alanyl-tRNA Synthetase Research Articles

Diptera-Specific Polymerase Chain Reaction Amplification Primers of use in Molecular Phylogenetic Research

Abstract DNA sequence data from a variety of mitochondrial and nuclear gene regions are significant components of phylogenetic research in entomology. Polymerase chain reaction (PCR) amplification primers for many gene regions have been developed that are specific to a range of dipteran groups. Here, we review the existing Diptera-specific PCR amplification primers that have been published for 11 mitochondrial and nuclear gene regions: 12S small ribosomal subunit, cytochrome b, cytochrome oxidase c subunit I, 28S ribosomal RNA, alanyl-tRNA synthetase, the carbamoyl phosphate synthase region of CAD, elongation factor-1α, 6-phosphogluconate dehydrogenase, triose phosphate isomerase, white, and wingless. We also have designed in total 94 new PCR amplification primers for use in these same gene regions. Our new primers have been developed and tested using our DNA sequence database of > 1,600 specimens representing 40 families of Diptera. All of the past and newly developed primer sequences are presented in tables, and their locations are shown on gene maps. This combined data will facilitate future molecular phylogenetic research within Diptera.

Clinical heterogeneity and prognostic features of South Australian patients with anti‐synthetase autoantibodies

To determine the clinical, serological and prognostic features of patients with autoantibodies against three aminoacyl-transfer RNA synthetases (ARS), namely Jo-1 (histidyl-tRNA synthetase), PL-7 (threonyl-tRNA synthetase) and PL-12 (alanyl-tRNA synthetase) in South Australia. Patients with autoantibodies against ARS detected by line immunoassay (anti-Jo1, anti-PL7, anti-PL12) or enzyme-linked immunosorbent assay (anti-Jo1) were identified from existing laboratory databases for the period 1994-2009. Demographic, clinical and serological data were obtained by retrospective review of patients' medical records and laboratory databases. Forty-two patients with autoantibodies were identified (anti-Jo1 = 37, anti-PL7 = 4, anti-PL12 = 1). Females were more commonly affected than males (M : F = 12:30). Twenty-one patients had polymyositis (anti-Jo1 = 17, anti-PL7 = 4), seven dermatomyositis (anti-Jo1 = 6, anti-PL12 = 1), 10 overlap syndrome (anti-Jo1 = 10; lupus = 4, scleroderma = 3, Sjögren's syndrome = 2 and rheumatoid arthritis = 2) and four had interstitial lung disease (ILD) only (anti-Jo1 = 4). ILD was present in 69%, polyarthritis in 59% and positive anti-nuclear antibody (ANA) in 43% of patients. Concurrence of autoantibodies against Ro-52 with Jo-1 was seen in 12 patients. The mean follow-up period was 8.3 years (95% CI 5.8-10.8) with 12 deaths. Poor prognostic indicators were age of onset >60 years (P= 0.001), cancer (P= 0.002), negative ANA (P= 0.006) and negative autoantibodies to extractable nuclear antigens (P= 0.02). Patients with autoantibodies against ARS present with varied clinical features and occasionally with isolated lung involvement (amyopathic ILD). Older age of onset, malignancy and negative immunologic tests are predictors of poor prognosis. Concurrence of autoantibodies against Jo-1 and Ro-52 may reflect a coupling effect during generation of autoimmunity.

Patterned Purkinje cell loss in the ataxic sticky mouse

The ataxic sticky (sti/sti) mouse is a spontaneous autosomal recessive mutant resulting from a disruption in the editing domain of the alanyl-tRNA synthetase (Aars) gene. The sticky phenotype is characterized by a small body size, a characteristic unkempt coat and neurological manifestations including marked tremor and ataxia starting at 6 weeks of age. The present study was undertaken to examine the spatiotemporal features of Purkinje cell degeneration in the sticky mouse. Purkinje cell loss was found to be both progressive and patterned, with vermal lobules VI, IX and X, crus 1 of the hemisphere, and the flocculus and paraflocculus being differentially resistant to degeneration. The pattern of Purkinje cell degeneration in sticky is not random - in general, the sphingosine kinase 1a-immunonegative Purkinje cell subset is preferentially susceptible to early cell death. In addition, zebrin II/aldolase C expression in the sticky cerebellum is profoundly downregulated, whereas the heat-shock protein 25 is both ectopically expressed in some scattered Purkinje cells and downregulated in other Purkinje cells in which it is normally expressed constitutively. Compared with many mouse mutants with patterned Purkinje cell death, in which successive stripes of cell loss are very clear, Purkinje cell loss in sticky shows a less clear-cut pattern between different Purkinje cell subtypes, with the result that preferential survival is less dramatic. This may represent a secondary consequence of the downregulation of zebrin II expression.

Exome Sequencing Identifies Mitochondrial Alanyl-tRNA Synthetase Mutations in Infantile Mitochondrial Cardiomyopathy

Infantile cardiomyopathies are devastating fatal disorders of the neonatal period or the first year of life. Mitochondrial dysfunction is a common cause of this group of diseases, but the underlying gene defects have been characterized in only a minority of cases, because tissue specificity of the manifestation hampers functional cloning and the heterogeneity of causative factors hinders collection of informative family materials. We sequenced the exome of a patient who died at the age of 10months of hypertrophic mitochondrial cardiomyopathy with combined cardiac respiratory chain complex I and IV deficiency. Rigorous data analysis allowed us to identify a homozygous missense mutation in AARS2, which we showed to encode the mitochondrial alanyl-tRNA synthetase (mtAlaRS). Two siblings from another family, both of whom died perinatally of hypertrophic cardiomyopathy, had the same mutation, compound heterozygous with another missense mutation. Protein structure modeling of mtAlaRS suggested that one of the mutations affected a unique tRNA recognition site in the editing domain, leading to incorrect tRNA aminoacylation, whereas the second mutation severely disturbed the catalytic function, preventing tRNA aminoacylation. We show here that mutations in AARS2 cause perinatal or infantile cardiomyopathy with near-total combined mitochondrial respiratory chain deficiency in the heart. Our results indicate that exome sequencing is a powerful tool for identifying mutations in single patients and allows recognition of the genetic background in single-gene disorders of variable clinical manifestation and tissue-specific disease. Furthermore, we show that mitochondrial disorders extend to prenatal life and are an important cause of early infantile cardiac failure.

Painful myositis in the anti-synthetase syndrome with anti-PL12 antibodies

The idiopathic inflammatory myopathies (IIMs) are characterized by muscle weakness, electromyography (EMG), histological and biochemical features of muscle inflammation. Their classification is evolving due to the myositis-associated autoantibody panel. Anti-aminoacyl-tRNA synthetase (ARS) antibodies are detected in 25-30% patients and define the anti-synthetase syndrome (ASS), a spectrum of interstitial lung disease (ILD), arthritis, fever, Raynaud’s phenomenon and mechanic’s hands. Anti-Jo1 antibodies are most common (20%), whereas anti-PL12 antibodies (alanyl-tRNA synthetase) occur in <3% cases. We report a 58-year-old male with IIM associated with anti-PL12 antibodies, who presented with a three-week history of severe widespread muscle pain, without overt muscle weakness. He also reported polyarthralgia, exertional dyspnoea, dry cough and weight loss. Examination revealed low-grade pyrexia, bi-basal crepitations and exquisitely tender muscles. Notably, there was no proximal muscle weakness or neurological deficit. Investigations revealed marked acute phase response (CRP 121 mg/l, ESR 79 mm/hr), polyclonal hypergammaglobulinaemia and raised ALT 276 U/l (0-40). Serology demonstrated high-titre anti-nuclear antibodies (1:1280, speckled). Serum Western blotting revealed anti-PL12 antibodies. No other autoantibodies were detected. Creatinine kinase was elevated 936 U/l (0-200), EMG was consistent with myositis. MRI thighs demonstrated high signal within the semitendinosis muscle. Muscle histology confirmed a florid inflammatory myopathy with disruption, oedema and considerable macrophage and lymphocytic infiltrate of perimysial connective tissue – typical features of ASS. Spirometry was restrictive with reduced corrected gas transfer. CT chest showed non-specific interstitial pneumonia. Prednisolone 60mg daily, resulted in improvement of dyspnoea and normalisation of CRP and CK. Significant muscle pain (requiring morphine) was steroid-responsive, but only to high doses, with recurrence on dose reduction. Pulsed cyclophosphamide was commenced, with improvement in muscle pain after the first dose. Severe muscular pain and tenderness in the absence of weakness, is atypical of ASS and has not been previously reported. Anti-PL12 antibodies are rare, therefore their associated clinical features are not well-described, unlike the Jo-1 syndrome. ILD is common, usually precedes muscle involvement and may occur in isolation. Previous reports suggest that muscle involvement is uncommon and mild (often subclinical). Further reports and prospective studies will help refine the clinical phenotype of anti-PL12 antibody-positive ASS subtype.

P23 H implicated as cis/trans regulator of AlaXp-directed editing for mammalian cell homeostasis

The toxicity of mistranslation of serine for alanine appears to be universal, and is prevented in part by the editing activities of alanyl-tRNA synthetases (AlaRSs), which remove serine from mischarged tRNA(Ala). The problem of serine mistranslation is so acute that free-standing, genome-encoded fragments of the editing domain of AlaRSs are found throughout evolution. These AlaXps are thought to provide functional redundancy of editing. Indeed, archaeal versions rescue the conditional lethality of bacterial cells harboring an editing-inactive AlaRS. In mammals, AlaXps are encoded by a gene that fuses coding sequences of a homolog of the HSP90 cochaperone p23 (p23(H)) to those of AlaXp, to create p23(H)AlaXp. Not known is whether this fusion protein, or various potential splice variants, are expressed as editing-proficient proteins in mammalian cells. Here we show that both p23(H)AlaXp and AlaXp alternative splice variants can be detected as proteins in mammalian cells. The variant that ablated p23(H) and encoded just AlaXp was active in vitro. In contrast, neither the p23(H)AlaXp fusion protein, nor the mixture of free p23(H) with AlaXp, was active. Further experiments in a mammalian cell-based system showed that RNAi-directed suppression of sequences encoding AlaXp led to a serine-sensitive increase in the accumulation of misfolded proteins. The results demonstrate the dependence of mammalian cell homeostasis on AlaXp, and implicate p23(H) as a cis- and trans-acting regulator of its activity.

Substrate Specificity and Catalysis by the Editing Active Site of Alanyl-tRNA Synthetase from Escherichia coli

Aminoacyl-tRNA synthetases (ARSs) enhance the fidelity of protein synthesis through multiple mechanisms, including hydrolysis of the adenylate and cleavage of misacylated tRNA. Alanyl-tRNA synthetase (AlaRS) limits misacylation with glycine and serine by use of a dedicated editing domain, and a mutation in this activity has been genetically linked to a mouse model of a progressive neurodegenerative disease. Using the free-standing Pyrococcus horikoshii AlaX editing domain complexed with serine as a model and both Ser-tRNA(Ala) and Ala-tRNA(Ala) as substrates, the deacylation activities of the wild type and five different Escherichia coli AlaRS editing site substitution mutants were characterized. The wild-type AlaRS editing domain deacylated Ser-tRNA(Ala) with a k(cat)/K(M) of 6.6 × 10(5) M(-1) s(-1), equivalent to a rate enhancement of 6000 over the rate of enzyme-independent deacylation but only 12.2-fold greater than the rate with Ala-tRNA(Ala). While the E664A and T567G substitutions only minimally decreased k(cat)/K(M,) Q584H, I667E, and C666A AlaRS were more compromised in activity, with decreases in k(cat)/K(M) in the range of 6-, 6.6-, and 15-fold. C666A AlaRS was 1.7-fold more active on Ala-tRNA(Ala) relative to Ser-tRNA(Ala), providing the only example of a true reversal of substrate specificity and highlighting a potential role of the coordinated zinc in editing substrate specificity. Along with the potentially serious physiological consequences of serine misincorporation, the relatively modest specificity of the AlaRS editing domain may provide a rationale for the widespread phylogenetic distribution of AlaX free-standing editing domains, thereby contributing a further mechanism to lower concentrations of misacylated tRNA(Ala).

An assessment of mechanisms underlying peripheral axonal degeneration caused by aminoacyl-tRNA synthetase mutations

Mutations in glycyl-, tyrosyl-, and alanyl-tRNA synthetases (GARS, YARS and AARS respectively) cause autosomal dominant Charcot–Marie–Tooth disease, and mutations in Gars cause a similar peripheral neuropathy in mice. Aminoacyl-tRNA synthetases (ARSs) charge amino acids onto their cognate tRNAs during translation; however, the pathological mechanism(s) of ARS mutations remains unclear. To address this, we tested possible mechanisms using mouse models. First, amino acid mischarging was discounted by examining the recessive “sticky” mutation in alanyl-tRNA synthetase (Aarssti), which causes cerebellar neurodegeneration through a failure to efficiently correct mischarging of tRNAAla. Aarssti/sti mice do not have peripheral neuropathy, and they share no phenotypic features with the Gars mutant mice. Next, we determined that the Wallerian Degeneration Slow (Wlds) mutation did not alter the Gars phenotype. Therefore, no evidence for misfolding of GARS itself or other proteins was found. Similarly, there were no indications of general insufficiencies in protein synthesis caused by Gars mutations based on yeast complementation assays. Mutant GARS localized differently than wild type GARS in transfected cells, but a similar distribution was not observed in motor neurons derived from wild type mouse ES cells, and there was no evidence for abnormal GARS distribution in mouse tissue. Both GARS and YARS proteins were present in sciatic axons and Schwann cells from Gars mutant and control mice, consistent with a direct role for tRNA synthetases in peripheral nerves. Unless defects in translation are in some way restricted to peripheral axons, as suggested by the axonal localization of GARS and YARS, we conclude that mutations in tRNA synthetases are not causing peripheral neuropathy through amino acid mischarging or through a defect in their known function in translation.

Painful myositis in the anti-synthetase syndrome with anti-PL12 antibodies

The idiopathic inflammatory myopathies (IIMs) are characterized by muscle weakness, electromyography (EMG), histological and biochemical features of muscle inflammation. Their classification is evolving due to the myositis-associated autoantibody panel. Anti-aminoacyl-tRNA synthetase (ARS) antibodies are detected in 25-30% patients and define the anti-synthetase syndrome (ASS), a spectrum of interstitial lung disease (ILD), arthritis, fever, Raynaud’s phenomenon and mechanic’s hands. Anti-Jo1 antibodies are most common (20%), whereas anti-PL12 antibodies (alanyl-tRNA synthetase) occur in <3% cases. We report a 58-year-old male with IIM associated with anti-PL12 antibodies, who presented with a three-week history of severe widespread muscle pain, without overt muscle weakness. He also reported polyarthralgia, exertional dyspnoea, dry cough and weight loss. Examination revealed low-grade pyrexia, bi-basal crepitations and exquisitely tender muscles. Notably, there was no proximal muscle weakness or neurological deficit. Investigations revealed marked acute phase response (CRP 121 mg/l, ESR 79 mm/hr), polyclonal hypergammaglobulinaemia and raised ALT 276 U/l (0-40). Serology demonstrated high-titre anti-nuclear antibodies (1:1280, speckled). Serum Western blotting revealed anti-PL12 antibodies. No other autoantibodies were detected. Creatinine kinase was elevated 936 U/l (0-200), EMG was consistent with myositis. MRI thighs demonstrated high signal within the semitendinosis muscle. Muscle histology confirmed a florid inflammatory myopathy with disruption, oedema and considerable macrophage and lymphocytic infiltrate of perimysial connective tissue – typical features of ASS. Spirometry was restrictive with reduced corrected gas transfer. CT chest showed non-specific interstitial pneumonia. Prednisolone 60mg daily, resulted in improvement of dyspnoea and normalisation of CRP and CK. Significant muscle pain (requiring morphine) was steroid-responsive, but only to high doses, with recurrence on dose reduction. Pulsed cyclophosphamide was commenced, with improvement in muscle pain after the first dose. Severe muscular pain and tenderness in the absence of weakness, is atypical of ASS and has not been previously reported. Anti-PL12 antibodies are rare, therefore their associated clinical features are not well-described, unlike the Jo-1 syndrome. ILD is common, usually precedes muscle involvement and may occur in isolation. Previous reports suggest that muscle involvement is uncommon and mild (often subclinical). Further reports and prospective studies will help refine the clinical phenotype of anti-PL12 antibody-positive ASS subtype.

A single sequence context cannot satisfy all non-AUG initiator codons in yeast†

BackgroundPrevious studies in Saccharomyces cerevisiae showed that ALA1 (encoding alanyl-tRNA synthetase) and GRS1 (encoding glycyl-tRNA synthetase) respectively use ACG and TTG as their alternative translation initiator codons. To explore if any other non-ATG triplets can act as initiator codons in yeast, ALA1 was used as a reporter for screening.ResultsWe show herein that except for AAG and AGG, all triplets that differ from ATG by a single nucleotide were able to serve as initiator codons in ALA1. Among these initiator codons, TTG, CTG, ACG, and ATT had ~50% initiating activities relative to that of ATG, while GTG, ATA, and ATC had ~20% initiating activities relative to that of ATG. Unexpectedly, these non-AUG initiator codons exhibited different preferences toward various sequence contexts. In particular, GTG was one of the most efficient non-ATG initiator codons, while ATA was essentially inactive in the context of GRS1.ConclusionThis finding indicates that a sequence context that is favorable for a given non-ATG initiator codon might not be as favorable for another.

Editing Mischarged Amino Acids: the Work of Paul R. Schimmel

RNA Determinants for Translational Editing: Mischarging a Minihelix Substrate by a tRNA Synthetase (Nordin, B. E., and Schimmel, P. (1999) J. Biol. Chem. 274, 6835–6838) Structure-specific tRNA Determinants for Editing a Mischarged Amino Acid (Beebe, K., Merriman, E., and Schimmel, P. (2003) J. Biol. Chem. 278, 45056–45061)

Placement of Conopidae (Diptera) within Schizophora based on mtDNA and nrDNA gene regions

The first attempt to phylogenetically place Conopidae using molecular characters, as well as the largest molecular analysis of relationships within Schizophora (Diptera) to date, is presented. Twenty-eight taxa from 11 acalyptrate families and seven acalyptrate superfamilies are represented. Nearly 12,800 bp of sequence data from 10 genes representing both mitochondrial (cytochrome oxidase I (COI), cytochrome b (cytB), and 12S) and nuclear genes (28S, the carbamoyl phosphate synthetase region of CAD (CAD), elongation factor-1α (EF-1α), white, alanyl-tRNA synthetase (AATS), triose phosphate isomerase (TPI), and phosphogluconate dehydrogenase (PGD)) are analysed. Parsimony and Bayesian analyses strongly support the monophyly of both Conopidae and Schizophora. While in the parsimony analysis, Conopidae are placed as sister to the remaining Schizophora, the Bayesian analysis recovers a Conopidae + Lauxaniidae clade. The value of nuclear, mitochondrial, ribosomal, and protein-coding gene sequence data for answering phylogenetic questions at different levels of divergence is evaluated.

Introduction of a leucine half-zipper engenders multiple high-quality crystals of a recalcitrant tRNA synthetase.

Although Escherichia coli alanyl-tRNA synthetase was among the first tRNA synthetases to be sequenced and extensively studied by functional analysis, it has proved to be recalcitrant to crystallization. This challenge remained even for crystallization of the catalytic fragment. By mutationally introducing three stacked leucines onto the solvent-exposed side of an alpha-helix, an engineered catalytic fragment of the synthetase was obtained that yielded multiple high-quality crystals and cocrystals with different ligands. The engineered alpha-helix did not form a leucine zipper that interlocked with the same alpha-helix from another molecule. Instead, using the created hydrophobic spine, it interacted with other surfaces of the protein as a leucine half-zipper (LHZ) to enhance the crystal lattice interactions. The LHZ made crystal lattice contacts in all crystals of different space groups. These results illustrate the power of introducing an LHZ into helices to facilitate crystallization. The authors propose that the method can be unified with surface-entropy reduction and can be broadly used for protein-surface optimization in crystallization.

A Major Determinant for Binding and Aminoacylation of tRNA Ala in Cytoplasmic Alanyl-tRNA Synthetase Is Mutated in Dominant Axonal Charcot-Marie-Tooth Disease

Charcot-Marie-Tooth disease (CMT) is the most common cause of inherited peripheral neuropathy, with an estimated frequency of 1/2500. We studied a large family with 17 patients affected by the axonal form of CMT (CMT2). Analysis of the 15 genes or loci known to date was negative. Genome-wide genotyping identified a CMT2 locus in 16q21-q23 between D16S3050 and D16S3106. The maximum two-point LOD score was 4.77 at theta = 0 for marker D16S3050. Sequencing of candidate genes identified a unique mutation, c.986G>A (p.Arg329His), affecting a totally conserved amino acid in the helical domain of cytoplasmic alanyl-tRNA synthetase (AlaRS). A second family with the same mutation and a different founder was then identified in a cohort of 91 CMT2 families. Although mislocation of mutant Arg329His-AlaRS in axons remains to be evaluated, experimental data point mostly to a quantitative reduction in tRNA(Ala) aminoacylation. Aminoacylation and editing functions closely cooperate in AlaRS, and Arg329His mutation could also lead to qualitative errors participating in neurodegeneration. Our report documents in 18 patients the deleterious impact of a mutation in human cytoplasmic AlaRS and broadens the spectrum of defects found in tRNA synthetases. Patients present with sensory-motor distal degeneration secondary to predominant axonal neuropathy, slight demyelination, and no atypical or additional CNS features.

Paradox of mistranslation of serine for alanine caused by AlaRS recognition dilemma

Mistranslation from confusion of serine for alanine by alanyl-tRNA synthetases (AlaRSs) has profound functional consequences1-3. Throughout evolution, two editing-checkpoints prevent disease-causing mistranslation from confusing glycine or serine for alanine at the active site of AlaRS. In both bacteria and mice, Ser poses a bigger challenge than Gly1,2. One checkpoint is the AlaRS editing center, while the other is from widely distributed AlaXps—free-standing, genome-encoded editing proteins that clear Ser-tRNAAla. The paradox of misincorporating both a smaller (glycine) and a larger amino acid (serine) suggests a deep conflict for nature-designed AlaRS. To understand the chemical basis for this conflict, kinetic and mutational analysis, together with nine crystal structures, provided snapshots of adenylate formation for each amino acid. An inherent dilemma is posed by constraints of a structural design that pins down the α–amino group of the bound amino acid using an acidic residue. This design, of more than 3 billion years, creates a serendipitous interaction with the serine OH that is difficult to avoid. Apparently not able to find better architecture for recognition of alanine, the serine misactivation problem was solved through free-standing AlaXps, which appeared contemporaneously with early AlaRSs. The results reveal unconventional problems and solutions arising from the historical design of the protein synthesis machinery.

The C-Ala Domain Brings Together Editing and Aminoacylation Functions on One tRNA

Protein synthesis involves the accurate attachment of amino acids to their matching transfer RNA (tRNA) molecules. Mistranslating the amino acids serine or glycine for alanine is prevented by the function of independent but collaborative aminoacylation and editing domains of alanyl-tRNA synthetases (AlaRSs). We show that the C-Ala domain plays a key role in AlaRS function. The C-Ala domain is universally tethered to the editing domain both in AlaRS and in many homologous free-standing editing proteins. Crystal structure and functional analyses showed that C-Ala forms an ancient single-stranded nucleic acid binding motif that promotes cooperative binding of both aminoacylation and editing domains to tRNA(Ala). In addition, C-Ala may have played an essential role in the evolution of AlaRSs by coupling aminoacylation to editing to prevent mistranslation.

The structure of alanyl-tRNA synthetase with editing domain

Alanyl-tRNA synthetase (AlaRS) catalyzes synthesis of Ala-tRNA(Ala) and hydrolysis of mis-acylated Ser- and Gly-tRNA(Ala) at 2 different catalytic sites. Here, we describe the monomer structures of C-terminal truncated archaeal AlaRS, with both activation and editing domains in the apo form, in complex with an Ala-AMP analog, and in a high-resolution lysine-methylated form. The structures show docking of the editing domain to the activation domain opposite from the predicted tRNA-binding surface. Thus, the editing site is positioned >35 A from the activation site, prompting us to model 2 different tRNA complexes: one binding tRNA at the activation site, and the other binding tRNA at the editing site. Interestingly, a gel-shift assay also implies the presence of 2 types of tRNA complex with different mobility. These results suggest that tRNA translocation via a canonical CCA flipping is unlikely to occur in AlaRS. The structure also demonstrated the binding of zinc in the editing site, in which the specific coordination of zinc would be facilitated by a conserved GGQ motif, implying that the editing mechanism may not be the same as in ThrRS. As Asn-194 in eubacterial AlaRS important for Ser misactivation is replaced by Thr-213 in archaeal AlaRS, a different Ser accommodation mechanism is proposed.

Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization

Alanyl-tRNA synthetase (AlaRS) specifically recognizes the major identity determinant, the G3:U70 base pair, in the acceptor stem of tRNA(Ala) by both the tRNA-recognition and editing domains. In this study, we solved the crystal structures of 2 halves of Archaeoglobus fulgidus AlaRS: AlaRS-DeltaC, comprising the aminoacylation, tRNA-recognition, and editing domains, and AlaRS-C, comprising the dimerization domain. The aminoacylation/tRNA-recognition domains contain an insertion incompatible with the class-specific tRNA-binding mode. The editing domain is fixed tightly via hydrophobic interactions to the aminoacylation/tRNA-recognition domains, on the side opposite from that in threonyl-tRNA synthetase. A groove formed between the aminoacylation/tRNA-recognition domains and the editing domain appears to be an alternative tRNA-binding site, which might be used for the aminoacylation and/or editing reactions. Actually, the amino acid residues required for the G3:U70 recognition are mapped in this groove. The dimerization domain consists of helical and globular subdomains. The helical subdomain mediates dimerization by forming a helix-loop-helix zipper. The globular subdomain, which is important for the aminoacylation and editing activities, has a positively-charged face suitable for tRNA binding.

ScanMoment: a web server for combinatorial analysis of basic residues in nucleic acid binding sites.

ScanMoment is a webserver designed to identify the presence of the basic faced alpha-helix (BFAH) motif in the nucleic acid binding sites of proteins. The program calculates the 'Basic Moment', a parameter that quantitizes the distribution of basic residues on the surface of an alpha-helix. A sliding window is used to generate a plot displaying regions of the protein sequence that possesses a high Basic Moment and hus likely to possess a BFAH motif. The user may vary the periodicity from that of an alpha-helix (100 degrees ), to those of other secondary structures such as beta sheets and 3(10) helices. The program can also plot the periodicity of basic residues in a protein sequence using a Fourier transformation. The procedure has been used to characterize the presence of BFAHs in the N-terminal extensions of the eukaryotic aminoacyl-tRNA synthetases and to indicate the presence of a BFAH in the tRNA binding site of alanyl-tRNA synthetase. www.scanmoment.org.

Aminoacyl-tRNA recognition by the FemXWv transferase for bacterial cell wall synthesis

Transferases of the Fem family catalyse peptide-bond formation by using aminoacyl-tRNAs and peptidoglycan precursors as donor and acceptor substrates, respectively. The specificity of Fem transferases is essential since mis-incorporated amino acids could act as chain terminators thereby preventing formation of a functional stress-bearing peptidoglycan network. Here we have developed chemical acylation of RNA helices with natural and non-proteinogenic amino acids to gain insight into the specificity of the model transferase FemXWv. Combining modifications in the RNA and aminoacyl moieties of the donor substrate revealed that unfavourable interactions of FemXWv with the acceptor arm of tRNAGly and with l-Ser or larger residues quantitatively accounts for the preferential transfer of l-Ala observed with complete aminoacyl-tRNAs. The main FemXWv identity determinant was identified as the penultimate base pair (G2-C71) of the acceptor arm instead of G3•U70 for the alanyl-tRNA synthetase. FemXWv tolerated a configuration inversion of the Cα of l-Ala but not the introduction of a second methyl on this atom. These results indicate that aminoacyl-tRNA recognition by FemXWv is distinct from other components of the translation machinery and relies on the exclusion of bulky amino acids and of the sequence of tRNAGly from the active site.