Bearing of some recent results on the mechanisms of polarity and messenger RNA stability

Molecular Biology Methods in Streptomyces rimosus, a Producer of Oxytetracycline

Streptomyces rimosus is used for production of the broad-spectrum antibiotic oxytetracycline (OTC). S. rimosus belongs to Actinomyces species, a large group of microorganisms that produce diverse set of natural metabolites of high importance in many aspects of our life. In this chapter, we describe specific molecular biology methods and a classical homologous recombination approach for targeted in-frame deletion of a target gene or entire operon in S. rimosus genome. The presented protocols will guide you through the design of experiment and construction of homology arms and their cloning into appropriate vectors, which are suitable for gene-engineering work with S. rimosus. Furthermore, two different protocols for S. rimosus transformation are described including detailed procedure for targeted gene replacement via double crossover recombination event. Gene deletion is confirmed by colony PCR, and colonies are further characterized by cultivation and metabolite analysis. As the final step, we present in trans complementation of the deleted gene, to confirm functionality of the engineering approach achieved by gene disruption. A number of methodological steps and protocols are optimized for S. rimosus strains including the use of the selected reporter genes. Protocols described in this chapter can be applied for studying function of any individual gene product in diverse OTC-producing Streptomyces rimosus strains.

Cloning, sequence analysis, and expression of alteration of the mRNA stability gene (ams+) of Escherichia coli

The ams+ gene, which influences the stability of mRNA in Escherichia coli was cloned in pBR322. The product of the gene, which is a 17,000-dalton protein, was expressed in expression vector pRC23, a derivative of pBR322. The molecular weight is consistent with sequencing analysis which shows that the gene contains 595 nucleotides and has an open reading frame of 149 amino acids. We discussed the possible role(s) of the ams+ gene product in affecting mRNA stability.

Lactose operon transcription from wild-type and L8-UV5 lac promoters in Escherichia coli treated with chloramphenicol

In cells treated with chloramphenicol and the inducer isopropyl-beta-D-thiogalacto-pyranoside, messenger ribonucleic acid transcription from the wild-type lac promoter was not detected. Transcription occurred from the mutant UV5-L8 promoter. The transcripts were of variable length; some included the whole Z gene. No major site of transcription arrest within the Z gene was apparent.

Evidence for endonucleolytic cleavage at the 5'-proximal segment of the trp messenger RNA in Escherichia coli

The 5'-proximal trp leader RNA segment (about 5S) decays at 2 to 3 times slower rates than the distal trp mRNA sequence. This has been demonstrated by employing the deletion mutants which lack a large portion of the structural genes but retain the promoter-proximal region of the trp operon. Relative stability of the leader RNA is not merely due to the presence of an untranslatable region in the segment; the internal untranslatable segment of trp mRNA downstream from the nonsense alteration site of a double mutant trpAD28.trpE9758 decays as fast as the normal trp mRNA sequence. These results suggest that the trp mRNA is endonucleolytically cleaved to yield the small 5'-proximal leader RNA segment before the distal mRNA decays and that the leader RNA sequence is not subject to usual mode of mRNA decay in the 5' to 3' direction.

PL-promoted transcription of the promoter-proximal N-trp region is insensitive to chloramphenicol in the absence of N function

When the trp operon is translocated into the early region of lambda phage, transcription originated at the PL promotor is known to be modified by function of the N gene product so that transcription of the operon continues when translation is blocked by nonsense mutations or by ribosomal antibiotics. When N function is deficient in a phage that joins the trp operon to a point distal to the N gene, deleting the tL site, nonsense mutations (Franklin, 1974) or chloramphenicol (Nakamura et al., accompanying paper) again block transcription of the bacterial operon. However, here we report that transcription over about the first 800 nucleotide pairs starting from the PL promotor of the N-trp operon is still insensitive to chloramphenicol even in the absence of N function. The region covers the full N gene and the initial bit of the trp operon.

Restoration of polarity by N-deficiency in lambda phage containing a translocated trp operon segment

When translation of trp mRNA is terminated by a nonsense codon or by antibiotics like chloramphenicol, the amount of the mRNA distal to the blocked ribosomes is found at much lower levels ("polarity"). Polarity is alleviated when the trp mRNA is formed as part of a long transcript from the phage lambda promoter PL (Segawa and Imamoto, 1974; Franklin, 1974); but the relief of polarity is itself largely dependent on the lambda protein N. In a phage that joins the trp operon segment (trpD, C, B A) to a point distal to the N gene, lacking the tL site, synthesis of trp mRNA starting at the PL promoter continues even when translation is generally inhibited by chloramphenicol, but in the absence of functional N gene product synthesis of the mRNA can be blocked by the antibiotic. Unexpectedly, in the absence of N function, even when translation is occurring, weak termination of transcription occurs at some sites in the translocated trp operon.

Function of the tof gene product in modifying chemical stability of trp messenger RNA synthesized from the PL promoter of lambda trp phage

The trp operon translocated into the early region of phage lambda can be transcribed under the control of two promoters, the authentic trp promoter (Ptrptrp mRNA) and the PL promoter of the N gene (PLtrp mRNA) (Imamoto and Tani, 1972; Ihara and Imamoto, 1976a). PLtrp mRNA is stabilized with time after infection: at early times after infection chemical degradation of PLtrp mRNA is two-fold slower than for Ptrptrp mRNA, while at later times the stabilization of PLtrp mRNA is almost total. The stabilization of PLtrp mRNA is markedly reduced when the activity of the tof gene product is low due to a missense mutation of the tof gene. In contrast there is no significant reduction in stabilization when N function is lost by an amber mutation. On the basis of these and other experiments with lambdatrp susN7 tof12 phage, it is inferred that stabilization of the PLtrp mRNA is brought about by a modification of the "decay trigger", at least in part by the protein product of the tof gene.

Gene affecting longevity of messenger RNA: a mutant of Escherichia coli with altered mRNA stability

We have screened 897 temperature sensitive growth mutants of E. coli for mutant strains showing longer mRNA half-life. The fate of pulse-labelled RNA was examined at 42 degrees C after cessation of RNA synthesis and with prior exposure to nonpermissive temperature (42 degrees C). Eight stains showed altered turnover of RNA (presumably mRNA), and further analysis on mutant strain JE15144 indicated that the stability of pulse-labeled RNA as well as of tryptophan (trp) mRNA increased four to seven fold over its parental strain at 42 degrees C. At 4 min or 10 min after addition of rifampicin, some 70 to 80% of polyribosome in the growing cells could still be conserved in JE15144 cultured at the nonpermissive temperature while little, if any, polyribosomes remained in its parental strain (PA3092) under the same condition. Two generation times were required for complete stoppage of growth of this mutant strain after shifting to 42 degrees C, and protein synthesis continued at a significant, but slightly reduced, rate at 42 degrees C. However, functional decay of mRNA in the mutant strain, with respect to the capacity for producing peptides, appeared to be similar to the parent strain, with half-lives of 3.5 min in PA3092 and 4.7 min in JE15144.

In vitro transcription of the tryptophan operon in isolated bacterial nucleoids

In vitro transcription of the trp operon in isolated nucleoids from Escherichia coli was studied. RNA synthesis in this system occurred primarily as a continuation of transcription which had been initiated in vivo; little or no initiation of new RNA chains was observed. Transcription of the trp operon in nucleoids by endogenous RNA polymerase procedded efficiently and ceases sequentially in the order of the gene sequence within the operon. Under these conditions, no appreciable exonuccleolytic digestion of nascent 3H-RNA was found, though some endonucleolytic cleavage was generally seen. Little or no incorporation of 14C-leucine into polypeptides was observed, inspite of tha fact that considerable number of ribosomes and nascent RNA chains were found attached to the isolated nucleoids. The synthesis of trp mRNA continued in the presence of chloramphenicol or fusidic acid, or under conditions where the rebosomal translocation factor G was inactivated. From these and other kinetic studies of trp mRNA synthesis in nucleoids obtained from nonsense strong polar mutants of the trp operon, it was shown that transcription in nucleoids was not connected functionally with transloational processes and thus unable to exhibit polarity effected by a nonsense mutation or by general translational blockage. In studies employing nucleoids from nonsense strong polar mutants of the trp operon, it was demonstrated that RNA polymerase are scantily distributed over the region downstream from the nonsense mutation site of the operon, thereby supporting a notion that in vivo transcription is eventually terminated near the nonsense mutation.

Stability of "spacer" sequences of pre-ribosomal RNA in Escherichia coli

"SPACER" SEQUENCES OF AN RRNA gene transcript were detected with high efficiency by hybridization with DNA of the specilized transducing phase phi80rrn. Hybridization-competition studies revealed that 20 to 23% of the 30S precursor rRNA, obtained from E. coli mutant strain AB301/105, consist of "spacer" sequences. The "spacer" sequences formed hybrids with E. coli DNA, but not with Vibrio DNA. Experiments with RNA labeling in the presence of rifampicin showed that more than 80% of the spacer sequences arrive in full-length 30S pre rRNA chains before any cleavage of the RNA occurs. The hybridization assays also permitted the detection of "spacer" sequences in pulse-labeled rRNA of wild-type cells, in which the 30S pre-rRNA is already cleaved during its synthesis. Many of these "spacer" sequences degraded to alcohol-soluble materials with a half-life time of 1.2 min. The half-life was not lengthened by the treatment of cells with chloramphenicol, which stabilizes bulk mRNA. However, unstable "spacer" sequences transcribed in cells deficient in RNase III exhibited slower degradation, with a half-life time of about 9 min, whereas the cleavage of 30S pre-rRNA to smaller RNA species occurred with a half-life of about 3 min. These results are consistent with the notion that a rate-limiting action of RNase III in the initial attack leads to degradation of "spacer" sequences in rRNA gene transcript; and that degradation is not at all connected with ribosome translocation.

Differential sensitivity to antibiotics of trp mRNA synthesis originating at the trp promoter and the lambda promoter

Transcription of the Escherichia coli trp operon translocated into the early region of bacteriophage lambda can occur under the control of either of two promoters, the trp promoter on the lambda promoter (OL of N gene). (Imamato, F. and Tani, S. (1972) Nat. New Biol. 240, 172-175 and Ihara S. and Imamoto, F. (1976) Biochim. Biophys. Acta 432, 199-211). Trp mRNA synthesis originating at the trp promoter stopped when translation was blocked by chloramphenicol tetracycline erythromycin or puromycin. In contrast, trp mRNA synthesis originating at the lambda promoter was not affected by antibiotic action. This probably is a reflection of the properties of the "immediate early" class of genes of lambda, whose transcription in initiated at the PL. promoter and is not inhibited by the antibiotic. The inference is strengthened by comparable results with phage lambdatrpE-A (carrying an intact tro operon) and lambdatrpBA (carrying the operator-distal two genes but missing the trp promoter and operator). Thus it seems that either the promoter or other gene(s) located at the beginning of the operon, either at polymerase addition or because of some feature of the transcript, can determine a requirement for "coupling" of RNA polymerase to the translational machinery in vivo.

Coupling of rates of transcription, translation, and messenger ribonucleic acid degradation in streptomycin-dependent mutants of Escherichia coli

The growth rates of streptomycin-dependent mutants varied in proportion to the level of streptomycin supplied; growth also varied characteristically from one dependent strain to another at a given streptomycin concentration. When cells growing at different rates (over a threefold range) were treated with rifampin, direct proportionality was observed for three parameters: (i) the rates of shutoff of transcription of total ribonucleic acid (RNA) and ribosomal RNA, as measured by pulse labeling at later times; (ii) the translation time for molecules of beta-galactosidase; and (iii) the rate of chemical degradation of messenger RNA. In contrast, the rate of functional inactivation of both total and beta-galactosidase messenger RNA was about the same at all growth rates. None of the variations of growth or other parameters were observed in an otherwise isogenic streptomycin-resistant strain treated with streptomycin. Since the mutational change in strd mutants and the site of action of streptomycin are in the 30S ribosomal subunits, it is suggested that the rate of ribosome function is set by the dependent lesion (and the level of streptomycin). One possibility is that the other correlated effects are mechanistically "coupled" to ribosome function, but the apparent coupling could also be an indirect result of differential effects of streptomycin on variables such as ribosomal miscoding and nucleotide pool size. However, since the rate of functional inactivation of messenger RNA is constant even when the RNA is broken down two- to fourfold more slowly, translation yield tends to be proportional to the growth rate of the dependent strains.