Growth rate modulation of four aminoacyl-transfer ribonucleic acid synthetases in enteric bacteria

Systematic identification of tRNAome and its dynamics in Lactococcus lactis

Transfer RNAs (tRNAs) through their abundance and modification pattern significantly influence protein translation. Here, we present a systematic analysis of the tRNAome of Lactococcus lactis. Using the next-generation sequencing approach, we identified 40 tRNAs which carry 16 different post-transcriptional modifications as revealed by mass spectrometry analysis. While small modifications are located in the tRNA body, hypermodified nucleotides are mainly present in the anticodon loop, which through wobbling expand the decoding potential of the tRNAs. Using tRNA-based microarrays, we also determined the dynamics in tRNA abundance upon changes in the growth rate and heterologous protein overexpression stress. With a fourfold increase in the growth rate, the relative abundance of tRNAs cognate to low abundance codons decrease, while the tRNAs cognate to major codons remain mostly unchanged. Significant changes in the tRNA abundances are observed upon protein overexpression stress, which does not correlate with the codon usage of the overexpressed gene but rather reflects the altered expression of housekeeping genes.

Pathotyping of Salmonella enterica by analysis of single-nucleotide polymorphisms in cyaA and flanking 23S ribosomal sequences

The egg-contaminating phenotype of Salmonella enterica serotype Enteritidis was linked to single-nucleotide polymorphisms (SNPs) occurring in cyaA, which encodes adenylate cyclase that produces cAMP and pyrophosphate from ATP. Ribotyping indicated that SNPs in cyaA were linked to polymorphisms occurring in the rrlC and rrlA 23S ribosomal subunits. Phylogenetic analysis of cyaA discriminated between Salmonella enterica serotypes and within serotype Enteritidis. Serotypes Typhimurium, Heidelberg and Enteritidis produced one, three and six cyaA allelic variants, respectively, among the set of 56 isolates examined. Asparagine(702) of CyaA was converted to serine in a biofilm-producing isolate. Statistical analysis was applied to 42 other genes encoding proteins between 800 and 1000 amino acids (aa). Results show that the 848 aa CyaA of serovar Enteritidis evolved by nucleotide substitutions that did not significantly alter the purine-to-pyrimidine nucleotide substitution ratio, which was a characteristic of large genes that was positively correlated with increasing gene size. In summary, these analyses link SNPs occurring in the rrlC-rrlA genomic fragment of S. enterica to genetic drift within S. Enteritidis that is associated with egg contamination.

Closely spaced and divergent promoters for an aminoacyl-tRNA synthetase gene and a tRNA operon in Escherichia coli. Transcriptional and post-transcriptional regulation of gltX, valU and alaW

The transcription of the gltX gene encoding the glutamyl-tRNA synthetase and of the adjacent valU and alaW tRNA operons of Escherichia coli K-12 has been studied. The alaW operon containing two tRNA(GGCAla) genes, is 800 base-pairs downstream from the gltX terminator and is transcribed from the same strand. The valU operon, containing three tRNA(UACVal) and one tRNA(UUULys) (the wild-type allele of supN) genes, is adjacent to gltX and is transcribed from the opposite strand. Its only promoter is upstream from the gltX promoters. The gltX gene transcript is monocistronic and its transcription initiates at three promoters, P1, P2 and P3. The transcripts from one or more of these promoters are processed by RNase E to generate two major species of gltX mRNA, which are stable and whose relative abundance varies with growth conditions. The stability of gltX mRNA decreases in an RNase E- strain and its level increases with growth rate about three times more than that of the glutamyl-tRNA synthetase. The 5' region of these mRNAs can adopt a stable secondary structure (close to the ribosome binding site) that is similar to the anticodon and part of the dihydroU stems and loops of tRNA(Glu), and which might be involved in translational regulation of GluRS synthesis. The gltX and valU promoters share the same AT-rich and bent upstream region, whose position coincides with the position of the upstream activating sequences of tRNA and rRNA promoters to which they are similar. This suggests that gltX and valU share transcriptional regulatory mechanisms.

Noncoordinate translation-level regulation of ribosomal and nonribosomal protein genes in the Escherichia coli trmD operon

The trmD operon of Escherichia coli contains the genes for the ribosomal protein S16, a 21-kilodalton polypeptide of unknown function, the tRNA(1-methylguanosine)methyltransferase, and the ribosomal protein L19, in that order. As reported elsewhere, the operon is transcribed as a single polycistronic mRNA species, and there is no significant difference in the steady-state amounts of different parts of the mRNA (A.S. Byström, A. von Gabain, and G.R. Björk, submitted for publication). Furthermore, accumulation of all parts of the transcript is altered in a stringently controlled manner upon starvation for valyl-tRNA. Here we show that the rate of synthesis of the trmD operon proteins increased with increasing growth rate and that the amount in steady state, at a specific growth rate (k = 1.0), of the tRNA(1-methylguanosine)methyltransferase was 260 molecules per gene copy, which is about 40 times lower than the amount of the two ribosomal proteins, whereas the 21-kilodalton protein was synthesized to the amount of about 850 molecules per gene copy. The lower steady-state amount of the two nonribosomal proteins was not due to a higher turnover rate. Synthesis of the 21-kilodalton and TrmD proteins responded differently from that of the two ribosomal proteins during conditions which provoked amino acid starvation, although accumulation of the entire mRNA molecule responds similarly to the rate of synthesis of the two ribosomal proteins. We conclude that the observed differential and noncoordinate expression is achieved by regulation at the level of mRNA translation.

Two control systems modulate the level of glutaminyl-tRNA synthetase in Escherichia coli

We studied the regulation of in vivo expression of Escherichia coli glutaminyl-tRNA synthetase at the transcriptional and translational level by analysis of glnS mRNA and glutaminyl-tRNA synthetase levels under a variety of growth conditions. In addition, strains carrying fusions of the beta-galactosidase structural gene and the glnS promoter were constructed and subsequently used for glnS regulatory studies. The level of glutaminyl-tRNA synthetase increases with the increasing growth rate, with a concomitant though much larger increase in glnS mRNA levels. Thus, transcriptional control appears to mediate metabolic regulation. It is known that glnR5, a regulatory mutation unlinked to glnS, causes overproduction of glutaminyl-tRNA synthetase. Here we showed that the glnR5 product enhances transcription of glnS 10- to 15-fold. The glnR5 mutation does not affect metabolic control. Thus, glnS appears to be regulated by two different control systems affecting transcription. Furthermore, our results suggest post-transcriptional regulation of glutaminyl-tRNA synthetase.

Different control circuits for growth rate-dependent regulation of 6-phosphogluconate dehydrogenase and protein components of the translational machinery in Escherichia coli

Previous studies showed that the level of 6-phosphogluconate (6PG) dehydrogenase increases about fourfold with increasing growth rate when the growth rate is varied by varying the carbon source. When the growth rate was reduced by anaerobic growth or by using mutations to divert metabolism to less efficient pathways, the level of 6PG dehydrogenase was the same as in a wild-type strain growing aerobically on other carbon sources that yielded the same growth rate. Thus, expression of gnd, which encodes 6PG dehydrogenase, is regulated by the cellular growth rate and not by specific nutrients in the medium. Growth rate-dependent regulation was independent of temperature. After a nutritional shift-up, 6PG dehydrogenase and total protein did not attain the postshift rate of accumulation for 30 min, whereas RNA accumulation increased immediately. The kinetics of accumulation of 6PG dehydrogenase and RNA were coincident after a nutritional shift-down. Partial amino acid starvation of a strain that controls RNA synthesis stringently (rel+) had no effect on the differential rate of accumulation of the enzyme. The level of 6PG dehydrogenase in cells harboring a gnd+ multicopy plasmid was in approximate proportion to gene dosage and somewhat higher at faster growth rates. Growth rate control of chromosomal gnd was normal in strains carrying multiple copies of the promoter-proximal and promoter-distal portions of gnd. These results show that gnd is not part of the same regulatory network as components of the translational apparatus since gnd shows a delayed response to a nutritional shift-up, is not autoregulated, and is not subject to stringent control. Models to account for growth rate-dependent regulation of gnd are discussed.

Regulation of small RNAs in Escherichia coli. Alteration in the intracellular concentrations of small RNAs during amino acid and energy starvation

The accumulation of low molecular weight RNAs in Escherichia coli cells following amino acid or energy source starvation was examined using two-dimensional polyacrylamide gel electrophoresis. 32P-labeled small RNA prepared from serine- or isoleucine-starved stringent strain (relA+) cells was shown to display gel patterns that were grossly different from that of unstarved cells. It appears that the deprivation of serine or isoleucine has little or no inhibitory effect on the accumulation of transfer RNA cognate to the deprived amino acid. This is demonstrated by a relative increase in the concentrations of small RNAs that can be charged with serine or isoleucine following starvation of these amino acids. However, small RNAs labeled during starvation of phenylalanine or energy source showed gel patterns similar to that of control cells. This suggested a heterogenous response in the accumulation of some low molecular weight RNAs, presumably transfer RNAs, following starvation of different amino acids.

Mutation in the structural gene for seryl-transfer ribonucleic acid synthetase of Escherichia coli which affects formation of its gene product at high temperature

The rate of formation of seryl-transfer ribonucleic acid (tRNA) synthetase activity was temperature dependent in a temperature-sensitive mutant of Escherichia coli (K28) with an altered seryl-tRNA synthetase structural gene and in a class of spontaneous revertants derived from it. These revertants, which were selected by their ability to grow at 45 degrees C, had high levels of the thermolabile enzyme. The rate of formation of seryl-tRNA synthetase activity in the mutant and in the revertants fell from 100% to near zero with a 4 degrees C temperature range from 40 to 44 degrees C. The temperature-dependent rate of formation of seryl-tRNA synthetase activity was reversible. Dropping the temperature from 44 to 37 degrees C resulted, after a 2- to 3-min delay, in a resumption of the initial rate of formation of enzyme activity. The results could not be accounted for by in vivo or in vitro degradation of the active enzyme. Addition of rifampin just before the temperature shift down from 44 to 37 degrees C inhibited the appearance of seryl-tRNA synthetase activity at the lower temperature. Explanations which might account for these phenomena are proposed.

Growth rate-dependent regulation of transfer ribonucleic acid (5-methyluridine) methyltransferase in Escherichia coli B/r

Enzymes catalyzing the transfer of methyl groups from S-adenosyl-l-methionine to a precursor transfer ribonucleic acid (tRNA) and forming 5-methyluridine (m(5)U), 1-methylguanine (m(1)G), or 5-methylaminomethyl-2-thio-uridine (mam(5)s(2)U) are denoted tRNA(m(5)U)-(EC 2.1.1.35), tRNA(m(1)G)-(EC 2.1.1.31), and tRNA(mam(5)s(2)U)methyltransferase. We have studied the regulation of these tRNA biosynthetic enzymes in Escherichia coli under various physiological conditions and in bacterial mutants known to affect the regulation of components of the translational apparatus. Such studies have revealed that tRNA(m(5)U)-methyltransferase increases with the growth rate in the same fashion as stable RNA, whereas the activity of two other tRNA methyltransferases remains constant in relation to the growth rate. Thus, these tRNA biosynthetic enzymes were not coordinately regulated. Regulation of both tRNA(m(5)U)methyltransferase and stable RNA was similar during shift-up and shift-down experiments. This enzyme showed a stringent regulation in relA(+) strain (T. Ny and G. R. Björk, J. Bacteriol. 130:635-641, 1977) but also in two temperature-sensitive mutants, fusA and fusB, known to influence the accumulation of guanosine 5'-diphosphate 3'-diphosphate and RNA synthesis at nonpermissive temperatures. The tRNA(m(5)U)methyltransferase showed a gene dose effect when its structural gene, trmA, was carried on a plasmid or on lambda transducing phages. Although the regulation of tRNA-(m(5)U)methyltransferase was surprisingly coupled to that of stable RNA, this enzyme was expressed at a much lower level.

Regulation of the biosynthesis of aminoacyl-transfer ribonucleic acid synthetases and of transfer ribonucleic acid in Escherichia coli. V. Mutants with increased levels of valyl-transfer ribonucleic acid synthetase

Spontaneous revertants of a temperature-sensitive Escherichia coli strain harboring a thermolabile valyl-transfer ribonucleic acid (tRNA) synthetase were selected for growth at 40 degrees C. Of these, a large number still contain the thermolabile valyl-tRNA synthetase. Three of these revertants contained an increased level of the thermolabile enzyme. The genetic locus, valX, responsible for the enzyme overproduction, is adjacent to the structural gene, valS, of valyl-tRNA synthetase. Determination (by radioimmunoassay) of the turnover rates of valyl-tRNA synthetase showed that the increased level of valyl-tRNA synthetase is due to new enzyme synthesis rather than decreased rates of protein degradation.

Escherichia coli mutants overproducing phenylalanyl- and threonyl-tRNA synthetase

The structural genes for threonyl-tRNA synthetase (ThrRS) and phenylalanyl-tRNA synthetase (PheRS) are closely linked on the Escherichia coli chromosome. To study whether these enzymes share a common regulatory element, we have investigated their synthesis in mutants which were selected for overproduction of either ThrRS or PheRS. It was found that mutants isolated previously for overproduction of ThrRS as strains resistant to the antibiotic borrelidin (strains Bor Res 3 and Bor Res 15) did not show an elevated level of PheRS. PheRS-overproducing strains were then isolated as revertants of strains with structurally altered enzymes. Strain S1 is a temperature-resistant derivative of a temperature-sensitive PheRS mutant, and strain G118 is a prototrophic derivative of a PheRS mutant which shows phenylalanine auxotrophy as a consequence of an altered K(m) of this enzyme for the amino acid. In both kinds of revertants, S1 and G118, the concentration of PheRS and ThrRS was increased by factors of about 2.5 and 1.8, respectively, whereas the level of other aminoacyl-tRNA synthetases was not affected by the mutations. Genetic studies showed that the simultaneous overproduction of PheRS and ThrRS in revertants G118 and S1 is based upon gene amplification, since this property was easily lost after growing the cells in the absence of the selective stimulus, and since this loss could be prevented by the presence of the recA allele. By similar criteria, the four- and eightfold overproduction of ThrRS in strains Bor Res 3 and Bor Res 15, respectively, was very stable genetically, indicating that it is caused by a mutational event other than gene amplification. From these results, we conclude that the concomitant increase of PheRS and ThrRS in strains G118 and S1 is an expression of gene duplication and not of a joint regulation of these two aminoacyl-tRNA synthetases. This conclusion is further supported by the result that, in mutant G118 as well as in its parental strain G1, growth in minimal medium lacking phenylalanine led to an additional twofold increase of their PheRS concentration. This increase was restricted to the PheRS, since the level of other aminoacyl-tRNA synthetases, including the ThrRS, stayed unchanged.

Two modes of metabolic regulation of lysyl-transfer ribonucleic acid synthetase in Escherichia coli K-12

Lysyl-transfer ribonucleic acid (tRNA) synthetase activity was compared in three independently isolated Escherichia coli K-12 mutants of the enzyme S-adenosyl-L-methionine synthetase (metK mutants) and their isogenic parents. In all three cases the activity of the lysyl-tRNA synthetase was elevated two- to fourfold in the mutant strains. Glycyl-L-leucine (3 mM) usually enhanced lysyl-tRNA synthetase activity two- to threefold in wild-type cells but did not further stimulate the synthetase activity in metK mutants. By two other criteria, the lysyl-tRNA synthetase from wild-type cells grown with the peptide and from the metK mutant RG62, grown in minimal medium, were similar. These criteria are enhanced resistance to thermal inactivation and altered susceptibility to endogenous proteases when compared with the synthetase from wild-type cells grown in minimal medium. In a separate set of experiments, the activities of the lysyl-, arginyl-, seryl-, and valyl-tRNA synthetases were measured in an isogenic pair of relt and rel strains of E. coli grown in a relatively poor growth medium (acetate) and in enriched medium. In the rel+ strain the level of all four synthetases was higher (two- to fourfold) in the enriched medium as expected. In the rel strain the difference in the activities of the synthetases between the two media were diminished. In all four cases the activities of the synthetases were higher in acetate medium in the rel strain. Evidence is presented that these two modes of metabolic regulation act independently.

Transient rates of synthesis of five amionacyl-transfer ribonucleic acid synthetases during a shift-up of Escherichia coli

The steady-state levels of a number of aminoacyl-transfer ribonucleic acid synthetases are known to be positively correlated with growth rate in Escherichia coli. To describe the regulation of these enzymes during a nutritional shift-up, use was made of the recent identification of polypeptide chains of several synthetases in whole cell lysates resolved by the O'Farrell two-dimensional gel system. A culture growing in acetate minimal medium was shifted to glucose-rich medium and pulse labeled with [3H]leucine and [3H]isoleucine for 30- or 6-s intervals during the 20 min after the shift. After mixing with a uniformly [35S]sulfate-labeled reference culture, the samples were subjected to two-dimensional gel electrophoresis. The 3H/35S ratio in the resolved synthetase polypeptides provided an accurate estimation of their transient rates of synthesis. Five aminoacyl-transfer ribonucleic acid synthetases (those for argnine, glycine, isoleucine, phenylalanine, and valine) exhibited an increase in formation within 30 to 90 s after the shift-up. The magnitude of the increases corresponded to the final steady-state values and were reached within 2 to 3 min. The addition to rifampin revealed that the increase in the differential rate of valyl-transfer ribonucleic acid synthetase formation was the result of increased messenger ribonucleic acid transcription and not of a relaxation of some translation restriction.

Chemical measurement of steady-state levels of ten aminoacyl-transfer ribonucleic acid synthetases in Escherichia coli

Polypeptide chains of 10 aminoacyl-transfer ribonucleic acid synthetases (those for arginine, glutamine, glutamic acid, glycine, isoleucine, leucine, lysine, phenylalanine, threonine, and valine) have been identified in lysates of Escherichia coli resolved by the O'Farrell two-dimensional gel system. By labeling cells uniformly with [14C]glucose and by measuring the total amounts of these polypeptides by their radioactivity, estimations of the steady-state, molecular amounts of these enzymes were made and compared to the number of ribosomes and elongation factors in these cells. Portions of a reference culture grown on glucose and labeled with [14C]leucine or [35S]sulfate were mixed with four cultures grown in widely different media containing [3H]leucine or [3H]leucine plus [3H]isoleucine. From the isotope ratios of the total protein and of the spots containing the synthetase chains, the chemical amount of each synthetase relative to that of the reference culture was determined. The results, where comparable, show reasonable agreement with enzyme activity measurements. In general, these synthetases each exhibit a positive correlation with growth rate in unrestricted media, indicating a strong tendency for the levels of transfer ribonucleic acid, synthetases, elongation factors, and ribosomes to remain approximately, though not exactly, in balance at different growth rates.