Cloning and characterization of the gene coding for cytoplasmic seryl-tRNA synthetase from Saccharomyces cerevisiae

E2/E3-independent ubiquitin-like protein conjugation by Urm1 is directly coupled to cysteine persulfidation

Post-translational modifications by ubiquitin-like proteins (UBLs) are essential for nearly all cellular processes. Ubiquitin-related modifier 1 (Urm1) is a unique UBL, which plays a key role in tRNA anticodon thiolation as a sulfur carrier protein (SCP) and is linked to the noncanonical E1 enzyme Uba4 (ubiquitin-like protein activator 4). While Urm1 has also been observed to conjugate to target proteins like other UBLs, the molecular mechanism of its attachment remains unknown. Here, we reconstitute the covalent attachment of thiocarboxylated Urm1 to various cellular target proteins in vitro, revealing that, unlike other known UBLs, this process is E2/E3-independent and requires oxidative stress. Furthermore, we present the crystal structures of the peroxiredoxin Ahp1 before and after the covalent attachment of Urm1. Surprisingly, we show that urmylation is accompanied by the transfer of sulfur to cysteine residues in the target proteins, also known as cysteine persulfidation. Our results illustrate the role of the Uba4-Urm1 system as a key evolutionary link between prokaryotic SCPs and the UBL modifications observed in modern eukaryotes.

Identification of factors that promote biogenesis of tRNACGASer

A wide variety of factors are required for the conversion of pre-tRNA molecules into the mature tRNAs that function in translation. To identify factors influencing tRNA biogenesis, we previously performed a screen for strains carrying mutations that induce lethality when combined with a sup61-T47:2C allele, encoding a mutant form of [Formula: see text]. Analyzes of two complementation groups led to the identification of Tan1 as a protein involved in formation of the modified nucleoside N⁴-acetylcytidine (ac⁴C) in tRNA and Bud13 as a factor controlling the levels of ac⁴C by promoting TAN1 pre-mRNA splicing. Here, we describe the remaining complementation groups and show that they include strains with mutations in genes for known tRNA biogenesis factors that modify (DUS2, MOD5 and TRM1), transport (LOS1), or aminoacylate (SES1) [Formula: see text]. Other strains carried mutations in genes for factors involved in rRNA/mRNA synthesis (RPA49, RRN3 and MOT1) or magnesium uptake (ALR1). We show that mutations in not only DUS2, LOS1 and SES1 but also in RPA49, RRN3 and MOT1 cause a reduction in the levels of the altered [Formula: see text]. These results indicate that Rpa49, Rrn3 and Mot1 directly or indirectly influence [Formula: see text] biogenesis.

Differential protective effects of extra virgin olive oil and corn oil in liver injury: a proteomic study

Extra virgin olive oil (EVOO) presents benefits against chronic liver injury induced by hepatotoxins such as carbon tetrachloride (CCl4); however, the protective mechanisms remain unclear. In the present study, a two-dimensional gel based proteomic approach was constructed to explore the mechanisms. Rats are injected with CCl4 twice a week for 4 weeks to induce liver fibrosis, and were fed laboratory chow plus 20% (w/w) of either corn oil or EVOO over the entire experimental period. Histological staining, MDA assay and fibrogenesis marker gene analysis illustrate that the CCl4-treated animals fed EVOO have a lower fibrosis and lipid peroxidation level in the liver than the corn oil fed group. The proteomic study indicates that the protein expression of thioredoxin domain-containing protein 12, peroxiredoxin-1, thiosulphate sulphurtransferase, calcium-binding protein 1, Annexin A2 and heat shock cognate 71 kDa protein are higher in livers from EVOO-fed rats with the CCl4 treatment compared with those from rats fed with corn oil, whereas the expression of COQ9, cAMP-dependent protein kinase type I-alpha regulatory subunit, phenylalanine hydroxylase and glycerate kinase are lower. Our findings confirmed the benefits of EVOO against chronic liver injury, which may be attributable to the antioxidant effects, hepatocellular function regulation and hepatic metabolism modification effects of EVOO.

Identifying Pex21p as a protein that specifically interacts with yeast seryl-tRNA synthetase

The interaction of Saccharomyces cerevisiae seryl-tRNA synthetase (SerRS) with peroxin Pex21p was identified in a two-hybrid screen with SerRS as bait. This was confirmed by an in vitro binding assay with truncated Pex21p fused to glutathione S-transferase. Furthermore, purified Pex21p acts as an activator of yeast seryl-tRNA synthetase in aminoacylation in vitro, revealing the functional significance of the Pex21p-SerRS interaction. Pex21p is a protein involved in the peroxisome biogenesis [Purdue, P.E., Yang, X. and Lazarow, P.B., J. Cell Biol. 143 (1998) 1859-1869]. Since eukaryotic aminoacyl-tRNA synthetases are known to participate in assembles with other synthetases and non-synthetase proteins, we propose that this unusual interaction reflects another function of the peroxin.

Detection of noncovalent tRNA.aminoacyl-tRNA synthetase complexes by matrix-assisted laser desorption/ionization mass spectrometry

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-MS) was used for the study of complexes formed by yeast seryl-tRNA synthetase (SerRS) and tyrosyl-tRNA synthetase (TyrRS) with tRNASer and tRNATyr. Cognate and noncognate complexes were easily distinguished due to a large mass difference between the two tRNAs. Both homodimeric synthetases gave MS spectra indicating intact desorption of dimers. The spectra of synthetase-cognate tRNA mixtures showed peaks of free components and peaks assigned to complexes. Noncognate complexes were also detected. In competition experiments, where both tRNA species were mixed with each enzyme only cognate alpha2.tRNA complexes were observed. Only cognate alpha2.tRNA2 complexes were detected with each enzyme. These results demonstrate that MALDI-MS can be used successfully for accurate mass and, thus, stoichiometry determination of specific high molecular weight noncovalent protein-nucleic acid complexes.

Genomic organization, cDNA sequence, bacterial expression, and purification of human seryl-tRNA synthase

In this paper, we report the cDNA sequence and deduced primary sequence for human cytosolic seryl-tRNA synthetase, and its expression in Escherichia coli. Two human brain cDNA clones of different origin, containing overlapping fragments coding for human seryl-tRNA synthetase were sequenced: HFBDN14 (fetal brain clone); and IB48 (infant brain clone). For both clones the 5' region of the cDNA was missing. This 5' region was obtained via PCR methods using a human brain 5' RACE-Ready cDNA library. The complete cDNA sequence allowed us to define primers to isolate and characterize the intron/exon structure of the serS gene, consisting of 10 introns and 11 exons. The introns' sizes range from 283 bp to more than 3000 bp and the size of the exons from 71 bp to 222 bp. The availability of the gene structure of the human enzyme could help to clarify some aspects of the molecular evolution of class-II aminoacyl-tRNA synthetases. The human seryl-tRNA synthetase has been expressed in E. coli, purified (95% pure as determined by SDS/PAGE) and kinetic parameters have been measured for its substrate tRNA. The human seryl-tRNA synthetase sequence (514 amino acid residues) shows significant sequence identity with seryl-tRNA synthetases from E. coli (25%), Saccharomyces cerevisiae (40%), Arabidopsis thaliana (41%) and Caenorhabditis elegans (60%). The partial sequences from published mammalian seryl-tRNA synthetases are very similar to the human enzyme (94% and 92% identity for mouse and Chinese hamster seryl-tRNA synthetase, respectively). Human seryl-tRNA synthetase, similar to several other class-I and class-II human aminoacyl-tRNA synthetases, is clearly related to its bacterial counterparts, independent of an additional C-terminal domain and a N-terminal insertion identified in the human enzyme. In functional studies, the enzyme aminoacylates calf liver tRNA and prokaryotic E. coli tRNA.

Only one nucleotide insertion to the long variable arm confers an efficient serine acceptor activity upon Saccharomyces cerevisiae tRNA(Leu) in vitro

Several tRNA species have a long variable arm composed of over ten nucleotides, which are relevant to those specific to serine, leucine and tyrosine in prokaryotes, while there are only serine and leucine-specific tRNAs in eukaryotes. To clarify the evolutionary aspects of the identity determination mechanism of these tRNAs, the tRNA(Ser) recognition in Saccharomyces cerevisiae was studied. Unmodified tRNA(Leu) transcript had serylation ability of low efficiency, but native tRNA(Leu) did not, indicating that some modification of tRNA(Leu) serves as a negative identity determinant for seryl-tRNA synthetase. Changing the discriminator base did not seriously affect the serine accepting efficiency. The tRNA(Leu) transcript possessing the variable arm of tRNA(Ser) was efficiently aminoacylated with serine. Eventually, it was found that only one nucleotide insertion to the variable arm of tRNA(Leu) was sufficient to confer an efficient serine accepting activity. The mode of serine tRNA recognition is similar to that in Escherichia coli in that the end of the long variable arm, but not the anticodon or discriminator base, is important. However, S. cerevisiae seryl-tRNA synthetase adopts a substantially different mechanism for rejection of tRNA(Leu) from that of its E. coli counterpart.

The C-terminal extension of yeast seryl-tRNA synthetase affects stability of the enzyme and its substrate affinity

Saccharomyces cerevisiae seryl-tRNA synthetase (SerRS) contains a 20-amino acid C-terminal extension, which is not found in prokaryotic SerRS enzymes. A truncated yeast SES1 gene, lacking the 60 base pairs that encode this C-terminal domain, is able to complement a yeast SES1 null allele strain; thus, the C-terminal extension in SerRS is dispensable for the viability of the cell. However, the removal of the C-terminal peptide affects both stability of the enzyme and its affinity for the substrates. The truncation mutant binds tRNA with 3.6-fold higher affinity, while the Km for serine is 4-fold increased relative to the wild-type SerRS. This indicates the importance of the C-terminal extension in maintaining the overall structure of SerRS.

Wide cross-species aminoacyl-tRNA synthetase replacement in vivo: yeast cytoplasmic alanine enzyme replaced by human polymyositis serum antigen

Because of variations in tRNA sequences in evolution, tRNA synthetases either do not acylate their cognate tRNAs from other organisms or execute misacylations which can be deleterious in vivo. We report here the cloning and primary sequence of a 958-aa Saccharomyces cerevisiae alanyl-tRNA synthetase. The enzyme is a close homologue of the human and Escherichia coli enzymes, particularly in the region of the primary structure needed for aminoacylation of RNA duplex substrates based on alanine tRNA acceptor stems with a G3.U70 base pair. An ala1 disrupted allele demonstrated that the gene is essential and that, therefore, ALA1 encodes an enzyme required for cytoplasmic protein synthesis. Growth of cells harboring the ala1 disrupted allele was restored by a cDNA clone encoding human alanyl-tRNA synthetase, which is a serum antigen for many polymyositis-afflicted individuals. The human enzyme in extracts from rescued yeast was detected with autoimmune antibodies from a polymyositis patient. We conclude that, in spite of substantial differences between human and yeast tRNA sequences in evolution, strong conservation of the G3.U70 system of recognition is sufficient to yield accurate aminoacylation in vivo across wide species distances.

Structure, function and evolution of seryl-tRNA synthetases: implications for the evolution of aminoacyl-tRNA synthetases and the genetic code

Two aspects of the evolution of aminoacyl-tRNA synthetases are discussed. Firstly, using recent crystal structure information on seryl-tRNA synthetase and its substrate complexes, the coevolution of the mode of recognition between seryl-tRNA synthetase and tRNA(ser) in different organisms is reviewed. Secondly, using sequence alignments and phylogenetic trees, the early evolution of class 2 aminoacyl-tRNA synthetases is traced. Arguments are presented to suggest that synthetases are not the oldest of protein enzymes, but survived as RNA enzymes during the early period of the evolution of protein catalysts. In this view, the relatedness of the current synthetases, as evidenced by the division into two classes with their associated subclasses, reflects the replacement of RNA synthetases by protein synthetases. This process would have been triggered by the acquisition of tRNA 3' end charging activity by early proteins capable of activating small molecules (e.g., amino acids) with ATP. If these arguments are correct, the genetic code was essentially frozen before the protein synthetases that we know today came into existence.

Seryl-tRNA synthetase from Escherichia coli: functional evidence for cross-dimer tRNA binding during aminoacylation

Escherichia coli seryl-tRNA synthetase (SerRS) is a homo-dimeric class II aminoacyl-tRNA synthetase. Each subunit is composed of two distinct domains: the N-terminal domain is a 60 A long, arm-like coiled coil structure built up of two antiparallel alpha-helices, whereas the C-terminal domain, the catalytic core, is an alpha-beta structure overlying a seven-stranded antiparallel beta-sheet. Deletion of the arm-like domain (SerRS delta 35-97) does not affect the amino acid activation step of the reaction, but reduces aminoacylation activity by more than three orders of magnitude. In the present study, it was shown that the formation of heterodimers from two aminoacylation defective homodimers, the N-terminal deletion and an active site mutant (SerRS E355Q), restored charging activity. The aminoacylation activity in a mixture containing the heterodimers was compared to that of solutions containing the same concentrations of homodimer. The activity of the mixture was eight times higher than the activities of the homodimer solutions, and reached 50% of the theoretical value that would be expected if 50% of the mixture was in the heterodimer form and assuming that a heterodimer contains only one active site. These results are in full agreement with the structural analysis of E. coli SerRS complexed with its cognate tRNA and provide functional evidence for the cross-dimer binding of tRNA in solution.

Reduced dosage of genes encoding ribosomal protein S18 suppresses a mitochondrial initiation codon mutation in Saccharomyces cerevisiae

A yeast mitochondrial translation initiation codon mutation affecting the gene for cytochrome oxidase subunit III (COX3) was partially suppressed by a spontaneous nuclear mutation. The suppressor mutation also caused cold-sensitive fermentative growth on glucose medium. Suppression and cold sensitivity resulted from inactivation of the gene product of RPS18A, one of two unlinked genes that code the essential cytoplasmic small subunit ribosomal protein termed S18 in yeast. The two S18 genes differ only by 21 silent substitutions in their exons; both are interrupted by a single intron after the 15th codon. Yeast S18 is homologous to the human S11 (70% identical) and the Escherichia coli S17 (35% identical) ribosomal proteins. This highly conserved family of ribosomal proteins has been implicated in maintenance of translational accuracy and is essential for assembly of the small ribosomal subunit. Characterization of the original rps18a-1 missense mutant and rps18a delta and rps18b delta null mutants revealed that levels of suppression, cold sensitivity and paromomycin sensitivity all varied directly with a limitation of small ribosomal subunits. The rps18a-1 mutant was most affected, followed by rps18a delta then rps18b delta. Mitochondrial mutations that decreased COX3 expression without altering the initiation codon were not suppressed. This allele specificity implicates mitochondrial translation in the mechanism of suppression. We could not detect an epitope-tagged variant of S18 in mitochondria. Thus, it appears that suppression of the mitochondrial translation initiation defect is caused indirectly by reduced levels of cytoplasmic small ribosomal subunits, leading to changes in either cytoplasmic translational accuracy or the relative levels of cytoplasmic translation products.

Coexpression of eukaryotic tRNASer and yeast seryl-tRNA synthetase leads to functional amber suppression in Escherichia coli

In order to gain insight into the conservation of determinants for tRNA identity between organisms, Schizosaccharomyces pombe and human amber suppressor serine tRNA genes have been examined for functional expression in Escherichia coli. The primary transcripts, which originated from E. coli plasmid promoters, were processed into mature tRNAs, but they were poorly aminoacylated in E. coli and thus were nonfunctional as suppressors in vivo. However, coexpression of cloned Saccharomyces cerevisiae seryl-tRNA synthetase led to efficient suppression in E. coli. This shows that some, but not all, determinants specifying the tRNASer identity are conserved in evolution.

Yeast seryl-tRNA synthetase expressed in Escherichia coli recognizes bacterial serine-specific tRNAs in vivo

The Saccharomyces cerevisiae serS gene which encodes seryl-tRNA synthetase (SerRS) was expressed in Escherichia coli from the promoter and the ribosome binding sequences contained in its own 5'-flanking region. The low level of yeast SerRS in the prokaryotic host was sufficient to permit in vivo complementation of two temperature-sensitive E. coli serS mutants at the nonpermissive temperature. Thus, yeast SerRS can aminoacylate E. coli tRNA(Ser) species in vivo. Yeast SerRS, isolated from an overexpressing E. coli strain by a rapid two-step purification on FPLC, aminoacylated E. coli tRNA with serine much more poorly (relative kcat/Km = 2 x 10(-4)) than its homologous tRNAs. DL-Serine hydroxamate, an inhibitor of E. coli SerRS, inhibits yeast SerRS in vivo and in vitro with an inhibition constant (Ki) of 2.7 mM, a value 90-fold higher than that for E. coli SerRS.

Human histidyl-tRNA synthetase: recognition of amino acid signature regions in class 2a aminoacyl-tRNA synthetases

We have determined the sequence of cDNA for the human histidyl-tRNA synthetase (HRS) in a hepatoma cell line and confirmed it in fetal myoblast and fibroblast cell lines. The newly determined sequence differs in 48 places, including insertions and deletions, from a previously published sequence. By sequence specific probing and by direct sequencing, we have established that only the newly determined sequence is present in genomic DNA and we have sequenced 500 hundred bases upstream of the translation start site. The predicted amino acid sequence now clearly demonstrates all three motifs recognized in class 2 aminoacyl-tRNA synthetases. Alignment of E. coli, yeast, and when available, mammalian predicted amino acid sequences for three of the four members of the class 2a subgroup (his, pro, ser, and thr) shows strong preservation of amino acid specific signature regions proximal to motif 2 and proximal to motif 3. These probably represent the active site binding regions for the proximal acceptor stem and for the amino acid. The first two exons of human HRS contain a 32 amino acid helical motif, first described in human QRS, a class 1 synthetase, which is found also in a yeast RNA polymerase, a rabbit termination factor, and both bovine and human WRS, suggesting that it may be an RNA binding motif.

Identification of cryptic lox sites in the yeast genome by selection for Cre-mediated chromosome translocations that confer multiple drug resistance

The Cre recombinase efficiently causes site-specific DNA recombination at loxP sites placed into the eukaryotic genome. Since the loxP site of phage P1 is 34 base-pairs in size, the natural occurrence of this exact sequence is unlikely in any eukaryotic genome. However, related sequences may exist in eukaryotic genomes that could recombine at low efficiency with an authentic loxP site. This work identifies such cryptic lox sites in the yeast genome using a positive selection procedure that allows the detection of events occurring at a frequency of less than 1 x 10(-7). The selection is based on the disruption/reconstruction of the yeast gene YGL022. Disruption of YGL022 confers multiple drug sensitivity. Recombination events at a loxP site 5' to the structural gene restore expression of YGL022 and result in a multiple drug resistant phenotype. These drug resistant mutants all display chromosomal rearrangements resulting from low-frequency Cre-mediated recombination with an endogenous cryptic lox site. Ten such sites have been found and they have been mapped physically to a number of different yeast chromosomes. Although the efficiency of Cre-mediated recombination between loxP and such endogenous sites is quite low, it may be possible to redesign recombination substrates to improve recombination efficiency. Because of the greater complexity of the human and mouse genomes compared with yeast, an analogous situation is likely to exist in these organisms. The availability of such sites would be quite useful in the development of alternative strategies for gene therapy and in the generation of transgenic animals.

Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetases

Class 2 aminoacyl-tRNA synthetases, which include the enzymes for alanine, aspartic acid, asparagine, glycine, histidine, lysine, phenylalanine, proline, serine and threonine, are characterised by three distinct sequence motifs 1,2 and 3 (reference 1). The structural and evolutionary relatedness of these ten enzymes are examined using alignments of primary sequences from prokaryotic and eukaryotic sources and the known three dimensional structure of seryl-tRNA synthetase from E. coli. It is shown that motif 1 forms part of the dimer interface of seryl-tRNA synthetase and motifs 2 and 3 part of the putative active site. It is further shown that the seven alpha 2 dimeric synthetases can be subdivided into class 2a (proline, threonine, histidine and serine) and class 2b (aspartic acid, asparagine and lysine), each subclass sharing several important characteristic sequence motifs in addition to those characteristic of class 2 enzymes in general. The alpha 2 beta 2 tetrameric enzymes (for glycine and phenylalanine) show certain special features in common as well as some of the class 2b motifs. In the alanyl-tRNA synthetase only motif 3 and possibly motif 2 can be identified. The sequence alignments suggest that the catalytic domain of other class 2 synthetases should resemble the antiparallel domain found in seryl-tRNA synthetase. Predictions are made about the sequence location of certain important helices and beta-strands in this domain as well as suggestions concerning which residues are important in ATP and amino acid binding. Strong homologies are found in the N-terminal extensions of class 2b synthetases and in the C-terminal extensions of class 2a synthetases suggesting that these putative tRNA binding domains have been added at a later stage in evolution to the catalytic domain.

Alanyl-tRNA synthetase from Escherichia coli, Bombyx mori and Ratus ratus. Existence of common structural features

Alanyl-tRNA synthetase from Escherichia coli, Bombyx mori and rat were examined with respect to the following functional and structural properties: the effect of substrates on sensitivity to proteolysis, secondary structure as determined by circular dichroism, amino acid composition and, in the case of the rat and insect enzymes, partial amino acid sequence determination on a 60-kDa C-terminal tryptic fragment. Digestion of the enzyme from all three sources with trypsin resulted in significant decline in aminoacyl-tRNA synthetase activity with little effect on pyrophosphate-exchange activity. In each case the presence of alanine and ATP together, but not separately, reduced the rate of digestion by trypsin; the largest effect was observed with the enzyme from rat liver. Trypsin digestion generated fragments of 47 kDa and 40 kDa with all three enzymes, but detection of significant quantities of the 47-kDa fragment from the rat enzyme required the presence of ATP and alanine. Trypsin digestion produced a fragment of 60 kDa with all three enzymes, but detection of significant quantities of this fragment with the bacterial enzyme required the presence of ATP and alanine. Limited sequence analysis of the 60-kDa fragment from the insect and rat enzymes indicated that trypsin cleaved both proteins at the same site to generate this species. Similar effects of substrates were observed when the enzymes were digested with chymotrypsin suggesting that the effects of substrates on protease sensitivity were not unique to trypsin. Circular dichroism spectra obtained for the three enzymes were qualitatively and quantitatively similar. There is some similarity in amino acid composition between the rat and insect enzymes.

Genomic organization of tRNA and aminoacyl-tRNA synthetase genes for two amino acids in Saccharomyces cerevisiae

The genomic organization in Saccharomyces cerevisiae of the tRNA and aminoacyl-tRNA synthetase genes for two amino acids was investigated. Aspartic acid and serine were chosen for the study because of the number and diversity of their tRNA gene sequences and the availability of cloned tRNA and aminoacyl-tRNA synthetase genes. Chromosome assignments were determined by hybridization to DNA gel blots of chromosomal DNA resolved by contour-clamped homogeneous electric field gel electrophoresis. Our results show that the tRNA and the cognate synthetase genes in such a family are dispersed and, therefore, cannot be regulated via a mechanism dependent on close proximity of genes. In general, the genome of S. cerevisiae contains randomly dispersed tRNA genes that are transcribed individually. We have supported and expanded this view by applying the facile method of contour-clamped homogeneous electric field gel electrophoresis to the investigation of these small multigene families.

Sequence and structural features associated with translational initiator regions in yeast--a review

We have compared the translational initiator regions of 131 yeast genes. 95% utilize the first AUG from the 5' end of the message as the start codon for translation. Yeast leader regions in general are rich in adenine nucleotides (nt), have an average length of 52 nt, and are void of significant secondary structure. Sequences immediately adjacent to AUG start codons are preferred, however, the bias in nucleotide distribution (5'-A-YAA-UAAUGUCU-3') does not reflect a higher eukaryotic consensus (5'-CACCAUGG-3') with the exception of an adenine nucleotide preference at the -3 position. A minority of yeast mRNAs that contain AUG codons in the leader region that do not serve as the start codon for the primary gene product differ from the majority of mRNAs by one or more of these general properties. This analysis appears to indicate that basic features associated with yeast leader regions are consistent with a general mechanism of initiation of protein synthesis in eukaryotes, as proposed by the ribosomal 'scanning' model, but perhaps only basic features associated with ribosomal recognition of an AUG start codon are intact.