In vivo stability, maturation and relative differential synthesis rates of individual ribosomal proteins in Escherichia coli B/r

Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources

Quantitative views of cellular functions require precise measures of rates of biomolecule production, especially proteins-the direct effectors of biological processes. Here, we present a genome-wide approach, based on ribosome profiling, for measuring absolute protein synthesis rates. The resultant E. coli data set transforms our understanding of the extent to which protein synthesis is precisely controlled to optimize function and efficiency. Members of multiprotein complexes are made in precise proportion to their stoichiometry, whereas components of functional modules are produced differentially according to their hierarchical role. Estimates of absolute protein abundance also reveal principles for optimizing design. These include how the level of different types of transcription factors is optimized for rapid response and how a metabolic pathway (methionine biosynthesis) balances production cost with activity requirements. Our studies reveal how general principles, important both for understanding natural systems and for synthesizing new ones, emerge from quantitative analyses of protein synthesis.

In silico method for modelling metabolism and gene product expression at genome scale

Transcription and translation use raw materials and energy generated metabolically to create the macromolecular machinery responsible for all cellular functions, including metabolism. A biochemically accurate model of molecular biology and metabolism will facilitate comprehensive and quantitative computations of an organism's molecular constitution as a function of genetic and environmental parameters. Here we formulate a model of metabolism and macromolecular expression. Prototyping it using the simple microorganism Thermotoga maritima, we show our model accurately simulates variations in cellular composition and gene expression. Moreover, through in silico comparative transcriptomics, the model allows the discovery of new regulons and improving the genome and transcription unit annotations. Our method presents a framework for investigating molecular biology and cellular physiology in silico and may allow quantitative interpretation of multi-omics data sets in the context of an integrated biochemical description of an organism.

Organelle growth control through limiting pools of cytoplasmic components

The critical importance of controlling the size and number of intracellular organelles has led to a variety of mechanisms for regulating the formation and growth of cellular structures. In this review, we explore a class of mechanisms for organelle growth control that rely primarily on the cytoplasm as a 'limiting pool' of available material. These mechanisms are based on the idea that, as organelles grow, they incorporate subunits from the cytoplasm. If this subunit pool is limited, organelle growth will lead to depletion of subunits from the cytoplasm. Free subunit concentration therefore provides a measure of the number of incorporated subunits and thus the current size of the organelle. Because organelle growth rates are typically a function of subunit concentration, cytoplasmic depletion links organelle size, free subunit concentration, and growth rates, ensuring that as the organelle grows, its rate of growth slows. Thus, a limiting cytoplasmic pool provides a powerful mechanism for size-dependent regulation of growth without recourse to active mechanisms to measure size or modulate growth rates. Variations of this general idea allow not only for size control, but also cell-size-dependent scaling of cellular structures, coordination of growth between similar structures within a cell, and the enforcement of singularity in structure formation, when only a single copy of a structure is desired. Here, we review several examples of such mechanisms in cellular processes as diverse as centriole duplication, centrosome and nuclear size control, cell polarity, and growth of flagella.

Decay of rplN and lacZ mRNA in Escherichia coli

To examine the previously proposed retroregulation model of spc mRNA degradation, two strains of Escherichia coli B/r were used; one has wild-type spc and lac operons and the other has a lac operon deletion, a wild-type spc operon, and a Pspc-rplN-lacZ fusion operon lacking the normal control sites of the spc operon (rplN is the first gene in the spc operon of ribosomal proteins). The decay of rplN mRNA and of lacZ mRNA in these strains was determined during exponential growth at different rates and after transcript initiation was inhibited by the antibiotic rifampicin. Functional decay of lacZ mRNA was monitored by measurements of beta-galactosidase activity and chemical decay was monitored using probes complementary to rplN, rplX, and to the 5' and 3'-terminal sections of lacZ. Analysis of the data was based on the assumption that the decay involves an endonucleolytic cleavage that functionally inactivates the mRNA and that this is followed by exonucleolytic degradation of the cleavage products. The major conclusions were: (1) During exponential growth, lacZ mRNA of the lac operon was translated about twice as frequently as lacZ mRNA of the spc-lac fusion, and both kinds of lacZ mRNA were translated at an elevated rate in the presence of rifampicin. (2) For lacZ mRNA from the lac operon, the endonuclease inactivation reaction was not affected by rifampicin, but the exonuclease reaction was inhibited. (3) The decay of rplN mRNA from the spc operon was accelerated in the presence of rifampicin; the average life was estimated to be six minutes during exponential growth in LB medium, and 2.8 minutes in the presence of rifampicin. (4) The decay of the rplN section of mRNA from the spc-lac operon fusion was coupled to the decay of the downstream lacZ mRNA section and was strongly inhibited (i.e. partially blocked) in the presence of rifampicin. These results show that the decay of spc mRNA differs in some important aspects from the decay of lac mRNA and support the retroregulation model. Moreover, the results indicate that rifampicin can have a significant and selective impact on the kinetics of both mRNA translation and decay.

Expression of lacZ from the promoter of the Escherichia coli spc operon cloned into vectors carrying the W205 trp-lac fusion

The expression of lacZ has been analyzed and compared in a series of promoter cloning vectors by measuring the amount of lacZ mRNA by hybridization and the amount of beta-galactosidase by standard enzymatic assay. Expression was driven by the promoter, Pspc, of the spc ribosomal protein operon. The vectors contained either the standard W205 trp-lac fusion with the trp operon transcription terminator, trpt, located in the lacZ leader sequence, or a deletion derivative that functionally inactivates trpt. In the presence of trpt, lacZ expression was temperature dependent so that increasing the growth temperature reduced the accumulation of lacZ mRNA and beta-galactosidase activity. The frequency of transcript termination at trpt was estimated to be near zero at 20 degreesC and at about 45% at 37 degreesC. The amount of Pspc-derived lacZ mRNA and the amount of beta-galactosidase produced per lacZ mRNA varied, depending on the mRNA 5' leader sequence between Pspc and lacZ. These results demonstrate that the quantitative assessment of promoter activities with promoter cloning vectors requires careful analysis and interpretation. One particular construct without trpt did not seem to contain fortuitous transcription or translation signals generated at the fusion junction. In this strain, lacZ expression from Pspc was compared at the enzyme activity and mRNA levels with a previously constructed strain in which lacZ was linked to the tandem P1 and P2 promoters of the rrnB operon. At any given growth rate, the different activities of beta-galactosidase in these two strains were found to reflect the same differences in their amounts of lacZ mRNA. Assuming that the promoter-lacZ fusions in these strains reflect the properties of the promoters in their normal chromosomal setting, it was possible to estimate the absolute transcription activity of Pspc and the relative translation efficiency of Pspc-lacZ mRNA at different growth rates. Transcription from the spc promoter was found to increase from about 10 transcripts per min at a growth rate of 1.0 doublings/h to a maximum plateau of about 23 transcripts per min at growth rates above 1.5 doublings/h. The translation frequency of lacZ mRNA expressed from Pspc was unaffected by growth rates.

The effects of mutations in the rpmB,G operon of Escherichia coli on ribosome assembly and ribosomal protein synthesis

The rpmB,G operon of Escherichia coli codes for proteins L28 and L33 of the larger (50S) ribosomal subunit. Strains with mutations in this operon can help define the roles of these proteins in ribosome synthesis and function. One such strain, BM108, makes neither protein and is unable to synthesize completed ribosomes; instead ribonucleoproteins accumulate, in the form of '30S material' and '47S particles'. However, when protein L28 is supplied from a plasmid, the growth rate, the kinetics of ribosome synthesis and the coordination of ribosomal protein synthesis are no different from that in wild-type organisms even though protein L33 is missing. This suggests that the latter protein can be redundant for ribosome synthesis and function. Another mutant strain, BM81, has a frameshift mutation that gives rise to an oversized protein L28. This mutant accumulates 30S material and 47S particles during slow exponential growth. The composition of the 47S particles from strains BM81, BM108 and a third mutant strain, TP28, suggests that their defining feature is the absence of L28; this is further evidence for an important role for this protein in ribosome assembly. Accumulation of ribonucleoproteins in strains BM81 and BM108 leads to some loss of the ordinarily precise coordination of synthesis of ribosomal proteins. We describe and discuss the characteristic features of this unbalanced synthesis.

Mutations in the rpmBG operon of Escherichia coli that affect ribosome assembly

The rpmBG operon of Escherichia coli codes for ribosomal proteins L28 and L33. Two strains with mutations in the operon are AM81, whose ribosomes lack protein L28, and AM90, whose ribosomes are without protein L33. Neither strain showed major defects in ribosome assembly. However, when the mutations were transferred to other strains of E. coli, ribosome synthesis was greatly perturbed and precursor ribonucleoproteins accumulated. In the new backgrounds, the mutation in rpmB was complemented by synthesis of protein L28 from a plasmid; the rpmG mutation was not complemented by protein L33 because synthesis of protein L28 from the upstream rpmB gene was also greatly reduced. The results suggest that protein L33, in contrast to protein L28, has at best a minor role in ribosome assembly and function.

Degradation of rRNA in Salmonella strains: a novel mechanism to regulate the concentrations of rRNA and ribosomes

We have previously shown that the 23S rRNA of Salmonella strains is highly fragmented by specific enzyme cleavages. In this article, we report that 23S rRNA of Salmonella strains is rapidly degraded as the cells enter the stationary phase. More than 90% of the 23S rRNA is degraded when the cells reach the stationary phase. The rate of degradation of 23S rRNA correlated with its degree of fragmentation. This degradation is probably mediated by newly synthesized protein factor(s), since treatment with chloramphenicol or rifampin inhibits the rRNA degradation. We propose that degradation of 23S rRNA is a novel mechanism in the regulation of the bacterial 23S rRNA and ribosome concentration and that this additional regulatory mechanism provides some selective advantage to cells.

Biomass growth rate during the prokaryote cell cycle

The rate of biomass growth throughout the cell cycle of prokaryotes is important in the study of global regulation. Two limiting cases have generally been considered: the exponential model and the linear model. The exponential model is a logical expectation because protein, the main component of biomass of a bacterial cell, increases continuously during the cell cycle and therefore the means for synthesis of other cell components and metabolites also increases. In addition, during the cell cycle, ribosomes, the means of production of proteins, increase monotonically. As a consequence, the increase of all should be autocatalytic and the content of cell substance should be an exponential function of time. Two cellular components would not be expected to increase exponentially: the DNA and the cell envelope. The former because of the intermittent synthesis of the chromosome, and the latter because of changes in the surface-to-volume ratio with growth and division. In contrast to the exponential model, the linear model of Kubitschek postulates that the cell only increases its membrane transport capability over a brief period during the cell cycle, and, thus limited by transport, all cell components can increase only at a constant linear rate during most of the cell cycle. Other proposed models are intermediate and assume that the growth rate of the cell depends on some cell cycle event, such as the initiation of chromosome replication. The models have relevance to prokaryotes undergoing balanced growth; they may not be relevant to eukaryotic microbes or to eukaryotic cells in tissue culture that have endogenous rhythms or are controlled by protein growth factors. Logically, the models could possibly apply to a free-living cell that does not respond to environmental cues. Even under rigidly constant conditions, however, cells may try to respond to a stimulus that was periodic or regulatory under natural conditions, but is present at a constant level under the experimental culture condition. There are four classes of experiments that have been used to measure the accumulation of dry biomass or its components during the cell cycle of a bacterium, as typified by Escherichia coli. For the first class of experiments, the dimensions of living cells are measured under the microscope. So far, the experiments have been limited by the resolving power of the phase microscope, but adequate resolution should be possible with the confocal scanning light microscope or various video computer systems. Such experiments are called integral because augmentation of cell constituents is followed. The second class involves pulse-chase labeling of cells and then their separation into different phases of the cycle or age groups and measurement of the radioactivity per cell in the fractions. Such experiments are called differential in that the rate is measured directly instead of being deduced by comparing the total size at different times.(ABSTRACT TRUNCATED AT 400 WORDS)

Autogenous control is not sufficient to ensure steady-state growth rate-dependent regulation of the S10 ribosomal protein operon of Escherichia coli

The regulation of the S10 ribosomal protein operon of Escherichia coli was studied by using a lambda prophage containing the beginning of the S10 operon (including the promoter, leader, and first one and one-half structural genes) fused to lacZ. The synthesis of the lacZ fusion protein encoded by the phage showed the expected inhibition during oversynthesis of ribosomal protein L4, the autogenous regulatory protein of the S10 operon. Moreover, the fusion gene responded to a nutritional shift-up in the same way that genuine ribosomal protein genes did. However, the gene did not exhibit the expected growth rate-dependent regulation during steady-state growth. Thus, the genetic information carried on the prophage is sufficient for L4-mediated autogenous control and a normal nutritional shift-up response but is not sufficient for steady-state growth rate-dependent control. These results suggest that, at least for the 11-gene S10 ribosomal protein operon, additional regulatory processes are required to coordinate the synthesis of ribosomal proteins with cell growth rate and, furthermore, that sequences downstream of the proximal one and one-half genes of the operon are involved in this control.

Non-autogenous control of ribosomal protein synthesis from the trmD operon in Escherichia coli

The trmD operon of Escherichia coli encodes the ribosomal proteins S16 and L19, the tRNA(m1G37)methyltransferase and a 21,000 Mr protein of unknown function. Here we demonstrate that, in contrast to the expression of other ribosomal protein operons, the amount of trmD operon mRNA and the rate of synthesis of the proteins encoded by the operon respond to increased gene dosage. The steady-state level of the mRNA was about 18 times higher, and the relative rate of synthesis of the ribosomal proteins S16 and L19, the tRNA(m1G37)methyltransferase and the 21,000 Mr protein was 15, 9, 25 and 23 times higher, respectively, in plasmid-containing cells than in plasmid-free cells. Overproduced tRNA(m1G37)methyltransferase and 21,000 Mr protein were as stable as E. coli total protein, whereas the two ribosomal proteins were degraded to a large extent. The steady-state amount of S16 and L19 in the plasmid-containing cells exceeded that in plasmid-free cells by threefold and twofold, respectively. No significant effect on the synthesis of the trmD operon proteins from the chromosomally located genes was observed when parts of the operon were expressed on different plasmids. Taken together, these results suggest that the expression of the trmD operon is not subject to transcriptional or translational feedback regulation, and demonstrate that not all ribosomal protein operons are regulated in the same manner. We propose that ribosomal protein operons that do not encode proteins that bind directly to rRNA are not under autogenous control. Metabolic regulation at the transcriptional level and protein degradation are plausible mechanisms for the control of expression of such operons.

Growth rate-dependent regulation of RNA polymerase synthesis in Escherichia coli

The rate of synthesis of the beta and beta' subunits of RNA polymerase relative to the rate of synthesis of total protein was found to remain constant with increasing steady state growth rate. This is in contrast to the relative synthesis rates of ribosomal proteins which are known to increase with growth rate. Yet the ratio of the rate of transcription of the ribosomal protein (rplJL) and RNA polymerase (rpoBC) domains of the rplKAJLrpoBC gene cluster was found to be invariant. Fusions to lacZ were used to relate the rate of transcription of the rplKAJL genes to the rate of synthesis of total protein. No change was seen at growth rates above 0.8 doublings per hour. This indicates that the growth rate-dependent expression of these ribosomal proteins is regulated at the post-transcriptional level. However because both the relative rate of transcription of rpoBC and rate of synthesis of beta and beta' were found to remain invariant over this growth range it suggests the expression of these RNA polymerase subunits is regulated at the transcriptional level.

Increased expression of ribosomal genes during inhibition of ribosome assembly in Escherichia coli

We have examined a prediction made from the ribosome feedback regulation model of ribosomal RNA and transfer RNA synthesis in Escherichia coli. This model proposes that non-translating "free" ribosomes act directly or indirectly as negative feedback inhibitors to regulate the transcription of rRNA and tRNA operons. One prediction of this model is that preferential inhibition of the assembly of ribosomes (without inhibiting macromolecular synthesis) should lead to a deficiency of free ribosomes which should, in turn, cause a stimulation of rRNA (and tRNA) synthesis. We have examined this prediction in vivo by causing the preferential inhibition of synthesis of certain ribosomal proteins by an overproduction of the translational repressor ribosomal protein S4. In agreement with our model, we have observed a preferential stimulation of ribosomal protein messenger RNA and rRNA synthesis under these conditions. These results suggest that ribosomes in the cellular pool, rather than incomplete ribosomal particles or free rRNA, are monitored by cells to regulate the rate of rRNA synthesis, and give further support to this proposed model.

Ribosomal protein synthesis by a mutant of Escherichia coli

The mutant strain of Escherichia coli, TP28, synthesises ribosomes by an abnormal pathway and accumulates large quantities of 47S ribonucleoprotein particles. The protein complement of mutant 70S ribosomes is normal but 47S particles contain only traces of proteins L28 and L33 and have a significantly reduced content of four other proteins. The mutation reduces the rates of synthesis of L28 and L33 by about half but other widespread alterations ensue. In particular, ribosomal protein synthesis in the mutant strain becomes less well balanced than in its parent: some proteins, particularly those from promoter-proximal genes, are oversynthesized and their excess then degraded.

Regulation of ribosome synthesis in Tetrahymena pyriformis. 1. Coordination of synthesis of ribosomal proteins and ribosomal RNA during nutritional shift-down

When exponentially growing cells of Tetrahymena pyriformis are transferred to a non-nutrient medium the loss of whole cell RNA, 90% of which is ribosomal RNA, exhibits biphasic kinetics, whereas whole cell protein is lost at a constant rate. The ratio RNA/protein declines during the first 5 h of starvation and then remains constant during the subsequent period of starvation. The synthesis of the majority of the ribosomal proteins is coordinately regulated during a nutritional shift-down. Exponentially growing cells devote 17% of their capacity for protein synthesis to the production of ribosomal proteins. Upon starvation this proportion is rapidly reduced 3.5-fold. In long-time-starved cells the absolute rate of ribosomal protein synthesis is only about 4.5% of that of exponentially growing cells. The synthesis of ribosomal RNA and ribosomal proteins appears tightly coupled during the transition from growth to starvation. In long-time-starved cells the synthesis of ribosomal RNA and ribosomal proteins are stoichiometrically balanced with no significant degradation of de novo synthesized ribosomal proteins.

Levels of ribosomal protein S1 and elongation factor G in the growth cycle of Escherichia coli

The relative levels of ribosomes, ribosomal protein S1, and elongation factor G in the growth cycle of Escherichia coli were examined with two-dimensional polyacrylamide gel electrophoresis. Nonequilibrium pH gradient polyacrylamide gel electrophoresis was used in the first dimension, and polyacrylamide gradient-sodium dodecyl sulfate gel electrophoresis was used in the second dimension. The identities of protein spots containing S1 and elongation factor G were confirmed by radioiodination of the proteins and peptide mapping of the radiolabeled peptides. The levels of ribosomes and ribosomal protein S1 were coordinately reduced during transition from exponential phase to stationary phase. There was no accumulation of S1 in the stationary phase. In marked contrast, the level of elongation factor G showed no significant change from exponential phase to stationary phase. The relative level of elongation factor G compared with ribosomes or S1 increased by about 2.5-fold during transition from exponential phase to stationary phase. The results show that there are differences between the regulation of the levels of elongation factor G and of ribosomal proteins, including S1, apparent during the transition from exponential to stationary phase.

Expression of the gene for ribosomal protein S20: effects of gene dosage

We have exploited the properties of three different plasmids which carry the gene for Escherichia coli ribosomal protein S20 (rpsT) to test the effects of gene dosage on the expression of rpsT. Over a range of total copies of rpsT of 1 to 58 per haploid genome equivalent, the rate of incorporation of uridine during a 30-s pulse into RNA annealing to either of two specific probes for S20 mRNA increased essentially in proportion to copy number. In contrast, the rate of synthesis of S20 protein increased no more than 2.1-fold at the highest copy number. We conclude, in contrast to an earlier report (D. Geyl, and A. Böck, Mol. Gen. Genet. 154:327-334, 1977), that the synthesis of S20 is regulated at a posttranscriptional step. We propose that S20 itself is the regulatory agent and that binding of S20 to its own mRNA in regions homologous in structure with 16S rRNA can account for our results.

The lethal effect of a plasmid resulting from transcriptional readthrough of rplJ from the rplKA operon in Escherichia coli

A high-copy plasmid, pGA217, which carries a deletion (lacking the carboxy-terminal 20 amino acids) of the structural gene for ribosomal protein L10 (rplJ) is lethal to the cell in the absence of the gene (rplL) for r-proteins L7/L12, but only if the upstream operon for r-proteins L11 (rplK) and L1 (rplA) is present on the same plasmid. Measurements of beta-galactosidase activity of a hybrid protein expressed by a rplL-lacZ fusion indicated that the L10 fragment peptide which lacks the carboxy-terminal 20 amino acids is capable of exerting feedback regulation. Double transformation experiments with two compatible plasmids showed that the detrimental effect of the rplJ deletion on pGA217 can be reversed by the addition of a second plasmid which carries a functional gene for L7/L12. These two pieces of evidence suggest that the lethal effect of pGA217 is due to its property of feeding back on L7/L12 production from the chromosomal rplK gene. The upstream rplKA operon was inferred to have a cis-acting, stimulating effect on rplJ expression from the following evidence: (1) donor plasmids carrying the genes for L11 and/or L1 fail to exert a trans-acting effect, (2) deletion mutants which removed portions of rplK and/or rplA, but maintained the rplKA promoter, rplKp, still retained a severe growth-inhibiting effect. We suggest that these results can be explained by assuming that there is transcription from the rplKA promoter through rplJ and perhaps beyond.

Mutations in the rpIJ leader of Escherichia coli that abolish feedback regulation

We have isolated mutants that fail to exhibit biosynthetic feedback regulation of a rpIJ-lacZ fusion. Analysis of these mutants and of others that were isolated earlier indicates that crucial sequences for both translational feedback regulation and efficient translation lie closely intermingled in the central region of the rpIJ mRNA leader 70-195 bases upstream from the translation start of rpIJ. We suggest that our point mutations define a region of the rpIJ leader mRNA to which L10 binds in effecting autogenous translational regulation.

Genetic analysis of a streptomycin-resistant Escherichia coli mutant temperature-sensitive for nonsense suppression

Continuing the genetic and biochemical characterization of the streptomycin-resistant Escherichia coli mutant LD1, we confirmed that LD1 is temperature-sensitive for suppression of nonsense codons, and that this phenotype of the mutant and its streptomycin-resistance are genetically linked and are probably caused by a single mutation, strA(LD1). We also isolated a spontaneous revertant, called LD1-R, which partially relieves the restriction of nonsense suppression caused by the strA(LD1) mutation. LD1-R is derived by an additional mutation (revA) which is closely linked to strA(LD1). We further demonstrate that the weak suppression of a lacZUGA mutation in a suppressor-free strain, which probably takes place by normal tRNA1rp, can be detected by the use of the chromagenic substance x-gal (5-Bromo-4-chloro-3-indolyl-beta-D-Galactopyranoside).

Chain initiation factor 3 crosslinks to E. coli 30S and 50S ribosomal subunits and alters the UV absorbance spectrum of 70S ribosomes

We report a direct procedure to determine the proteins near the IF-3 binding site in purified 30S and 50S ribosomal subunits. This procedure introduces only limited numbers of cleavable crosslinks between IF-3 and its nearest neighbors. The cleavable crosslinking reagent, 2-iminothiolane, was used to crosslink IF-3 in place to both 30S and 50S subunits. Ribosomal proteins S9/S11, S12, L2, L5 and L17 were found, by this approach, to be in close proximity to the factor in purified IF-3-subunit complexes. In addition, IF-3 was shown to alter the ultraviolet absorbance spectrum of E. coli 70S ribosomes at 10 mM Mg2+. The magnitude of the observed difference spectrum at a constant IF-3/ribosome ratio of 1.0, is linearly dependent upon ribosome concentration over the range 5 nM - 55 nM. Titration experiments indicated that the observed effect is maximal at an IF-3/ribosome ratio of approximately 1.0. These results are taken to indicate a conformational change in the 70S ribosome induced by IF-3.

Ribosomal protein genes rp 39(10 - 78), rp 39(11 - 40), rp 51, and rp 52 are not contiguous to other ribosomal protein genes in the Saccharomyces cerevisiae genome

A library of recombinant phage containing EcoR1 fragments of Saccharomyces cerevisiae DNA has been constructed. This library was screened with four different recombinant plasmids, each containing a different yeast ribosomal protein gene, in order to isolate chromosomal fragments extending in both directions from these genes. These chromosomal fragments were assayed for the presence of additional ribosomal protein genes by hybridization selection and cell free translation, and none were found. These four regions are not closely linked to each other, since DNA from one domain does not cross hybridize with DNA from any of the other three, except for the sequences within the homologous ribosomal protein 39 gene pair. Northern blots demonstrate that although the concentrations of ribosomal protein mRNAs are diminished significantly in a strain containing the ts mutation rna2, transcripts from genes in these flanking segments are relatively unaffected.

Transcriptional and post-transcriptional control of ribosomal protein and ribonucleic acid polymerase genes

A partial restriction of ribonucleic acid (RNA) polymerase activity has been used to dissociate the coordinate synthesis of ribosomal proteins and subunits of RNA polymerase and to identify transcriptional and post-transcriptional control signals which regulate the expression of these component genes. Within the beta operon [which has the genetic organization: promoter (p beta), rplJ (L10), r;lL (L7/L12), attenuator, rpoB (beta), rpoC (beta'), terminator], the restriction caused a disproportionate increase between proximal and distal gene transcriptions; the transcriptional intensities of the proximal ribosomal protein genes and the distal RNA polymerase genes were elevated about two- and fourfold, respectively. Transcription within the operon containing four ribosomal protein genes and the RNA polymerase alpha gene was also enhanced, whereas transcription within operons containing only ribosomal protein genes was virtually unaffected by the restriction. It was thus concluded that the mechanisms controlling transcription initiation or attenuation or both in operons containing RNA polymerase subunit genes are coupled to the global rate of RNA synthesis. By introducing the composite ColE1 plasmid pJC701 carrying the proximal portion of the L10 operon, including the beta subunit gene, it was possible to achieve a 10- and a 30-fold range in the transcriptional intensities of the genes specifying L10 and L7/L12 and beta, respectively. Under these conditions, the relative synthesis rates of L7/L12 and beta protein varied by less than 2-fold and by about 15-fold, respectively. These observations corroborate the existence of a post-transcriptional mechanism which severely restricts translation of excess L7/L12 and L10 ribosomal protein messenger RNA; this mechanism is probably important in maintaining the balanced synthesis of ribosome components under conditions in which their messenger RNA levels are dissociated. Furthermore, the observed reduction in the translation efficiency of beta subunit messenger RNA may be related to an inhibitory effect caused by accumulation of RNA polymerase assembly intermediates.

Lodish model and regulation of ribosomal protein synthesis by insulin-deficient chick embryo fibroblasts

The production of ribosomal proteins in chick embryo fibroblasts that have been deprived of insulin is depressed in a much greater degree than that of most or all other cell proteins. Previous observations ruled out explanations for the preferential decrease in ribosomal protein formation that depend upon a selective destruction of ribosomal protein messages or a regulatory role for nascent ribosomal ribonucleic acid. The proposition has now been examined that ribosomal protein messenger ribonucleic acids (mRNAs) in the hormone-deficient chick embryo cells have a lower affinity for a limiting, early acting component of the initiating machinery than do most other cell messages and, in consequence, suffer from a translational disadvantage. The approach that was used depends upon the findings of Lodish and others that all mRNAs are not initiated with equal ease, that inhibitors of elongation favor the initiation of low-affinity mRNAs, and that agents that dampen an early step in initiation discriminate against the low-affinity messages. The idea was tested by comparing the effects of various inhibitors on the rates of synthesis of total cell protein and individual nonribosomal proteins, on the one hand, with those of individual ribosomal proteins, on the other. The results fit the Lodish model and are consistent with the conclusions that ribosomal protein mRNAs are more poorly initiated in the resulting fibroblasts than are most or all other cell messages and that this condition is largely or entirely responsible for the low rate of ribosomal protein formation.

Reduction of ribosome activity and synthesis of stable RNA in Neurospora crassa

The addition of cycloheximide (0.02 micrograms/ml) to exponentially growing cultures of Neurospora crassa causes a reduction in growth rate and a decrease in the rate of protein accumulation, due to a partial inhibition of protein synthesis, while RNA accumulation is unaffected for about 1 h. Thus, an increased RNA:protein ratio is established in the presence of the inhibitor. RNA that accumulates during treatment with cycloheximide has the same characteristics as that of the control cultures and this, together with the enhancement of the relative rate of synthesis of ribosomal proteins induced by cycloheximide, seems to indicate that more mature ribosomes are present in cycloheximide-treated cultures. The endocellular level of several amino acids begins to increase significantly only 60 min after cycloheximide addition. A possible explanation of the stimulation of ribosome production induced by cycloheximide is given in terms of the existence of a feed-back mechanism controlling ribosome synthesis.

Synthesis of ribosomal proteins in merodiploid strains of Escherichia coli

The regulation of the synthesis of r-proteins in Escherichia coli was investigated by increasing the dosage of the genes for a limited number of ribosomal proteins (r-proteins) using either transducing phage lambda fus 3 (Lindahl et al. 1977) or lambda rifd 18 (Kirschbaum and Konrad 1973). During exponential growth the presence in the cell of either lysogenised transducing phage did not increase the rate of synthesis or degradation of any of the 31 r-proteins whose genes are duplicated. Experiments were also performed to determine whether r-protein synthesis during the period of unbalanced r-protein synthesis that follows nutritional enrichment was sensitive to an increase in gene dosage. Duplication of the 27 r-protein genes on lambda fus 3 did not alter the rate of synthesis of any of the r-proteins after enrichment. However, gene dosage effects were detected for at least 3 of the r-proteins whose genes were duplicated on lambda rifd 18.

Post-transcriptional regulatory mutants in a ribosomal protein-RNA polymerase operon of E. coli

A high copy number plasmid that carries the promoter PJ, intact rplJ and a deletion of the 3' terminal portion of rplL is detrimental to the growth of the host bacterium. Six independent point mutations on the plasmid that overcome this detriment have been isolated. Nucleotide sequence analysis demonstrates that all six mutants are single base pair alterations, occur within the leader region of the rplJ operon and are well removed from the presumed position of the primary promoter, PJ. These mutant plasmids exhibit normal transcription of rplJ-rplL but do not translate rplJ messenger RNA to yield plasmid-specified L10 ribosomal protein. We suggest that these mutations define a regulatory region within the leader sequence of the RNA transcript that serves to modulate the translational efficiency of rplJ messenger RNA.

Post-transciptional control of coordinated ribosomal protein synthesis in Escherichia coli

The synthesis of the approximately 50 different ribosomal proteins (r proteins) is very well coordinated in Escherichia coli. As the r-protein genes are arranged in many different operons, placed at separate locations on the E. coli chromosome, it is not obvious how this coordination is maintained. The first indication that special controls are involved in the coordination came from the observations that merodiploid strains containing F' factors with some of the ribosomal genes also synthesise the r proteins in balanced amounts. The overall regulation of r-protein synthesis in reponse to changes in growth conditions is primarily mediated by changes in the rate of transcription of the r-protein genes. To investigate whether the gene dosage control seen in merodiploid strains is also transcriptional in nature or whether other mechanisms are involved, we compared the transcriptionof r-protein mRNA in haploid and merodiploid strains. It was found that the rate of transcription of the r-protein mRNA from the str-spc cluster of genes changes in proportion to the gene dosage and it is concluded that the expression of r-protein genes is adjusted by post-transcriptional control.

Ribosome biosynthesis in Tetrahymena thermophila. IV. Regulation of ribosomal RNA synthesis in growing and growth arrested cells

Three parameters involved in the production of new ribosomal RNA (rRNA) were measured in Tetrahymena thermophilia: (i) the rate of synthesis of the rRNA precursor, (ii) the rate of processing of the RNA precursor and rRNA intermediates and (iii) the efficiency of utilization of the rRNA precursor in producing mature ribosomal RNA. These parameters were measured in cells in exponential growth and in cells starved in a dilute salt solution. Growing cells synthesize rRNA 20 times faster and process rRNA precursors and intermediates 10 to 15 times more rapidly than do starved cells. Both utilize their rRNA precursors with an efficiency of one in converting them to mature rRNA.

Post-translational modification of Escherichia coli ribosomal protein S6

Escherichia coli has multiple forms of ribosomal protein S6, differing in number of glutamyl resideus at the C-terminal end. Three forms are revealed when crude cell extracts are fractionated by a two-dimensional gel electrophoresis technique. Pulse-chase experiments show that the shortest and most alkaline form of S6 is the first to appear. In about one doubling time this form reaches equilibrium with the two other forms of S6, implicating the existence of an enzyme, which adds glutamic acid residues to S6. We show that the relative levels of these three S6 forms are not affected by the growth rate of the culture.

Analysis of rpsD mutations in Escherichia coli. II. Physiology of some representative mutants

The effects of ribosomal ambiguity mutations (ram A-) on the assembly of ribosomal 30S subunits in Escherichia coli were studied in some representative mutant strains. It was found that the inability of these strains to produce active 30S subunits at nonpermissive temperatures is correlated with a halt in the accumulation of protein S4. It is demonstrated that 30S-precursor particles lacking this protein accumulate and break down at nonpermissive temperatures and that most of the 30S proteins as well as the 17S RNA constituting these particles are similarly unstable. These findings are discussed and related to the finding that merodiploid strains containing genes for both mutant and wild type protein S4 do not accumulate the mutant form of the protein. Experiments indicating that ribosomal precursor particles are associated with polysomes are presented. The implications of these findings are discussed and it is suggested that the assembly of ribosomes is tightly coupled to the synthesis of ribosomal proteins.

DNA sequences of promoter regions for the str and spc ribosomal protein operons in E. coli

The DNA sequences have been determined for promoter regions of two ribosomal protein operons in E. coli, the str operon and the spc operon. The site of in vitro transcription initiation within each of these promoter regions has been determined. The start site of the str operon occurs 69 bases upstream from the initiation codon of the S12 gene. The start site of the spc operon occurs 72 bases upstream from the L14 gene, and only 91 bases downstream from the termination codon of the S17 gene (which is in the preceding S10 operon). Both promoters are similar to other sequenced promoters in that they each have an identifiable "Pribnow box" sequence 5 bases upstream from the transcription start site. The spc promoter has a long sequence of 2 fold symmetry centered within the Pribnow box; the str promoter has a shorter but similar symmetry. At positions -69 through -40 in the spc operon, another long region of symmetry is present which may be the termination signal of the preceding S10 operon. Extensive sequence similarity between the str and spc promoter regions is found downstream from the Pribnow box-that is, in a transcribed region preceding the translation start sites.