tRNA Availability Research Articles

TRNA Turnaround

Two recently published papers (Takano et al., 2005 and Shaheen and Hopper, 2005) demonstrate that in S. cerevisiae, cytoplasmic tRNAs can be transported into the nucleus. This retrograde movement may expose mature tRNAs to nuclear proofreading or it may regulate tRNA availability in response to amino acid availability.

Conformational diseases and the protein folding problem: role of amino-acid propensity to be embedded in context of specific usage of synonymous codons. Genetic code degeneracy and folding

Translation was long thought to be a smooth process, producing invariably native proteins. However, it appeared recently that this may not always be the case. First, a family of apparently unconnected diseases, including important neurodegenerative conditions, like Alzheimer, Parkinson, Huntington, and prion disorders, was shown to be linked to misfolded proteins ('conformational diseases'). Secondly, up to 70% of nascent proteins are recognized as misfolded and tagged for proteolysis whilst still attached to the ribosome. Misfolding seems therefore to be a quite common event, which is however most often corrected by efficient proteolysis of the misconformers produced. Misfolding therefore usually remains unnoticed, and safe when proteolysis is unable to remove the misconformers, which is the case in conformational diseases. Since the latter usually onset in the second half of human life, the mechanism of misfolding is likely to be linked to defects in the cellular translation and proteolysis machinery. This speculation is further substantiated by the observation that the amount of nascent proteins, recognized as misconformers whilst still attached to the ribosome, depends on the cellular state. On the other hand, the large amount of work devoted to prion proteins has highlighted the fact that certain proteins are prone to become easily misfolded. This implies that particular motifs in the primary structure of proteins enter metastable or 'soft' conformations upon synthesis, which can easily flip from one state to another. The present study investigates a possible link between particular primary structures and soft conformations. The study is based on experimental evidence, showing that silent codon exchange can affect protein conformation. Synonymous codons correspond to cognate tRNAs that may be present in the cell in rather different concentrations. Since tRNA availability determines the cognate codon translation rate, it follows that synonymous codons may have rather different translation rates. Taken together, part at least of the factors determining the native protein conformation may be encoded in the protein translation rate, i.e. in the selection of synonymous codons. Finally, the codon translation rate can be approximately estimated from the relative codon usage. Indeed, since the cellular concentration of charged tRNA on one hand controls the translation rate of the cognate codon, and on the other correlates closely with the usage of that codon in the cell, a reasonable approximation is to take as relative rate of codon translation the inverse of the usage of this codon. These various assumptions allow us to compute the local translation rate at any codon of a given messenger RNA. We were struck by the observation that 'fast' (frequent) or 'slow' (rare) codons tend to cluster in most mRNAs, and that the clusters tend to harbour preferentially certain amino acids. We therefore set out to analyse all the genes of E. coli, identify the 'fastest' and 'slowest' codon window in each and check if certain amino-acids are favored, or disfavored, within these windows, with respect to the general amino-acid usage in the genome of the species under investigation. We find that indeed, most aminoacids are constrained within these windows, and more so as the size of the window is reduced from 21 to 5 codons. Significant correlations are found between the type (excess or depletion) of constraint and the physical characteristics of the amino acids (hydrophobic, aromatic, charged or polar) or their propensity to enter particular secondary structure. It is therefore likely that synonymous codon selection in the mRNA locally sets kinetic factors contributing to the native conformation of the protein. Modifications of these kinetic factors, whether by silent codon exchange or by changes of the translation rate due to modifications of the cellular concentrations of components of the translation machinery (charged tRNA, elongation factor, foldases, etc.) would then possibly result in misconformation of the protein. We surmise that conformational diseases may result from spontaneous protein misfolding resulting from the incompatibility of the translation machinery components with the folding-specific translation rate. The misfolded proteins would either adopt a conformation that cannot be proteolyzed, or aggregate so as to be unable to enter the proteasome.

Codon-usage based regulation of colicin K synthesis by the stress alarmone ppGpp.

The molecular mechanism of the upregulation of Escherichia coli colicin K (Cka) synthesis during stress conditions was studied. Nutrient starvation experiments and the use of relA spoT mutant strains, IPTG-regulated overproduction of ppGpp and lacZ fusions revealed that the stringent response alarmone guanosine 3',5'-bispyrophosphate (ppGpp) is the main positive effector of Cka synthesis. Comparison of the amounts of protein produced (Western blotting) and specific mRNA (Northern blotting) before and after nutrient starvation demonstrated increases in Cka protein with unaltered specific mRNA levels, suggesting a post-transcriptional regulatory mechanism. Reporter (beta-galactosidase) assays using truncated cka of variable length fused to lacZ located the key regulatory region close to the 5' end of the cka mRNA. Closer analysis of this region indicated the presence of several rare codons, including the leucine-encoding codon CUA. Synonymous exchange of the rare codons with more frequently used ones abolished the regulatory effect of ppGpp. Supplementation of the strain with the plasmid CodonPlus carrying several rare tRNA genes yielded similar results, indicating that codon usage (in particular, the fifth codon for the amino acid leucine) and tRNA availability (i.e. tRNAleu) are the key elements of the regulatory function of ppGpp. We conclude that ppGpp regulates Cka synthesis via a novel post-transcriptional mechanism that is based on rare codon usage and variable cognate tRNA availability.

The EMAPII Cytokine Is Released from the Mammalian Multisynthetase Complex after Cleavage of Its p43/proEMAPII Component

Endothelial-monocyte-activating polypeptide II (EMAPII) is an inflammatory cytokine released under apoptotic conditions. Its proEMAPII precursor proved to be identical to the auxiliary p43 component of the aminoacyl-tRNA synthetase complex. We show here that the EMAPII domain of p43 is released readily from the complex after in vitro digestion with caspase 7 and is able to induce migration of human mononuclear phagocytes. The N terminus of in vitro-processed EMAPII coincides exactly with that of the mature cytokine isolated from conditioned medium of fibrosarcoma cells. We also show that p43/proEMAPII has a strong tRNA binding capacity (K(D) = 0.2 microm) as compared with its isolated N or C domains (7.5 microm and 40 microm, respectively). The potent general RNA binding capacity ascribed to p43/proEMAPII is lost upon the release of the EMAPII domain. This suggests that after onset of apoptosis, the first consequence of the cleavage of p43 is to limit the availability of tRNA for aminoacyl-tRNA synthetases associated within the complex. Translation arrest is accompanied by the release of the EMAPII cytokine that plays a role in the engulfment of apoptotic cells by attracting phagocytes. As a consequence, p43 compares well with a molecular fuse that triggers the irreversible cell growth/cell death transition induced under apoptotic conditions.

Ribosome Traffic in E. coli and Regulation of Gene Expression

The ribosome traffic during translation of E. coli coding sequences was simulated, assuming that the rate of translation of individual codons is limited by the cognate tRNA availability. Actual translation rates were taken from Solomovici et al. (J. theor. Biol.185, 511–521, 1997). The mean translation rates of the 4271 sequences cover a broad, two-fold range, whereas the local rate of translation along messengers varies three-fold on average. The simulation allows one to sketch the ribosome traffic on the polysome, in particular by providing the extent of mRNA sequences uncovered between consecutive ribosomes and the time during which these sequences are exposed. These parameters may participate in the control of mRNA stability and transcriptional polarity. By averaging the translation rates in a 17-codon window, assumed to be the sequence covered by a translating ribosome, and sliding this window along a given coding sequence, the addresses KMAX and KMIN, and the times TMAX and TMIN of respectively the slowest and the fastest translated window were determined. It is shown that under the assumptions made, TMAX sets the number of proteins translated from a given mRNA molecule per unit time, in case the delay between consecutive translation starts is below TMAX. Both windows display two strong biases, one as expected on the usage of codon frequencies, and the other surprisingly on the occurrence of aminoacids.

Papillomavirus capsid protein expression level depends on the match between codon usage and tRNA availability.

Translation of mRNA encoding the L1 and L2 capsid proteins of papillomavirus (PV) is restricted in vivo to differentiated epithelial cells, although transcription of the L1 and L2 late genes occurs more widely. The codon composition of PV late genes is quite different from that of most mammalian genes. To test the possibility that PV late gene codon composition determines the efficiency of PV late gene expression in some cell types, synthetic bovine papillomavirus type 1 (BPV1) late genes were constructed with codon composition modified to resemble the typical mammalian gene. Expression of these genes from a strong promoter in Cos-1 cells was compared with expression of wild-type BPV1 late genes from the same promoter. Both unmodified and modified PV late genes were transcribed in Cos-1 cells, but only the codon-modified genes were translated. In vitro translation of wild-type but not synthetic BPV1 L1 mRNA was markedly enhanced by addition of aminoacyl-tRNAs. Codon composition thus limits BPV1 late gene translation in Cos-1 cells, and this limitation can be overcome by modification of the codon composition of the genes or by provision of excess tRNA. Replacement of codons in the green fluorescent protein (gfp) gene with those frequently used in PV late genes did not alter gfp transcription in Cos-1 cells but almost abolished translation, supporting the hypothesis that the observed differences in efficiency of translation of modified and unmodified PV capsid genes were related to codon usage rather than mRNA structure. As tRNA populations vary within and between tissues in the same eukaryotic organism, we speculate that matching of tRNA availability to codon usage may be one determinant of the restriction of expression of PV late genes to differentiated epithelium.

Eukaryotic release factor 1 (eRF1) abolishes readthrough and competes with suppressor tRNAs at all three termination codons in messenger RNA.

It is known from experiments with bacteria and eukaryotic viruses that readthrough of termination codons located within the open reading frame (ORF) of mRNAs depends on the availability of suppressor tRNA(s) and the efficiency of termination in cells. Consequently, the yield of readthrough products can be used as a measure of the activity of polypeptide chain release factor(s) (RF), key components of the translation termination machinery. Readthrough of the UAG codon located at the end of the ORF encoding the coat protein of beet necrotic yellow vein furovirus is required for virus replication. Constructs harbouring this suppressible UAG codon and derivatives containing a UGA or UAA codon in place of the UAG codon have been used in translation experiments in vitro in the absence or presence of human suppressor tRNAs. Readthrough can be virtually abolished by addition of bacterially-expressed eukaryotic RF1 (eRF1). Thus, eRF1 is functional towards all three termination codons located in a natural mRNA and efficiently competes in vitro with endogenous and exogenous suppressor tRNA(s) at the ribosomal A site. These results are consistent with a crucial role of eRF1 in translation termination and forms the essence of an in vitro assay for RF activity based on the abolishment of readthrough by eRF1.

The tendency of lentiviral open reading frames to become A-rich: constraints imposed by viral genome organization and cellular tRNA availability

Human immunodeficiency virus type 1 (HIV-1) and other lentiviridae demonstrate a strong preference for the A-nucleotide, which can account for up to 40% of the viral RNA genome. The biological mechanism responsible for this nucleotide bias is currently unknown. The increased A-content of these viral genomes corresponds to the typical use of synonymous codons by all members of the lentiviral family (HIV, SIV, BIV, FIV, CAEV, EIAV, visna) and the human spuma retrovirus, but not by other retroviruses like the human T-cell leukemia viruses HTLV-1 and HTLV-II. In this article, we analyzed A-bias for all codon groups in all open reading frames of several lentiviruses. The extent of lentiviral codon bias could be related to host cellular translation. By calculating codon bias indices (CBIs), we were able to demonstrate an inverse correlation between the extent of codon bias and the rate of translation of individual reading frames in these viruses. Specifically, the shift toward A-rich codons is more pronounced in pol than in gag lentiviral genes. Since it is known that Gag synthesis exceeds Pol synthesis by a factor of 20 due to infrequent ribosomal frame-shifting during translation of the gap-pol mRNA molecule, we propose that the aminoacyl-tRNA availability in the host cell restricts the lentiviral preference for A-rich codons. In addition, less A-nucleotides were found in regions of the viral genome encoding multiple functions; e.g., overlapping reading frames (tat-rev-env) or in genes that overlap regulatory sequences (nef-LTR region).(ABSTRACT TRUNCATED AT 250 WORDS)

Codon bias in Escherichia coli may modulate translation initiation.

Codons with low corresponding intracellular tRNA concentrations are generally used less frequently (i .e. rare) compared to synonymous codons associated with higher tRNA concentrations 11 1. The differential use of codons with defined tRNA concentrations causes a given mRNA sequence to be translated at variable rates 121. Rare codons with extremely low tRNA concentrations may stall translation until an appropriate tRNA becomes available [31. Translational pauses caused by low tRNA availability may also influence the folding of a nascent polypeptide chain, and it has been proposed that in several proteins (e.g. Rabbit a and p globins, Cytochromes C and Yeast Pyruvate Kinase 131) translational pausing may allow discrete protein domains to fold and interact. Translational pausing of this type therefore complements the kinetics of a protein folding reaction. Translational pauses could also influence the targeting of exported polypeptides. In E . coli proteins are generally exported by interactions of a N-terminal signal sequence with the translocation machinery [4,5,6]. Translational pausing could therefore favour export in two ways. With proteins exported posttranslationally, an increase in time required for translation elongation would also increase the time a nascent polypeptide chain is exposed in the cytoplasm. Chaperone proteins 17) involved specifically in protein translocation (e.g. Sec B [6]) could then bind to the protein chain, increasing both the efficiency of export and the probability of the protein adopting a loose fold suitable for translocation. Proteins exported in a co-translational fashion could also benefit from translational pauses within approximately the first 100 codons. Pauses located around this region would expose the nascent signal sequence in the cytoplasm prior to pausing and this should allow i t to act independently of the un-translated protein. The export process would then be more efficient since direct interactions with the translocation machinery could ensue and the un-translated portion of the protein would not have to be maintained in a translationally competent state. This would be of particular importance in prokaryotic species where there is no evidence for elongation arrest by a Signal Recognition Particle (SRP). We therefore developed analytical software to examine rare codon usage & distribution in a sample containing 47 exported and 46 cytoplasmic polypeptides. The necessary coding regions of Escherichia coli were selected from the Linkage map of E . ccdi K12 181, and subsequently exuacted from the Gembl database using ‘GCG Navigator’ software. To locate potential pause sites we selected 8 rarely used codons 191, with minor concentrations of tRNA [ 11. These were CTA (Leu), ATA (Ile), ACA (Thr), CCT, CCC (Pro), CGG, AGA & AGG (Arg). If translational pausing was a widely used folding strategy, it would be reasonable to assume a longer polypeptide would require more pauses during translation to achieve this. Preliminary data demonstrated that frequency of rare ctdon use appears to be independent of polypeptide chain length. This does not prevent translational pauses regulating protein folding events, but we found no evidence to support this. In order to analyse the role translational pausing may play, detailed structural data on protein domain boundaries is required. Analysis of the distribution of rare The distribution of rare codons in the first 120 codons of 47 exported and 46 cytoplasmic polypeptides.

Chloroplast DNA codon use: Evidence for selection at the psb A locus based on tRNA availability

Codon use in the three sequenced chloroplast genomes (Marchantia, Oryza, and Nicotiana) is examined. The chloroplast has a bias in that codons NNA and NNT are favored over synonymous NNC and NNG codons. This appears to be a consequence of an overall high A + T content of the genome. This pattern of codon use is not followed by the psb A gene of all three genomes and other psb A sequences examined. In this gene, the codon use favors NNC over NNT for twofold degenerate amino acids. In each case the only tRNA coded by the genome is complementary to the NNC codon. This codon use is similar to the codon use by chloroplast genes examined from Chlamydomonas reinhardtii. Since psb A is the major translation product of the chloroplast, this suggests that selection is acting on the codon use of this gene to adapt codons to tRNA availability, as previously suggested for unicellular organisms.

Synonymous codon preferences in bacteriophage T4: A distinctive use of transfer RNAs from T4 and from its host Escherichia coli

Codon usage data of bacteriophage T4 genes were compiled and synonymous codon preferences were investigated in comparison with tRNA availabilities in an infected cell. Since the genome of T4 is highly AT rich and its codon usage pattern is significantly different from that of its host Escherichia coli, certain codons of T4 genes need to be translated by appropriate host transfer RNAs present in minor amounts. To avoid this predicament, T4 phage seems to direct the synthesis of its own tRNA molecules and these phage tRNAs are suggested to supplement the host tRNA population with isoacceptors that are normally present in minor amounts. A positive correlation was found in that the frequency of E. coli optimal codons in T4 genes increases as the number of protein monomers per phage particle increases. A negative correlation was also found between the number of protein monomers per phage and the frequency of "T4 optimal codons", which are defined as those codons that are efficiently recognized by T4 tRNAs. From these observations it was proposed that tRNAs from the host are predominantly used for translation of highly expressed T4 genes while tRNAs from T4 tend to be used for translation of weakly expressed T4 genes. This distinctive tRNA-usage in T4 may be an optimization of translational efficiency, and an adjustment of T4-encoded tRNAs to the synonymous codon preferences, which are largely influenced by the high genomic AT-content, would have occurred during evolution.

Ribosomal frameshifting in the yeast retrotransposon Ty: tRNAs induce slippage on a 7 nucleotide minimal site

Ribosomal frameshifting regulates expression of the TYB gene of yeast Ty retrotransposons. We previously demonstrated that a 14 nucleotide sequence conserved between two families of Ty elements was necessary and sufficient to support ribosomal frameshifting. This work demonstrates that only 7 of these 14 nucleotides are needed for normal levels of frameshifting. Any change to the sequence CUU-AGG-C drastically reduces frameshifting; this suggests that two specific tRNAs, tRNALeuUAG and tRNAArgCCU, are involved in the event. Our tRNA overproduction data suggest that a leucyl-tRNA, probably tRNALeuUAG, an unusual leucine isoacceptor that recognizes all six leucine codons, slips from CUU-Leu onto UUA-Leu (in the +1 reading frame) during a translational pause at the AGG-Arg codon induced by the low availability of tRNAArgCCU, encoded by a single-copy essential gene. Frameshifting is also directional and reading frame specific. Interestingly, frameshifting is inhibited when the “slip” CUU codon is located three codons downstream, but not four or more codons downstream, of the translational initiation codon.

Expression of a wheat α-gliadin gene in Saccharomyces cerevisiae

A vector was constructed that directs the expression of foreign genes in the yeast Saccharomyces cerevisiae. This vector contains an expression site that was constructed by in vitro modification of the iso-1-cytochrome c ( CYC1) gene of S. cerevisiae. The expression of heterologous sequences can be experimentally controlled by catabolite control sequences, promoter and transcription initiation sequences and termination sequence derived from the CYC1 gene. A portion of a genomic wheat a-gliadin gene consisting of the entire 861 bp of protein-coding sequence, 18 bp of 5' leader sequence and 54 bp of 3'-noncoding sequence was inserted into the expression site. A CYC1 : : α-gliadin transcript of approx. 1050 nucleotides was synthesized in transformed yeast under the control of the CYC1 regulatory region. The transcripts terminated within the α-gliadin 3'-noncoding region, near a nucleotide sequence similar to the yeast transcription termination consensus sequence. The α-gliadin was immunochemically detected in total protein extracts from transformed cells and accounted for approx. 0.1% of the total cellular protein. The size of a-gliadin synthesized in yeast is the same as that of mature wheat α-gliadin. This is consistent with recognition and cleavage of the signal peptide by yeast. Due to the amino acid composition of α-gliadin, the availability of glutamine tRNA is a potential translational limitation to high-level synthesis in yeast.

Translation rate modification by preferential codon usage: Intragenic position effects

We present a model for calculating the protein production rate as a function of the translation rate. The model takes into account that the elongation rate along an mRNA molecule is non-uniform as a result of different tRNA availabilities for different codons. Initiation of ribosomes on an mRNA is normally the rate-limiting step in the translation process, and blocking of the initiation site can be avoided if the codons closest to this site allow fast translation by the ribosome. Hence, different selective forces may act on the choice of synonymous codons in the initiation region than elsewhere on a given mRNA. We show that the elongation rate along the whole mRNA influences the production rate of abundant proteins, whereas only the elongation rate in the initiation region is of importance for the production rate of rare proteins. We also present an analysis of the codon distribution along known mRNAs coding for abundant and rare proteins.

Characterization of a bacteriocinogenic plasmid from Clostridium perfringens and molecular genetic analysis of the bacteriocin-encoding gene.

The bacteriocinogenic plasmid pIP404 from Clostridium perfringens was isolated and cloned in Escherichia coli, and its physical map was deduced. Expression of the bcn gene, encoding bacteriocin BCN5, is inducible by UV irradiation of C. perfringens and thus resembles the SOS-regulated bacteriocin genes of enteric bacteria. The location of bcn on pIP404 was established by a dot-blot procedure, using specific hybridization probes to analyze mRNA samples from induced and uninduced cultures. From the nucleotide sequence of its gene, the molecular weight of BCN5 was deduced to be 96,591, and a protein of this size was secreted by bacteriocin-producing cultures of C. perfringens. The primary structure of the protein suggests that it may function as an ionophore, since a hydrophobic domain, resembling those of the ionophoric colicins, is present at the COOH terminus. No bacteriocin activity could be detected in E. coli harboring plasmids bearing the bcn gene, even when the transcriptional and translational signals were replaced by those of lacZ. A possible explanation may be found in the unusual codon usage of the adenine-thymine-rich bcn gene, as this shows a preference for codons with a high adenine-plus-thymine content, especially in the wobble position. Many of the frequently used codons correspond to those recognized by minor tRNA species in E. coli. Consequently, bcn expression might be limited by tRNA availability in this bacterium.

Translation is a non-uniform process: Effect of tRNA availability on the rate of elongation of nascent polypeptide chains

We reported elsewhere (Varenne et al., 1982) that, during synthesis of a number of colicins in Escherichia coli, intermediate nascent chains of discrete sizes accumulated, suggesting a variable rate of translation. In this paper, a detailed analysis provides arguments that this phenomenon, at least for the proteins under study, is not related to aspects of messenger RNA such as secondary structure. It is linked to the difference in transfer RNA availability for the various codons. Experimental analysis of translation of other proteins in E. coli confirms that the main origin for the discontinuous translation in the polypeptide elongation cycle is the following. For a given codon, the stochastic search of the cognate ternary complex (aminoacyl-tRNA-EF-Tu-GTP) is the rate-limiting step in the elongation cycle: transpeptidation and translocation steps are much faster. The degree of slackening in ribosome movement is almost proportional to the inverse of tRNA concentrations. The verification of this model and its possible physiological significance are discussed.

Development of methods to measure activity of polysomes and cytoplasmic enzymes from bovine skeletal muscle in in vitro protein-synthesis assays.

A cell-free, protein-synthesis system containing components from bovine skeletal muscle was developed as prerequisite to attempts to learn whether polysomes or cytoplasmic enzymes limit rate of muscle protein synthesis in the current population of domestic animals. Amino acid incorporation into trichloroacetic acid-precipitable protein was optimal at pH 7.5 and, if Tris buffer was used, at K+ and Mg2+ concentrations of 40 mM and 4 mM, respectively. Optimal concentrations of compounds that provide energy for amino acid incorporation were 1 mM ATP, .2 mM GTP, 20 micrograms creatine phosphokinase/ml and 20 mM creatine phosphate; .03 mM of each of the 20 amino acids was required for assays lasting up to 60 min. Neither rate of tRNA acylation nor availability of aminoacyl-tRNA was rate-limiting in the cell-free system established; hence, the cytoplasmic enzyme fraction from bovine skeletal muscle contains ample tRNA and has aminoacyl-tRNA synthases that are sufficiently active to form aminoacyl-tRNA faster than these compounds are used to form polypeptides in the cell-free system developed. Reinitiation of ribosomes onto new mRNA occurred very slowly, if at all, in the protein-synthesis system developed. Cytoplasmic enzymes were rate-limiting whenever cytoplasmic enzyme protein to polysomal protein ratios were 3.2:1 or lower in the cell-free system. Polysomes were rate-limiting whenever cytoplasmic enzyme protein to polysomal protein ratios were 400:1 or higher in the cell-free system. These ratios define the conditions needed to assay activity of cytoplasmic enzymes or polysomes from different animals quantitatively.

Functional interrelationship between two tandem E. coli ribosomal RNA promoters.

The Escherichia coli chromosome carries seven cistrons encoding ribosomal RNA sequences. In all cases studied, in vitro and in vivo, it has been established that transcription is initiated from two tandem promoters. The expression of the rRNA cistrons is regulated in response to growth rate as well as to aminoacyl tRNA availability. In the present study, a plasmid (pPS1) carrying the promoter region of the rrnA cistron fused to the terminator region of rrnB has been used for in vitro transcription experiments. The presence of the terminators (T1 and T2) together with the fact that supercoiled DNA is found to be a highly efficient template, provide an ideal in vitro system in which to study the functional interrelationship between the two tandem promoters of E. coli rRNA cistrons. The results suggest that the rate of rRNA synthesis in E. coli cells growing in various conditions, as reflected by the availability of RNA polymerase, is primarily dependent on the properties of the two tandem rRNA promoters.

Evidence for use of rare codons in the dnaG gene and other regulatory genes of Escherichia coli.

Amino acid sequence and composition data of Escherichia coli dnaG primase protein and its tryptic peptides have confirmed that the dnaG gene contains an unusually high number of codons that are not frequently used in most E. coli genes. In 25 E. coli proteins analyzed the codons AUA, UCG, CCU, CCC, ACG, CAA, AAT, and AGG are infrequently used, occurring as 4% of the total codons in the reading frame and 11% and 10% in the nonreading frames. In dnaG they occur as 11% in the reading frame and 12% in the nonreading frames. The rpsU and rpoD genes, which flank the dnaG gene [Smiley, B. L., Lupski, J. R., Svec, P. S., McMacken, R. & Godson, G. N. (1982) Proc. Natl. Acad. Sci. USA 79, 4550-4554], however, have normal codon usage. Translational modulation using isoaccepting tRNA availability may therefore be part of the mechanism of keeping the dnaG gene expression low, while expression of the adjacent rpsU and rpoD genes on the same mRNA transcript is high.

Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes: Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs

There exists a similarity among the synonymous codon choice patterns of the yeast nuclear genes that have been sequenced thus far although these genes encode different types of protein molecules, and the patterns are significantly different from those of Escherichia coli genes. Based on constraints caused by the availability of E. coli transfer RNAs and the nature of their codon recognition related to the modified nucleotides at the anticodon wobble position, the characteristic patterns of synonymous codon choice commonly found for E. coli genes have been almost completely explained (Ikemura, 1981 a, b). In the present paper, tRNAs of the yeast Saccharomyces cerevisiae were separated by two-dimensional polyacrylamide gel electrophoresis and the relative abundance of purified tRNA molecules was measured on the basis of molecular numbers in cells. A strong correlation between tRNA abundance and codon choice was found for each nuclear gene of yeast, but the correlation was less significant for 2μ plasmid genes. According to the criteria proposed for E. coli genes (Ikemura, 1981 b) the order of codon preference in yeast nuclear genes was predicted based on the abundance of yeast isoaccepting tRNAs and on the nature of the modified nucleotides at their anticodons. Clear correlations between predictions and the actual preferences among synonymous codons were revealed, indicating that the codon choices in yeast genes are also constrained by a combination of tRNA availability and nature of its codon recognition. Then the difference in synonymous codon use between the two organisms can be attributed to the difference in these two factors.