Search Results (316)

Background: Mycobacterium avium (Mav) is a leading cause of pulmonary disease among non-tuberculous mycobacteria (NTMs) due to its extensive antibiotic resistance profile. The essential Rel protein is a bifunctional enzyme, which is sensitive to environmental stress and regulates cellular guanosine-3′,5′-bispyrophosphate ((p)ppGpp). Increased levels of the alarmone thereby initiate a survival response, contributing to bacterial persistence and virulence. Objectives: MavRel harbors an unusual extension at the N-terminal domain (NTD), which we aim to characterize its possible regulatory role in maintaining (p)ppGpp homeostasis. We also studied whether the TGS domain retains its regulation capacity in MavRel and the binding propensity of the ACT domain to valine. Methods: Molecular dissection of MavRel was performed to generate a series of truncates to quantify the synthetase and hydrolase activities. Binding experiments with tRNA and valine were carried out via tryptophan quenching assay and NMR, respectively. Results: Bi-catalytic regulation of MavRel was found to be predominantly governed by the residues 37–50 at the NTD extension in its free state. The TGS domain was shown to harbor the capacity to bind with deacylated tRNA and represses synthetase activity to a lower degree compared to the NTD extension. We also characterized the dimeric Mav ACT-domain and the interacting residues contributing to its affinity with valine to function as a nutrient sensor. Conclusions: The mapping of the unique NTD regulatory element of MavRel reveals its functional relevance to coordinate the catalytic states of synthetase and hydrolase, hence underscores the prospect to drive inhibitor development targeting this novel site against Mav infections. Full article

Aminoacyl-tRNA synthetases (AARSs), traditionally recognized for their essential role in protein synthesis, are now emerging as critical players in cancer pathogenesis through translation-independent functions. Lactate-derived lactylation, a post-translational modification, plays an increasingly important role in tumorigenesis in the context of high levels of lactate in tumor cells due to the Warburg effect. Current research has highlighted AARS1/2 as lactate sensors and lactyltransferases that catalyze global lysine lactylation in cancer cells and promote cancer proliferation, providing a new perspective for cancer therapy. This review synthesizes the canonical and non-canonical functions of AARS1/2, with a particular focus on their lactylation-related mechanisms; details how lactylation acts as a mechanistic bridge linking AARS1/2 to diverse oncogenic signaling pathways, thereby promoting cancer hallmarks such as metabolic reprogramming, uncontrolled proliferation, immune escape, and therapy resistance; and proposes strategies to target AARS1/2 or modulate relative lactylation, offering a potential avenue to translate these insights into effective cancer therapies. Full article

Background: Aminoacyl-tRNA synthetases (ARSs) are a group of enzymes responsible for the first step of protein translation. Among them, the KARS1 gene encodes lysyl-tRNA synthetase 1, an enzyme essential for charging tRNA-Lys with lysine in both the cytoplasm and mitochondria. Mutations in KARS1 are associated with a wide range of clinical phenotypes, including leukoencephalopathy, hereditary deafness, peripheral neuropathies, and multisystemic involvement. Methods: We hereby report a detailed case study of a 15-month-old boy presenting at age 5 months with developmental delay, microcephaly, hypotonia, sensorineural deafness, retinopathy, visual impairment, nystagmoid eye movements, and hepatic and immuno-hematological abnormalities. In addition, he exhibited a severe hyperkinetic movement disorder, not previously reported in the literature, and developed epilepsy at 13 months. Genetic testing identified two rare compound heterozygous variants in the KARS1 gene. Results: With this report, we aim to contribute to the expanding of both the clinical phenotype and the allelic spectrum of lysyl-tRNA synthetase-related disorders. Our study also includes a review of previously described KARS1 cases presenting with movement disorders. Conclusions: Our findings further highlight the importance of assessing systemic involvement and performing brain and spinal neuroimaging, as well as implementing genetic screening, in infants presenting with global developmental delay, sensory deficits, and movement disorders—features that may suggest a mitochondrial disorder such as those involving ARS mutations. Full article

A novel Gram-negative bacterium, designated strain SN16^T, was isolated from a harmful algal bloom (HAB). Strain SN16^T exhibited potent, broad-spectrum algicidal activity against the colony-forming alga Phaeocystis globosa and eight other HAB-causing species, highlighting its potential as a promising candidate for the biological control of HABs. A phylogenetic analysis of 16S rRNA gene sequences placed strain SN16^T within the genus Flagellimonas. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain SN16^T and its relatives were 75.4–91.4% and 19.3–44.0%, respectively. These values fall below the established thresholds for species delineation, confirming that SN16^T represents a novel species. A chemotaxonomic analysis revealed its dominant cellular fatty acids to be iso-C_15:0 and iso-C_15:1 G. The major polar lipid was phosphatidylethanolamine, and the primary respiratory quinone was menaquinone-6. Genome mining identified 11 biosynthetic gene clusters (BGCs), including those encoding for terpenes, ribosomal peptide synthetases, and non-ribosomal peptide synthetases. By integrating BGC analysis with the observed algicidal activities, we predicted that pentalenolactone and xiamycin analogues are the likely causative compounds. Based on this polyphasic evidence, strain SN16^T is proposed as a novel species of the genus Flagellimonas, named Flagellimonas algicida sp. nov. This is the first report of Flagellimonas species exhibiting broad-spectrum algicidal activity, including activity against the colonial form of P. globosa—a key ecological challenge in HAB mitigation. Full article

Bacillus cereus AS_3 and Bacillus cereus AS_5 are bacterial endophytes isolated from sterilized leaves of the medical plant Alectra sessiliflora, which were previously identified using 16S rRNA sequencing. Here, we present the whole-genome sequencing and annotation of strains AS_3 and AS_5, the first genome report of Bacillus cereus strains from A. sessiliflora. The genome of strain AS_3 has 59 contigs, 5 503 542 bp draft circular chromosome, an N₅₀ of 211,274 bp, and an average G+C content of 35.2%; whereas strain AS_5 has 38 contigs, 5,510,121 bp draft circular chromosome, an N₅₀ of 536,033 bp, and an average G+C content of 35.2%. A total of 5679 protein-coding genes, 62 genes coding for RNAs, and 122 pseudogenes in the strain AS_3 genome were identified by the National Center for Biotechnology Information Prokaryotic Annotation pipeline, whereas a total of 5688 gene protein-coding genes were identified in AS_5, with 60 genes coding for RNAs and 120 pseudogenes. Phenotypic analysis and whole-genome sequencing analysis showed that AS_3 and AS_5 share similar characteristics, including Gram-positive, motile, rod-shaped, and endospore-forming have shown a high sequence similarity with Bacillus cereus, type strain ATCC 14579^T. Strains AS_3 and AS_5 had genomic digital DNA–DNA hybridization (dDDH) with the type strain Bacillus cereus ATCC 14579^T of 85.8% and 86%, respectively, and average nucleotide identities (ANIs) of 98% and 98.01%, respectively. Phylogenomic analysis confirmed that strains AS_3 and AS_5 share very similar genomic and phenotypic characteristics, and are closely related to the type strain Bacillus cereus type strain ATCC 14579^T, supporting their classification within the Bacillus cereus species. A total of 10 secondary metabolite gene clusters, including siderophore type petrobactin, terpene type molybdenum cofactor, non-ribosomal peptide synthetase (NRPS) type bacillibactin, and β-lactone type fengycin, were predicted using AntiSMASH software (version 5.0). Putative genes potentially involved in bioremediation and endophytic lifestyle were identified in the genome analysis. Genome sequencing of Bacillus cereus AS_3 and Bacillus cereus AS_5 has provided genomic information and demonstrated potential biotechnological applications. Full article

Background/Objectives: Trypanosoma evansi (T. evansi) is an etiological agent of surra, and it causes significant economic losses in livestock. Rising trypanocide resistance demands alternatives that control parasitemia while mitigating oxidative and genotoxic damage. Therefore, the present study was designed to explore both the in vivo and in silico potential of Zingiber officinale (Z. officinale) as a novel phytotherapy to counter growing resistance against conventional trypanocides. Methods: Methanolic extract of Z. officinale (MZ) was orally administered at dosages of 200 mg/kg (MZ 200), 400 mg/kg (MZ 400), and 800 mg/kg (MZ 800) on a daily basis to the experimentally infected mice and compared against treated control (TC) and untreated control (UC) groups. After the infection, different parameters such as parasitemia counts, body weight changes, and the survival of infected mice were monitored for up to 7 days post-infection, while hematobiochemical parameters, oxidative stress profiles (catalase, malondialdehyde, and superoxide dismutase), and genotoxicity in brain tissues were compared at the end of the trial. Moreover, computational tools were used to predict the affinities of key bioactive compounds with twenty-one essential proteins of T. evansi. Results: The findings showed that the administration of MZ significantly (p < 0.05) reduced parasitemia and improved the survival rates in the experimentally infected mice in a dose-dependent manner. Noteworthy, significant (p < 0.05) improvements in hematological parameters and liver enzyme profiles were also recorded in MZ-treated groups. Compared to the untreated control, MZ-treated groups showed a significant amelioration in oxidative stress and genotoxicity in brain tissue in a dose-dependent fashion. The current study’s findings suggest that MZ potentially inhibits various essential proteins of T. evansi, including adenosine transporter-1, casein kinase, leucyl-tRNA synthetase, and multidrug resistance E protein. Among its constituents, 6-Isoshogaol and 6-Gingerol showed the most stable interactions in the molecular dynamics simulation. Conclusions: MZ efficiently reduced parasitemia, oxidative stress, and genotoxicity, and increased the survival rate in infected mice, suggesting it as a promising natural trypanicidal agent. Full article

In the standard genetic code, the CUG triplet is translated as leucine. The pathogenic yeast Candida albicans and other CTG-clade yeasts contain tRNA_CAG, which is recognized by both leucine- and serine-tRNA synthetases. The CUG codon in these yeasts is translated most often as serine, and only in 3–5% of cases as leucine. Therefore, CTG Candida species have unstable proteomes. The effect of serine–leucine exchange on the structure and function of proteins has only been experimentally examined for a few cases. In C. albicans, CUG codons occur even in genes deemed to be essential. This means that serine–leucine ambiguity either does not affect the structure and function of the respective proteins, or that the presence of these amino acids at specific positions is associated with meaningful alteration of the proteins’ function. This study employed AlphaFold2 to evaluate the potential effects of serine-to-leucine exchange in 12 proteins encoded by essential genes lacking orthologs in other yeasts and human genomes. The low homology with known proteins allowed us to make only low-confidence predictions. The analyzed proteins could be grouped into subsets based on the structural outcomes. Structural changes were observed only in four proteins. The remaining eight proteins showed no significant differences between serine and leucine variants. Full article

Haloxylon articulatum is traditionally used for treating infections, digestive issues, and oxidative stress. Despite its ethnopharmacological relevance, its phytochemistry and biological activities, particularly in Iraq, are underexplored. This study investigated the phytochemical composition of H. articulatum extracts and evaluated their antioxidant and anti-Helicobacter pylori activities, supported by molecular docking and in silico ADMET analysis. Methanol/water and ethyl acetate extracts from roots and aerial parts were analyzed using LC-HRMS/MS. Antioxidant capacity was measured via DPPH assay, and anti-H. pylori activity was assessed using broth microdilution. Molecular docking targeted bacterial isoleucyl-tRNA synthetase, and ADMET predictions were carried out with SwissADME and ADMETlab. Phytochemical profiling identified 32 compounds, including phenolamides, flavonoids, alkaloids, and triterpenoid glycosides. Root extracts exhibited stronger antioxidant and antibacterial effects than aerial parts. Ethyl acetate extracts were inactive. Phenolamides, N-caffeoyltyramine, and sinapoyltyramine, present in the extract, showed significant activity (MICs = 54 ± 0.92 and 74 ± 1.05 µg/mL). Docking supported their strong binding to the target enzyme. ADMET results indicated good oral bioavailability and low toxicity. This study is the first to report the anti-H. pylori activity of H. articulatum and to characterize its Iraqi chemotype through advanced metabolomics. The findings highlight the plant’s potential as a source of multifunctional phytochemicals with antioxidant and antibacterial applications, warranting further preclinical development and toxicological investigation. Full article

Combined oxidative phosphorylation deficiency type 8 (COXPD8) is an autosomal recessive mitochondrial disorder caused by a mutation of the nuclear encoded mitochondrial alanyl-tRNA synthetase gene (AARS2). Clinical manifestations of COXPD8 include lethal infantile hypertrophic cardiomyopathy, pulmonary hypoplasia, generalized muscle weakness, and neurological involvement. We report a patient with COXPD8 caused by two mutations in the AARS2 gene. The c.1738 C>G mutation has not been previously reported, while the c.2872 C>T mutation has been associated with pulmonary hypoplasia and hypertrophic cardiomyopathy. Cardiac tissue, obtained through the LungMAP program, showed that, compared to other patients of similar ages, these two mutations affect not only the assembly of functional monomeric complexes (Cx) I and IV of the electron transport chain (ETC) but also limit the formation of respiratory supercomplexes. This patient had altered expression of some ETC proteins but normal expression of several enzymes of the tricarboxylic acid cycle. We also show that one of the control/comparison patients had an undiagnosed ETC Cx IV deficiency. In conclusion, our data demonstrate that the two mutations of the AARS2 gene are associated with failed assembly of Cx I and Cx IV and reduced formation of respiratory supercomplexes of the ETC, likely leading to acute bioenergetic stress. Full article

Background: Basal-like breast cancer (BLBC) is a highly aggressive molecular subtype characterized by the strong expression of a gene cluster found in the basal or outer epithelial layer of the adult mammary gland. Patients with BLBC typically face a poor prognosis, with a shorter disease-free period and overall survival. Methods: In this study, we explored the proteomic profiles of BLBC patients using publicly available data from two large cohorts of breast cancer patients. By integrating cluster analysis, predictive modeling, protein differential abundance expression, and network analysis, we identified and validated the presence of two distinct subgroups, characterized by 256 upregulated and 99 downregulated proteins. Results: We report the upregulation of spliceosome components, especially SNRPG and its partners (BUD13, CWC15, SNRNP70, ZMAT12), indicating altered splicing activity between TNBC subgroups. Collagen proteins (COL1A1, COL1A2, COL3A1, COL11A1) were associated with tumor progression and metastasis. Proteins in the CCT complex and microtubule-associated proteins (TUBA1C, TUBB) were linked to cytoskeletal structure and chemotherapy resistance. Aminoacyl-tRNA synthetases (DARS1, IARS1, KARS1) may also play a role in TNBC development. Conclusions: These findings suggest the existence of novel molecular signatures that could improve TNBC classification, prognosis, and potential therapeutic targeting. Full article

Background and Clinical Significance: Antisynthetase syndrome (ASyS) is a rare autoimmune entity defined by the presence of anti-aminoacyl-t ribonucleic acid (RNA) synthetase autoantibodies and classically associated with a triad of interstitial lung disease (ILD), inflammatory myopathy, and arthritis. Additional clinical features may include Raynaud’s phenomenon and “mechanic’s hands”. Among antisynthetase antibodies, anti-PL-12 is notably associated with predominant or isolated ILD and may occur in the absence of clinically evident myositis, thereby complicating timely diagnosis. Case Presentation: We are presenting a 45-year-old non-smoking female patient with a prior diagnosis of seronegative rheumatoid arthritis (RA) who developed progressive dyspnea, dry cough, and sicca symptoms. High-resolution computed tomography revealed a nonspecific interstitial pneumonia (NSIP) pattern. Despite normal creatine kinase and lactate dehydrogenase levels, serological work-up revealed positive anti-PL-12 and anti-Ro52 antibodies, supporting a diagnosis of antisynthetase syndrome without myositis, fulfilling the diagnostic criteria for ASyS per Connors and Solomon. Treatment with corticosteroids and cyclophosphamide induced clinical and functional respiratory improvement, while azathioprine was initiated for maintenance. Conclusions: This case underscores the clinical heterogeneity of antisynthetase syndrome and highlights the diagnostic challenge posed by anti-PL-12–associated ILD in the absence of myositis. Importantly, it demonstrates that in patients with pre-existing rheumatologic diagnoses, the emergence of atypical pulmonary manifestations warrants repeat serologic evaluation to assess ASyS and other autoimmune conditions. Early diagnosis and immunosuppressive treatment are essential to optimize outcomes. Full article

Background/Objectives: Accurate determination of malignancy in pancreatic masses through endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) is crucial for appropriate clinical management and prognostic assessment. However, the diagnostic sensitivity of conventional cytology using Papanicolaou (Pap) staining remains limited, often leading to inconclusive results. In this study, we investigated the diagnostic utility of methionyl-tRNA synthetase 1 (MARS1) through immunohistochemical (IHC) and immunofluorescence (IF) staining as a potential biomarker for pancreatic cancer. IHC analysis was conducted on resected tissue samples from 10 patients, including both pancreatic ductal adenocarcinoma and corresponding non-neoplastic pancreatic tissue. Additionally, cytologic samples were obtained from 198 patients with pancreatic masses who underwent EUS-FNA for diagnostic evaluation. Pap staining and MARS1 IF staining were performed on liquid-based cytology slides derived from EUS-FNA specimens. Results: MARS1 was detected by IHC staining in the 10 surgical specimens diagnosed with pancreatic adenocarcinomas. After Pap staining, 37 patients were excluded because of unsuitable specimens, leaving 161 patients who underwent both Pap and MARS1 IF staining. EUS-FNA specimens from the 151 patients with pancreatic ductal adenocarcinoma were classified by Pap staining as atypia (n = 36), suspicious for malignancy (n = 55), or malignancy (n = 60). MARS1 IF staining was positive in 147 of these patients and negative in 4. MARS1 IF staining distinguished pancreatic cancer in specimens with atypia on Pap staining. The sensitivity for detecting pancreatic cancer was significantly higher for MARS1 IF staining than for conventional Pap staining (97.4% vs. 79.1%, p < 0.0001). Conclusions: The high sensitivity of MARS1 IF staining improved malignancy detection in pancreatic masses. Further prospective studies are required to validate our findings. Full article

A novel actinobacterial strain, designated E54^T, was isolated from a hyper-arid desert soil sample collected from the Kumtagh Desert in Dunhuang, Gansu Province, China. Phylogenetic analysis based on 16S rRNA gene sequences placed strain E54^T within the genus Lentzea, showing highest similarity to Lentzea waywayandensis DSM 44232^T (98.9%) and Lentzea flava NBRC 15743^T (98.5%). However, whole-genome comparisons revealed that the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between E54^T and these related strains were below the thresholds for species delineation. Strain E54^T exhibited typical morphological characteristics of the genus Lentzea, forming a branched substrate. It grew optimally at 28–30 °C, pH 7.0–9.0, and tolerated up to 10% NaCl. The cell wall contained meso-diaminopimelic acid, the predominant menaquinone was MK-9(H₄), and major fatty acids included iso-C_16:0. The polar lipid profile comprised diphosphatidyl glycerol, phosphatidyl ethanolamine, phosphatidyl inositol, hydroxyphosphatidyl ethanolamine, and an unidentified lipid. The characteristic amino acid type of the cell wall was meso-DAP. Whole-cell hydrolysis experiments revealed the characteristic cell wall sugar fractions: ribose and galactose. The genome of strain E54^T is approximately 8.0 Mb with a DNA G+C content of 69.38 mol%. Genome mining revealed 39 biosynthetic gene clusters (BGCs), including non-ribosomal peptide synthetases (NRPS), polyketide synthases (PKS), terpenes, and siderophores. Comparative antiSMASH-based genome analysis across 38 Lentzea strains further demonstrated the genus’ remarkable biosynthetic diversity. NRPS and type I PKS (T1PKS) were the most prevalent BGC types, indicating a capacity to synthesize structurally complex and pharmacologically relevant metabolites. Together, these findings underscore the untapped biosynthetic potential of the genus Lentzea and support the proposal of strain E54^T as a novel species. The strain E54^T (=JCM 34936^T = GDMCC 4.216^T) should represent a novel species, for which the name Lentzea xerophila sp. nov. is proposed. Full article

Influenza viruses are characterized by their high variability and pathogenicity, and effective therapeutic options remain limited. Given these challenges, targeting host cell proteins that facilitate viral replication presents a promising strategy for antiviral drug discovery. In the present study, we observed a significant upregulation of Glycyl-tRNA synthetase (GlyRS) within 24 h post-PR8 virus infection. The inhibition of GlyRS expression in A549 cells resulted in a marked reduction in infection rates across multiple influenza virus strains, while the overexpression of GlyRS led to an increase in viral infectivity during the early stages of infection. These findings suggest that GlyRS plays a critical role in the replication of influenza virus. Accordingly, we screened for potential inhibitors targeting GlyRS and identified Lycobetaine and Scutellarein using a multifaceted approach. Through a combination of molecular dynamics simulations, we further elucidated the mechanisms of action and potential binding sites of these compounds. Both inhibitors effectively suppressed the replication of influenza viruses, and their antiviral activity was confirmed to be mediated by GlyRS targeting. Therefore, GlyRS inhibitors, such as Lycobetaine and Scutellarein, represent promising candidates for combating influenza infections and provide novel insights into the treatment of influenza and aaRS-related diseases, opening new avenues for the development of aaRS-targeted therapeutics. Full article

3,4-Dihydroxy-L-phenylalanine (DOPA) is a promising noncanonical amino acid (ncAA) that introduces novel catechol chemical features into proteins, expanding their functional potential. However, the most common approach to incorporating ncAAs into proteins relies on stop codon suppression, which is often limited by the competition of endogenous translational termination machinery. Here, we employed a special in vitro protein expression system that facilitates the efficiency of DOPA incorporation into proteins by removing essential Class I peptide release factors through targeted degradation. In the absence of both RF1 and RF2, we successfully demonstrated DOPA incorporation at all three stop codons (TAG, TAA, and TGA). By optimizing the concentration of engineered DOPA-specific aminoacyl-tRNA synthetase (DOPARS), DOPA, and DNA template, we achieved a synthesis yield of 2.24 µg of sfGFP with 100% DOPA incorporation in a 20 μL reaction system. DOPARS exhibited a dissociation constant (Kd) of 11.7 μM for DOPA but showed no detectable binding to its native counterpart, tyrosine. Additionally, DOPA was successfully incorporated into a reverse transcriptase, which interfered with its activity. This system demonstrates a fast and efficient approach for precise DOPA incorporation into proteins, paving the way for advanced protein engineering applications. Full article