Bacterial elongation factors EF-Tu, their mutants, chimeric forms, and domains: isolation and purification.

Prokaryotic elongation factors EF-Tu form a family of homologous, three-domain molecular switches catalyzing the binding of aminoacyl-tRNAs to ribosomes during the process of mRNA translation. They are GTP-binding proteins, or GTPases. Binding of GTP or GDP regulates their conformation and thus their activity. Because of their particular structure and regulation, various activities (also outside of the translation system) and a relative abundance they represent attractive tools for studies of many basic but still not fully understood mechanisms both of the translation process, the structure-function relationships in EF-Tu molecules themselves and proteins and energy transduction mechanisms in general. The review critically summarizes procedures for the isolation and purification of native and engineered eubacterial elongation factors EF-Tu and their mutants on a large as well as small scale. Current protocols for the purification of both native and polyHis-tagged or glutathione-S-transferase (GST)-tagged EF-Tu proteins and their variants using conventional procedures and the Ni-NTA-Agarose or Glutathione Sepharose are presented.

The c-SRC1 gene visualized by in situ hybridization on Xenopus laevis chromosomes.

Fluorescent in situ hybridization followed by tyramide signal amplification was used to map the site of the c-SRC1 gene on XENOPUS LAEVIS chromosomes. Positive results were obtained with a cDNA probe of about 1 kb. The c-SRC1 gene is located in the subcentromeric region in the long arm of one of the acrocentric chromosomes of the G category (classified according to Graf and Kobel, 1991). The c-SRC1 gene and the XENOPUS major histocompatibility complex (MHC) 1b locus, which consists of 20 tandemly arranged gene copies, are situated on different chromosomes of the G category.

Genomic organization of the mouse src gene. Sequencing of src introns revealed a new chromosome 2 microsatellite marker.

Ten introns interrupting the coding sequence of the mouse src protooncogene were sequenced (in total 11260 bp) and their general characteristics compared with the homologous genes in human and chicken. While the study of genome organization of the src gene was performed only in the inbred mouse strain BALB/cHeA (Mus musculus domesticus), one special region in the intron 5 was also sequenced in additional mouse strains (M. musculus musculus and M. spretus), because the discovered CA and GT repeat array differences could serve as a new polymorphic marker in the chromosome No. 2 and help elucidate some evolutionary relations between mouse strains.

Cloning and characterization of the str operon and elongation factor Tu expression in Bacillus stearothermophilus.

The complete primary structure of the str operon of Bacillus stearothermophilus was determined. It was established that the operon is a five-gene transcriptional unit: 5'-ybxF (unknown function; homology to eukaryotic ribosomal protein L30)-rpsL (S12)-rpsG (S7)-fus (elongation factor G [EF-G])-tuf (elongation factor Tu [EF-Tu])-3'. The main operon promoter (strp) was mapped upstream of ybxF, and its strength was compared with the strength of the tuf-specific promoter (tufp) located in the fus-tuf intergenic region. The strength of the tufp region to initiate transcription is about 20-fold higher than that of the strp region, as determined in chloramphenicol acetyltransferase assays. Deletion mapping experiments revealed that the different strengths of the promoters are the consequence of a combined effect of oppositely acting cis elements, identified upstream of strp (an inhibitory region) and tufp (a stimulatory A/T-rich block). Our results suggest that the oppositely adjusted core promoters significantly contribute to the differential expression of the str operon genes, as monitored by the expression of EF-Tu and EF-G.

Sperm-mediated preparation of transgenic Xenopus laevis and transmission of transgenic DNA to the next generation.

Sperm-mediated transgenesis of frogs Xenopus laevis with retroviral Rous sarcoma virus DNA is described and the transgenic progeny is characterized. Correlation between the high expression of src gene and defective morphogenesis of frog embryos is discussed.

Depression in the level of cadherin and alpha-, beta-, gamma-catenins in transgenic Xenopus laevis highly expressing c-Src.

Aberrant morphogenesis of transgenic Xenopus laevis 5-day embryos carrying Rous sarcoma virus LTR in their DNA and expressing a high level of c-Src protein kinase was found to be accompanied with a profound depression in the level of cadherins and alpha-, beta-, and gamma-(plakoglobin) catenins in their tissues, as revealed by immunohistochemical analysis. Simultaneously, an increased level of phosphotyrosine staining was detected. However, an analogous increase in the level of phosphotyrosine immunostaining and a slightly higher level of Src were also detected in tissues of originally defective but later spontaneously repaired frog embryos that displayed essentially normal patterns of staining for cadherins and catenins. Our results provide evidence that the defective morphogenesis of frog embryos expressing a high level of c-Src is characterized by the loss of the cadherin-catenin complexes. It appears that to induce frog morphogenetic malformations, the c-Src overproduction and the loss of cadherins-catenins are simultaneously required. Phosphorylation is not likely to be the cause of cadherin and catenin disappearance from the tissues of strongly aberrant frog embryos.

Effect of host bacteria genotype on spontaneous reversions of Bacillus subtilis bacteriophage phi29 sus17 nonsense codon.

Gene 17 of Bacillus subtilis bacteriophage Phi29 is an early gene playing a role in DNA replication. Its mutant sus17(112) carries the TAA nonsense triplet at the fifth codon of the gene. We isolated and sequenced 73 spontaneous revertants producing normal-size plaques on bacteria without an informational suppressor gene. In all revertants, the TAA triplet was changed by a one-base substitution and the sequences CAA, AAA, TTA, TAC and TAT were recovered at its place. The spectrum of these mutations was markedly influenced by the genotype of the bacteria in which the revertants arose. In agreement with the results described in Escherichia coli, the ratio of transversions to transitions (CAA being the only transition acceptable) was higher in strains harboring the functional allele recA(+) than in those with recA4. Our results support the idea that also in the Gram-positive B. subtilis, the spectra of spontaneous mutations are specifically modified by an SOS function. It is assumed that the single-stranded DNA chains generated in the course of phage DNA replication might act as an inducing factor.

Structure and expression of elongation factor Tu from Bacillus stearothermophilus.

The tuf gene coding for elongation factor Tu (EF-Tu) of Bacillus stearothermophilus was cloned and sequenced. This gene maps in the same context as the tufA gene of Escherichia coli str operon. Northern-blot analysis and primer extension experiments revealed that the transcription of the tuf gene is driven from two promoter regions. One of these is responsible for producing a 4.9-kb transcript containing all the genes of B. stearothermophilus str operon and the other, identified adjacent to the stop codon of the fus gene and designated tufp, for producing a 1.3-kb transcript of the tuf gene only. In contrast to the situation in E. coli, the ratio between the transcription products was found to be about 10:1 in favour of the tuf gene transcript. This high transcription activity from the tufp promoter might be accounted for by the presence of an extremely A+T-rich block consisting of 29 nucleotides which immediately precedes the consensus -35 region of the promoter. A very similar tuf gene transcription strategy and the same tufp promoter organization with the identical A/T block were found in Bacillus subtilis. The tuf gene specifies a protein of 395 amino acid residues with a molecular mass of 43,290 Da, including the N-terminal methionine. A computer-generated three-dimensional homology model shows that all the structural elements essential for binding guanine nucleotides and aminoacyl-tRNA are conserved. The presence of serine at position 376 and a low affinity for kirromycin determined by zone-interference gel electrophoresis (Kd approximately 8 microM) and by polyacrylamide gel electrophoresis under non-denaturing conditions are in agreement with the reported resistance of this EF-Tu to the antibiotic. The replacement of the highly conserved Leu211 by Met was identified as a possible cause of pulvomycin resistance.

Development of transgenic Xenopus laevis with a high C-src gene expression.

Xenopus laevis larvae with an elevated expression of c-src were generated by mating a transgenic X. laevis male frog carrying proviral Rous sarcoma virus (RSV) long terminal repeat (LTR) and most of the pol gene sequences in its sperm DNA and a normal X. laevis female frog. Offspring (15-20%) with a higher dosage of c-Src, detected in disorganized myotomal musculature and in cerebral and spinal neuronal cells by immunohistochemical analysis, developed abnormally, with edemas (in most cases), head deformities, and eye and axial system defects. In the remaining embryos, a small increase in c-src expression seemed to be compatible with normal embryogenesis. The dosage of c-Src correlated with the dosage of RSV LTR integrated in frog DNA as revealed by Southern and polymerase chain reaction (PCR) analyses. Authenticity of the integrated RSV LTR including enhancer sequence was proved by sequencing. Probing of total RNA from aberrant larvae demonstrated several times higher dosage of c-src mRNA in their tissues than in control tadpoles. We hypothesize that the integrated RSV regulatory sequences can stimulate the expression of c-src proto-oncogene of X. laevis above a threshold that interferes with the early developmental program of frog embryos.

Interaction of EF-Tu with EF-Ts: substitution of His-118 in EF-Tu destabilizes the EF-Tu x EF-Ts complex but does not prevent EF-Ts from stimulating the release of EF-Tu-bound GDP.

Elongation factor Tu from Escherichia coli with His-118 substituted by glycine (EF-TuH118G) was found to be defective in complex formation with EF-Ts. EF-Ts in excess failed to dissociate kirromycin from the EF-TuH118G x kirromycin complex and to form a stable complex with EF-TuH118G on column chromatography. However, the stimulatory effect of EF-Ts on GDP dissociation from EF-TuH118G x GDP and on poly(U)-directed poly(Phe) synthesis catalyzed by EF-TuH118G was only partially influenced. These results indicate that His-118, while very important for the formation of a stable EF-Tu-EF-Ts complex, is not essential for the transmission of the EF-Ts-dependent signal accelerating the release of the EF-Tu-bound GDP.

The pyrAb gene coding for the large subunit of carbamoylphosphate synthetase from Bacillus stearothermophilus: molecular cloning and functional characterization.

The Bacillus stearothermophilus pyrAb gene, encoding the large subunit of carbamoylphosphate synthetase, was isolated and characterized. The DNA sequence is a 3195-nucleotide long reading frame coding for a polypeptide of 1064 amino acids and deduced Mr approximately 116,160 Da. The pyrAb gene is part of the B. stearothermophilus pyrimidine biosynthesis operon pyr. The 5' end of thepyrAb gene overlaps with the 3' end of the pyrAa gene coding for the small subunit of carbamoylphosphate synthetase, while the 3' end of the pyrAb gene is overlapped with the 5' end of the pyrD gene, which by analogy with the B. subtilis genomic organization, codes for dihydroorotate dehydrogenase. The deduced amino acid sequence of the large subunit of B. stearothermophilus carbamoylphosphate synthetase was compared with the known sequences of the large subunit of carbamoylphosphate synthetase enzymes from other organisms via the NCBI database. Extremely high (98%) identity in amino acid sequence with the large subunit of carbamoylphosphate synthetase from Bacillus caldolyticus was detected.

Uptake of plasmid RSV DNA by frog and mouse spermatozoa.

Xenopus laevis spermatozoa and mouse epididymal spermatozoa were compared in their ability to bind plasmid DNA. Spermatozoa of both species are endowed with a very similar binding capacity for plasmid pAPrC DNA carrying the complete Rous sarcoma virus (RSV) DNA. Our experiments failed to detect any substantial differences between both types of sperm cells in the kinetics of DNA binding, maximum DNA binding capacity, effect of various ions, metabolic inhibitors and substrates on DNA binding, etc. Each X. laevis and mouse sperm cell associates, on an average, with about 50 and 45 molecules, respectively, of the plasmid DNA in a DNase resistant form, if spermatozoa were exposed to the DNA at a concentration of 0.5 microgram/5 x 10(6) sperm cells. The uptake of the DNA by both types of sperm cells is strongly inhibited by heparin. The 37-kDa factor IF-1 shown by Zani et al. (1995) to specifically block DNA binding to mouse sperm cells inhibited the interaction between pAPrC DNA and frog spermatozoa with a similar intensity.

Association of rous sarcoma virus DNA with Xenopus laevis spermatozoa and its transfer to ova through fertilization.

Mature Xenopus laevis spermatozoa are capable of binding plasmid pAPrC carrying the complete Rous sarcoma virus (RSV) DNA. Each sperm cell associates, on an average, with 70-160 molecules of the plasmid DNA in a DNase resistant form, if the spermatozoa were exposed to the DNA at a concentration of 1.0-1.4 micrograms/10(7) sperm cells. Fertilization with pAPrC-treated spermatozoa induced developmental malformations in 25-30% of embryos. Immunohistochemical analysis of tissue sections from defective animals revealed aberrations in myotomal structures, and increased expression of pp60src protein in myoblasts, neuronal tube, and epidermis. The presence of characteristic v-src and RSV-long terminal repeat (LTR) sequences in X. laevis DNA was detected by PCR analysis. Embryonic RNA hybridized with a src-specific and an RSV-LTR specific probes indicating expression of the viral DNA. Plasmid DNAs without the v-src gene (pATV9) or completely free of any RSV sequences (pBR322) did not induce any changes in embryonic development. Our results provide evidence that the pBR322-cloned DNA form of the RSV genome associates with frog sperm cells in a DNase-resistant manner suggesting internalization and may be subsequently carried into eggs during the process of artificial fertilization. Correlation between the defective morphogenesis of X. laevis and increased expression of the src gene as well as an interference of RSV DNA with the developmental programs of frog embryos are discussed.

Histidine-118 of elongation factor Tu: its role in aminoacyl-tRNA binding and regulation of the GTPase activity.

The function of His118 in elongation factor (EF)-Tu from Escherichia coli was investigated by its substitution with glycine. The substitution had a differential effect on individual functions of the protein. The affinity for aminoacyl (aa)-tRNA and the intrinsic GTPase activity of the mutant EF-Tu were decreased whereas the response of its GTPase center to aa-tRNA was strongly increased. These results suggest that the region around His118 is involved in the binding of aa-tRNA and in the transmission of a turn-off signal generated by the interaction with aa-tRNA and directed to the GTPase center of EF-Tu.

Site-directed mutagenesis of elongation factor Tu. The functional and structural role of residue Cys81.

A Cys residue located in the second consensus sequence element (DCPG) of the GTP-binding region is highly conserved in bacterial elongation factors (EF) Tu. Chemical modification of this Cys81 in EF-Tu from Escherichia coli by N-tosyl-L-phenylalanine chloromethane [Jonák, J., Petersen, T. E., Clark, B. F. C. & Rychlík, I. (1982) FEBS Lett. 150, 485-488], and of homologous Cys residues in other bacterial EF-Tu, selectively blocks the binding of Xaa-tRNA. We have substituted Cys81 with Gly using site-directed mutagenesis of the EF-Tu-encoding tuf A gene. This substitution induces a partial inhibition (20-70%) of: (a) poly(U)-directed poly(Phe) synthesis; (b) EF-Tu/Xaa-tRNA interaction, determined as protection by EF-Tu of the non-enzymic deacylation of Xaa-tRNA; (c) EF-Tu-dependent binding of Xaa-tRNA to the mRNA/ribosome complex and (d) the intrinsic GTPase reaction, that is also less sensitive to stimulation by Xaa-tRNA. Our results thus provide evidence that Cys81, though important, is not essential for the binding of Xaa-tRNA to EF-Tu. The accuracy in poly(Phe) synthesis, measured as misincorporation of Leu, was increased. Both the binding affinity of [C81G]EF-Tu for the nucleotide and the resistance against thermal denaturation are more strongly decreased in the case of the GDP-bound state than in the case of the GTP-bound state, suggesting that Cys81 plays a more specific role in the former conformation. The sensitivity to N-tosyl-L-phenylalanine chloromethane is decreased by 80% but not totally lost. The inhibition by N-tosyl-L-phenylalanine chloromethane treatment of the function of EF-Tu appears to be a consequence of steric hindrance and/or of an altered conformation of EF-Tu.GTP. The lower activities of [C81G]EF-Tu are probably due to long-range effects, mediated by an overall destabilization of the molecule that is particularly pronounced for the GDP-bound state.

Microinjection of cloned proviral Rous sarcoma virus DNAs into Xenopus laevis one cell embryos.

Plasmid pATV8 carrying Rous sarcoma virus (RSV) DNA with one long terminal repeat (LTR) or plasmid pAPrC carrying complete RSV proviral DNA was injected into fertilized eggs of Xenopus laevis. The fate of the exogenous DNAs was followed during embryogenesis. In both cases a new form of DNA, comigrating with endogenous DNA, began to appear shortly after the injection. This new form represented a linear dimer of the injected plasmid that had formed by ligation of linear monomers of the plasmid DNAs. All forms of the exogenous pATV8 DNA disappeared gradually during neurulation. No traces of virus-specific RNA were ever found in any of the following stages. The intensity of replication of plasmid pAPrC DNA in fertilized eggs was greater than that of pATV8 DNA and, in contrast to pATV8, a small amount of pAPrC persisted through the neurula till higher stages. In some experiments virus-specific DNA was even observed in 6-day-old embryos. Digestion with Nsi I and Sac I proved integration of the plasmid into the frog genome. At the stage of gastrula and at later stages a weak signal of viral RNA was also detected.

Substitution of proline 82 by threonine induces autophosphorylating activity in GTP-binding domain of elongation factor Tu.

Mutation of Pro82 into Thr, a residue situated in the second element (D80CPG83) of the consensus sequence proposed to interact with GTP/GDP in GTP-binding proteins was introduced via site-directed mutagenesis in the isolated guanine nucleotide-binding domain (G domain) of elongation factor Tu. G domainPT82 displays virtually no GTPase activity. As a major change, the apparent inhibition of the GTPase reaction is associated with the appearance of autophosphorylating activity, as in ras product p21 in the case of mutation Ala59----Thr, corresponding to 82 in elongation factor Tu. Dependence of this reaction on mono- and divalent cation concentration and on pH is essentially the same as for the GTPase of wild-type G domain. The autokinase reaction follows an apparent first order rate, suggesting an intermolecular mechanism. Analysis of amino acid and peptide composition of the 32P-labeled G domainPT82, as well as Edman degradation of the tryptic peptide containing the covalently bound 32P, shows that Thr82 is the phosphorylated residue. Taken together, these results point out that Thr82 is in close proximity to the gamma-phosphate of GTP, as in the case of Thr59 in p21. These results are in agreement with the observations derived from x-ray diffraction analysis that the tertiary structure of the GTP-binding domain of elongation factor Tu and that of p21 are similar.

The influence of different modifications of elongation factor Tu from Escherichia coli on ternary complex formation investigated by fluorescence spectroscopy.

A fluorescence titration assay was used to detect the effects of various modifications of E.coli elongation factor Tu on the formation of the ternary complex with aminoacyl-tRNAs. The treatment of EF-Tu.GDP with TPCK, an analogue of the 3'terminus of aminoacyl-tRNA, was found to have no influence on the conversion of EF-Tu.GDP to 'active' EF-Tu.GTP, but does decrease the affinity of the activated protein for yeast aminoacyl-tRNA by more than three orders of magnitude. Modification of the elongation factor by limited cleavage with trypsin, leading to the excision of amino acid residues 45-58, has only a minor influence on ternary complex formation. The equilibrium dissociation constant of the ternary complex with this trypsin-treated EF-Tu.GTP and E.coli Phe-tRNA(Phe) is only one order of magnitude higher than that of the ternary complex with native EF-Tu. Mutations in the amino acid residues 222 and 375 of EF-Tu also have little effect on ternary complex formation. Compared with TPCK-treated EF-Tu, the affinities of the two mutant species, designated EF-tuAR and EF-TuBO respectively, for [AEDANS-s2C]Tyr-tRNA(Tyr) are only slightly reduced and in the same range as trypsin-cleaved EF-Tu.

Identification of the N-tosyl-L-phenylalanyl chloromethylketone modification site in Thermus thermophilus elongation factor Tu.

EF-Tu from Thermus thermophilus was first labelled with N-[14C]tosyl-L-phenylalaninechloromethylketone and then cleaved by the combined action of CNBr and trypsin. The resulting peptides were separated by reversed-phase HPLC. Analysis of the isolated, labelled peptide led to the identification of a sequence which was identical to residues 76-88 in T. thermophilus EF-Tu. The TPCK reactive site is at Cys-82. Kinetic measurements of the incorporation of TPCK into native EF-Tu and EF-Tu nicked at position Arg-59 were performed. The results provide evidence that the cleavage of the peptide bond between Arg-59 and Gly-60 does not lead to a dramatic conformational change of EF-Tu at the aa-tRNA binding site.

Modification of Bacillus subtilis elongation factor Tu by N-tosyl-L-phenylalanyl chloromethane abolishes its ability to interact with the 3'-terminal polynucleotide structure but not with the acyl bond in aminoacyl-tRNA.

Modification of B. subtilis EF-Tu by N-tosyl-L-phenylalanyl chloromethane destroyed its ability to promote protein synthesis and resulted in selective dissociation of the two binding activities of the protein for aminoacyl-tRNA. The modified EF-Tu was completely ineffective in the protection of the 3'-terminal CCA structure of tRNA against pancreatic ribonuclease, while remaining almost fully active in the protection of the ester bond between the 3'-terminal adenosine and the amino acid residue in aminoacyl-tRNA.