Aminoacyl-tRNA synthetases

Impact of pathogenic mutations on the refolding ability and stability of human mitochondrial Phenylalanyl-tRNA synthetase

Human mitochondrial phenylalanyl-tRNA synthetase (hmtPheRS) requires partial unfolding for mitochondrial import and subsequent refolding to maintain proper functionality. Mutations in the FARS2 gene, encoding hmtPheRS, cause disorders such as early-onset epileptic encephalopathy and spastic paraplegia. This study was intended to investigate the impact of mutations on hmtPheRS refolding ability, stability, and solubility. We have selected two mutations associated with early-onset epileptic encephalopathy (G309S, D325Y) with severe phenotype and three mutations associated with spastic paraplegia (P136H, D142Y, P361L) with less severe phenotypes. Some of those mutations were reported to have diminished aminoacylation activity. However, the molecular connection of pathogenicity remained elusive for these mutants. We observed that hmtPheRS showed exceptional structural flexibility and refolding ability even at lower pH. Mutations associated with severe phenotypes (G309S, D325Y) exhibited impaired refolding ability and stability, whereas other mutant versions of hmtPheRS linked to hereditary spastic paraplegia (P136H, D142Y, P361L) retained some stability and refolding capacity. Mutants exhibited expansion in hydrodynamic diameter, indicating significant perturbation in the internal architecture. Molecular simulation studies suggested the presence of structural deformities in hmtPheRS mutants at mildly acidic pH. This analysis reveals how mutations affect protein stability and function, which may play a role in mitochondrial disorders. It may act as a probable model for predicting pathogenicity-related mutants.

Residue-Specific Incorporation of Noncanonical Amino Acids in Auxotrophic Hosts: Quo Vadis?

The residue-specific incorporation of noncanonical amino acids in auxotrophic hosts allows the global exchange of a canonical amino acid with its noncanonical analog. Noncanonical amino acids are not encoded by the standard genetic code, but they carry unique side chain chemistries, e.g., to perform bioorthogonal conjugation reactions or to manipulate the physicochemical properties of a protein such as folding and stability. The method was introduced nearly 70 years ago and is still in widespread use because of its simplicity and robustness. In our study, we review the trends in the field during the last two decades. We give an overview of the application of the method for artificial post-translational protein modifications and the selective functionalization and directed immobilization of proteins. We highlight the trends in the use of noncanonical amino acids for the analysis of nascent proteomes and the engineering of enzymes and biomaterials, and the progress in the biosynthesis of amino acid analogs. We also discuss the challenges for the scale-up of the technique.

Streamlining tRNA-Synthetase Evolution for Genetic Code Expansion and Deep Sequencing Analyses of Its Evolved Variants

Proteins are typically composed of 20 amino acids encoded by 61 codons. However, some bacteria and archaea have evolved to incorporate additional amino acids by repurposing stop codons, a phenomenon that led to the development of genetic code expansion (GCE) in the early 21st century. This approach introduces orthogonal tRNA and aminoacyl-tRNA-synthetase (aaRS) pairs into target organisms, enabling the incorporation of noncanonical amino acids (ncAAs) with distinct side chains into proteins. GCE has broad applications, including site-specific cross-linking, fluorescence labeling, and electron-transfer functionalities. Despite its versatility, improving the efficiency of ncAA incorporation remains a challenge. Directed evolution provides a powerful solution by introducing mutations into the aaRS sequence and applying selection to identify variants with enhanced activity. Here, we present a simplified directed evolution system designed to improve the activity of pyrrolysyl-tRNA synthetase (PylRS) from Methanosarcina mazei. Our approach is accessible, requiring only basic laboratory equipment, making it suitable and facile to implement by graduate students. We evolved PylRS variants toward three distinct substrates, each pathway yielding unique, substrate-specific mutations. We characterized the impact of these mutations on both PylRS activity and expression levels, demonstrating that tandem codon randomization can be an effective strategy for improving PylRS function through additive effects of the mutations. Additionally, deep sequencing validated our approach, confirming its efficiency, revealing conserved and mutationally flexible sites and reinforcing the advantage of tandem mutations in PylRS evolution. Collectively, these findings streamline the process of evolving PylRS and provide insights into strategies for enhancing ncAA incorporation in synthetic biology and protein engineering.

Allosteric modulation of Plasmodium falciparum Isoleucyl tRNA synthetase by South African natural compounds

Targeting Plasmodium falciparum (Pf) aminoacyl tRNA synthetases is a viable strategy to overcome malaria parasite multi-drug resistance. Here, we focused on Pf Isoleucyl tRNA synthetase (PfIleRS) to identify potential allosteric inhibitors from 1019 South African Natural Compounds (SANC). Eleven potential hits, which passed ADMET and PAINS, were selected based on their docking binding affinity which was higher for PfIleRS than for human IleRS. Molecular dynamics simulations revealed that the compounds, particularly SANC456, commonly induced considerable changes in the global conformation and dynamics of PfIleRS, suggesting potential allosteric modulatory effects. Importantly, all 11 SANC hits reduced the binding affinity of the nucleotide AMP molecule by at least 25%. Some SANC ligand-bound systems (SANC456, SANC1095, and SANC1104) significantly increased the distance between the AMP and Ile ligands. Possible explanations for these changes were explored using three dynamic residue network centrality metrics. Betweenness centrality identified a major allosteric pathway in holo PfIleRS spanning the entire protein length. In contrast, SANC382, SANC456, SANC522, SANC806 and SANC1095 ligand-bound systems exhibited delta BC pathways (SANC-protein minus holo-protein), induced by the ligands, extending from their respective pockets into the active site. Additionally, eigenvector centrality revealed two important residue clusters either side of the holo active site which became altered in the ligand-bound systems, indicating possible allosteric activity. Lastly, many SANC systems showed decreased closeness centrality of zinc finger and active site residues, including the HYGH and KMSKR motifs. We believe that the compounds identified in this study as potential allosteric inhibitors have strong translational potential and warrant further investigation through in vitro and in vivo experiments. Overall, they hold promise as starting points for the development of new and effective antimalarial therapies, particularly against multidrug-resistant Plasmodium parasites.

Architecture of Pseudomonas aeruginosa glutamyl-tRNA synthetase defines a subfamily of dimeric class Ib aminoacyl-tRNA synthetases

The aminoacyl-tRNA synthetases (AaRSs) are an ancient family of structurally diverse enzymes that are divided into two major classes. The functionalities of most AaRSs are inextricably linked to their oligomeric states. While GluRSs were previously classified as monomers, the current investigation reveals that the form expressed in Pseudomonas aeruginosa is a rotationally pseudosymmetrical homodimer featuring intersubunit tRNA binding sites. Both subunits display a highly bent, "pipe strap" conformation, with the anticodon binding domain directed toward the active site. The tRNA binding sites are similar in shape to those of the monomeric GluRSs, but are formed through an approximately 180-degree rotation of the anticodon binding domains and dimerization via the anticodon and D-arm binding domains. As a result, each anticodon binding domain is poised to recognize the anticodon loop of a tRNA bound to the adjacent protomer. Additionally, the anticodon binding domain has an α-helical C-terminal extension containing a conserved lysine-rich consensus motif positioned near the predicted location of the acceptor arm, suggesting dual functions in tRNA recognition. The unique architecture of PaGluRS broadens the structural diversity of the GluRS family, and member synthetases of all bacterial AaRS subclasses have now been identified that exhibit oligomerization.

Adaptive dynamics of extrachromosomal circular DNA in rice under nutrient stress

Extrachromosomal circular DNAs (eccDNAs) have been identified in various eukaryotic organisms and are known to play crucial roles in genomic plasticity. However, in crop plants, the role of eccDNAs in responses to environmental cues, particularly nutritional stresses, remains unexplored. Rice (Oryza sativa ssp. japonica), a vital crop for over half the world's population and an excellent model plant for genomic studies, faces numerous environmental challenges during growth. Therefore, we conduct comprehensive studies investigating the distribution, sequence, and potential responses of rice eccDNAs to nutritional stresses. We describe the changes in the eccDNA landscape at various developmental stages of rice in optimal growth. We also identify eccDNAs overlapping with genes (ecGenes), transposable elements (ecTEs), and full-length repeat units (full-length ecRepeatUnits), whose prevalence responds to nitrogen (N) and phosphorus (P) deficiency. We analyze multiple-fragment eccDNAs and propose a potential TE-mediated homologous recombination mechanism as the origin of rice's multiple-fragment eccDNAs. We provide evidence for the role of eccDNAs in the rice genome plasticity under nutritional stresses and underscore the significance of their abundance and specificity.

Serine mistranslation induces the integrated stress response through the P stalk

Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes that support robust and accurate protein synthesis. A rapidly expanding number of studies show that mutations in aaRSs lead to multiple human diseases, including neurological disorders and cancer. How aaRS mutations impact human health is not fully understood. In particular, our knowledge of how aminoacylation errors affect stress responses and fitness in eukaryotic cells remains limited. The integrated stress response (ISR) is an adaptive mechanism in response to multiple stresses. However, chronic activation of the ISR contributes to the development of multiple diseases such as neuropathies. In this study, we show that Ser misincorporation into Ala and Thr codons, resulting from either aaRS-editing defects or mutations in tRNAs, activates the ISR. We further demonstrate that activation of the ISR by Ser mistranslation does not depend on the accumulation of uncharged tRNAs but rather requires the P stalk associated with the ribosome, implying that ribosome stalling and collision are involved. Our work highlights that certain types of aminoacylation errors can lead to chronic activation of the ISR, potentially affecting fitness and disease progression.

Direct and quantitative analysis of tRNA acylation using intact tRNA liquid chromatography-mass spectrometry

Aminoacyl-tRNA synthetases (aaRSs) provide an essential functional link between an mRNA sequence and the protein it encodes. aaRS enzymes catalyze a two-step chemical reaction that acylates specific tRNAs with a cognate α-amino acid. In addition to their role in translation, acylated tRNAs contribute to non-ribosomal natural product biosynthesis and are implicated in multiple human diseases. In synthetic biology, the acylation of tRNAs with a non-canonical α-amino acid or, more recently, a non-α-amino acid monomer is a critical first step in the incorporation of these monomers into proteins, where they can be used for fundamental and applied science. These endeavors all demand an understanding of aaRS activity and specificity. Here, we describe a liquid chromatography-mass spectrometry assay that directly monitors aaRS activity by detecting the intact acyl-tRNA product. After a simple tRNA acylation reaction workup, acyl- and non-acyl-tRNA molecules are resolved by using ion-pairing reverse-phase chromatography, and their exact masses are determined by using high-resolution time-of-flight mass spectrometry. Our assay is fast and simple, quantifies reaction yields as low as 0.23% and can also be used on tRNAs acylated with flexizyme to detect products that are undetectable by using standard techniques. The protocol requires basic expertise in molecular biology, liquid chromatography-mass spectrometry and RNase-free techniques. This protocol takes ≥5 h to complete, depending on the number of samples.

Evolution is coupled with branching across many granularities of life

Across many scales of life, the rate of evolutionary change is often accelerated at the time when one lineage splits into two. The emergence of novel protein function can be facilitated by gene duplication (neofunctionalization); rapid morphological change is often accompanied by speciation (punctuated equilibrium); and the establishment of cultural identity is frequently driven by sociopolitical division (schismogenesis). In each case, the changes resist re-homogenization; promoting assortment into distinct lineages that are susceptible to different selective pressures, leading to rapid divergence. The traditional gradualistic view of evolution struggles to detect this phenomenon. We propose a probabilistic framework that constructs phylogenies, tests for saltative branching and improves divergence time estimation by estimating the independent contributions of gradual and abrupt change on each lineage. We provide evidence of saltative branching for proteins (aminoacyl transfer RNA (tRNA) synthetases), animal morphologies (cephalopods) and human languages (Indo-European). These three cases provide unique insights: for aminoacyl-tRNA synthetases, the trees are substantially different from those obtained under gradualist models; we estimate that 99% of cephalopod morphological changes coincided with speciation events; and Indo-European dispersal is estimated to have started around 6000 BCE, corroborating the recently proposed hybrid explanation. Our open-source code is available under a General Public License.

Neonatal exposure to morphine results in prolonged pain hypersensitivity during adolescence, driven by gut microbial dysbiosis and gut-brain axis-mediated inflammation

Opioids, such as morphine, are used in the Neonatal Intensive Care Unit (NICU) for pain relief in neonates. However, the available evidence concerning the benefits and harms of opioid therapy in neonates remains limited. While previous studies have reported that neonatal morphine exposure (NME) results in long-term heightened pain sensitivity, the underlying mechanisms are not well understood. This study proposes that dysbiosis of the gut microbiome contributes to pain hypersensitivity following NME. Using an adolescent female murine model, pain sensitivity was evaluated using the tail flick and hot plate assays for thermal pain and the Von Frey assay for mechanical pain. Gut microbiome composition was assessed using 16S rRNA sequencing, while transcriptomic changes in midbrain samples were investigated using bulk RNA sequencing. NME induced prolonged hypersensitivity to thermal and mechanical pain in adolescence, accompanied by persistent gut microbial dysbiosis and sustained systemic inflammation, characterized by elevated circulating cytokine levels (e.g., IL-1α, IL-12p70, IFN-γ, IL-10). Transplantation of the microbiome from NME adolescents recapitulated pain hypersensitivity in naïve adolescent mice, while neonatal probiotic intervention with Bifidobacterium infantis (B. infantis) reversed the pain hypersensitivity by preventing gut dysbiosis and associated systemic inflammation. Furthermore, transcriptomic analysis of midbrain tissues revealed that NME upregulated several genes and key signaling pathways, including those related to immune activation and excitatory signaling, which were notably mitigated with neonatal B. infantis administration. Together, these findings highlight the critical role of the gut-brain axis in modulating pain sensitivity and suggest that targeting the gut microbiome offers a promising therapeutic strategy for managing neurobiological disorders following early opioid exposure.

A genome-wide investigation of Mycoplasma hominis genes associated with gynecological infections or infertility

Background and aim

Mycoplasma hominis is a human pathogenic bacterium that causes a wide range of genital infections and reproductive issues. Previously, based on an extended multilocus sequence typing scheme, we provided evidence for the segregation of M. hominis clinical strains into two distinct pathotypes: gynecological infections or infertility. Here, based on whole genome sequencing (WGS) data, we sought to provide a more refined picture of the phylogenetic relationship between these two M. hominis pathotypes, with the aim to delineate the underlying genetic determinants.

Methods

We carried out WGS of 62 Tunisian M. hominis clinical strains collected over a 17-year period. The majority of these clinical strains are associated with infertility (n = 53) and the remaining nine isolates are from gynecological infections cases. An alignment-free distance-based procedure (Jolytree) was used to infer phylogenetic relationships among M. hominis isolates, while the phylogenetic method treeWAS was used to determine the statistical association between pathotypes of interest and genotypes at all loci.

Results

The total pangenome of M. hominis strains was found to contain 1,590 genes including 966 core genes and 592 accessory genes, representing 60 and 37% of the total genome, respectively. Collectively, phylogenetic analyses based on WGS confirmed the distinction between the two M. hominis pathotypes. Strikingly, genome wide association analyses identified 4 virulence genes associated with gynecological infections, mainly involved in nucleotide salvage pathways and tolerance to oxidative stress, while five genes have been associated with infertility cases, two of which are implicated in biofilm formation.

Conclusion

In sum, this study further established the categorization of M. hominis into two pathotypes, and led to the identification of the associated genetic loci, thus holding out promising prospects for a better understanding of the differential interaction of M. hominis with its host.

Membrane-permeable trehalose 6-phosphate precursor spray increases wheat yields in field trials

Trehalose 6-phosphate (T6P) is an endogenous sugar signal in plants that promotes growth, yet it cannot be introduced directly into crops or fully genetically controlled. Here we show that wheat yields were improved using a timed microdose of a plant-permeable, sunlight-activated T6P signaling precursor, DMNB-T6P, under a variety of agricultural conditions. Under both well-watered and water-stressed conditions over 4 years, DMNB-T6P stimulated yield of three elite varieties. Yield increases were an order of magnitude larger than average annual genetic gains of breeding programs and occurred without additional water or fertilizer. Mechanistic analyses reveal that these benefits arise from increased CO2 fixation and linear electron flow ('source') as well as from increased starchy endosperm volume, enhanced grain sieve tube development and upregulation of genes for starch, amino acid and protein synthesis ('sink'). These data demonstrate a step-change, scalable technology with net benefit to the environment that could provide sustainable yield improvements of diverse staple cereal crops.

Proteomic analysis of hippocampus reveals metabolic reprogramming in a piglet model of mild hypoxic ischemic encephalopathy

Neonatal hypoxic-ischemic encephalopathy (HIE) remains a leading cause of long-term neurologic morbidity. Fifty percent of HIE cases are mild and do not have clearly defined therapeutic interventions. Emergent evidence now demonstrates that up to 25% of children with mild HIE suffer motor and developmental delay by 18 months and 35% have cognitive impairments by age 5 years. Interestingly, the hippocampus, which is responsible for learning and memory, does not show overt injury but does demonstrate volume changes on imaging that correlate with cognitive and behavioral outcomes. Although there is extensive data regarding pathophysiological changes following moderate and severe HIE, there is a paucity of understanding regarding the extent, duration, and compensatory adaptations in the mild neonatal HIE brain. We performed hippocampal proteomic analysis using a swine model of mild neonatal hypoxia-asphyxia. Hippocampi were collected at 24 or 72 hours after injury, and proteomics was performed by liquid chromatography tandem mass spectrometry (LC-MS/MS). Pathway analysis demonstrated that several metabolic pathways are temporally regulated after mild HIE. Specifically, amino acid, carbohydrate, and one-carbon metabolism increased at 24 hours while fat metabolism and oxidative phosphorylation decreased at 24 hours. Downregulation of oxidative phosphorylation was more pronounced at 72 hours. Our data demonstrate that metabolic reprogramming occurs after mild HIE, and these changes persist up to 72 hours after injury. These results provide new evidence that mild HIE disrupts brain metabolism, emphasizing the need for a better understanding of the underlying pathophysiology of mild HIE and development of targeted therapeutic interventions for this population.

Unexpected enzymatic function of an ancient nucleic acid-binding fold

Aminoacyl-tRNA synthetases (ARSs) are indispensable for all living organisms and their associated aminoacyl-tRNA editing domains ensure the fidelity of translation. In eukaryotes, ARSs form a multi-aminoacyl-tRNA synthetase complex (MSC), which is assembled together with several nonsynthetase scaffolding proteins. The MSC found in Trypanosoma brucei (Tb) includes two proteins with oligosaccharide/oligonucleotide-binding (OB) folds-MSC-associated protein 1 (MCP1) and MCP2-and one known trans-editing factor, MCP3, an Ala-tRNA deacylase. The activity of MCP1 was unexplored until now. Our study shows that recombinantly-expressed and purified MCP1 also deacylates Ala-tRNAs despite lacking known tRNA-editing domain homology. Domain deletion studies reveal that the OB-fold houses the catalytic pocket and mutation of any one of three conserved OB-fold residues (K326, R331, S335) abolishes activity. Assays with Saccharomyces cerevisiae Arc1p reveal that MCP1's deacylation activity is conserved across organisms. This discovery explains the 3' CCA-end binding activity of this protein family and uncovers an ancient nucleic acid binding domain's unexpected enzymatic function.

Mass spectrometry-based characterisation of the cardiac microtissue metabolome and lipidome

INTRODUCTION

The use of large, non-sample specific metabolite reference libraries often results in high proportions of false positive annotations in untargeted metabolomics.

OBJECTIVE

This study aimed to measure and curate a library of polar metabolites and lipids present in cardiac microtissues.

RESULTS

Untargeted ultra-high performance liquid chromatography-coupled mass spectrometry measurements of cardiac microtissue intracellular extracts were annotated by comparison against four spectral databases and a retention time library. The annotations were combined to create a library of 313 polar metabolites and 1004 lipids.

CONCLUSIONS

The curated library will facilitate higher confidence metabolite annotation in mass spectrometry-based untargeted metabolomics of cardiac microtissues.

Mendelian randomization analysis of blood metabolites and immune cell mediators in relation to GVHD and relapse

BACKGROUND

Graft-versus-host disease (GVHD) and relapse are major complications following allogeneic hematopoietic stem cell transplantation (allo-HSCT). Metabolites play crucial roles in immune regulation, but their causal relationships with GVHD and relapse remain unclear.

METHODS

We utilized genetic variants from genome-wide association studies (GWAS) of 309 known metabolites as instrumental variables to evaluate their causal effects on acute GVHD (aGVHD), gut GVHD, chronic GVHD (cGVHD), and relapse in different populations. Multiple causal inference methods, heterogeneity assessments, and pleiotropy tests were conducted to ensure result robustness. Multivariable MR analysis was performed to adjust for potential confounders, and validation MR analysis further confirmed key findings. Mediation MR analysis was employed to explore indirect causal pathways.

RESULTS

After correction for multiple testing, we identified elevated pyridoxate and proline levels as protective factors against grade 3-4 aGVHD (aGVHD3) and relapse, respectively. Conversely, glycochenodeoxycholate increased the risk of aGVHD3, whereas 1-stearoylglycerophosphoethanolamine had a protective effect. The robustness and stability of these findings were confirmed by multiple causal inference approaches, heterogeneity, and horizontal pleiotropy analyses. Multivariable MR analysis further excluded potential confounding pleiotropic effects. Validation MR analyses supported the causal roles of pyridoxate and 1-stearoylglycerophosphoethanolamine, while mediation MR revealed that pyridoxate influences GVHD directly and indirectly via CD39 + Tregs. Pathway analyses highlighted critical biochemical alterations, including disruptions in bile acid metabolism and the regulatory roles of vitamin B6 derivatives. Finally, clinical metabolic analyses, including direct fecal metabolite measurements, confirmed the protective role of pyridoxate against aGVHD.

CONCLUSIONS

Our findings provide novel insights into the metabolic mechanisms underlying GVHD and relapse after allo-HSCT. Identified metabolites, particularly pyridoxate, may serve as potential therapeutic targets for GVHD prevention and management.

Yeast models for Charcot-Marie-Tooth disease-causing aminoacyl-tRNA synthetase alleles reveal the cellular basis of disease

Charcot-Marie-Tooth disease (CMT) is a genetically diverse hereditary disorder that affects the motor and sensory nerves, impacting about 1 in 2500 people. It can be inherited through autosomal dominant (AD), autosomal recessive (AR), or X-linked genetic patterns. CMT2, one of the primary subtypes, is characterized by axonal degeneration and commonly presents with muscle weakness, atrophy, foot deformities, and sensory loss. Aminoacyl-tRNA synthetases (aaRSs) play an important role in the genetic underpinnings of CMT2, with more than 60 disease-causing alleles identified across eight different aaRSs, including alanyl-, asparaginyl-, histidyl-, glycyl-, methionyl-, tryptophanyl-, seryl-, and tyrosyl-tRNA synthetases. Mutations in aaRS genes can lead to destabilization of the enzyme, reduced aminoacylation, and aberrant protein complex formation. Yeast as a simple organism provides a robust model system to study the pathogenic effects of aaRS CMT mutations. In this review, we discuss the advantages and limitations of the yeast model systems for CMT2-causative mutations in aaRS.

The crystal structures of apo and tryptophan-bound tryptophanyl-tRNA synthetase from Neisseria gonorrhoeae

Neisseria gonorrhoeae, the causative agent of the human disease gonorrhea, is the second most common sexually transmitted pathogen in the United States. Gonorrhea has a significantly high morbidity rate due to the ability of N. gonorrhoeae to rapidly develop antibiotic resistance. In this paper, crystal structures of tryptophanyl-tRNA synthetase (TrpRS) from N. gonorrhoeae (NgTrpRS) were determined in both its apo form and in complex with tryptophan. The structures reveal conserved HIGH and KMSKS motifs critical for ATP binding and catalysis, and highlight conformational changes in the active site upon tryptophan binding, including a methionine flip and the rearrangement of hydrogen-bonding residues. Structural alignments with human TrpRS isoforms demonstrate significant differences between the bacterial and human cytosolic forms, particularly in their active sites. While NgTrpRS and human mitochondrial TrpRS share conserved catalytic residues that are essential for binding tryptophan and indolmycin, the cytosolic TrpRS contains substitutions that introduce steric hindrance, limiting the binding of indolmycin. These results provide insight for the development of inhibitors targeting bacterial TrpRS without affecting the human mitochondrial or cytosolic isoforms, contributing to efforts to combat antibiotic-resistant N. gonorrhoeae infections.

Kinetic characterization of amino acid activation by aminoacyl-tRNA synthetases using radiolabelled γ-[32P]ATP

Aminoacyl-tRNA synthetases (AARSs) are fundamental enzymes that pair amino acids and tRNAs for protein synthesis. Aminoacylation occurs in two discrete steps. The amino acid is first activated by ATP, leading to an aminoacyl-adenylate intermediate and pyrophosphate (PPi) formation. In a subsequent step, the aminoacyl moiety is transferred to the tRNA. Kinetic assays were developed to follow each of these steps independently, as well as cumulative two-step aminoacylation. The main advantage of following the activation step over two-step aminoacylation is that most AARSs can activate amino acids in the absence of the tRNA, the production of which is laborious. Hence, the activation step is often tested first in the kinetic analysis, including large screens exploring AARS-targeting inhibitors. Since the 1960s, the activation reaction has been routinely followed by the standard ATP/[32P]PPi exchange assay, which relies on the equilibrium exchange of radiolabel between PPi and ATP using [32P]PPi as a labelled compound. However, this method became much less convenient when [32P]PPi was discontinued in 2022. As a solution, we developed a modified assay that uses easily attainable γ-[32P]ATP as a labelled compound in the equilibrium-based assay. Using this assay, herein named the [32P]ATP/PPi assay, we followed the activation step of several AARSs. The obtained data are in good agreement with the previously published kinetic constants obtained with the standard ATP/[32P]PPi exchange assay.

Insecticidal effect and mechanism of Metarhizium anisopliae ZHKUJGZ1 against Solenopsis invicta (Hymenoptera: Formicidae)

The red imported fire ant (RIFA), Solenopsis invicta Buren, poses threats to biodiversity, public safety, agriculture, and the economy, especially as global trade expands its reach into China. To address this, researchers screened fungal isolates from soil in Dongguan City, Guangdong Province, aiming to develop a biopesticide against RIFA. Metarhizium anisopliae, known for its biocontrol potential, was identified as a candidate. This insect pathogenic fungus parasitizes Lepidoptera pest larvae and Hemiptera stinkbugs, causing green rigidity and repeated infestations. Microscopic, morphological, and molecular analyses were conducted on the fungal isolates, with ZHKUJGZ1, a strain of M. anisopliae, showing promise. Tests revealed that inoculating RIFA workers with 1 × 107 cfu/mL of ZHKUJGZ1 resulted in an 83.33 ± 1.57 % mortality rate, with an LC50 of 8.36 × 106 cfu/mL. Untargeted metabolomics suggested that ZHKUJGZ1 enhances insecticidal activity by disrupting the nervous system, signaling, digestive system, amino acid metabolism, and biosynthesis in RIFA. This study highlights the potential of using entomopathogenic fungi like M. anisopliae isolated from Dongguan as an effective strategy for controlling RIFA, offering a promising biocontrol option for agricultural pests.

The origins and evolution of translation factors

Translation is an ancient molecular information processing system found in all living organisms. Over the past decade, significant progress has been made in uncovering the origins of early translation. Yet, the evolution of translation factors - key regulators of protein synthesis - remains poorly understood. This review synthesizes recent findings on translation factors, highlighting their structural diversity, evolutionary history, and organism-specific adaptations across the tree of life. We examine conserved translation factors, their coevolution, and their roles in different steps in translation: initiation, elongation, and termination. The early evolution of translation factors serves as a natural link between modern genetics and the origins of life. Traditionally rooted in chemistry and geology, incorporating evolutionary molecular biology into the studies of life's emergence provides a complementary perspective on this complex question.

BmWARS inhibits BmNPV infection via the PI3K-Akt pathway

Bombyx mori Tryptophanyl-tRNA synthetase (BmWARS) belongs to the family of Ic-like aminoacyl-tRNA synthetases (aaRSs), whose specific recognition of the substrate Trp, tRNA, maintains the fidelity of protein synthesis. In this study, BmWARS was cloned and characterized from the midgut of the silkworm, Bombyx mori, resulting in an open reading frame (ORF) with a full length of 1,149 bp, which can encode 382 Aa. BmWARS is localized in the cytoplasm, and is expressed in all tissues of the silkworm, with higher expression in the testis, ovary, silk gland and malpighian tubule. The expression of BmWARS was significantly up-regulated in the midgut and silk gland after infection with Bombyx mori nuclear polyhedrosis virus (BmNPV). In addition, overexpression of BmWARS inhibited BmNPV infection and replication extremely significantly, while interference with BmWARS expression promoted BmNPV infection and replication. Analysis of the immune pathways in which BmWARS may be involved revealed that the expression of the key genes of the PI3K-Akt pathway, BmPI3K, BmAkt, BmPDK1, BmeIF4E, BmS6, and p-Akt protein was significantly reduced, whereas the expression of BmPTEN, BmFoxO, and BmCaspase9 was significantly increased in the cells that overexpressed BmWARS and were infected with BmNPV. Meanwhile, the results of the study interfering with the expression of BmWARS were completely opposite to those of the study overexpressing BmWARS. This is the first report that BmWARS has antiviral effects in Bombyx mori. Moreover, BmWARS inhibits BmNPV infection and replication in Bombyx mori cells by promoting apoptosis and inhibiting cell proliferation.

Glycyl-tRNA sequestration is a unifying mechanism underlying GARS1-associated peripheral neuropathy

Dominantly inherited mutations in eight cytosolic aminoacyl-tRNA synthetase genes cause hereditary motor and sensory neuropathy, characterized by degeneration of peripheral motor and sensory axons. We previously identified a pathogenic gain-of-toxic function mechanism underlying peripheral neuropathy (PN) caused by heterozygous mutations in the GARS1 gene, encoding glycyl-tRNA synthetase (GlyRS). Specifically, PN-mutant GlyRS variants sequester tRNAGly, which depletes the cellular tRNAGly pool, leading to insufficient glycyl-tRNAGly available to the ribosome and consequently ribosome stalling at glycine codons. Given that GlyRS functions as a homodimer, a subset of PN-GlyRS mutations might alternatively cause peripheral neuropathy through a dominant negative loss-of-function mechanism. To explore this possibility, we here generated three novel PN-GlyRS Drosophila models expressing human PN-GlyRS (hGlyRS) variants that do not alter the overall GlyRS protein charge (S211F and H418R) or the single reported PN-GlyRS variant that renders the GlyRS protein charge more negative (K456Q). High-level expression of hGlyRS-K456Q did not induce peripheral neuropathy and the K456Q variant does not affect aminoacylation activity, suggesting that K456Q is not a pathogenic mutation. Expression of hGlyRS-S211F or hGlyRS-H418R in Drosophila did induce peripheral neuropathy and de novo protein synthesis defects. Genetic and biochemical evidence indicates that these phenotypes were attributable to tRNAGly sequestration rather than a dominant negative mechanism. Our data identify tRNAGly sequestration as a unifying pathogenic mechanism underlying PN-GlyRS. Thus, elevating tRNAGly levels may constitute a therapeutic approach for all PN-GlyRS patients, irrespective of their disease-causing mutation.

Aminoisothiazolamides, a new class of potent inhibitors of lysyl-tRNA synthetase

BACKGROUND

Owing to the economic relevance of resistance evolution against herbicides, new chemical entities addressing unprecedented molecular targets are urgently needed to develop future sustainable weed control solutions. As part of our discovery research, the new class of aminoisothiazolamides was investigated.

RESULTS

Aminoisothiazolamide 3-amino-4-chloro-N-(cyclohexylmethyl)isothiazole-5-carboxamide 1a and several of its derivatives displayed potent herbicidal and fungicidal in vivo activity in initial glasshouse tests. Lysyl-tRNA synthetase 1 (KRS1) was identified as the putative target for 1a and was validated as a key contributor to the biochemical mode-of-action of aminoisothiazolamides. Thermal stability shift analysis with KRS1 from Arabidopsis thaliana (AtKRS1) revealed that 1a specifically increased the thermostability of this enzyme, proving the KRS1 enzyme as the aminoisothiazolamide target. It turned out that the inhibition of AtKRS1 and HsKRS was strongly correlated, as was the inhibition of AtKRS1 and the herbicidal activity of the aminoisothiazolamides. Hence, in vivo acute toxicity tests were initiated at a very early project stage complementing the enzyme tests.

CONCLUSION

The observed toxicological effects paired with the anticipated likelihood to overcome this problem, owing to the highly conserved active sites in different species, finally resulted in the conclusion to stop the further exploration of the otherwise promising class of herbicidal aminoisothiazolamides. Thus, we opted to discard several further herbicidal lead structures before the start of in-depth investigations when sequence analyses suggested similar levels of conservation between the respective binding pockets in plants and mammalians. © 2025 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Remodelled ribosomal populations synthesize a specific proteome in proliferating plant tissue during cold

Plant acclimation occurs through system-wide mechanisms that include proteome shifts, some of which occur at the level of protein synthesis. All proteins are synthesized by ribosomes. Rather than being monolithic, transcript-to-protein translation machines, ribosomes can be selective and cause proteome shifts. In this study, we use apical root meristems of germinating seedlings of the monocotyledonous plant barley as a model to examine changes in protein abundance and synthesis during cold acclimation. We measured metabolic and physiological parameters that allowed us to compare protein synthesis in the cold to optimal rearing temperatures. We demonstrated that the synthesis and assembly of ribosomal proteins are independent processes in root proliferative tissue. We report the synthesis and accumulation of various macromolecular complexes and propose how ribosome compositional shifts may be associated with functional proteome changes that are part of successful cold acclimation. Our study indicates that translation initiation is limiting during cold acclimation while the ribosome population is remodelled. The distribution of the triggered ribosomal protein heterogeneity suggests that altered compositions may confer 60S subunits selective association capabilities towards translation initiation complexes. To what extent selective translation depends on heterogeneous ribo-proteome compositions in barley proliferative root tissue remains a yet unresolved question.This article is part of the discussion meeting issue 'Ribosome diversity and its impact on protein synthesis, development and disease'.

Mechanistic insights into the viral microorganism inactivation during lime stabilization for wastewater sludges

The pathogens inactivation in wastewater sludges is vitally important for safely managing solid wastes and protecting public and environmental health especially in the emergency. Reports have shown the effectiveness of lime to kill virus pathogens in sludges, but mechanism of virus inactivation and related human diseases is unclear. This study evaluated representative limes of CaO/CaO2 on actual viral microorganism inactivation by viral metagenomic sequencing technology. As results, the CaO2 treatment enhanced the sludge hydrolysis and enveloped viral pathogens suppression via EPS structure destruction by oxidative radical generations; while CaO suppressed most of none-enveloped plant related viral pathogens. Most of the viromes of plant virus including Virgaviridae and Nodaviridae were inactivated by CaO, but the human virus-Feirsviridae and plant virus-Solemoviridae were occurred after lime stabilization compared to untreated sludge, with abundances of 1 %-37 % and 21 %-32 % in CaO-treated (CaO-T) and CaO2-treated (CaO2-T) samples, respectively. In addition, metatranscriptome analysis revealed distinct gene expression patterns between the CaO-T and CaO2-T sludges, in which lipopolysaccharide biosynthesis (LPS) and aminoacyl-tRNA synthetases (ARSs) in CaO-T, the formation of ribosome in CaO2-T were crucial to RNA virus regrowth in sludge. These findings suggested neither of CaO and CaO2 could completely suppress pathogens in sludge, and the effect of representative limes of CaO and CaO2 on the viral pathogen diversity, abundance, and metabolic function of the core microbiome on virus suppression and regrowth were ignored. Therefore, combined processes were recommended to provide possible alternatives for sludge safe management in pandemic emergencies.

Aminoacyl-tRNA synthetase urzymes optimized by deep learning behave as a quasispecies

Protein design plays a key role in our efforts to work out how genetic coding began. That effort entails urzymes. Urzymes are small, conserved excerpts from full-length aminoacyl-tRNA synthetases that remain active. Urzymes require design to connect disjoint pieces and repair naked nonpolar patches created by removing large domains. Rosetta allowed us to create the first urzymes, but those urzymes were only sparingly soluble. We could measure activity, but it was hard to concentrate those samples to levels required for structural biology. Here, we used the deep learning algorithms ProteinMPNN and AlphaFold2 to redesign a set of optimized LeuAC urzymes derived from leucyl-tRNA synthetase. We select a balanced, representative subset of eight variants for testing using principal component analysis. Most tested variants are much more soluble than the original LeuAC. They also span a range of catalytic proficiency and amino acid specificity. The data enable detailed statistical analyses of the sources of both solubility and specificity. In that way, we show how to begin to unwrap the elements of protein chemistry that were hidden within the neural networks. Deep learning networks have thus helped us surmount several vexing obstacles to further investigations into the nature of ancestral proteins. Finally, we discuss how the eight variants might resemble a sample drawn from a population similar to one subject to natural selection.

Effects of positive mGlu5 modulation on D2 signaling and nicotine-conditioned place preference: Mechanisms of epigenetic inheritance in a transgenerational model of drug abuse vulnerability in psychosis

BACKGROUND

The metabotropic glutamate type 5 (mGlu5) receptor has emerged as a potential target for the treatment of psychosis that is suggested to have greater efficacy than antipsychotic medications that are currently utilized.

AIMS

This study sought to elucidate mechanisms of therapeutic action associated with the modulation of the mGlu5 receptor in a disordered system marked by dopamine dysfunction. We further explored epigenetic mechanisms contributing to heritable transmission of a psychosis-like phenotype in a novel heritable model of drug abuse vulnerability in psychosis.

METHODS

F1 generation male and female Sprague-Dawley rats that were the offspring of two neonatal quinpirole-treated (QQ) or two saline-treated (SS) animals were tested on nicotine-conditioned place preference (CPP). Regulators of G protein signaling 9 (RGS9) and β-arrestin 2 (βA2), which mediate dopamine (DA) D2 signaling, were measured in the nucleus accumbens shell, prelimbic and infralimbic cortices. Reduced Representation Bisulfite Sequencing (RRBS) was used to analyze the cytosine methylation in these brain regions.

RESULTS

Pretreatment with the mGlu5-positive allosteric modulator 3-Cyano-N-(1,3-diphenyl-1H-pyrazol-5-yl)benzamide (CDPPB) 20 min prior to conditioning trials blocked enhanced nicotine CPP and mitigated aberrant G protein-dependent and -independent signaling in QQ animals. RRBS analysis revealed region-specific changes in several pathways, including nicotine addiction, dopamine synapses, and neural connectivity.

CONCLUSIONS

These results reveal an important region-specific mechanism of action for CDPPB in a system marked by enhanced DAD2 receptor signaling. Results additionally reveal DNA methylation as an epigenetic mechanism of heritability, further validating the current model as a useful tool for the study of psychosis and comorbid nicotine use.

Structural basis for aminoacylation of cellular modified tRNALys3 by human lysyl-tRNA synthetase

The average eukaryotic transfer ribonucleic acid (tRNA) contains 13 post-transcriptional modifications; however, their functional impact is largely unknown. Our understanding of the complex tRNA aminoacylation machinery in metazoans also remains limited. Herein, using a series of high-resolution cryo-electron microscopy (cryo-EM) structures, we provide the mechanistic basis for recognition and aminoacylation of fully modified cellular tRNALys3 by human lysyl-tRNA synthetase (h-LysRS). The tRNALys3 anticodon loop modifications S34 (mcm5s2U) and R37 (ms2t6A) play an integral role in recognition by h-LysRS. Modifications in the T-, variable-, and D-loops of tRNALys3 are critical for ordering the metazoan-specific N-terminal domain of LysRS. The two catalytic steps of tRNALys3 aminoacylation are structurally ordered; docking of the 3'-CCA end in the active site cannot proceed until the lysyl-adenylate intermediate is formed and the pyrophosphate byproduct is released. Association of the h-LysRS-tRNALys3 complex with a multi-tRNA synthetase complex-derived peptide shifts the equilibrium toward the 3'-CCA end "docked" conformation and allosterically increases h-LysRS catalytic efficiency. The insights presented here have broad implications for understanding the role of tRNA modifications in protein synthesis, the human aminoacylation machinery, and the growing catalog of metabolic and neurological diseases linked to it.

Structural insights into dynamics of the BMV TLS aminoacylation

Brome Mosaic Virus (BMV) utilizes a tRNA-like structure (TLS) within its 3' untranslated region to mimic host tRNA functions, aiding aminoacylation and viral replication. This study explores the structural dynamics of BMV TLS interacting with tyrosyl-tRNA synthetase (TyrRS) during aminoacylation. Using cryo-EM, we capture multiple states of the TLS-TyrRS complex, including unbound TLS, pre-1a, post-1a, and catalysis states, with resolutions of 4.6 Å, 3.5 Å, 3.7 Å, and 3.85 Å, respectively. These structural comparisons indicate dynamic changes in both TLS and TyrRS. Upon binding, TLS undergoes dynamic rearrangements, particularly with helices B3 and E pivoting, mediated by the unpaired A36 residue, ensuring effective recognition by TyrRS. The dynamic changes also include a more compact arrangement in the catalytic center of TyrRS and the insertion of 3' CCA end into the enzyme's active site, facilitating two-steps aminoacylation. Enzymatic assays further demonstrated the functional importance of TLS-TyrRS interactions, with mutations in key residues significantly impacting aminoacylation efficiency. Furthermore, Electrophoretic Mobility Shift Assay (EMSA) demonstrated that BMV TLS binds elongation factors EF1α and EF2, suggesting a multifaceted strategy to exploit host translational machinery. These findings not only enhance our knowledge of virus-host interactions but also offer potential targets for antiviral drug development.

Purification and validation of asparaginyl-tRNA synthetase heterodimer with indistinguishable subunits

Oligomerization can influence the stability and activity of a protein. The majority of enzymes, including aminoacyl-tRNA synthetases, become catalytically active upon forming homodimers. Residues located at the dimerization interface are highly conserved and mutations arising within can cause severe disease phenotypes. Beyond homozygous mutations, other disease-causing mutations, such as compound heterozygous and mono-allelic mutations, can lead to the formation of heterodimers between two distinct subunits. Purifying a recombinant heterodimer is required for its thorough characterization in vitro, yet there is a lack of established biochemical methods for the preparation. Here we describe a heterodimer purification and validation method with the example of a disease-causing mono-allelic, nonsense mutation R534* in cytoplasmic asparaginyl-tRNA synthetase (NARS1 or AsnRS). Our method involves co-expression of two separately tagged constructs to allow for purification of the wild-type and the R534* mutant heterodimers. While the two subunits can hardly be distinguished by size, their separate detection is achieved by western blotting against the tags. Quantification analysis confirmed that the subunits within the heterodimer are present in nearly equal proportions. This simple protocol can be adapted to study other size-indistinguishable heterodimers.

From sequence to significance: A thorough investigation of the distinctive genome features uncovered in C. Werkmanii strain NIB003

Citrobacter werkmanii (C. werkmanii), an opportunistic urinary bacterium that causes diarrhea, is poorly understood. Our research focuses on genetic features that are crucial to disease development, such as pathogenic interactions, antibiotic resistance, virulence genes and genetic variation. Following its morphological, biochemical, and molecular identification, the whole genome of C. werkmanii strain NIB003 was sequenced in Bangladesh for the first time. Despite having around 80% whole genome conservation, the research shows that the Bangladeshi strain forms a separate phylogenetic cluster. This emphasises the genetic variability within C. werkmanii, resulting in particular modifications at the strain level and changes in its ability to cause disease. The results of the genetic diversity analysis indicate that the Bangladeshi sequenced genome is more diverse than the other strains due to the existence of unique features, such as the presence of t-RNA binding domain and N-6 adenine-specific DNA methylases.

Isoleucine-to-valine substitutions support cellular physiology during isoleucine deprivation

Aminoacyl-tRNA synthetases (ARSs) couple tRNAs with their corresponding amino acids. While ARSs can bind structurally similar amino acids, extreme specificity is ensured by subsequent editing activity. Yet, we found that upon isoleucine (I) restriction, healthy fibroblasts consistently incorporated valine (V) into proteins at isoleucine codons, resulting from misacylation of tRNAIle with valine by wildtype IARS1. Using a dual-fluorescent reporter of translation, we found that valine supplementation could fully compensate for isoleucine depletion and restore translation to normal levels in healthy, but not IARS1 deficient cells. Similarly, the antiproliferative effects of isoleucine deprivation could be fully restored by valine supplementation in healthy, but not IARS1 deficient cells. This indicates I > V substitutions help prevent translational termination and maintain cellular function in human primary cells during isoleucine deprivation. We suggest that this is an example of a more general mechanism in mammalian cells to preserve translational speed at the cost of translational fidelity in response to (local) amino acid deficiencies.

The Plethora of RNA-Protein Interactions Model a Basis for RNA Therapies

The notion of RNA-based therapeutics has gained wide attractions in both academic and commercial institutions. RNA is a polymer of nucleic acids that has been proven to be impressively versatile, dating to its hypothesized RNA World origins, evidenced by its enzymatic roles in facilitating DNA replication, mRNA decay, and protein synthesis. This is underscored through the activities of riboswitches, spliceosomes, ribosomes, and telomerases. Given its broad range of interactions within the cell, RNA can be targeted by a therapeutic or modified as a pharmacologic scaffold for diseases such as nucleotide repeat disorders, infectious diseases, and cancer. RNA therapeutic techniques that have been researched include, but are not limited to, CRISPR/Cas gene editing, anti-sense oligonucleotides (ASOs), siRNA, small molecule treatments, and RNA aptamers. The knowledge gleaned from studying RNA-centric mechanisms will inevitably improve the design of RNA-based therapeutics. Building on this understanding, we explore the physiological diversity of RNA functions, examine specific dysfunctions, such as splicing errors and viral interactions, and discuss their therapeutic implications.

A comprehensive review of the proline mimic azetidine-2-carboxylic acid (A2C)

The imino acid azetidine-2-carboxylic acid (A2C), a proline homologue, was first identified in liliaceous plants in 1955. Its ability to exchange for proline in protein synthesis is responsible for its teratogenic effects and has made it a very useful tool for generating non-native proteins to study proteotoxic stress and ER stress. The tRNA synthetases from some A2C-producing plants can discriminate between proline and A2C, but for most plants and for mammalian cells, A2C is mistakenly used in protein synthesis in place of proline and can avoid cell proof-reading mechanisms. Human exposure to A2C would be very limited had it not been for the development of sugar beets as an alternative source of dietary sucrose to sugar cane, and the widespread use of the plentiful byproducts as livestock fodder. Fodder beets, a very high yielding forage crop, are also used as livestock fodder particularly for lactating cows. It is therefore possible for A2C to enter the human food chain and impact human health. It was hypothesised that its ability to replace proline in protein synthesis generates immunogenic neo-epitopes in myelin basic protein and could therefore be a causative factor for multiple sclerosis. In this review we discuss the distribution of A2C in nature, what is known about its toxicity, and the impact of the proline to A2C exchange on protein structure and function and in particular the proteins collagen and myelin basic protein. We summarise analytical approaches that can be used to quantify A2C in complex biological samples and the adaptations made by some organisms to avoid its toxic effects. We summarise the evidence for human exposure to A2C and the geographical and temporal links to higher incidences of MS. Finally, we highlight gaps in our knowledge that require addressing before we can determine if this non-protein amino acid is a threat to human health.

Human disease-causing missense genetic variants are enriched in the evolutionarily ancient domains of the cytosolic aminoacyl-tRNA synthetase proteins

All life depends on accurate and efficient protein synthesis. The aminoacyl-tRNA synthetases (aaRSs) are a family of proteins that play an essential role in protein translation, as they catalyze the esterification reaction that charges a transfer RNA (tRNA) with its cognate amino acid. However, new domains added to the aaRSs over the course of evolution in eukaryotes confer novel functions unrelated to protein translation. To date, damaging variants that affect aaRS-encoding genes have been linked to over 50 human diseases. In this study, we leverage the evolutionary history of the aaRS proteins to better understand the distribution of disease-causing missense variants in human cytosolic aaRSs. We hypothesized that disease-causing missense variants in human aaRSs were more likely to be located in the ancient domains of the aaRS, essential for the aminoacylation reaction, rather than in the evolutionarily more recent domains found in eukaryotes. We determined the locations of the modern and ancient domains in each aaRS protein found in humans. We then statistically assessed the positional conservation across each domain and examined the distribution of pathogenic and benign/unknown missense human genetic variants across these domains. We establish that pathogenic missense variants in the human aaRS proteins are enriched in the evolutionarily ancient domains while benign/unknown missense variants are enriched in the modern domains. In addition to defining the evolutionary history of human aaRS proteins through domain identification, we anticipate that this work will improve the ability to diagnose patients affected by damaging genetic variants in the aaRS protein family.

High lead-tolerant mutant Bacillus tropicus AT31-1 from rhizosphere soil of Pu-erh and its remediation mechanism

In this study, we successfully generated the mutant strain Bacillus tropicus AT31-1 from AT31 through atmospheric room-temperature plasma mutagenesis. This mutant strain AT31-1 demonstrated an impressive 48.6 % removal efficiency in 400 mg/L lead medium. Comparative genomic analysis showed that the mutant strain AT31-1 had three mutation sites, which affect the efflux RND transporter permease subunit, the response regulator transcription factor, and a gene with unknown function. The transcriptional analysis showed a notable upregulation in the expression of 283 genes in AT31-1 as lead concentrations increased from 0 to 200 mg/L and then to 400 mg/L, which include zinc-transporting ATPase, ferrous iron transport protein B, NADH dehydrogenase, and others. The Gene ontology function of the peptide metabolic process, along with the KEGG pathway of carbon metabolism were identified as closely linked to the extreme lead tolerance of AT31-1. This study presents novel insights into the lead tolerance mechanisms of bacteria.

Aminoacyl-tRNA synthetase defects in neurological diseases

Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes to support protein synthesis in all organisms. Recent studies, empowered by advancements in genome sequencing, have uncovered an increasing number of disease-causing mutations in aaRSs. Monoallelic aaRS mutations typically lead to dominant peripheral neuropathies such as Charcot-Marie-Tooth (CMT) disease, whereas biallelic aaRS mutations often impair the central nervous system (CNS) and cause neurodevelopmental disorders. Here, we review recent progress in the disease onsets, molecular basis, and potential therapies for diseases caused by aaRS mutations, with a focus on biallelic mutations in cytoplasmic aaRSs.

A kinetic model for compound heterozygous pathogenic variants in Tyrosyl-tRNA synthetase gene YARS2-Associated neonatal phenotype

Human genetic disorders are often caused by mutations of compound heterozygosity, where each allele of the mutant gene harbors a different genetic lesion. However, studies of such mutations are hampered due to the lack of an appropriate model. Here we describe a kinetic model of compound heterozygous variants in an obligate enzyme dimer that contains one mutation in one monomer and the other mutation in the second monomer. This enzyme is encoded by human YARS2 for mitochondrial tyrosyl-tRNA synthetase (mt-TyrRS), which aminoacylates tyrosine to mt-tRNATyr. YARS2 is a member of the genes for mt-aminoacyl-tRNA synthetases, where pathogenic mutations present limited correlation between disease severity and enzyme activity. We identify a pair of compound heterozygous variants in YARS2 that is associated with neonatal fatality. We show that, while each mutation causes a minor-to-modest defect in aminoacylation in the homodimer of mt-TyrRS, the two mutations in trans synergistically reduce the enzyme activity to a greater effect. This kinetic model thus accurately recapitulates the disease severity, emphasizing its utility to study YARS2 mutations and its potential for generalization to other diseases with compound heterozygous mutations.

Transfer RNA and small molecule therapeutics for aminoacyl-tRNA synthetase diseases

Aminoacyl-tRNA synthetases catalyze the ligation of a specific amino acid to its cognate tRNA. The resulting aminoacyl-tRNAs are indispensable intermediates in protein biosynthesis, facilitating the precise decoding of the genetic code. Pathogenic alleles in the aminoacyl-tRNA synthetases can lead to several dominant and recessive disorders. To date, disease-specific treatments for these conditions are largely unavailable. We review pathogenic human synthetase alleles, the molecular and cellular mechanisms of tRNA synthetase diseases, and emerging approaches to allele-specific treatments, including small molecules and nucleic acid-based therapeutics. Current treatment approaches to rescue defective or dysfunctional tRNA synthetase mutants include supplementation with cognate amino acids and delivery of cognate tRNAs to alleviate bottlenecks in translation. Complementary approaches use inhibitors to target the integrated stress response, which can be dysregulated in tRNA synthetase diseases.

Exploring the Proteomic Landscape and Immunomodulatory Functions of Edwardsiella piscicida Derived Extracellular Vesicles

Extracellular vesicles (EVs) have garnered attention in research for their potential as biochemical transporters and immune modulators, crucial for regulating the host immune system. The present study was conducted to isolate and characterize EVs from Gram negative bacteria Edwardsiella piscicida (EpEVs) and investigate their proteomic profile and immune responses. Isolation of EpEVs was carried out using ultracentrifugation method. Transmission electron microscopy results confirmed the spherical shape of EpEVs. The average size and zeta potential were 85.3 ± 1.8 nm and -8.28 ± 0.41 mV, respectively. EpEVs consisted of 1,487 distinct proteins. Subcellular localization analysis revealed that "cell" and "cell part" were the most predominant areas for protein localization. Proteins associated with virulence, along with several chaperones that facilitate protein folding and stability, were also present. No toxicity was detected when EpEVs were treated to fathead minnow (FHM) cells up to 100 μg/ml. Fluorescent-labeled EpEVs showed cellular internalization in FHM cells at 24 h post treatment (hpt). In-vitro gene expression in Raw 264.7 cells showed upregulation of interleukin (Il)6, Il1β, and interferon (Ifn)β with simultaneous upregulation of anti-inflammatory Il10. In vivo, gene expression revealed that except for heat shock protein (hsp)70, all other genes were upregulated suggesting that EpEVs induced the expression of immune-related genes. Western blot analysis showed increased protein levels of tumor necrosis factor (Tnf)α in EpEVs-treated spleen tissue of zebrafish. Our results confirm that EpEVs can be successfully isolated using the ultracentrifugation method. Furthermore, exploring immunomodulatory mechanism of EpEVs is essential for their potential use as novel therapeutics in fish medicine.

Chemotherapeutic agents and leucine deprivation induce codon-biased aberrant protein production in cancer

Messenger RNA (mRNA) translation is a tightly controlled process frequently deregulated in cancer. Key to this deregulation are transfer RNAs (tRNAs), whose expression, processing and post-transcriptional modifications are often altered in cancer to support cellular transformation. In conditions of limiting levels of amino acids, this deregulated control of protein synthesis leads to aberrant protein production in the form of ribosomal frameshifting or misincorporation of non-cognate amino acids. Here, we studied leucine, an essential amino acid coded by six different codons. Surprisingly, we found that leucine deprivation leads to ribosomal stalling and aberrant protein production in various cancer cell types, predominantly at one codon, UUA. Similar effects were observed after treatment with chemotherapeutic agents, implying a shared mechanism controlling the downstream effects on mRNA translation. In both conditions, a limitation in the availability of tRNALeu(UAA) for protein production was shown to be the cause for this dominant effect on UUA codons. The induced aberrant proteins can be processed and immune-presented as neoepitopes and can direct T-cell killing. Altogether, we uncovered a novel mode of interplay between DNA damage, regulation of tRNA availability for mRNA translation and aberrant protein production in cancer that could be exploited for anti-cancer therapy.

Structural basis for aminoacylation of cellular modified tRNALys3 by human lysyl-tRNA synthetase

The average eukaryotic tRNA contains 13 posttranscriptional modifications; however, their functional impact is largely unknown. Our understanding of the complex tRNA aminoacylation machinery in metazoans also remains limited. Herein, using a series of high-resolution cryo-electron microscopy (cryo-EM) structures, we provide the mechanistic basis for recognition and aminoacylation of fully-modified cellular tRNALys3 by human lysyl-tRNA synthetase (h-LysRS). The tRNALys3 anticodon loop modifications S34 (mcm5s2U) and R37 (ms2t6A) play an integral role in recognition by h-LysRS. Modifications in the T-, variable-, and D-loops of tRNALys3 are critical for ordering the metazoan-specific N-terminal domain of LysRS. The two catalytic steps of tRNALys3 aminoacylation are structurally ordered; docking of the 3'-CCA end in the active site cannot proceed until the lysyl-adenylate intermediate is formed and the pyrophosphate byproduct is released. Association of the h-LysRS-tRNALys3 complex with a multi-tRNA synthetase complex-derived peptide shifts the equilibrium towards the 3'-CCA end 'docked' conformation and allosterically enhances h-LysRS catalytic efficiency. The insights presented here have broad implications for understanding the role of tRNA modifications in protein synthesis, the human aminoacylation machinery, and the growing catalog of metabolic and neurological diseases linked to it.

AARS Online: A collaborative database on the structure, function, and evolution of the aminoacyl-tRNA synthetases

The aminoacyl-tRNA synthetases (aaRS) are a large group of enzymes that implement the genetic code in all known biological systems. They attach amino acids to their cognate tRNAs, moonlight in various translational and non-translational activities beyond aminoacylation, and are linked to many genetic disorders. The aaRS have a subtle ontology characterized by structural and functional idiosyncrasies that vary from organism to organism, and protein to protein. Across the tree of life, the 22 coded amino acids are handled by 16 evolutionary families of Class I aaRS and 21 families of Class II aaRS. We introduce AARS Online, an interactive Wikipedia-like tool curated by an international consortium of field experts. This platform systematizes existing knowledge about the aaRS by showcasing a taxonomically diverse selection of aaRS sequences and structures. Through its graphical user interface, AARS Online facilitates a seamless exploration between protein sequence and structure, providing a friendly introduction to the material for non-experts and a useful resource for experts. Curated multiple sequence alignments can be extracted for downstream analyses. Accessible at www.aars.online, AARS Online is a free resource to delve into the world of the aaRS.

Mechanism of action of the toxic proline mimic azetidine 2-carboxylic acid in plants

Plants have an amazing capacity to outcompete neighboring organisms for space and resources. Toxic metabolites are major players in these interactions, which can have a broad range of effectiveness by targeting conserved molecular mechanisms, such as protein biosynthesis. However, lack of knowledge about defensive metabolite pathways, their mechanisms of action, and resistance mechanisms limits our ability to manipulate these pathways for enhanced crop resilience. Nonproteogenic amino acids (NPAAs) are a structurally diverse class of metabolites with a variety of functions but are typically not incorporated during protein biosynthesis. Here, we investigate the mechanism of action of the NPAA azetidine-2-carboxylic acid (Aze), an analog of the amino acid proline (Pro). Using a combination of plate-based assays, metabolite feeding, metabolomics, and proteomics, we show that Aze inhibits the root growth of Arabidopsis and other plants. Aze-induced growth reduction was restored by supplementing L-, but not D-Pro, and nontargeted proteomics confirm that Aze is misincorporated for Pro during protein biosynthesis, specifically on cytosolically translated proteins. Gene expression analysis, free amino acid profiling, and proteomics show that the unfolded protein response is upregulated during Aze treatment implicating that Aze misincorporation results in accumulation of misfolded proteins triggering a global stress response. This study demonstrates the mechanism of action of Aze in plants and provides a foundation for understanding the biological functions of proteotoxic metabolites.

Translation regulation in response to stress

Cell stresses occur in a wide variety of settings: in disease, during industrial processes, and as part of normal day-to-day rhythms. Adaptation to these stresses requires cells to alter their proteome. Cells modify the proteins they synthesize to aid proteome adaptation. Changes in both mRNA transcription and translation contribute to altered protein synthesis. Here, we discuss the changes in translational mechanisms that occur following the onset of stress, and the impact these have on stress adaptation.

Characterization of a novel heterozygous variant in the histidyl-tRNA synthetase gene associated with Charcot-Marie-Tooth disease type 2W

Heterozygous pathogenic variants in the histidyl-tRNA synthetase (HARS) gene are associated with Charcot-Marie-Tooth (CMT) type 2W disease, classified as an axonal peripheral neuropathy. To date, at least 60 variants causing CMT symptoms have been identified in seven different aminoacyl-tRNA synthetases, with eight being found in the catalytic domain of HARS. The genetic data clearly show a causative role of aminoacyl-tRNA synthetases in CMT; however, the cellular mechanisms leading to pathology can vary widely and are unknown in the case of most identified variants. Here we describe a novel HARS variant, c.412T>C; p.Y138H, identified through a CMT gene panel in a patient with peripheral neuropathy. To determine the effect of p.Y138H we employed a humanized HARS yeast model and recombinant protein biochemistry, which identified a deficiency in protein dimerization and a growth defect which shows mild but significant improvement with histidine supplementation. This raises the potential for a clinical trial of histidine.

A genomic database furnishes minimal functional glycyl-tRNA synthetases homologous to other, designed class II urzymes

The hypothesis that conserved core catalytic sites could represent ancestral aminoacyl-tRNA synthetases (AARS) drove the design of functional TrpRS, LeuRS, and HisRS 'urzymes'. We describe here new urzymes detected in the genomic record of the arctic fox, Vulpes lagopus. They are homologous to the α-subunit of bacterial heterotetrameric Class II glycyl-tRNA synthetase (GlyRS-B) enzymes. AlphaFold2 predicted that the N-terminal 81 amino acids would adopt a 3D structure nearly identical to our designed HisRS urzyme (HisCA1). We expressed and purified that N-terminal segment and the spliced open reading frame GlyCA1-2. Both exhibit robust single-turnover burst sizes and ATP consumption rates higher than those previously published for HisCA urzymes and comparable to those for LeuAC and TrpAC. GlyCA is more than twice as active in glycine activation by adenosine triphosphate as the full-length GlyRS-B α2 dimer. Michaelis-Menten rate constants for all three substrates reveal significant coupling between Exon2 and both substrates. GlyCA activation favors Class II amino acids that complement those favored by HisCA and LeuAC. Structural features help explain these results. These minimalist GlyRS catalysts are thus homologous to previously described urzymes. Their properties reinforce the notion that urzymes may have the requisite catalytic activities to implement a reduced, ancestral genetic coding alphabet.

Dietary Intake of Chromista Oil Alters Hepatic Metabolomic Profile of Mice With Excess Fat Mass

Increasing dietary intake of fish oil is frequently recommended for decreasing the risk for cardiovascular diseases and improving metabolic health. We hypothesised that dietary intake of chromista oil (a marine food product and a rich source of long-chain n-3 polyunsaturated fatty acids) ameliorates metabolic impairments in mice with established excess adiposity. Three-to 4-week-old mice (male) were fed a control (n = 12) or a high-fat diet (HFD, n = 24) for 12 weeks to establish body fat mass. Then, mice on the HFD were assigned to 2 groups (n = 12 each) with 1 continuing being fed the HFD and the other fed the HFD with chromista oil for an additional 12 weeks. Intake of chromista oil did not affect body weight and body adiposity of the mice fed the HFD; mice fed the HFD had significantly more body weight and fat mass than control mice. The flattened daily oscillations of respiratory exchange ratio induced by the HFD were not changed by chromista oil intake. Intake of chromista oil significantly increased plasma concentration of insulin, the calculated value of HOMA-IR, and plasma concentration of adiponectin in the mice fed the HFD. However, blood glucose was unaffected by chromista oil. Transcription of genes encoding circadian rhythm and fatty acid metabolism of the 2 HFD-fed groups were similar. Untargeted metabolomic analysis showed that intake of chromista oil altered the hepatic metabolomic profile with substantial alterations in amino acid metabolism. Findings from this study indicate that dietary intake of chromista oil does not improve glucose homeostasis or alter the diminished metabolic flexibility in mice with excess adiposity induced by the HFD. argeted metabolomic analysis is warranted to investigate the effects of dietary chromista oil, as a source of n-3 poly unsaturated fatty acids, on metabolism in models of obesity.

Blood expression of NADK2 as a diagnostic biomarker for sciatica

Sciatica is characterized by radiating pain along the sciatic nerve, with a lifetime prevalence of up to 43%. This study explored blood biomarkers for sciatica using transcriptomic microarray data (GSE124272 and GSE150408). Differential gene expression analysis identified NADK2 as a potential diagnostic biomarker. A diagnostic model based on NADK2 showed strong validation performance in 200 clinical cases. Gene set enrichment analysis (GSEA) suggested a connection between NADK2 and the aminoacyl-tRNA biosynthesis pathway. In conclusion, NADK2 emerges as promising diagnostic and therapeutic targets for sciatica, significantly advancing our comprehension of potential pathogenic mechanisms and offering perspectives for early diagnosis and treatment.