Mutations in the Gene for a Trna That Functions as a Regulator of a Transcriptional Attenuator in Bacillus Subtilis

It has been proposed that uncharged tRNA molecules may act as positive regulatory factors to control the expression of a number of operons in Bacillus subtilis and related bacteria by interacting with leader sequences to cause antitermination. In this study we report the isolation and characterization of regulatory mutations that modify one of the tRNA molecules predicted to have such a regulatory role. Three different alleles of the B. subtilis leucine tRNA gene leuG were found that resulted in higher expression of the ilv-leu biosynthetic operon. Each resulted in a base change in the D-loop of the leucine tRNA molecule with the anticodon 5''-GAG-3'' (leucine tRNA(GAG)). Experiments with strains that are diploid for mutant and wild-type alleles suggested that both charged and uncharged tRNA molecules may interact with leader sequences to control expression of the operon.     

Stringent control of ribonucleic acid synthesis in Bacillus subtilis treated with granaticin.

The antibiotic granaticin interferes in Bacillus subtilis with the charging process of tRNALeu causing both the arrest of protein synthesis and bacteriostasis [A. Ogilvie, K. Wiebauer & W. Kersten (1975) Biochem. J. 152, 511-515]. A concomitant inhibition of RNA synthesis is observed. This inhibition was studied with mutant strains of B. subtilis. 2. Granaticin inhibits protein and RNA synthesis in stringently controlled B. subtilis (rel+) to about the same extent. In a relaxed mutant strain (rel-) of B. subtilis, protein synthesis is also inhibited, but the accumulation of RNA continues after the addition of the drug. 3. Chloramphenicol, which is known to abolish the stringent control mechanism, added simultaneously with granaticin, allows the synthesis of RNA to proceed in the stringent strain. 4. Guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp) accumulate in granaticin-treated stringently controlled B. subtilis but not in the rel- mutant. 5. It is concluded that the inhibition of RNA synthesis granaticin can adequately be explained as a stringent response caused by the interference by the drug with leucyl-tRNA synthetase.     

A cluster of nine tRNA genes between ribosomal gene operons in Bacillus subtilis.

A cluster of nine tRNA genes located in the 1-kb region between ribosomal operons rrnJ and rrnW in Bacillus subtilis has been cloned and sequenced. This cluster contains the genes for tRNA(UACVal), tRNA(UGUThr), tRNA(UUULys), tRNA(UAGLeu). tRNA(GCCGly), tRNA(UAALeu), tRNA(ACGArg), tRNA(UGGPro), and tRNA(UGCAla). The newly discovered tRNA gene cluster combines features of the 3'-end of trnI, a cluster of 6 tRNA genes between ribosomal operons rrnI and rrnH, and of the 5'-end of trnB, a cluster of 21 tRNA genes found immediately 3' to rrnB. Neither the tRNA(UAGLeu) gene nor its product has been found previously in B. subtilis. With the discovery of this new set of tRNA genes, a total of 60 such genes have now been found in B. subtilis. These known genes account for almost all of the tRNA hybridizing restriction fragments of the B. subtilis genome. The 60 known tRNA genes of B. subtilis code for only 28 different anticodons, compared with a total of 41 different anticodons for 78 tRNA genes in Escherichia coli. This may indicate that B. subtilis does not need as many anticodons because of more flexible translation rules, similar to the situation in Mycoplasma capricolum.     

Interaction of granaticin B with the transcription system ofBacillus subtilis

The interaction of granaticin B, a quinone antibiotic produced by Streptomyces granaticolor, with some biologically important bivalent metal ions, DNA and ATP was demonstrated spectrophotometrically. The activity of isolated RNA polymerase was higher when the DNA of phage SP 50 served as template than with DNA isolated from Bacillus subtilis. Granaticin B inhibited in vitro RNA synthesis, similarly to certain other antibiotics (the inhibition was three times lower than that caused by actinomycin D or streptolydigin and slightly higher than that by epsilon-pyrromycinone). The inhibitory effect was higher when the Mg2+ concentration in the reaction mixture was decreased. The inhibition was then proportional to the concentration of the DNA template. DNA-dependent RNA synthesis is thus inhibited in vitro by granaticin B but this does not appear to be the only site of action of this antibiotic in vivo.     

Modified nucleotides in Bacillus subtilis tRNA(Trp) hyperexpressed in Escherichia coli.

In the present study, modified nucleotides in the B. subtilis tRNA(Trp) cloned and hyperexpressed in E. coli have been identified by TLC and HPLC analyses. The modification patterns of the two isoacceptors of cloned B. subtilis tRNA(Trp) have been compared with those of native tRNA(Trp) from B. subtilis and from E. coli. The modifications of the A73 mutant of B. subtilis tRNA(Trp), which is inactive toward its cognate TrpRS, were also investigated. The results indicate the formation of the modified nucleotides S4U8, Gm18, D20, Cm32, i6A/ms2i6A37, T54 and psi 55 on cloned B. subtilis tRNA(Trp). This modification pattern resembles the pattern of E. coli tRNA(Trp), except that m7G is missing from the cloned tRNA(Trp), probably on account of its short extra loop. In contrast, the pattern departs substantially from that of native B. subtilis tRNA(Trp). Therefore, the cloned B. subtilis tRNA(Trp) has taken on largely the modification pattern of E. coli tRNA(Trp) despite the 26% sequence difference between the two species of tRNA, gaining in particular the Cm32 and Gm18 modifications from the E. coli host. A notable difference between the isoacceptors of the cloned tRNA(Trp) was seen in the extent of modification of A37, which occurred as either the hypomodified i6A or the hypermodified ms2i6A form. Surprisingly, base substitution of guanosine by adenosine at position 73 of the cloned tRNA(Trp) has led to the abolition of the 2'-O-methylation modification of the remote G18 residue.     

Purification of Leucine tRNA Isoaccepting Species from Soybean Cotyledons: I. Benzoylated Diethylamino Cellulose Fractionation, N-Hydroxysuccinimide Modification, and Characterization of Product

Transfer RNA from soybean (Glycine max) cotyledons was purified to homogeneity followed by the purification of the family of leucine tRNA via benzoylated diethylaminoethyl cellulose (BDC) chromatography. Nonacylated total purified tRNA was salicylhydroxamate (SHAM) modified by the phenoxyacetyl method and fractionated into three peaks on a BDC column. The first peak containing bulk tRNA with no hydrophobic character amounted to 78% of the added tRNA. The second peak containing 19% of the added tRNA and represents the tRNA with intrinsic hydrophobic properties. The third peak containing 3% of the tRNA represents the SHAM modified tRNA and nonspecifically modified tRNA. Transfer RNA peaks I and II were pooled and subsequently stoichiometrically acylated in two batches, one containing [¹⁴C]leucine while the other contained unlabeled leucine. The acylated tRNA was loaded on and step-eluted from a BDC column. The purified acylated-tRNA was phenoxyacetyl modified and following ethanol precipitation was fractionated on a BDC column. A double peak eluted from the column in the ethanol gradient contained 5.3% of the starting optical density and 85.3% of the starting counts per minute. Characterization of this leucine tRNA showed typical ultraviolet spectra properties and appeared to be homogeneous on a G-100 Sephadex column. The minimum purity of the tRNA was 32 to 35%. Finally, the acylated tRNA was chromatographed on an RPC-2 column giving six leucine isoaccepting tRNAs. The data indicate that leucine tRNA was highly purified without losing the integrity of the family of isoacceptors.     

Patterns of E. coli leucine tRNA isoacceptors following bacteriophage MS2 infection.

The RNA extracted from MS2 phage particles can accept radioactive leucine and serine in the presence of tRNA activating enzymes. Leucine acceptance is due to the presence of E. coli leucine tRNA that binds very tightly to the virus particle. RPC-5 column chromatography shows that the pattern of virus associated leucyl-tRNA isoacceptors is different from that of normal E. coli leucyl-tRNA. It is also different from the pattern of host leucyl-tRNA isoacceptors found in E. coli lysate following MS2 phage infection. The RPC-5 pattern of the latter tRNA shows several new peaks of leucine tRNA isoacceptors. The possibility that these tRNAs are some modified forms of normal leucine tRNA isoacceptors is suggested.     

Role of aminoacyl-transfer ribonucleic acid in the regulation of ribonucleic acid synthesis in Escherichia coli

Morris, D. W. (University of California, San Diego), and J. A. DeMoss. Role of aminoacyl-transfer ribonucleic acid in the regulation of ribonucleic acid synthesis in Escherichia coli. J. Bacteriol. 90:1624-1631. 1965.-A leucine auxotroph of Escherichia coli was examined for its rate of ribonucleic acid (RNA) synthesis and the level of charged leucine-, arginine-, and valine-specific transfer RNA (tRNA) during the exponential growth period and when growth was limited by leucine starvation. During the logarithmic growth period, the leucine-specific tRNA was 70% charged, arginine-specific tRNA was 30% charged, and the valine-specific tRNA was 80% charged. When leucine became limiting, RNA synthesis was inhibited and the levels of charged arginine- and valine-specific tRNA remained constant, whereas the level of charged leucine-specific tRNA dropped to 40%. Examination of the leucyl-tRNA during the leucine starvation period showed that this 40% level is maintained by protein turnover. Addition of chloramphenicol or puromycin to a leucine-starved culture derepressed RNA synthesis. In the presence of chloramphenicol, the leucine-specific tRNA was fully charged; however, in the presence of puromycin the amount of charged leucine-specific tRNA remained at the starved level. Therefore, during leucine starvation the level of uncharged leucine-specific tRNA is not invariably correlated with the rate of RNA synthesis. We propose that it is the availability of charged tRNA and not the amount of uncharged tRNA which is the important factor in the amino acid control of RNA synthesis.     

Presence and Function of Sulfur-containing Transfer Ribonucleic Acid of Bacillus subtilis

Bacillus subtilis transfer ribonucleic acid (tRNA) was analyzed for the occurrence of thionucleotides by in vivo labeling with (35)S and fractionation by methylated albumin kieselguhr column chromatography. Alkaline hydrolysates of tRNA were also examined by column chromatography and paper electrophoresis, and the amino acid-accepting ability of thionucleotide-containing tRNA was tested after iodine oxidation. The results showed that B. subtilis tRNA contains 4-thiouridylate, a second nucleotide with properties similar to 2-thiopyrimidine, and a third unidentified thionucleotide. The amino acid-accepting ability for serine, tyrosine, lysine, and glutamic acid was markedly inhibited after oxidation of the tRNA with iodine, suggesting the presence of thionucleotides in these tRNA species. This inhibition could be reversed by thiosulfate reduction. The iodine treatment totally inactivated all lysine tRNA species, partially inactivated the serine tRNA species, and did not affect the accepting ability for valine. A comparison of tRNA from cells in the log and stationary phases and from spores revealed similar iodine inactivation patterns in all cases. The thionucleotide content in B. subtilis tRNA differed from that in Escherichia coli, both in extent and in distribution. A possible function of the thionucleotides in tRNA is discussed.     

A study of the method to pick up a selenocysteine tRNA in Bacillus subtilis.

In Bacillus subtilis, selenocysteine tRNA has not been identified in a total genome sequence so far (1). To explore the system of selenocysteine incorporation in B. subtilis, we screened serine-acceptable tRNAs to find an unknown tRNA for selenocysteine by the combined method of specific biotinylation of aa-tRNA (2) and RT-PCR (3). cDNAs obtained from the serine-acceptable tRNA pool were amplified and cloned into plasmid to read its sequence. This procedure gave cDNA library corresponding known serine tRNAs, but no candidate for selenocysteine has been found. Thus, this result, together with the previous data (4), might reveal that there is no selenocysteine tRNA in B. subtilis and/or metabolism of selenium is considerably different from known one as seen in other bacteria.     

Evidence That the Majority of Leucine Transfer Ribonucleic Acid Is Not Involved in Repression in Salmonella typhimurium

Leucine transfer ribonucleic acid (tRNA) was almost fully charged, and the isoleucine-valine and leucine enzymes remained derepressed when trifluoroleucine was added to a leucine auxotroph. High levels of charged leucine tRNA and derepression were also found in a leucyl-tRNA synthetase mutant.     

Transfer RNA genes in the cap-oxil region of yeast mitochondrial DNA.

A cytoplasmic "petite" (rho-) clone of Saccharomyces cerevisiae has been isolated and found through DNA sequencing to contain the genes for cysteine, histidine, leucine, glutamine, lysine, arginine, and glycine tRNAs. This clone, designated DS502, has a tandemly repeated 3.5 kb segment of the wild type genome from 0.7 to 5.6 units. All the tRNA genes are transcribed from the same strand of DNA in the direction cap to oxil. The mitochondrial DNA segment of DS502 fills a sequence gap that existed between the histidine and lysine tRNAs. The new sequence data has made it possible to assign accurate map positions to all the tRNA genes in the cap-oxil span of the yeast mitochondrial genome. A detailed restriction map of the region from 0 to 17 map units along with the locations of 16 tRNA genes have been determined. The secondary structures of the leucine and glutamine tRNAs have been deduced from their gene sequences. The leucine tRNA exhibits 64% sequence homology to an E. coli leucine tRNA.     

Evolution of tRNAs and tRNA genes in Acholeplasma laidlawii.

The genes for 22 tRNA species from Acholeplasma laidawii, belonging to the class Mollicutes (Mycoplasmas), have been cloned and sequenced. Sixteen genes are organized in 3 clusters consisting of eleven, three and two tRNA genes, respectively, and the other 6 genes exist as a single gene. The arrangement of tRNA genes in the 11-gene, the 3-gene and the 2-gene clusters reveals extensive similarity to several parts of the 21-tRNA or 16-tRNA gene cluster in Bacillus subtilis. The 11-gene cluster is also similar to the tRNA gene clusters found in other mycoplasma species, the 9-tRNA gene cluster in M.capricolum and in M.mycoides, and the 10-tRNA gene cluster in Spiroplasma meliferm. The results suggest that the tRNA genes in mycoplasmas have evolved from large tRNA gene clusters in the ancestral Gram-positive bacterial genome common to mycoplasmas and B.subtilis. The anticodon sequences including base modifications of 15 tRNA species from A.laidlawii were determined. The anticodon composition and codon-recognition patterns of A.laidlawii resemble those of Bacillus subtilis rather than those of other mycoplasma species.     

Control of Isoleucine, Valine, and Leucine Biosynthesis VI. Effect of 5′,5′,5′-Trifluoroleucine on Repression in Salmonella typhimurium

The leucine analogue 5',5',5',-trifluoroleucine (fluoroleucine) replaced leucine for repression of the isoleucine-valine biosynthetic enzymes in Salmonella typhimurium. In contrast, the analogue had no effect on derepression of the leucine biosynthetic enzymes in leucine auxotrophs grown on limiting amounts of leucine. The effect of fluoroleucine on repression appeared to be specific for leucine since derepression of the isoleucine-valine enzymes due to an isoleucine or valine limitation was not affected by the analogue. The prevention of derepression by fluoroleucine was probably due to repression and not to the formation of false proteins, since the analogue had no effect on the derepression of a number of enzymes unrelated to the isoleucine-valine pathway. Fluoroleucine was able to attach to leucine transfer ribonucleic acid (tRNA) as evidenced by the ability of the analogue to protect about 70% of leucine tRNA from oxidation by periodate. We propose that the differential effects of fluoroleucine on repression are due to differences in the ability of the analogue to bind to the various species of leucine tRNA.