Synthesis and turnover of phage messenger RNA in E. coli infected with bacteriophage T4 in the presence of chloromycetin

A Grad-seq View of RNA and Protein Complexes in Pseudomonas aeruginosa under Standard and Bacteriophage Predation Conditions

The Gram-negative rod-shaped bacterium Pseudomonas aeruginosa is not only a major cause of nosocomial infections but also serves as a model species of bacterial RNA biology. While its transcriptome architecture and posttranscriptional regulation through the RNA-binding proteins Hfq, RsmA, and RsmN have been studied in detail, global information about stable RNA-protein complexes in this human pathogen is currently lacking. Here, we implement gradient profiling by sequencing (Grad-seq) in exponentially growing P. aeruginosa cells to comprehensively predict RNA and protein complexes, based on glycerol gradient sedimentation profiles of >73% of all transcripts and ∼40% of all proteins. As to benchmarking, our global profiles readily reported complexes of stable RNAs of P. aeruginosa, including 6S RNA with RNA polymerase and associated product RNAs (pRNAs). We observe specific clusters of noncoding RNAs, which correlate with Hfq and RsmA/N, and provide a first hint that P. aeruginosa expresses a ProQ-like FinO domain-containing RNA-binding protein. To understand how biological stress may perturb cellular RNA/protein complexes, we performed Grad-seq after infection by the bacteriophage ΦKZ. This model phage, which has a well-defined transcription profile during host takeover, displayed efficient translational utilization of phage mRNAs and tRNAs, as evident from their increased cosedimentation with ribosomal subunits. Additionally, Grad-seq experimentally determines previously overlooked phage-encoded noncoding RNAs. Taken together, the Pseudomonas protein and RNA complex data provided here will pave the way to a better understanding of RNA-protein interactions during viral predation of the bacterial cell.

Dip-a-Dee-Doo-Dah: Bacteriophage-Mediated Rescoring of a Harmoniously Orchestrated RNA Metabolism

RNA turnover and processing in bacteria are governed by the structurally divergent but functionally convergent RNA degradosome, and the mechanisms have been researched extensively in Gram-positive and Gram-negative bacteria. An emerging research field focuses on how bacterial viruses hijack all aspects of the bacterial metabolism, including the host machinery of RNA metabolism. This review addresses research on phage-based influence on RNA turnover, which can act either indirectly or via dedicated effector molecules that target degradosome assemblies. The structural divergence of host RNA turnover mechanisms likely explains the limited number of phage proteins directly targeting these specialized, host-specific complexes. The unique and nonconserved structure of DIP, a phage-encoded inhibitor of the Pseudomonas degradosome, illustrates this hypothesis. However, the natural occurrence of phage-encoded mechanisms regulating RNA turnover indicates a clear evolutionary benefit for this mode of host manipulation. Further exploration of the viral dark matter of unknown phage proteins may reveal more structurally novel interference strategies that, in turn, could be exploited for biotechnological applications.

Expression of arg genes of Escherichia coli during arginine limitation dependent upon stringent control of translation

The transcription and translation of operons for arginine biosynthetic enzymes after arginine removal (arginine down shift) were studied in relA and relA+ strains of Escherichia coli. After arginine down shift, derepression of synthesis of the arginine biosynthetic enzymes ornithine carbamoyltransferase (argF) and argininosuccinate lyase (argH) began at about 15 min in relA+ cells but was delayed in relA cells for more than 2 h. However, both relA+ and relA cells accumulated high levels of argCBH mRNA, as shown by dot blot hybridization, after arginine down shift. After 15 min of arginine limitation, the proportion of ribosome-bound argCBH mRNA was equivalent in both relA+ and relA cells. During the 15 min after the arginine down shift, relA+ cells produced a significant burst of argF and argH enzyme synthesis when arginine was added back to the culture, whereas relA cells did not produce this burst of enzyme synthesis. The relA cells regained the ability to produce a burst of argF and argH enzyme synthesis when alpha-methylglucose-induced glucose starvation was combined with arginine limitation. Significant guanosine 5'-diphosphate 3'-diphosphate accumulated in relA cells under this condition. Our results support the view that during periods of severe amino acid limitation guanosine 5'-diphosphate 3'-diphosphate acts in some way to ensure the translation of argCBH mRNA.

Requirement of protein synthesis for the induction of ribonucleoside diphosphate reductase mRNA in Escherichia coli

An RNA-DNA hybridization assay was used to quantitate the ribonucleoside diphosphate reductase mRNA synthesis (nrd mRNA) to show that gene expression was dependent on protein synthesis. The increased nrd mRNA synthesis induced by inhibition of DNA synthesis was eliminated by simultaneous inhibition of protein synthesis. It was further found that protein synthesis is required not only initially but continuously during DNA inhibition for increased expression of nrd mRNA synthesis.

Regulation of ribonucleoside diphosphate reductase mRNA synthesis in Escherichia coli

A RNA-DNA hybridization assay for ribonucleoside diphosphate reductase (RDP reductase) mRNA was used to determine whether control of RDP reductase synthesis in Escherichia coli is at the level of RNA transcription. The correlation observed between the level of RDP reductase enzymatic activity and the rate of RDP reductase mRNA synthesis suggested that the control is at the level of RNA transcription. No increase in RDP reductase enzymatic activity or RDP reductase mRNA was observed during the first 15 min after removal of thymine from a thymine-requiring culture. Thereafter, the rate of RDP reductase mRNA synthesis increased linearly for approximately 75 min before beginning to level off. The addition of thymine to a culture starved for thymine resulted in a decreasing rate of RDP reductase mRNA synthesis. However, 30 min of growth in the presence of thymine was required before the rate of RDP reductase mRNA synthesis dropped to the rate observed in an exponentially growing culture. Inhibition of DNA synthesis caused by shifting a culture of a polC mutant or a dnaB mutant to nonpermissive growth conditions resulted in an increase in the rate of RDP reductase mRNA synthesis similar to that observed for a thymine-starved culture.

Physical location of the ilvO determinant in Escherichia coli K-12 deoxyribonucleic acid

A plasmid carrying the 4,6-kilobase (kb) HindIII-derived fragment from an ilvO mutant derivative of lambda h80dilv imparted a valine-resistant phenotype on strains it carried. This fragment carries a small amount of the promoter-proximal end of ilvE, the ilvO determinant, and apparently the entire ilvG gene, which specifies the valine-insensitive acetohydroxy acid synthase. Comparable deoxyribonucleic acid (DNA) from the original lambda h80dilv did not carry the valine resistance marker. The valine-resistant phenotype was always correlated with the formation of the resistant enzymes. The ilvO determinant was shown to be carried within an approximately 600-based-pair region lying between the SalI and KpnI sites on the HindIII fragment and perhaps within the ilvG gene itself. Ribonucleic acid that hybridizes with the DNA corresponding to the ilvG gene is formed in wild-type K-12 cells. This fact, coupled with the fact that ilvG is transcribed from the same DNA strand as the ilvE, D, and A genes, led to the idea that transcription is normally initiated upstream from ilvG in both wild-type and ilvO strains. In wild-type strains either the formation or the translation of the transcript would be terminated with the ilvG gene, thus preventing expression of that gene.

Regional replication of the bacterial chromosome induced by derepression of prophage lambda. III. Role of the replication in escape synthesis of gal operon

Recent evidence suggests that the escape synthesis of gal operon following derepression of the prophage lambda in Escherichia coli K12 involves transcription originating at the lambda promoter (PL) to extend through gal under the conditions in which lambda DNA replication is prevented. Whether the observed expression of gal is due to transcription initiating at PL or at the bacterial promoter for gal (Pgal) was examined in the case of lambda DNA replication being normal. The experiments are based on that two types of transcription are distinguished from each other by the following properties: 1. Pgal-promoted transcription is inhibited by chloramphenicol, while PL-promoted transcription is not. 2. PL-promoted transcription suppresses the polar effect caused by nonsense mutation in a bacterial gene, while Pgal-promoted transcription does not do so. -he results have suggested that gal escape synthesis in lambda-induced lysogen results from transcription which initiates not only at PL but also at Pgal. The Pgal-promoted transcription may be a consequence, direct or indirect, of the concomitant replication of gal DNA.

Isolation of a lambdadcys transducing bacteriophage and its use in determining the regulation of cysteine messenger ribonucleic acid synthesis in Escherichia coli K-12

A defective specialized lambda transducing phage carrying the cysJ, cysI, cysH, and cysD genes has been isolated from a secondary-site lysogen. Deoxyribonucleic acid-ribonucleic acid (DNA-RNA) hybridization studies utilizing this phage have been carried out to detect cysteine-specific messenger RNA (cys mRNA) synthesized in vivo. A vivo. A 3.5- to 9-fold increase in the rate of synthesis of cys mRNA has been detected in the derepressed wild-type (Cys+) strain grown on glutathione compared with a repressed control grown on cystine. Pleiotropic cysE and cysB mutants grown on glutathione were found to possess rates of synthesis of cys mRNA that were significantly lower than their derepressed isogenic parent. The addition of O-acetyl-L-serine to the cysE strain produced a 5.5-fold increase in the rate of synthesis of cys mRNA. These results indicate that cysteine biosynthesis is controlled at the level of transcription by the inducer O-acetylserine, the cysB protein and cyst(e)ine.

Origin and metabolic properties of the RNA species formed during the replication cycle of virus 2C

When short pulses of [(3)H]uracil were administered to Bacillus subtilis infected with phage 2C, the main species of labeled RNA was a 10S component that hybridized chiefly, but not exclusively, with the heavy strand of 2C DNA. After long pulses, most of the radioactivity was found in the 23S, 16S, and 5S rRNA's, which are coded for by the cell genome. Formation of such RNA species was reduced but not suppressed upon infection, the extent of inhibition being proportional to the virus-to-cell ratio. When bacteria were incubated with virginiamycin, an inhibitor of protein synthesis, and then infected with phage 2C, formation of virus-specific RNA decreased. This antibiotic also reduced the preferential transcription of the heavy strand of 2C DNA. The methylation pattern of rRNA remained unchanged upon infection with phage 2C. Virginiamycin reduced both the methylation and stability of rRNA in uninfected cells; this effect, however, was clearly reduced during the viral cycle. It can be concluded that in 2C-infected B. subtilis, cellular and viral RNA species are simultaneously synthesized and a preferential transcription of viral message depends not only on the number of available copies of viral template, but also on their translation. Moreover, virus-dictated proteins are responsible for the inhibition of cellular RNA formation as well as for the asymmetrical transcription of phage genome. Finally, virginiamycin and phage 2C have antagonistic, nonoverlapping effects on the metabolism and function of the RNA of the host cell.

Deoxyribonucleic acid-directed in vitro synthesis of ilv-specific messenger ribonucleic acid by extracts of Escherichia coli K-12

The synthesis of ilv-specific messenger ribonucleic acid (mRNA) by extracts of Escherichia coli K-12 has been demonstrated in a deoxyribonucleic acid (DNA)-dependent, coupled transcription-translation system. ilv-Specific mRNA was determined by hybridization either to double-stranded lambdacI857St68h80dilv DNA (lambdah80dilv DNA) immobilized on nitrocellulose filters or to its separate l and r strands in liquid. During conditions optimal for protein synthesis, slightly more than 6% of the total [(3)H]RNA synthesized by S-30 extracts of the threonine deaminase-negative strain CU5136 was ilv-specific. Of this RNA, nearly 30% was complementary to the l (correct) strand. Total ilv-specific mRNA synthesis in vitro was not affected by omission of valine or all 20 amino acids from the reaction mixture. Hybridization of ilv-specific mRNA made in vitro to the l strand of lambdah80dilv DNA was effectively reduced in the presence of unlabeled RNA extracted from an ilv derepressed strain but not from an ilv deletion strain. In a purified transcription system, employing commercial RNA polymerase, twofold more ilv-specific mRNA was synthesized than in the coupled system, but this increase was entirely due to greater transcription of the r (incorrect) strand. An S-30 extract prepared from a strain isogenic to strain CU5136 but derepressed for ilvA gene expression synthesized twofold more ilv-specific mRNA in the coupled system. The significance of these findings is discussed.

Isoleucine and valine metabolism in Escherichia coli K-12: detection and measurement of ilv-specific messenger ribonucleic acid

Ribonucleic acid-deoxyribonucleic acid (RNA-DNA) hybridization was employed for the determination of messenger RNA transcribed from the ilv gene cluster of Escherichia coli K-12. Strains with derepressed levels of the isoleucine and valine biosynthetic enzymes owing to linked or unlinked genetic lesions were found to exhibit ilv messenger RNA levels from 1.5- to 4-fold higher than did their isogenic parents. When grown under conditions that specifically repressed the synthesis of isoleucine- and valine-forming enzymes, most strains exhibited drastically reduced ilv messenger RNA levels. Hybridization performed with the separated strands of ilv DNA showed that all the ilv genes are transcribed from the same strand, the "l strand" of lambdaphi80CI857St68dilv DNA. Sucrose gradient analyses of RNA extracted from cells starved for isoleucine, valine, or leucine resulted in the detection of at least two distinct types of ilv messenger RNA.

Inhibition of transcription of the histidine operon in vitro by the first enzyme of the histidine pathway

An in vitro system was developed for transcription of the histidine operon of Esherichia coli carried in the genome of a defective varphi80 transducing phage. The messenger RNA (mRNA) of the histidine operon synthesized in the in vitro system was detected by hybridization to single strands of both varphi80 and varphi80dhis DNA, and by competition of this hybridization with unlabeled histidine mRNA that had been synthesized in vivo (RNA extracted from cells in which the histidine operon had been derepressed). Under the conditions used, RNA complementary to the histidine operon was about 15% of the total RNA that was synthesized in vitro from the varphi80dhis DNA template. The RNA complementary to the histidine operon was synthesized on the "sense" strand (the R strand) of varphi80dhis in the form of a polycistronic message with a sedimentation coefficient (about 38 S) very close to that observed for the histidine mRNA synthesized in vivo. Synthesis of the histidine operon RNA appears to be subject to control in vitro. Addition of the first enzyme of the pathway for histidine biosynthesis blocked transcription of the histidine operon specifically, strongly suggesting that this enzyme acts as a regulatory protein for the histidine operon.

Transcriptional control of the calactose operon by the capR (lon) and capT genes

Mutations in capR or capT cause derepression of the enzymes of the gal operon. The gal-specific messenger ribonucleic acid is directly proportional to the gal enzyme levels in wild type, capR, and capT strains. These results indicate that capR and capT control the gal operon at the transcriptional level.

Asymmetric transcription of bacteriophage Mu-1

The deoxyribonucleic acid (DNA) of bacteriophage Mu-1 can be separated into its complementary strands by poly(U,G) binding and equilibrium centrifugation. DNA-ribonucleic acid (RNA) hybridizations in liquid show that more than 98% of "early" phage-specific RNA and over 96% of "late" messenger species bind to the heavy [poly(U,G)-binding] strand of Mu-1 DNA. A small (1.45%) but significant amount of late RNA binds to the light strand. The significance of this RNA fraction is discussed in connection with the peculiar structure of denatured and reannealed Mu-1 DNA.

Arginine control of transcription of argECBH messenger ribonucleic acid in Escherichia coli

The level of messenger ribonucleic acid specific for the argECBH gene cluster (arg-mRNA) of Escherichia coli was measured by deoxyribonucleic acid-ribonucleic acid hybridization in a number of strains. During the first 10 min after removal of arginine (derepression), the rate of arg-mRNA accumulation was six to ten times greater than that found in arginine-repressed argR(+) cells. In the absence of arginine, l-canavanine (200 mug/ml) repressed arg-mRNA synthesis to a level only 20 to 30% lower than that found after arginine deprivation. High levels of arg-mRNA were produced by argR(-) strains with or without added arginine. Within about 2 min after arginine addition to argR(+) cells, the rate of synthesis of arg-mRNA reached the repressed level. Likewise, 2.5 min after rifampin addition, all transcription of arg-mRNA was completed. These data are consistent with the view that arginine signals repression by inhibiting the initiation of transcription of arg-mRNA mediated in some way by the argR gene. The kinetics of arg-mRNA accumulation and the kinetics of completion of transcription together with the profile of hybridizable arg-mRNA in sucrose density gradients (major component 16S) suggest that the argECBH gene cluster is transcribed in short pieces rather than as a single unit.

New polarity suppressors in Escherichia coli: suppression and messenger RNA stability

Two new polarity suppressors (Su27 and Su78) have been isolated in Escherichia coli. Both suppress polarity in the trp and lac operons, and neither shows codon specificity for suppression. Extreme polar mutants of the lac z gene that contain either Su27 or Su78 make mRNA from the entire operon; however, no active beta-galactosidase is translated from the z-gene messenger, and the amount of distal messenger is greater than would be expected from corresponding enzyme activities. Puromycin treatment of lac(+) strains mimics the effect of polar chain-termination mutations in destabilizing lac mRNA. This effect is completely reversed by Su27, and it is partially reversed by Su78. The results suggest that these suppressors act by stabilizing mRNA after premature termination of protein synthesis.

Abortive infection of sporulating Bacillus subtilis 168 by phi 2 bacteriophage

Bacteriophage phi2 is unable to replicate in Bacillus subtilis 168. Although some phage deoxyribonucleic acid (DNA) synthesis can occur, the DNA made is not biologically active and sedimentation analysis reveals that it is smaller in size than that of mature DNA or DNA isolated from phi2-infected permissive hosts. Messenger ribonucleic acid hybridizable with phi2 DNA is also synthesized in phi2-infected cells of 168. Mutants of 168 which are permissive hosts for phi2 have been isolated. These mutants are defective in sporulation and possess the phenotype of "early sporulation mutants." The majority map in two locations, one near the lys locus opposite the trp locus (spoA locus) and the other tightly linked to a phe locus.

Biological activity of bacteriophage ghosts and "take-over" of host functions by bacteriophage

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Complementarity of RNA produced by enzymic transcription of native and denatured B. subtilis DNA

This paper describes the preparation and some of the properties of the RNA specimens synthesized with the aid of the RNA polymerase of E. coli by transcription of the following DNA templates: (a) undenatured B. subtilis DNA (yielding N-RNA); (b) separated strand fractions L and H isolated by chromatography of the denatured DNA on methylated albumin (yielding L-RNA and H-RNA, respectively). The study of the hybridization behavior of the various RNA products showed that N-RNA, though able to form hybrids with either strand, hybridized with H-DNA to twice as great an extent as with L-DNA. The transcripts of the separated L and H fractions exhibited complete specificity with respect to complexing: L-RNA hybridized only with L-DNA, H-RNA only with H-DNA.