells which have arrested proliferation in response to glucose exhaustion is drastically different from that of exponentially growing cells (Boucherie, 1985). In this study, we used two-dimensional gel electrophoresis to characterize the protein events responsible for these alterations. We found that the induction of heat-shock proteins is one of the major events responsible for these changes. This induction accounts for the synthesis of 18 of the 35 novel polypeptides observed in glucose-limited cells. It was shown to occur in combination with two other protein events: the derepression of carbon catabolite repressed proteins, which accounts for the synthesis of the other novel polypeptides, and an arrest of the synthesis of almost all the proteins present in exponentially growing cells. The time course of each of these events was determined by carrying out a detailed analysis of the pattern of proteins synthesized at various stages of a culture exhausting its glucose supply, and by the measurement of the rate of synthesis of individual polypeptides. The results showed in particular that the synthesis of most of the heat-shock proteins synthesized in glucose-limited cells was induced closely before glucose exhaustion, and that this synthesis was transient, climaxing by the time glucose was exhausted. Under the culture condition investigated, the entry into stationary phase associated with glucose limitation began several hours before glucose exhaustion. It was thus concluded that the observed induction of heat-shock proteins is directly related to the nutritional limitation and is independent from the arrest of cell proliferation.

A PMR2 tandem repeat with a modified C-terminus is located downstream from the KRS1 gene encoding lysyl-tRNA synthetase in Saccharomyces cerevisiae

The KRS1 gene encodes the cytoplasmic form of Saccharomyces cerevisiae lysyl-tRNA synthetase. The KRS1 locus has been characterized. The lysyl-tRNA synthetase gene is unique in the yeast genome. The gene is located on the right arm of chromosome IV and disruption of the open reading frame leads to lethality. These results contrast with the situation encountered in Escherichia coli where lysyl-tRNA synthetase is coded by two distinct genes, lysS and lysU, and further address the possible biological significance of this gene duplication. The nucleotide sequence of the 3'-flanking region has been established. It encodes a long open reading frame whose nucleotide and amino acid structures are almost identical to PMR2, a cluster of tandemly repeated genes coding for P-type ion pumps. The sequence alterations relative to PMR2 are mainly located at the C-terminus of the protein.

Partial characterization of a lysU mutant of Escherichia coli K-12

The Escherichia coli K-12 strain GNB10181 shows no inducible lysyl-tRNA synthetase (LysRS) activity. Two-dimensional gel electrophoretic analysis of the polypeptides synthesized by this strain indicates that the normal lysU gene product, LysU, is absent. When both GNB10181 and its parent, MC4100, were grown at elevated temperatures (42 to 45 degrees C) no significant difference between their growth rates was observed. The lysU mutation was transferred to other E. coli K-12 backgrounds by using P1 transduction. The lysU transductants behaved comparably to their lysU+ parents at different growth temperatures. Therefore, the LysU proteins does not appear to be essential for growth at high temperatures, at least under the conditions examined here. In addition, lysU transductants were found to be defective for inducible lysine decarboxylase, (LDC), inducible arginine decarboxylase (ADI), and melibiose utilization (Mel), which are all missing in GNB10181. Complementation of the above missing functions was achieved by using the Clarke-Carbon plasmids pLC4-5 (LysU LDC) and pLC17-38 (LysU Mel ADI). From these experiments, it appears that GNB10181 has suffered a chromosomal deletion between 93.4 and 93.7 min, which includes the lysU gene. By using plasmid pLC17-38, the position of ADI on two-dimensional gels was identified. Finally, lysS delta lysU double mutants were constructed which can potentially be used as positive selection agents for the isolation of LysRS genes from other sources.

Heat shock response of murine Chlamydia trachomatis

We have investigated the heat shock response in the mouse pneumonitis strain of Chlamydia trachomatis. The kinetics of the chlamydial heat shock response resembled that of other procaryotes: the induction was rapid, occurring over a 5- to 10-min time period, and was regulated at the level of transcription. Immunoblot analysis and immunoprecipitations with heterologous antisera to the heat shock proteins DnaK and GroEL demonstrated that the rate of synthesis, but not the absolute amount of these two proteins, increased after heat shock. Using a general screen for genes whose mRNAs are induced by heat shock, we identified and cloned two of these. DNA sequence analysis demonstrated that one of the genes is a homolog of dnaK. Further sequence analysis of the region upstream of the dnaK gene revealed that the chlamydial homolog of the grpE gene is located just adjacent to the dnaK gene. The second locus encoded three potential nonoverlapping open reading frames. One of the open reading frames was 52% homologous to the ribosomal protein S18 of Escherichia coli and thus presumably encodes the chlamydial homolog. Interestingly, this ribosomal protein is not known to be induced by heat shock in E. coli. S1 nuclease and primer extension analyses located the start site of the dnaK transcript to the last nucleotide of the grpE coding sequence, suggesting that these two genes, although tandemly arranged, are transcribed separately. No promoter sequences resembling the E. coli consensus heat shock promoter could be identified upstream of either the C. trachomatis dnaK, grpE, or S18 gene. The induction of the dnaK and S18 mRNAs by heat shock occurred at a transcriptional level; their induction could be blocked by rifampin. The mechanisms of induction for these two loci were not the same, however; they were differentially sensitive to chloramphenicol. Whereas the induction of dnaK mRNA required de novo protein synthesis, the induction of the S18 mRNA did not. Thus, C. trachomatis utilizes at least two different pathways to induce the transcription of mRNAs encoding proteins induced in the heat shock response.

Independent genes for two threonyl-tRNA synthetases in Bacillus subtilis

With the exception of Escherichia coli lysyl-tRNA synthetase, the genes coding for the different aminoacyl-tRNA synthetases in procaryotes are always unique. Here we report on the occurrence and cloning of two genes (thrSv and thrS2), both encoding functional threonyl-tRNA synthetase in Bacillus subtilis. The two proteins share only 51.5% identical residues, which makes them almost as distinct from each other as each is from E. coli threonyl-tRNA synthetase (42 and 47%). Both proteins complement an E. coli thrS mutant and effectively charge E. coli threonyl tRNA in vitro. Their genes have been mapped to 250 degrees (thrSv) and 344 degrees (thrS2) on the B. subtilis chromosome. The regulatory regions of both genes are quite complex and show structural similarities. During vegetative growth, only the thrSv gene is expressed.

Roles of the two lysyl-tRNA synthetases of Escherichia coli: analysis of nucleotide sequences and mutant behavior

The complete nucleotide sequence of lysU, the gene for the heat-inducible lysyl-tRNA synthetase of Escherichia coli, was determined and compared with the published sequence of lysS (herC), the gene for the constitutive lysyl-tRNA synthetase. These unlinked genes were found to be identical over 72% of their lengths. The deduced amino acid sequences of the respective gene products, LysU and LysS, were identical over 85% and similar over 92% of their lengths. Accumulation of high levels of LysU during growth of strains carrying the wild-type allele of lysU on multicopy plasmids had no observable effect on growth or on the synthesis of LysS. A lysU deletion strain was constructed and was shown to grow normally at low temperature (28 degrees C) but poorly at 44 degrees C; the slow growth (45% of normal) at elevated temperature was fully reversed by plasmids bearing wild-type lysU. The implications of these findings for the existence of two aminoacyl-tRNA synthetases for lysine are discussed.

Homology of lysS and lysU, the two Escherichia coli genes encoding distinct lysyl-tRNA synthetase species

In Escherichia coli, two distinct lysyl-tRNA synthetase species are encoded by two genes: the constitutive lysS gene and the thermoinducible lysU gene. These two genes have been isolated and sequenced. Their nucleotide and deduced amino acid sequences show 79% and 88% identity, respectively. Codon usage analysis indicates the lysS product being more efficiently translated than the lysU one. In addition, the lysS sequence exactly coincides with the sequence of herC, a gene which is part of the prfB-herC operon. In contrast to the recent proposal of Gampel and Tzagoloff (1989, Proc. Natl. Acad. Sci. USA 86, 6023-6027), the lysU sequence is distinct from the open reading frame located adjacent to frdA, although large homologies are shared by these two genes.

In vivo synthesis of adenylylated bis(5'-nucleosidyl) tetraphosphates (Ap4N) by Escherichia coli aminoacyl-tRNA synthetases

The role of aminoacyl-tRNA synthetases in the in vivo synthesis of adenylylated bis(5'-nucleosidyl) tetraphosphates (Ap4N) was studied by measuring the concentration of these nucleotides in Escherichia coli cells overproducing lysyl-, methionyl- phenylalanyl-, or valyl-tRNA synthetase. Overproduction of each aminoacyl-tRNA synthetase (20- to 80-fold) was accompanied by a significant increase in intracellular Ap4N concentration (3- to 14-fold). As expected, non-adenylylated bis(5'-nucleosidyl) tetraphosphate concentration was not changed by synthetase overproduction. It was also verified that overproduction of an inactive methionyl-tRNA synthetase mutant did not modify Ap4N concentration. Ap4N accumulation during heat shock occurred in all strains studied. The increase factor (approximately 50-fold after 1 hr at 48 degrees C) was not changed by overproduction of any of the aminoacyl-tRNA synthetases studied, including that of the heat-inducible form of lysyl-tRNA synthetase from the lysU gene. Together, these results establish that aminoacyl-tRNA synthetases are involved in Ap4N biosynthesis during exponential growth as well as during heat shock.

Homology of aspartyl- and lysyl-tRNA synthetases

The yeast nuclear gene MSD1 coding for mitochondrial aspartyl-tRNA synthetase has been cloned and sequenced. The identity of the gene is confirmed by the following evidence. (i) The primary structure of the protein derived from the gene sequence is similar to that of the yeast cytoplasmic aspartyl-tRNA synthetase. (ii) In situ disruption of MSD1 in a respiratory-competent haploid strain of yeast induces a pleiotropic phenotype consistent with a lesion in mitochondrial protein synthesis. (iii) Mitochondria from a mutant with a disrupted chromosomal copy of MSD1 are unable to acylate mitochondrial aspartyl-tRNA. The primary structures of the cytoplasmic and mitochondrial aspartyl-tRNA synthetases are similar to the yeast cytoplasmic lysyl-tRNA synthetase, suggesting that the two types of synthetases may have a common evolutionary origin. Searches of the current protein banks also have revealed a high degree of sequence similarity of the lysyl-tRNA synthetase to the product of the Escherichia coli herC gene and to the partial sequence of a protein encoded by an unidentified reading frame located adjacent to the E. coli frdA gene. Based on the sequence similarities and the map positions of the herC and frdA loci, we propose herC to be the structural gene of the constitutively expressed lysyl-tRNA synthetase of E. coli and the unidentified reading frame to be the structural gene of the heat-inducible lysyl-tRNA synthetase.

The binding activities of proteins that bind Ap4A, an alarmone, are stimulated in the presence of ethanol or phosphatidylethanolamine

Three proteins binding Ap4A which is known to increase in the heat-shocked cells or to trigger DNA synthesis in G1-arrested eukaryotic cells were purified from E. coli cell extract. For the binding activities of the proteins, glutathione or dithiothreitol and manganese or iron ion were absolutely required. Glutathione, which exists in relatively high concentration in the cells and had been reported to be related to oxidant shock, was far more effective than an artificial antioxidant, dithiothreitol. Ethanol, which has an effect similar to heat or oxidant shock on microbial or eukaryotic cells, enhanced several fold the Ap4A-binding activity. Phosphatidylethanolamine, a major component of phospholipids of cytoplasma and membrane of E. coli cell also stimulated the Ap4A-binding activity.

Construction of lac fusions to the inducible arginine- and lysine decarboxylase genes of Escherichia coli K12

The induction of several amino acid decarboxylases under anaerobic conditions at low pH has been known for many years, but the mechanism associated with this type of regulation has not been elucidated. To study the regulation of the biodegradative arginine and lysine decarboxylases of Escherichia coli K12, Mudlac fusions to these genes were isolated. Mudlac fusion strains deficient for lysine decarboxylase or arginine decarboxylase were identified using decarboxylase indicator media and analysed for their regulation of beta-galactosidase expression. The position of the Mudlac fusion in lysine decarboxylase-deficient strains has been mapped to the cadA gene at 93.7 minutes, while the Mudlac fusions exhibiting a deficiency in the inducible arginine decarboxylase have been mapped to 93.4 minutes.

The groES and groEL heat shock gene products of Escherichia coli are essential for bacterial growth at all temperatures

The products of the groES and groEL genes of Escherichia coli, constituting the groE operon, are known to be required for growth at high temperature (42 degrees C) and are members of the heat shock regulon. Using a genetic approach, we examined the requirement for these gene products for bacterial growth at low temperature (17 to 30 degrees C). To do this, we constructed various groES groEL heterodiploid derivative strains. By inactivating one of the groE operons by a polar insertion, it was shown by bacteriophage P1 transduction that at least one of the groE genes was essential for growth at low temperature. Further P1 transduction experiments with strains that were heterodiploid for only one of the groE genes demonstrated that both groE gene products were required for growth at low temperature, which suggested a fundamental role for the groE proteins in E. coli growth and physiology.

Identification, characterization, and mapping of the Escherichia coli htrA gene, whose product is essential for bacterial growth only at elevated temperatures

We identified and cloned an Escherichia coli gene called htrA (high temperature requirement). The htrA gene was originally discovered because mini-Tn10 transposon insertions in it allowed E. coli growth at 30 degrees C but prevented growth at elevated temperatures (above 42 degrees C). The htrA insertion mutants underwent a block in macromolecular synthesis and eventually lysed at the nonpermissive temperature. The htrA gene was located at approximately 3.7 min (between the fhuA and dapD loci) on the genetic map of E. coli and between 180 and 187.5 kilobases on the physical map. It coded for an unstable, 51-kilodalton protein which was processed by removal of an amino-terminal fragment, resulting in a stable, 48-kilodalton protein.

Modulation of stability of the Escherichia coli heat shock regulatory factor sigma

The heat shock response of Escherichia coli is under the positive control of the sigma 32 protein (the product of the rpoH gene). We found that overproduction of the sigma 32 protein led to concomitant overproduction of the heat shock proteins, suggesting that the intracellular sigma 32 levels limit heat shock gene expression. In support of this idea, the intracellular half-life of the sigma 32 protein synthesized from a multicopy plasmid was found to be extremely short, e.g., less than 1 min at 37 and 42 degrees C. The half-life increased progressively with a decrease in temperature, reaching 15 min at 22 degrees C. Finally, conditions known previously to increase the rate of synthesis of the heat shock proteins, i.e., a mutation in the dnaK gene or expression of phage lambda early proteins, were shown to simultaneously result in a three- to fivefold increase in the half-life of sigma 32.

Lysyl-tRNA synthetase from Escherichia coli K12. Chromatographic heterogeneity and the lysU-gene product

In contrast with most aminoacyl-tRNA synthetases, the lysyl-tRNA synthetase of Escherichia coli is coded for by two genes, the normal lysS gene and the inducible lysU gene. During its purification from E. coli K12, lysyl-tRNA synthetase was monitored by its aminoacylation and adenosine(5')tetraphospho(5')adenosine (Ap4A) synthesis activities. Ap4A synthesis was measured by a new assay using DEAE-cellulose filters. The heterogeneity of lysyl-tRNA synthetase (LysRS) was revealed on hydroxyapatite; we focused on the first peak, LysRS1, because of its higher Ap4A/lysyl-tRNA activity ratio at that stage. Additional differences between LysRS1 and LysRS2 (major peak on hydroxyapatite) were collected. LysRS1 was eluted from phosphocellulose in the presence of the substrates, whereas LysRS2 was not. Phosphocellulose chromatography was used to show the increase of LysRS1 in cells submitted to heat shock. Also, the Mg2+ optimum in the Ap4A-synthesis reaction is much higher for LysRS1. LysRS1 showed a higher thermostability, which was specifically enhanced by Zn2+. These results in vivo and in vitro strongly suggest that LysRS1 is the heat-inducible lysU-gene product.

Mapping of the constitutive lysyl-tRNA synthetase gene of Escherichia coli K-12

The constitutive lysyl-tRNA synthetase gene (lysS) was mapped at 62.1 min on the Escherichia coli chromosome by a combination of conjugation and transduction, with physical confirmation by two-dimensional gel electrophoresis. Revertant analysis suggests that the altered isoelectric point and the low amount of the mutant LysS protein may be due to a single mutational event.

Effects of cycloheximide on thermotolerance expression, heat shock protein synthesis, and heat shock protein mRNA accumulation in rat fibroblasts

A single hyperthermic exposure can render cells transiently resistant to subsequent high temperature stresses. Treatment of rat embryonic fibroblasts with cycloheximide for 6 h after a 20-min interval at 45 degrees C inhibits protein synthesis, including heat shock protein (hsp) synthesis, and results in an accumulation of hsp 70 mRNA, but has no effect on subsequent survival responses to 45 degrees C hyperthermia. hsp 70 mRNA levels decreased within 1 h after removal of cycloheximide but then appeared to stabilize during the next 2 h (3 h after drug removal and 9 h after heat shock). hsp 70 mRNA accumulation could be further increased by a second heat shock at 45 degrees C for 20 min 6 h after the first hyperthermic exposure in cycloheximide-treated cells. Both normal protein and hsp synthesis appeared increased during the 6-h interval after hyperthermia in cultures which received two exposures to 45 degrees C for 20 min compared with those which received only one treatment. No increased hsp synthesis was observed in cultures treated with cycloheximide, even though hsp 70 mRNA levels appeared elevated. These data indicate that, although heat shock induces the accumulation of hsp 70 mRNA in both normal and thermotolerant cells, neither general protein synthesis nor hsp synthesis is required during the interval between two hyperthermic stresses for Rat-1 cells to express either thermotolerance (survival resistance) or resistance to heat shock-induced inhibition of protein synthesis.

Accumulation of dinucleoside polyphosphates in Saccharomyces cerevisiae under stress conditions. High levels are associated with cell death

Adenosine tetraphosphonucleosides (Ap4X) were measured in Saccharomyces cerevisiae by a coupled phosphodiesterase-luciferase assay. After exposure of the cells to cadmium or to hyperthermic treatment (46 degrees C) a marked increase of the cellular pool from 0.08 microM (base level) to 4 microM or higher was observed. The accumulation of Ap4X to high levels is associated with irreversible processes leading to cell death.

Effects of cycloheximide on thermotolerance expression, heat shock protein synthesis, and heat shock protein mRNA accumulation in rat fibroblasts

A single hyperthermic exposure can render cells transiently resistant to subsequent high temperature stresses. Treatment of rat embryonic fibroblasts with cycloheximide for 6 h after a 20-min interval at 45 degrees C inhibits protein synthesis, including heat shock protein (hsp) synthesis, and results in an accumulation of hsp 70 mRNA, but has no effect on subsequent survival responses to 45 degrees C hyperthermia. hsp 70 mRNA levels decreased within 1 h after removal of cycloheximide but then appeared to stabilize during the next 2 h (3 h after drug removal and 9 h after heat shock). hsp 70 mRNA accumulation could be further increased by a second heat shock at 45 degrees C for 20 min 6 h after the first hyperthermic exposure in cycloheximide-treated cells. Both normal protein and hsp synthesis appeared increased during the 6-h interval after hyperthermia in cultures which received two exposures to 45 degrees C for 20 min compared with those which received only one treatment. No increased hsp synthesis was observed in cultures treated with cycloheximide, even though hsp 70 mRNA levels appeared elevated. These data indicate that, although heat shock induces the accumulation of hsp 70 mRNA in both normal and thermotolerant cells, neither general protein synthesis nor hsp synthesis is required during the interval between two hyperthermic stresses for Rat-1 cells to express either thermotolerance (survival resistance) or resistance to heat shock-induced inhibition of protein synthesis.