Ribonuclease V of escherichia coli. I. Dependence on ribosomes and translocation

Killer and protective ribosomes

In prokaryotes, translation influences mRNA decay. The breakdown of most Escherichia coli mRNAs is initiated by RNase E, a 5'-dependent endonuclease. Some mRNAs are protected by ribosomes even if these are located far upstream of cleavage sites ("protection at a distance"), whereas others require direct shielding of these sites. I argue that these situations reflect different modes of interaction of RNase E with mRNAs. Protection at a distance is most impressive in Bacilli, where ribosomes can protect kilobases of unstable downstream sequences. I propose that this protection reflects the role in mRNA decay of RNase J1, a 5'-->3' exonuclease with no E. coli equivalent. Finally, recent years have shown that besides their protective role, ribosomes can also cleave their mRNA under circumstances that cause ribosome stalling. The endonuclease associated with this "killing" activity, which has a eukaryotic counterpart ("no-go decay"), is not characterized; it may be borne by the distressed ribosome itself.

Genetic analysis of mutations affecting ribonuclease II in Escherichia coli

Exonuclease activity in an Escherichia coli K12 mutant S296 is less than 1% of that in the wild type strain (Nikolaev et al., 1976). Another mutant N464 has thermolabile ribonuclease II (Castles and Singer, 1968; Kuwano et al., 1969). Genetic analysis of these mutants by Hfr conjugation and P1 transduction indicates that the structural gene (rnb) for ribonuclease II is located near the pyrF gene (28 min on the E. coli genetic map of Bachmann, Low and Taylor (1976)), and the most probable gene order is tyrT-trp-pyrF-rnb.

Heterogeneity of 5' -termini of nucleolar 45S, 32S and 28S RNA in mouse hepatoma

The 5'-termini of nucleolar 45S, 32S and 28S RNA's were analyzed by means of thin layer chromatography and Dowex-1 colum chromatography. 45S RNA did not bear a triphosphate at the 5'-terminus, but various monophosphates are found. 5'-termini of 32S and 28S RNA's were also heterogeneous. These results indicate that 45S molecules as isolated with the conventional procedure may not contains the primary transcript of the ribosomal gene, but a collection of large precursors with different degrees of processing at the 5'-terminus. The processing of the primary transcript may thus involve some unknown trimming processes at the 5'-terminus before the first major cleavage takes place.

Inhibition of messenger ribonucleic acid synthesis in Escherichia coli by thiolutin

Thiolutin, at concentrations of 5 to 40 mug/ml, inhibited the induced synthesis of beta-galactosidase in Escherichia coli CA8000. Thiolutin had no effect on the rate of in vitro hydrolysis of o-nitrophenyl-beta-d-galactoside by purified beta-galactosidase. Examination of the effects of thiolutin on the kinetics of appearance of beta-galactosidase in the presence and absence of rifampin in induced E. coli cells indicated that thiolutin interferes with the transcription process at the level of elongation of messenger ribonucleic acid (mRNA) chains. The data indicated that, in the presence of thiolutin, beta-galactosidase mRNA has a half-life of 1.6 min and that the first completed beta-galactosidase mRNA is produced about 1.5 min after induction. These data are consistent with estimates of transcription time and messenger half-life obtained by conventional means, and suggest that thiolutin does not affect translation of mRNA or its breakdown in vivo. After removal of thiolutin, cells fully regained the ability to be induced for synthesis of beta-galactosidase within 10 min, but mRNA which was incomplete at the time of thiolutin addition did not subsequently become functional.

Effect of isoleucine, valine, or leucine starvation on the potential for formation of the branched-chain amino acid biosynthetic enzymes

The derepression of the isoleucine and valine biosynthetic enzymes in Escherichia coli and Salmonella typhimurium was examined under conditions of restriction of isoleucine, valine, or leucine (the three amino acids needed for multivalent repression of these enzymes). A procedure was used that allowed the measurement of enzyme-forming potential that accumulated during the starvation period, but could not be expressed unless the missing amino acid was supplied. The threonine deaminase (the product of the ilvA gene)-forming potential that accumulated under such conditions was found to be unstable and decayed with a half-life of about 2.5 min (at 37 C). Evidence was obtained that indicates the threonine deaminase-forming potential that accumulates under conditions of isoleucine starvation is in the form of initiated (rifampin-resistant), but uncompleted (actinomycin D-sensitive), messenger ribonucleic acid chains. Furthermore, it appears that a large portion of the threonine deaminase- and dehydrase (the product of the ilvD gene)-forming potential, under such conditions, is in the form of initiated polypeptide chains. Based on these results and results obtained with SuA(-) strains, a model is presented that explains how the second gene (D) in the ilvADE operon can be partially transcribed and translated under conditions in which there are no completed messenger ribonucleic acids for the gene (A) transcribed before it.

Messenger ribonucleic acid synthesis and degradation in Escherichia coli during inhibition of translation

Various aspects of the coupling between the movement of ribosomes along messenger ribonucleic acids (mRNA) and the synthesis and degradation of mRNA have been investigated. Decreasing the rate of movement of ribosomes along an mRNA does not affect the rate of movement of some, and possibly most, of the RNA polymerases transcribing the gene coding for that mRNA. Inhibiting translation with antibiotics such as chloramphenicol, tetracycline, or fusidic acid protects extant mRNA from degradation, presumably by immobilizing ribosomes, whereas puromycin exposes mRNA to more rapid degradation than normal. The promoter distal (3') portion of mRNA, synthesized after ribosomes have been immobilized by chloramphenicol on the promoter proximal (5') portion of the mRNA, is subsequently degraded.

Salmonella typhimurium mutants lacking ribonuclease I: effect on the polarity of histidine mutants

Mutants of Salmonella typhimurium containing 1 to 2% of wild-type ribonuclease I activity were isolated. The rns mutation had no effect on the polarity of mutations in the S. typhimurium histidine operon. Even in the presence of an rns mutation, it was not possible to obtain strong suppressors of the polarity of two polar mutations in the his operon.

Inhibition of ribonuclease II of Escherichia coli by sodium ions, adenosine-5'-triphosphate, and transfer ribonucleic acid

Ribonuclease II action on polyuridylate is competitively inhibited by transfer ribonucleic acid and noncompetitively inhibited by sodium ions. At low substrate levels, adenosine-5'-triphosphate is also inhibitory.

Translational repression in the arginine system of Escherichia coli

Translation of bacterial mRNA, divorced from transcription, has been obtained for enzymes of arginine synthesis; evidence has been acquired for repression by arginine at the level of translation. mRNAs for acetylornithinase and ornithine transcarbamylase were accumulated by arginine starvation of argR(+) and argR(-) arginine auxotrophs derived from Escherichia coli K12. Further transcription was inhibited with rifampicin or miracil D, and enzyme formation was measured in the presence of either an excess of, or a restricted supply of, arginine. For the argR(+) strain 961, little mRNA was found without starvation; for the argR(-) strain 977, a considerable amount of mRNA was demonstrated even without starvation. There was relatively little translation for the argR(+) strain, but not for the argR(-) strain, in the presence of excess arginine, apparently due to an accelerated degradation of mRNA in the argR(+) strain under repressive conditions.

Spermidine requirement for Bacillus thuringiensis ribosomes in cell-free phenylalanine incorporation

A cell-free system from Bacillus thuringiensis was found to actively incorporate phenylalanine into hot trichloroacetic acid-precipitable material in the presence of synthetic polynucleotide, ribosomes, S-100 supernatant, an energy-generating system, and guanosine triphosphate. Phenylalanine incorporation was absolutely dependent on the presence of spermidine in addition to magnesium ions, even when highly purified ribosomes were used. The spermidine effect could not be attributed to inhibition of nucleases. The ribosomal and supernatant fractions from Escherichia coli and B. thuringiensis could be substituted for each other in this system. The spermidine requirement was shown to be limited to the B. thuringiensis ribosome fraction.

Ribonuclease V of Escherichia coli: susceptibility of heated ribosomal RNA and stability of R17 phage RNA

Native ribosomal RNA anid inttact pliage R17 RNA are insensitive to attack by ribonuclease V, an exonucleolytic activity associated with ribosome movement on the substrate RNA. However, ribosomal RNA becomes a substrate when it is heated under conditions that make it a template for protein synthesis, and R17 RNA is attacked if it is either heated or fragmnented. Accessibility of the 5' terminus of an RNA molecule is probably inzcreased by heating or fragmnentation and may determine its susceptibility to ribonuclease V.

Regulation of ribonucleic acid synthesis in Escherichia coli during diauxie lag: accumulation of heterogeneous ribonucleic acid

The synthesis of ribonucleic acid (RNA) and of protein in Escherichia coli during glucose-lactose diauxie lag have been examined. The rate of RNA synthesis is about 7%, of the corresponding rate during exponential growth and the rate of protein synthesis 10 to 15%. Inhibition of RNA synthesis occurs to the same extent in both rel and rel(+) strains. The RNA which accumulates during 20 min in diauxie lag is composed of about 50% ribosomal and transfer RNA species and about 50% of a fraction which resembles messenger RNA (mRNA) in its heterogeneous sedimentation properties. Decay of the heterogeneous fraction occurs in the presence of glucose and actinomycin D with a half-life of 3 min, the same as that of pulse-labeled mRNA; however, during the diauxie lag, the half-life of this RNA is about 25 min. Accumulation of the heterogeneous RNA is further increased when protein synthesis is blocked by chloramphenicol. The data suggest that the disproportionate accumulation of mRNA during diauxie lag and energy source shift-down may be attributed at least in part to increased stability of mRNA, but do not rule out a preferential synthesis of mRNA.

Binding of adenosine 3':5'-cyclic phosphate to G factor of Escherichia coli, and its effects on GTPase, RNase V, and protein synthesis

Unique among adenine nucleotides tested by filter binding assays, 3':5'-cyclic AMP binds to the G translocation factor. Binding is dependent on the presence of GTP, and is inhibited by GDP, by the analog 5'-beta,gamma-methylene GTP, and by the antibiotic fusidic acid. The cAMP seems to be released during the ribosome-dependent translocation of charged tRNA catalyzed by G factor. Bound cAMP inhibits GTPase and ribosome-associated degradation of messenger RNA, but does not inhibit protein synthesis. cAMP might thereby regulate the ratio of productive to degradative transits of ribosomes on messenger RNA, and this may account for some part of its profound effect on levels of specific bacterial messenger RNA species.