Difference between functional and structural integrity of messenger RNA

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.

The functional stability of the lacZ transcript is sensitive towards sequence alterations immediately downstream of the ribosome binding site

Various synthetic DNA sequences were inserted downstream of the fourth codon of the Escherichia coli lacZ gene on plasmids containing a hybrid lacZ-galK operon. Several different sequences, one as short as 10 bp, reduced the functional stability of the lacZ message three- to fourfold, whereas others had little or no effect. Introduction of synthetic sequences into a plasmid containing the intact lac operon resulted in similar reductions of mRNA stability. The sequence alterations also reduced the translational efficiency and transcription through lacZ as monitored by measurements of galactokinase synthesis from the downstream galK gene. There was no correlation between the average translational frequency and the stability of the lacZ message indicating that some of the inserted sequences reduced mRNA stability directly and not as a consequence of their effect on translation. The reduction of transcription through the lacZ gene correlated with the reduction of translation in agreement with current models of transcriptional polarity.

Exclusion of bacteriophage T1 by bacteriophage lambda. II. Synthesis of T1-specific macromolecules under N-mediated excluding conditions

The results of experiments investigating T1 macromolecular synthesis under N-mediated excluding conditions failed to demonstrate a substantial alteration in the T1 mRNA production in excluding cultures at any stage in the T1 infectious cycle. The number of T1 DNA sequences in the excluding culture was found to be one-third to one-half that found in T1-infected cultures. The most severe reduction in T1-specific macromolecules was seen in protein synthesis. Total incorporation of labeled amino acids was reduced sixfold, and gel experiments confirmed that the T1-specific proteins capable of detection are reduced in excluding cells.

Transcriptional regulation of the yeast cytochrome c gene

DNA from the cloned yeast iso-1-cytochrome c, cycl, gene was used in a hybridization assay to measure levels and rates of synthesis of cycl RNA. Derepressed cells synthesized cycl RNA at 6 times the rate of that of glucose-repressed cells. Upon glucose addition to a derepressed culture, the transcription of the cycl gene was repressed within 2.5 min. The half-life of hybridizable cycl RNA was determined to be 12-13.5 min under repressed and derepressed conditions and during repression. The results demonstrate that the expression of the cycl gene is subject to transcriptional regulation.

Unusual stability and translation kinetics of an Escherichia coli lac messenger RNA synthetized during amino-acids deprivation

Escherichia coli, cultured on minimal medium and deprived of its required amino-acids, was induced for lac genes transcription. After inducer removal and restoration of growth, beta-galactosidase synthesis was measured. Two different kinetics of enzyme synthesis were observed depending on the starvation conditions employed during the induction period: 1. beta-galactosidase synthesis was immediately obtained and a plateau was reached, in 20 min after restoration of growth, when cells had been induced during deprivation of amino-acids and carbon source. 2. beta-galactosidase displayed an unusually long rate of synthesis, and plateau was not reached before two doubling times, when cells had been induced during the deprivation of the sole amino-acids. The latter result points out a problem of messenger stability during those long translation kinetics and led us to study the behaviour of strains carrying lac genetic determinants on different replicative structures; chromosomic and plasmidic. In those two situations, induction of lac messenger RNA was obtained and ratify our previous observations. However, their translation kinetics suggest a DNA linkage of this induced messenger.

Functional half-lives of bacteriophage m13 gene 5 and gene 8 messages

The half-lives of the M13 gene 5 and gene 8 messages were determined by measuring the decay in the rate of synthesis of the gene 5 and gene 8 proteins after inhibition of new RNA chain initiations with rifampin. The gene 5 and gene 8 messages decay with half-lives of approximately 2.5 and 5 min, respectively. We found no evidence of a functional M13 message with a half-life as long as that reported for hybridizable mRNA.

Early gene expression in bacteriophage T7. I. In vivo synthesis, inactivation, and translational utilization of early mRNA's

In vivo decay rates for the individual T7 early mRNA species were determined. The physical half-lives, measured at 37 C, range from 1.1 min for gene 0.7 RNA to 4.5 min for gene 0.3 RNA. Physical half-lives, as observed after rifampin inhibition of RNA synthesis and polyacylamide electrophoresis of RNAs, are approximately 30% longer than functional half-lives, as observed by 14C-labeled amino acid uptake into individual T7 early proteins. The different RNA species are synthesized at grossly different rates, 0.3 RNA at four times the rate of 1.0 RNA, 0.7 RNA at twice the rate, and 1.1 and 1.3 RNAs at about the same or a slightly lower rate than 1.0 RNA. Rho-factor-mediated termination of transcription behind genes 0.3, 0.7, and perhaps behind 1.0 is inferred from these data. The in vivo translational utilization of the individual T7 early-message species was found to vary by not more than a factor of 2.

Effects of triiodothyronine on rat-liver mitochondrial transcription process

1. In order to demonstrate that triiodothyronine affects mitochondrial RNA synthesis by acting on the enzyme component of the DNA. RNA polymerase complex, mitochondrial RNA polymerase from thyroidectomized and hormone-treated rats was purified up to a stage in which activity was dependent on the addition of exogenous template. In these conditions and using different DNAs as templates, the enzyme from hormone-treated animals displayed an activity about double that of the activity of thyroidectomized animals. 2. Measurements of stability of mitochondrial RNA synthesized in vitro suggest, however, that the hormone can act also at the template level in mitochondrial transcription: the RNA population synthesized in vitro from hormone-treated rats is indeed much more enriched in unstable, probably messenger, RNA species. 3. The turnover of mitochondrial messenger RNA is higher after hormone treatment. 4. Adenosine cyclic 3':5'-monophosphate (cAMP) and its dibutyryl derivative added in vitro to mitochondria from thyroidectomized animals do not affect the incorporation of labeled precursor into mitochondrial RNA, suggesting that the level of the cyclic nucleotide in mitochondria is probably not involved in the hormone action. 5. It is concluded from these and previous studies that the thyroid hormone affects more than one parameter in the mitochondrial transcription process. The interrelationship between these events at molecular level remains, however, to be clarified.