Mass spectra of partial protein hydrolysates as a multiple phase check for long polypeptides deduced from DNA sequences: NH2-terminal segment of alanine tRNA synthetase

A strategy has been developed for rapid and accurate determination of the amino acid sequence of large proteins, such as many of the members of the class of proteins known as aminoacyl tRNA synthetases. This strategy involves combining DNA sequencing of the gene for the protein of interest with gas chromatographic mass spectrometric identification of tetra- and pentapeptides in partial hydrolysates of the entire protein or very large fragments thereof. These peptides are matched to blocks of codons at locations scattered throughout the entire structural gene. Tetra- and pentapeptide sequences are sufficiently long that they are unlikely to be repeated in the protein sequence or to occur in an incorrect reading frame; therefore, they can be placed at unique clusters of codons on the DNA. This procedure rigorously establishes the proper phasing of the DNA throughout the entire length of the structural gene, and the protein sequence is thereby accurately read from the DNA sequence. This approach is being used to determine the amino acid sequence of EScherichia coli alanine tRNA synthetase, a protein that has approximately 900 amino acids. This paper reports the sequence of the first 165 amino acids from the NH2 terminus.

Assignment of a human genetic locus to chromosome 5 which corrects the heat sensitive lesion associated with reduced leucyl-tRNA synthetase activity in ts025Cl Chinese hamster cells

A heat-sensitive (hs) leucyl-tRNA synthetase (leuRS) deficient CHO mutant, ts025Cl, was fused with human leukocytes and hybrids isolated in HAT medium at the nonpermissive temperature. Nineteen heat-resistant (hr) and 14 hs subclones were isolated from four independent primary hybrids and tested for the expression of 24 human isozymes which have been assigned to 17 human chromosomes. Four hr independent subclones and three hs independent subclones were analyzed for the presence of human chromosomes. A pattern of concordant segregation was noted for the hr phenotype, human hexosaminidase B (EC 3.2.1.30) and human chromosome 5. Based on these results, we have defined the human genetic locus which corrects the heat-sensitive lesion in ts025Cl as hr025Cl and have assigned this locus to human chromosome 5. Two hr hybrids exhibited leuRS activity 2.5 and 4 times the leuRS activity of ts025Cl but a wild-type level of activity was not restored. One hs hybrid had only 73% of the leuRS activity exhibited by ts025Cl while another hs hybrid had 1.8 times the leuRS activity of ts025Cl.

Genetic analysis of mutations causing borrelidin resistance by overproduction of threonyl-transfer ribonucleic acid synthetase

Mutations leading to borrelidin resistance in Escherichia coli by overproduction of threonyl-transfer ribonucleic acid synthetase were anaylzed genetically. The regulatory mutations were closely linked to the treonyl-transfer ribonucleic acid synthetase structural gene (thrS), located clockwise to it. The mutation that causes the threefold-increased enzyme level was more distant from thrS than the mutation responsible for the ninefold overproduction. Both mutations were cis dominant in merodiploid strains, indicating that they affected promoter-operator-like control elements. Overproduction was restricted to threonyl-transfer ribonucleic acid synthetase and was not observed for the products of genes neighboring thrS (e.g., infC, pheS, pheT, and argS), providing evidence that thrS is transcribed singly and that gene amplificationis not a likely basis for increased thrS experession.

Improved mapping of the tyrS locus in Escherichia coli

A tyrosyl-tRNA synthetase mutant of Escherichia coli was isolated and the tyrS gene assigned a map position between man and pdxH at 36.0 min on the chromosome. The tyrS mutant grew badly on broth as did previously described tyrS mutants. This sensitivity to broth was suppressed by tyrR mutations. F-prime factors were found to complement the tyrS mutation.

A temperature-sensitive mutant in prolinyl-tRNA ligase of Escherichia coli K-12

A mutant with a defective prolinyl-tRNA ligase has been found in a collection of spontaneous temperature-sensitive mutants. The mutated gene, which is designated proS, is closely linked to metD.

Mutation in the structural gene for seryl-transfer ribonucleic acid synthetase of Escherichia coli which affects formation of its gene product at high temperature

The rate of formation of seryl-transfer ribonucleic acid (tRNA) synthetase activity was temperature dependent in a temperature-sensitive mutant of Escherichia coli (K28) with an altered seryl-tRNA synthetase structural gene and in a class of spontaneous revertants derived from it. These revertants, which were selected by their ability to grow at 45 degrees C, had high levels of the thermolabile enzyme. The rate of formation of seryl-tRNA synthetase activity in the mutant and in the revertants fell from 100% to near zero with a 4 degrees C temperature range from 40 to 44 degrees C. The temperature-dependent rate of formation of seryl-tRNA synthetase activity was reversible. Dropping the temperature from 44 to 37 degrees C resulted, after a 2- to 3-min delay, in a resumption of the initial rate of formation of enzyme activity. The results could not be accounted for by in vivo or in vitro degradation of the active enzyme. Addition of rifampin just before the temperature shift down from 44 to 37 degrees C inhibited the appearance of seryl-tRNA synthetase activity at the lower temperature. Explanations which might account for these phenomena are proposed.

Evolutionary relationship between Halobacterium cutirubrum and eukaryotes determined by use of aminoacyl-tRNA synthetases as phylogenetic probes

The cross-species reactivities between tRNAs and aminoacyl-tRNA synthetases have been employed as a basis to estimate the relatedness of various prokaryotes to the eukaryotes. The tRNA of Halobacterium cutirubrum, unlike that of other prokaryotes tested, including Agrobacterium tumefaciens, Arthrobacter luteus, Bacillus subtilis, Bacillus stearothermophilus, Escherichia coli, Micrococcus luteus, Myxococcus xanthus, Rhodopseudomonas spheroides, and Thermus aquaticus, was found to share with yeast, rat liver, and wheat germ tRNA a distinct preference for aminoacylation by eukaryotic synthetases from yeast as opposed to prokaryotic synthetases from either E. coli or R. spheroides. These results suggest that phylogenetically H. cutirubrum is more closely related to the eukaryotes than to the eubacteria.

Temperature-sensitive mutants in cysteinyl-tRNA ligase of E. coli K-12

Two mutants with a defective cysteinyl-tRNA synthetase have been found in a collection of spontaneous temperature sensitive mutants. The mutated gene, which is designated cysS, is closely cotransduced with purE.

Regulation of biosynthesis of aminoacyl-transfer RNA synthetases and of transfer-RNA in Escherichia coli

We have isolated temperature resistant revertants from temperature sensitive E. coli strains containing either a thermolabile glutaminyl-tRNA synthetase or leucyl-tRNA synthetase. Among the revertants which still contained the thermolabile leucyl-tRNA synthetase we found two classes of regulatory mutants (leuX and leu Y) which have elevated levels of this enzyme. The leuX mutation specifies an operator-promoter region adjacent to the structural gene (leuS) for the enzyme. The leuY gene maps away from the leuS gene and codes for a protein. Using these mutants we demonstrated that the levels of leucyl-tRNA are related to the derepression of the leucine and isoleucine-valine operons. Among the revertants which still contained the thermolabile glutaminyl-tRNA synthetase were characterized three classes of mutants, glnT, glnU, and glnR. The glnT and glnU mutants contain elevated levels of tRNAgln, while the glnR mutant possesses elevated levels of glutaminyl-tRNA synthetase. The level of glutamine synthetase, the enzyme responsible for the formation of glutamine, is also derepressed in the glnT and glnR mutants.

Specialized lambda transducing bacteriophage which carries hisS, the structural gene for histidyl-transfer ribonucleic acid synthetase

A number of specialized lambda transducing bacteriophages which carry the Escherichia coli gene guaB were isolated from E. coli. One of these bacteriophages, lambda cI857 Sam7 d guaB-2, also carries hisS, the structural gene for histidyl-transfer ribonucleic acid synthetase (EC 6.1.1.21). Histidyl-transfer ribonucleic acid synthetase activities in induced and uninduced lysogens carrying lambda d guaB-2 indicate that the phage carries the entire structural gene and that the gene is under the control of an E. coli promoter. These conclusions were confirmed by the in vivo production of a protein encoded by the phage which comigrates with authentic histidyl-transfer ribonucleic acid synthetase on two-dimensional polyacrylamide gels.

Mapping hisS, the structural gene for histidyl-transfer ribonucleic acid synthetase, in Escherichia coli

The structural gene for histidyl-tRNA synthetase was localized to 53.8 min on the Escherichia coli genome. The gene order in this region was determined to be dapE-purC-upp-purG-(guaA, guaB)-hisS-glyA.

Characterization of cell lines showing growth control isolated from both the wild type and a leucyl-tRNA synthetase mutant of Chinese hamster ovary cells

The genetic approach to the problem of cellular growth control is limited by the availability of recessive mutations in cell lines which are capable of growth control in vitro. The CHO cell line has yielded many recessive mutations including, for example, tsH1, a temperature sensitive leucyl-tRNA synthetase mutant, which under non-permissive conditions rapidly shuts down protein synthesis and generates uncharged tRNA. Both CHO and tsH1 are transformed, however, and do not respond to environmental stimuli with the coordinated regulation of macromolecular processes observed in normal diploid fibroblasts. We describe here the isolation and characterization of growth control revertants obtained from both CHOwt and tsH1. The best of these GRC+L-73, isolated from tsH1, had 20 chromosomes, one less than tsH1, had normal fibroblastic morphology, would not grow in suspension, required high serum concentrations for growth, grew to relatively low cell densities at saturation in monolayer culture and showed a stationary phase characterized by arrest in a G1-like state with maintenance of high viability for several weeks. It is expected that this line as well as a ts revertant GRC+LR-73 will greatly facilitate the genetic investigation of growth control and, in particular, will help to elucidate the role of uncharged tRNA in the regulation of macromolecular synthesis in mammalian cells.

The effect of amino acids on the temperature sensitive phenotype of the mammalian leucyl-tRNA synthetase mutant tsHl and its revertants

The temperature sensitive leucyl-tRNA synthetase mutant tsHl and two revertants have been compared to the parental Chinese hamster ovary cells with respect to the effects of amino acid concentrations in the medium on growth. Elevating the leucine concentration 30- or 100-fold allowed tsHl to grow exponentially at 38.5 degrees C, normally the nonpermissive temperature. Partial revertants that had recovered some enzyme activity required smaller supplements for growth. Measurements of the leucine pools indicated that they respond directly to the extracellular leucine concentration and may mediate the effect. Use of combinations of amino acids confirmed that isoleucine has a similar though weaker effect on tsHl and identified an even weaker protection by valine. The triple combination of leucine, isoleucine and valine was a much more efficient medium supplement and three times normal concentrations of these amino acids supported growth of tsHl at 38.5 degrees C. It is postulated that they are acting at their respective aminoacyl-tRNA synthetases to help stabilize a complex which also contains the mutant leucyl-tRNA synthetase. The pool size measurements also showed that the leucine pools of tsHl and a revertant increased 2-fold more in a response to increased temperature than those of WT. It is suggested that this is a regulatory response to low leucyl-tRNA synthetase activity and is important in determining growth phenotypes.

Isolation and characterization of revertants of the mammalian temperature sensitive leucyl-tRNA synthetase mutant tsHl

Nine spontaneous and seven ethyl methanesulfonate induced revertants of the Chinese hamster ovary cell line mutant (tsHl), which possesses a temperature sensitive leucyl-tRNA synthetase, were isolated and characterized with respect to growth rate, leucyl-tRNA synthetase activity and thermolability, intracellular leucine pool size, and rRNA content. Although most revertants had increased leucyl-tRNA synthetase activity, and of those tested, all but one had increased thermostability, each appears to be unique. One revertant may be an intergenic suppressor since it appears to contain an elevated level of tsHl-like synthetase. There was no evidence for any of the revertants having increased rRNA and tRNA contents, however, many showed leucine pools two to three times larger than wild type cells. Since similar increases have been observed in tsHl cells they are believed to result from regulation of leucine pool size by the leucyl-tRNA synthetase and are of a magnitude sufficient to affect significantly the growth of revertants at 38.5 degrees C.

Regulation of the biosynthesis of aminoacyl-tRNA synthetases and of tRNA in Escherichia coli. IV. Mutants with increased levels of leucyl- or seryl-tRNA synthetase

Spontaneous revertants of a temperature-sensitive Escherichia coli strain harboring a thermolabile leucyl-tRNA synthetase and seryl-tRNA synthetase were selected for growth at 40 degrees C. Among these, strains were found with increased levels of both thermolabile synthetases. Two distinct genetic loci were found responsible for enzyme overproduction. leuR, located near xyl, causes elevated levels of leucyl-tRNA synthetase; while serR, located near leu, causes elevated levels of seryl-tRNA synthetase.

Aminoacyl-tRNA synthetase mutants degrade protein at a normal rate

The stability of both rapidly and slowly degraded proteins in wild type CHO cells is similar to that in three ts aminoacyl-tRNA synthetase mutants at both permissive and non-permissive temperatures, although the degree of tRNA charging in the synthetase mutants differs considerably with temperature. These results indicate that the altered rate of protein breakdown seen under a variety of physiological conditions in eukaryotic systems is not mediated by uncharged tRNA.

Aminoacyl-tRNA synthetase families and their significance to the origin of the genetic code

A correlation of various aspects of the protein structures and substrate and mechanistic specificities of the aminoacyl-tRNA synthetases has led to the identification of at least one family of enzymes probably derived from a common ancestral synthetase. While strong correlations exist only in one part of the array of 64 codons comprising the Genetic Code, this itself may be interpreted as a meaningful pattern, most consistent with a development of the present code from earlier codes containing fewer amino acids and fewer available codons. Specifically, strong correlations in the enzymes whose cognate tRNAs respond to codons containing a central pyrimidine, including the enzyme family of Ile-, Phe-, Val-, Met-, and Leu-tRNA synthetases, suggests that these enzymes evolved last, and that, therefore, an earlier version of the Genetic Code was comprised solely of codons containing a central purine. It is suggested that further study of the historical interrelationships of these enzymes could lead to a fairly detailed picture of how the Genetic Code developed.

Evidence for structural gene alterations affecting aminoacyl-tRNA synthetases in CHO cell mutants and revertants

Aminoacyl-tRNA synthetase (aaRS) activities in extracts of mutant strains of the Chinese hamster ovary line (CHO) were examined for alterations in thermal stability. Mutants having low activity for MetRS, AsnRS, or GlnRS contained aaRSs that were inactivated much more rapidly upon heating than those from wild-type cells. Revertant lines, isolated from cultures of these mutants (Asn-5, Met-2, and Gln-2) after treatment with nitrosoguanidine or ethyl methanesulfonate, had thermolabilities intermediate between mutant and wild-type, and consistently had higher activities than the mutants. With a modified in vivo aminoacylation procedure, two previously exceptional mutants. Arg-1 and His-1, showed pronounced reductions in the amount of arginyl-tRNA or histidyl-tRNA, respectively, under restrictive conditions, compared to wild type. Revertants of Arg-1 (like the mutant itself) had no measurable ArgRS in vitro activity (less than 0.4% of wild type) although in vivo aminoacylation in the one revertant tested was partially restored. These data provide evidence that the forward mutations have occurred in the structural genes of the aaRSs and that most of the reversions are probably the result of second-site point mutations in the aaRS genes.

Mutations in the tryptophanyl-transfer ribonucleic acid ligase of E. coli causing temperature-sensitivity for growth

Strains of Escherichia coli K-12 with altered tryptophanyl-tRNA ligases, conferring temperature-sensitivity for growth, have been isolated as spontaneous one-step mutants. The mutated enzymes differ markedly in activity from the wildtype, even at the permissive temperature. When assayed at the non-permissive temperature, the mutant enzymes are completely inactive. In one of the mutant strains, growth can be completely inhibited by addition of L-phenylalanine or L-tyrosine to the medium.

Mutations in the structural genes of CHO cell histidyl-, valyl-, and leucyl-tRNA synthetases

Forty-three temperature-sensitive mutants were isolated in the CHO cell line by selecting for noncycling cells using [3H]TdR and cytosine arabinoside. Cell division was extremely temperature sensitive in eight of the mutants, and these were studied in more detail. In seven of these eight mutants, the in vitro specific activity of a single aminoacyl-tRNA synthetase was greatly reduced; four had reduced levels of histidyl-tRNA synthetase, two of valyl-tRNA synthetase, and one of leucyl-tRNA synthetase. Cell hybridization studies showed that the mutants formed three complementation groups. In six of the seven mutants the aminoacyl-tRNA synthetase which had reduced activity was also more thermolabile than the wild-type enzyme. The spontaneous reversion frequency was low for these mutants, and in most cases could be increased by treatment with a chemical mutagen. The isolation of the valyl-tRNA synthetase mutant reported here brings to eight the number of different aminoacyl-tRNA synthetase mutants isolated in the CHO cell line.

Effect of mutations affecting lysyl-tRNAlys on the regulation of lysine biosynthesis in Escherichia coli

When studying mutants affecting lysyl-tRNA synthetase or tRNAlys (hisT, hisW), a lack of correlation is clearly observed between the amount of lysyl-tRNA and the level of derepression of several lysine biosynthetic enzymes. This exlcudes the possible role of lysyl-tRNA as the specific corepressor of the lysine regulon. However, the level of derepression of DAP-decarboxylase, the last enzyme of the lysine pathway, is very low in the hisT mutant; this indicates that tRNAlys is a secondary effector involved in the regulation of the synthesis of this enzyme.

Biochemical characterization of a mutant asparaginyl-tRNA synthetase from Chinese hamster ovary cells

The biochemical and physical properties of asparaginyl-tRNA synthetase from wild type Chinese hamster ovary cells and a temperature sensitive mutant strain (lys 65a) are compared. The asparaginyl-tRNA synthetase in the mutant strain exhibits a greater temperature lability in vitro, a higher temperature-independent Km for asparagine, and a lower temperature-dependent catalytic capacity than the enzyme from the wild type strain. The mutant enzyme shows no differences in its molecular weight, its Km for tRNAAsn, or its ability to aminoacylate tRNAAsn isoacceptor species compared to the wild type enzyme. These observations, as well as the growth properties of the mutant cells as a function of temperature and exogenous asparagine concentrations, are consistent with their decreased ability to aminoacylate tRNAAsn in vivo.

Six complementation classes of conditionally lethal protein synthesis mutants of CHO cells selected by 3H-amino acid

Using a tritiated amino acid suicide procedure designed specifically to select conditional protein synthesis mutants, we have isolated and characterized a large number of such mutants of Chinese hamster ovary cells. All of the mutants are genetically stable and behave as recessives in somatic cell hybrids. Most of the new mutants are phenotypically dependent on the concentration of a specific amino acid as well as on temperature. In addition to identifying many additional leucyl- and asparagyl-tRNA synthetase mutants, complementation analysis has distinguished four new genetic classes representing methionine-, glutamine-, histidine-, and arginine-dependent mutants. Biochemical characterization of representative mutants from each of these six classes has identified the primary lesions as being defective aminoacyl-tRNA synthetases. Our selection results further demonstrate the high specificity of the 3H-amino acid procedure for isolating protein synthesis mutants. Reconstruction experiments performed with two representative mutants indicated a selection efficiency of approximately 10% under standard conditions.

Identification of a temperature-sensitive asparaginyl-transfer ribonucleic acid synthetase mutant of Escherichia coli

A temperature-sensitive mutant of Escherichia coli K-12 isolated previously (H. Ohsawa and B. Maruo, J. Bacteriol. 127:1157-1166, 1976) was found to have an alteration in asparaginyl-transfer ribonucleic acid synthetase. This alteration can account for the temperature-sensitive phenotype of the mutant. No evidence was obtained to support the previous suggestion that ribosomal protein S1 is altered in this mutant. Combined with the previous genetic studies, we conclude that the newly defined genetic locus, asnS, for the asparaginyl-transfer ribonucleic acid synthetase maps near pyrD at 21 min on the E. coli chromosome.

Intrachromosomal gene mapping in man: the gene for tryptophyl-tRNA synthetase maps in region q21 leads to qter of chromosome 14

A gene for tryptophanyl-tRNA synthetase (EC 6.1.1.2), the enzyme which attaches tryptophan to its tRNA, has previously been assigned to human chromosome 14 by analysis of man-mouse somatic cell hybrids. We report here a method for the electrophoretic separation of Chinese hamster and human tryptophanyl-tRNA synthetases and its application to a series of independently derived Chinese hamster-human hybrids in which part of the human chromosome 14 has been translocated to the human X chromosome. When this derivative der (X),t(X;14) (Xqter leads to Xp22::14q21 leads to 14qter) chromosome carrying the human gene for hypoxanthine-guanine phosphoribosyltransferase was selected for and against in cell hybrid lines by the appropriate selective conditions, the human tryptophanyl-tRNA synthetase activity was found to segregate concordantly. These results provide additional confirmation for the assignment of the tryptophanyl-tRNA synthetase gene to human chromosome 14 and define its intrachromosomal location in the region 14q21 leads to 14qter. Our findings indicate that the genes for tryptophanyl-tRNA synthetase and for ribosomal RNA are not closely linked on chromosome 14.

A genetic study of erythrocyte arginine-tRNA synthetase activity in man

To search for evidence of genetic variation among the aminoacyl-tRNA synthetases, a semi-automated assay procedure employing a Technicon AutoAnalyzer was used to measure erythrocyte arginine-tRNA synthetase activity in samples obtained from normal human twins of various ages. Variation in enzyme activity within the older DZ twins was five times that of the MZ twins suggesting the existence of genetically determined variation in enzyme activity. Higher enzyme activity was observed in newborn DZ unlike-sexed twins than in like-sexed twins for either zygosity. Possible explanations for this observation are discussed.