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Two complementing in vivo selection systems based on CCA-trimming exonucleases as a tool to monitor, select and evaluate enzymatic features of tRNA nucleotidyltransferases

tRNA nucleotidyltransferase represents a ubiquitous and essential activity that adds the indispensable CCA triplet to the 3'-end of tRNAs. To fulfill this function, the enzyme contains a set of highly conserved motifs whose coordinated interplay is crucial for the sequence-specific CCA polymerization. In the human enzyme, alterations within these regions have been shown to lead to the manifestation of disease. Recently, we developed an in vivo screening system that allows for the selection and analysis of tRNA nucleotidyltransferase variants by challenging terminal AMP incorporation into tRNA during induced RNase T-catalyzed CCA-decay. Here, we extend this method for screening of full CCA-end repair by utilizing the CCA-trimming activity of exonuclease LCCR4. To demonstrate the combined potential of these two in vivo selection systems, we applied a semi-rational library design to investigate the mode of operation of catalytically important motifs in the human CCA-adding enzyme. This approach revealed unexpected requirements for amino acid composition in two motifs and gives new insights into the mechanism of CCA addition. The data show the potential of these RNase-based screening systems, as they allow the detection of enzyme variations that would not have been identified by a conventional rational approach. Furthermore, the combination of both RNase T and LCCR4 systems can be used to investigate and dissect the effects of pathogenic mutations on C- and A-addition.

The major component of Heteractis magnifica sea anemone venom, RpIII, exhibits strong subtype selectivity for insects over mammalian voltage-gated sodium channels

Voltage-gated sodium channels (NaV) are molecular targets for the development of drugs for the treatment of diseases such as epilepsy, neuropathic pain, long QT syndrome, etc., as well as for insecticides. Therefore, the search for novel selective NaV channel ligands is relevant. Using amplicon deep sequencing of tentacle cDNA libraries from sea anemones Heteractis magnifica, 36 transcripts related to RpIII neurotoxin, a NaV channel modulators, were revealed. The recombinant RpIII was moderately toxic for mice (LD50 0.030 ± 0.004 mg/kg) but did not demonstrate any activity towards NaV in human SH-SY5Y cells. The toxin inhibited inactivation of heterologously expressed mammalian, insect, and arachnid NaV channels with higher specificity to insect channels. Cockroach (Blattella germanica) sodium channel BgNaV1 (EC50 of 2.4 ± 0.2 nM) and yellow fever mosquito (Aedes aegypti) channel AaNaV1 (EC50 of 1.5 ± 0.3 nM) were the most sensitive to RpIII, while mammals NaV had EC50 values above 100 nM except mNaV1.6 (EC50 of 43.8 ± 3.6 nM). The low nanomolar RpIII affinity to insect AaNaV1 may be explained by the extensive intermolecular contacts found by docking study. According to the predicted data, the toxin lands on the ion channel between voltage-sensing domain IV and pore domain I, also known as toxin site 3, followed by stabilizing the channels in the open state what was measured at electrophysiological experiments.

Structure of the microtubule-anchoring factor NEDD1 bound to the γ-tubulin ring complex

The γ-tubulin ring complex (γ-TuRC) is an essential multiprotein assembly that provides a template for microtubule nucleation. The γ-TuRC is recruited to microtubule-organizing centers (MTOCs) by the evolutionarily conserved attachment factor NEDD1. However, the structural basis of the NEDD1-γ-TuRC interaction is not known. Here, we report cryo-EM structures of NEDD1 bound to the human γ-TuRC in the absence or presence of the activating factor CDK5RAP2. We found that the C-terminus of NEDD1 forms a tetrameric α-helical assembly that contacts the lumen of the γ-TuRC cone and orients its microtubule-binding domain away from the complex. The structure of the γ-TuRC simultaneously bound to NEDD1 and CDK5RAP2 reveals that both factors can associate with the "open" conformation of the complex. Our results show that NEDD1 does not induce substantial conformational changes in the γ-TuRC but suggest that anchoring of γ-TuRC-capped microtubules by NEDD1 would be structurally compatible with the significant conformational changes experienced by the γ-TuRC during microtubule nucleation.

Enhancing catalytic activity of thermostable 4-α-glucanotransferase from Thermus filiformis through semi-rational design

4-α-glucanotransferases (4GT) are valuable enzymatic tools with application in the food and pharmaceutical industries, particularly for producing thermoreversible starch gels. The screening of thermostable 4GT enzymes with high catalytic activity presents a significant challenge. In this study, a comprehensive screening of potential 4GT in the UniProt database led to the identification of a 4GT from Thermus filiformis (TfGT) with superior catalytic activity and thermal stability. To further improve its catalytic efficiency, a semi-rational design approach based on protein sequence conservation analysis was employed. The optimized mutant, M3 (Q60S/Y452I/R455K), exhibited a 3.76-fold increase in specific activity compared to the wild type (WT) enzyme and retained more than 50 % of its activity after incubation at 70 ℃ for 24 h. Additionally, molecular dynamics simulations revealed that the enhanced activity of M3 was largely due to the reshaping of the substrate tunnel, which facilitated substrate entry to the active pocket and promoted the reaction. This study not only provides a robust approach for enhancing 4GT enzyme performance but also paves the way for broader industrial applications of 4GT enzymes.

Transcriptomic comparison unveils saxitoxin biosynthesis genes in the marine dinoflagellate Gymnodinium catenatum

The marine dinoflagellate Gymnodinium catenatum is known to produce saxitoxins (STXs) that are responsible for paralytic shellfish poisoning (PSP); however, the genes involved in STX synthesis are insufficiently understood. In the present study, we determined transcriptome sequences of toxic G. catenatum isolated from Korea (Gc-KR) and compared them with G. catenatum strains reported in other regions such as Spain (Gc-SP) and the United States (Gc-US). Toxin analysis showed that the Korean strain produced the toxins at 6.0 ± 1.9 STXs eq fmol/cell. Comparative transcriptomics of the three strains identified more than 1000 homologs of nearly all STXs biosynthesis genes in dinoflagellates, except sxtB, sxtN, and sxtY. Gene expression analysis revealed similar sxt expression patterns across all strains, with the highest expression levels observed for sxtA and sxtG. Phylogenetic analysis of sxtA, sxtG, sxtI, sxtU, and sxtS revealed distinct evolutionary patterns, with sxtA being more conserved across G. catenatum, Alexandrium spp., and toxic cyanobacteria, particularly at the sxtA4 domain, suggesting its significance in STXs synthesis. Other sxt genes in G. catenatum showed distinct patterns and significant divergence from Alexandrium spp., suggesting independent acquisition in G. catenatum. Moreover, the absence of core genes, such as sxtB, indicates it may not be essential for STXs production in G. catenatum. These findings provide insight into the sxt candidate genes in G. catenatum, enhancing our understanding of STXs biosynthesis in dinoflagellates.

Mutation-induced rigidity in the Fyn SH2 domain enhances pY-binding affinity at the cost of peptide specificity

Interactions between SH2 domains and tyrosine-phosphorylated (pY) peptides are essential for cellular signaling. While structural studies have revealed how triple-point Fyn SH2 mutants achieve ultra-high pY-peptide affinity, the dynamic consequences of these mutations remain unexplored. In this study, we performed extensive all-atom molecular dynamics simulations on the isolated wild-type Fyn SH2 domain, its mutant, and their complexes with the pY-peptide (EPQpYEEIPIYL). Comparative analyses of these simulations provided dynamic insights into how mutations within the pY-binding pocket alter the interaction between Fyn SH2 domain and the pY-peptide. Our results demonstrate that the mutations significantly influence the dynamic stability of unstructured regions within the SH2 domain and the domain-peptide interface. Specifically, the mutations enhance the rigidity and stability of the pY-binding pocket, as well as the overall structural stability of the domain, including the central β-sheet and terminal regions. This increased rigidity in the mutant enhances interactions between the pY-binding pocket and pY but weakens the interaction with the peptide residue at the +3 position relative to pY, thereby compromising the specificity of the domain-peptide interaction. These findings highlight that the interaction between SH2 domains and pY-peptides is governed not only by the structural properties of the pY-binding pocket but also by the dynamic stability of the domain itself. This insight could guide the experimental design of SH2 domains engineered to recognize post-translational modifications with diverse characteristics.

Simple and robust in vivo engineering of plasmid DNA at any copy number in Escherichia coli

Plasmids and the model bacterium Escherichia coli are at the heart of recombinant gene technologies. Plasmids are handled in test tubes with enzymes such as restriction endonucleases, ligases, and polymerases. However, with the increasing demand for larger and more complex designs, in vitro manipulation constitutes a bottleneck. By combining recombination with genetic selection, in vivo manipulation of genomic DNA is becoming routine but is yet to be developed as a versatile and reliable way to make plasmid DNA. Here, we present a robust methodology for plasmid recombineering in E. coli using a triple-selection system customized for efficient performance at any copy number. Equipped with this genetic selection cassette, we generate a toolbox of plasmids in a standardized framework with popular genetic modules. By reducing the time and resources for making recombinant DNA, this approach should enable automation and accelerate the development of biological solutions.

Comparative immunobiology and cross-species validations of pan-MHC-II epitopes on Hantaan virus nucleocapsid protein

During viral infection, CD4+ helper T-cell is indispensable for the establishment of the humoral immune protection, CTL activation, and even long-term memory response. It requires MHC-II molecules in viral structural antigens process and presentation. HTNV NP epitopes exhibited high affinity to both of HLA-II superfamilies and H-2-I genes in the present study. Immunogenicity and conservation analyses identified 34 selective epitopes, later validated by molecular docking (MD) with MHC-II structures. NP 15-mer peptides and MHC-II haplotypes were found to interact bidirectionally through hierarchical clustering. In brief, epitopes that exhibit immunoreactivities for a wide range of MHC-II molecules reflect the biomedical practice of vaccination, while haplotype clusters reflect individual differences in T-cell antigen presentation. Then, 11 HTNV variants showed three amino acid substitutions in three epitopes, with little impact on their pan-HLA-II immunoreactivity. Safety analyses indicated that the 34 selective epitopes exhibit favorable safety profiles for potential applications. Finally, we validated the immunogenicity of the selective epitopes using ELISA, ELISpot, and flow cytometry. In conclusion, our work provides a comprehensive assessment of the pan-MHC-II immunoreactivity of HTNV NP and lays the theoretical and technical foundations for the development of protective epitope vaccines in the context of population immunity.

Coordinated histone methylation loss and MYC activation promote translational capacity under amino acid restriction

BACKGROUND

Cells adapt to nutrient fluctuations through both signaling and epigenetic mechanisms. While amino acid (AA) deprivation is known to suppress protein synthesis via mTORC1 inactivation, the epigenetic pathways that support cellular adaptation and recovery remain poorly understood. We investigated how chromatin and transcriptional changes contribute to maintaining translational capacity during AA restriction and priming cells for growth upon AA repletion.

METHODS

Human cells were cultured under amino acid-replete or -depleted conditions, and global histone methylation levels were assessed by Western blotting and ChIP-seq. RNA-seq and chromatin-associated RNA-seq (chromRNA-seq) were used to evaluate gene expression and transcriptional output. Ribosome profiling and [35S]-methionine/cysteine or O-propargyl-puromycin (OPP) incorporation assays measured protein synthesis. Functional contributions of SETD8 and MYC were tested through knockdown and overexpression experiments.

RESULTS

AA deprivation induced a selective, genome-wide loss of H4K20me1, particularly from gene bodies, and led to increased MYC expression and binding at promoter regions. These changes were most pronounced at genes encoding ribosomal proteins and translation initiation factors. Although overall protein synthesis declined during AA restriction, these cells showed increased translational capacity evidenced by accumulation of monomeric ribosomes and enhanced translation upon AA repletion. Loss of H4K20me1 was independent of mTORC1 signaling and partly driven by SETD8 protein downregulation. While MYC overexpression alone was insufficient to upregulate translation-related genes, its combination with SETD8 knockdown in nutrient-rich conditions was both necessary and sufficient to induce expression of these genes and enhance protein synthesis.

CONCLUSIONS

Our findings reveal a chromatin-based mechanism by which cells integrate metabolic status with transcriptional regulation to adapt to amino acid limitation. Loss of H4K20me1 and increased MYC activity act in parallel to prime the translational machinery during AA deprivation, enabling rapid recovery of protein synthesis upon nutrient restoration. This mechanism may help explain how cells maintain competitive growth potential under fluctuating nutrient conditions and has implications for understanding MYC-driven cancer progression.

The lumenal domain of Cyt b559 interacting with extrinsic subunits is crucial for accumulation of functional photosystem II

Cytochrome b559 (Cyt b559) is an essential component of the photosystem II (PSII) reaction center core. It consists of two subunits, PsbE and PsbF, which together coordinate a redox-active heme. While extensive studies have revealed the importance of Cyt b559, its structural and functional roles are not fully understood. Previous studies have implied that the lumenal region of Cyt b559, interacting with the PSII extrinsic subunit PsbP in green plant PSII, may have important roles. However, few studies have investigated its lumenal region. Here, we have focused on a well-conserved lumenal region of PsbE, which was found to interact with the N-terminal region of PsbP in green-lineage PSII (from green algae and land plants). In red-lineage PSII (from red algae and algae possessing red algal-derived plastids), very similar interactions were observed between the same lumenal region of PsbE and the N-terminal region of PsbQ'. We generated Arabidopsis thaliana mutants harboring mutations in the well-conserved lumenal region of PsbE through targeted base editing of the plastid genome by ptpTALECD. The mutations led to strong growth defects and extremely low Fv/Fm. This study suggests the importance of the lumenal regions of Cyt b559, and gives insight into possible structural and functional compensation between the N-terminal regions of PsbP in green-lineage PSII and PsbQ' in red-lineage PSII.

Flexibility and Hydration of the Qo Site Determine Multiple Pathways for Proton Transfer in Cytochrome bc1

The detailed catalytic activity of cytochrome bc1 (or respiratory complex III) and the molecular mechanism of the Q cycle remain elusive. At the Qo site, the cycle begins with oxidation of the coenzyme-Q substrate (quinol form) in a bifurcated two-electron transfer to the iron-sulfur (FeS) cluster and the heme bL center. The release of two protons during quinol oxidation and their transfer is less understood, with one proton likely delivered to the histidine side chain attached to the FeS cluster. Here, we present extensive molecular dynamics simulations with enhanced sampling of side-chain torsions at the Qo site and analyze available sequences and structures of several bc1 homologs to probe the interactions of quinol with potential proton acceptors and identify viable pathways for proton transfer. Our findings reveal that side chains at the Qo site are highly flexible and can adopt multiple conformations. Consequently, the quinol head is also flexible, adopting three distinct binding modes. Two of these modes are proximal to the heme bL and represent reactive conformations capable of electron and proton transfer, while the third, more distal mode likely, represents a prereactive state, consistent with recent cryo-EM structures of bc1 with bound coenzyme-Q. The Qo site is highly hydrated, with several water molecules bridging interactions between the quinol head and the conserved side chains Tyr147, Glu295, and Tyr297 in cytochrome b (numbering according to Rhodobacter sphaeroides), facilitating proton transfer. A hydrogen bond network and at least five distinct proton wires are established and possibly transport protons via a Grotthuss mechanism. Asp278 and propionate-A of heme bL in cytochrome b are in direct contact with external water and are proposed as the final proton acceptors. The intervening water molecules in these proton wires exhibit low mobility, and some have been resolved in recent experimental structures. These results help to elucidate the intricate molecular mechanism of the Q-cycle and pave the way to a detailed understanding of chemical proton transport in several bioenergetic enzymes that catalyze coenzyme-Q redox reactions.

Disruption of SETD3-mediated histidine-73 methylation by the BWCFF-associated β-actin G74S mutation

Histidine-73 methylation of β-actin by SETD3 modulates ATPase activity, filament assembly, and protein interactions. The pathogenic G74S mutation in cytoskeletal β-actin, associated with Baraitser-Winter cerebrofrontofacial syndrome (BWCFF), alters the adjacent phosphate sensor loop, disrupting SETD3-mediated methylation. Molecular docking indicates that SETD3 undergoes structural rearrangements to accommodate the mutant β-actin, leading to reduced catalytic efficiency. Enzymatic assays confirm slower turnover of mutant actin peptides, while mass spectrometry reveals decreased histidine-73 methylation in both recombinant mutant β-actin and patient-derived fibroblasts. This perturbance of SETD3-mediated methylation likely generates β-actin pools with distinct methylation states, varying across cell types and developmental stages, thereby impairing cytoskeletal dynamics and contributing to BWCFF pathology. Impact statement This study reveals that the BWCFF-linked G74S mutation in β-actin disrupts SETD3-mediated histidine-73 methylation, impairing a critical post-translational modification. It provides the first direct mechanistic link between a cytoskeletal actinopathy and altered methylation, highlighting potential targets for therapeutic intervention in β-actin-related developmental disorders.

Genome-wide maps of UV damage repair and mutation suppression by CPD photolyase

Ultraviolet (UV) light causes cyclobutane pyrimidine dimers (CPDs) and other DNA lesions that must be efficiently repaired to prevent cell death and mutagenesis. While mammals utilize the nucleotide excision repair (NER) pathway to repair CPDs, many species primarily utilize photolyase enzymes to repair UV damage. Our understanding of how different genomic and chromatin features impact photolyase repair across a eukaryotic genome is limited. Here, we map repair of CPDs by photolyase across the yeast genome at single-nucleotide resolution. Our data indicate that yeast photolyase repairs CPDs more rapidly than NER, but photolyase activity is inhibited at certain classes of transcription factor binding sites and in nucleosomes. Repair in nucleosomes is particularly inhibited when CPDs are located along the 3' side of the nucleosomal DNA or at minor-in rotational settings. Our data indicate that photolyase efficiently repairs the non-transcribed strand of yeast genes, but repair of the transcribed strand (TS) is inhibited. Genome-wide analysis of UV-induced mutations in NER-deficient photoreactivated yeast reveals a striking enrichment of mutations along the TS of yeast genes. These data indicate that inhibition of photolyase repair along the TS, likely due to occlusion of CPDs by RNA polymerase II stalling, promotes UV mutagenesis.

PlantDeepMeth: A Deep Learning Model for Predicting DNA Methylation States in Plants

Cytosine DNA methylation (5mCs) is an important epigenetic modification in genomic research. However, the methylation states of some cytosine sites are not available due to the limitations of different studies, and there are few tools developed to deal with this problem, especially in plants, which have more methylation types than animals. Here, we report PlantDeepMeth, a novel deep learning model that utilizes deep learning to predict DNA methylation states in plants. The evaluation of PlantDeepMeth on known cytosine sites in both the Brassica rapa and Arabidopsis thaliana genomes shows good performance in predicting methylation states, indicating that the tool is good at learning patterns for methylation imputation. Motif analysis of the model's predictions identified specific motifs associated with hypo- or hyper-methylation states in B. rapa and A. thaliana, further revealing key regulatory patterns captured by the model. Moreover, cross-species validation between B. rapa and A. thaliana demonstrated the generalizability of PlantDeepMeth, with the model maintaining high performance across different plant species. These results highlight the effectiveness of PlantDeepMeth and demonstrate the potential of deep learning to advance plant genomics research.

Secreted retropepsin-like enzymes are essential for stress tolerance and biofilm formation in Pseudomonas aeruginosa

Proteases regulate important biological functions. Here, we present the structural and functional characterization of three previously uncharacterized aspartic proteases in Pseudomonas aeruginosa. We show that these proteases have structural hallmarks of retropepsin peptidases and play redundant roles for cell survival under hypoosmotic stress conditions. Consequently, we named them retropepsin-like osmotic stress tolerance peptidases (Rlo). Our research shows that while Rlo proteases are homologous to RimB, an aspartic peptidase involved in rhizosphere colonization and plant infection, they contain N-terminal signal peptides and perform distinct biological functions. Mutants lacking all three secreted Rlo peptidases show defects in antibiotic resistance, biofilm formation, and cell morphology. These defects are rescued by mutations in the inactive transglutaminase transmembrane protein RloB and the cytoplasmic ATP-grasp protein RloC, two previously uncharacterized genes in the same operon as one of the Rlo proteases. These studies identify Rlo proteases and rlo operon products as critical factors in clinically relevant processes, making them appealing targets for therapeutic strategies against Pseudomonas infections.IMPORTANCEBacterial infections have become harder to treat due to the ability of pathogens to adapt to different environments and the rise of antimicrobial resistance. This has led to longer illnesses, increased medical costs, and higher mortality rates. The opportunistic pathogen Pseudomonas aeruginosa is particularly problematic because of its inherent resistance to many antibiotics and its capacity to form biofilms, structures that allow bacteria to withstand hostile conditions. Our study uncovers a new class of retropepsin-like proteases in P. aeruginosa that are required for biofilm formation and bacterial survival under stress conditions, including antibiotic exposure. By identifying critical factors that determine bacterial fitness and adaptability, our research lays the foundation for developing new therapeutic strategies against bacterial infections.

RPAD locus controls prostrate growth habit in Oryza nivara

The development of ideal plant architecture is crucial for optimizing grain yield in crop breeding. The transition from prostrate growth habit in wild rice to erect growth habit in cultivated rice is one of the important events during rice domestication. Here, we identified a yield-related quantitative trait locus (QTL) cluster on the short arm of chromosome 7 using Teqing/W2014 (Oryza nivara) derived BC3F6 population. The introgression line TIL81 containing this QTL cluster exhibited significantly larger tiller angle, increased tiller numbers, and prostrate growth habit compared to the recipient parent Teqing. Using a segregating F2 population derived from a cross between TIL81 and Teqing, this yield-related QTL cluster was mapped to a similar position as the known rice plant architecture domestication (RPAD) locus controlling rice plant architecture domestication. CRISPR/Cas9-mediated genome (where CRISPR is clustered regularly interspaced short palindromic repeats) editing of four zinc finger transcription factors (OnZnF1, OnZnF6, OnZnF8, and OnZnF9) within the RPAD locus demonstrated their collective involvement in regulating plant architecture and yield-related traits. Notably, the knockout lines harboring all four zinc finger gene mutations exhibited plant architecture traits and grain yield per plant comparable to the control Teqing. These findings demonstrated that RPAD locus in O. nivara functions in prostrate growth habit and provided new insights into the molecular mechanism of plant architecture during rice domestication.

Nitric oxide production and protein S-nitrosation in algae

Key roles for nitric oxide in signalling processes and plant physiological processes are now well established. In particular, the identification and functional characterisation of proteins regulated by S-nitrosation, a NO-dependent post-translational modification, provided remarkable insights into the subtle mechanisms by which NO mediates its effects. Nevertheless, and despite the considerable progress in understanding NO signalling, the question of how plant cells produce NO is not yet fully resolved. Interestingly, there is now compelling evidence that algae constitute promising biological models to investigate NO production and functions in plants. This article reviews recent highlights of research on NO production in algae and provides an overview of S-nitrosation in these organisms at the proteome level.

Protein identification using Cryo-EM and artificial intelligence guides improved sample purification

Protein purification is essential in protein biochemistry, structural biology, and protein design, enabling the determination of protein structures, the study of biological mechanisms, and the characterization of both natural and de novo designed proteins. However, standard purification strategies often encounter challenges, such as unintended co-purification of contaminants alongside the target protein. This issue is particularly problematic for self-assembling protein nanomaterials, where unexpected geometries may reflect novel assembly states, cross-contamination, or native proteins originating from the expression host. Here, we used an automated structure-to-sequence pipeline to first identify an unknown co-purifying protein found in several purified designed protein samples. By integrating cryo-electron microscopy (Cryo-EM), ModelAngelo's sequence-agnostic model-building, and Protein BLAST, we identified the contaminant as dihydrolipoamide succinyltransferase (DLST). This identification was validated through comparisons with DLST structures in the Protein Data Bank, AlphaFold 3 predictions based on the DLST sequence from our E. coli expression vector, and traditional biochemical methods. The identification informed subsequent modifications to our purification protocol, which successfully excluded DLST from future preparations. To explore the potential broader utility of this approach, we benchmarked four computational methods for DLST identification across varying resolution ranges. This study demonstrates the successful application of a structure-to-sequence protein identification workflow, integrating Cryo-EM, ModelAngelo, Protein BLAST, and AlphaFold 3 predictions, to identify and ultimately help guide the removal of DLST from sample purification efforts. It highlights the potential of combining Cryo-EM with AI-driven tools for accurate protein identification and addressing purification challenges across diverse contexts in protein science.

Specific DNA features of the RNA polymerase I core promoter element targeted by core factor

RNA polymerase I (Pol I) is essential for ribosomal RNA (rRNA) synthesis, driving ribosome biogenesis in eukaryotes. Transcription initiation by Pol I requires core factor (CF) binding to the core element (CE) of the ribosomal DNA (rDNA) promoter. Despite structural conservation across species, significant sequence variability suggests CF recognizes DNA through structural features rather than specific sequences. We investigated CF's DNA binding preferences to elucidate the role of DNA structural properties in CE recognition. Analysis of CE sequences from 35 fungal species revealed conserved structural features, notably a rigid AT-rich patch at positions -22 to -20 and a conserved G base pair at position -24. Competition-based electrophoretic mobility shift assays (EMSA) with single base-pair substitutions showed CF tolerates mutations at many positions but is sensitive to changes in the AT-rich patch. Loss of CF binding correlated with alterations in DNA structural properties such as increased bendability, decreased curvature, widened minor groove width, and altered helix twist. In vitro SELEX experiments identified novel CE sequences preferentially bound by CF, exhibiting increased GC content, higher bendability, and decreased curvature despite lacking sequence conservation. Classification based on bendability profiles revealed CF preferentially binds bendable sequences. In vivo selection assays confirmed these findings, demonstrating consistent CF binding preferences within a cellular context. Our results indicate that CF recognizes and binds to the CE primarily through specific DNA structural features rather than nucleotide sequences. Structural properties like bendability, curvature, and minor groove width are critical determinants of CF binding, facilitating effective Pol I transcription initiation.

Mild and ultrafast GLORI enables absolute quantification of m6A methylome from low-input samples

Methods for absolute quantification of N6-methyladenosine (m6A) have emerged as powerful tools in epitranscriptomics. We previously reported GLORI, a chemical-assisted approach to achieve unbiased and precise m6A measurement. However, its lengthy reaction time and severe RNA degradation have limited its applicability, particularly for low-input samples. Here, we present two updated GLORI approaches that are ultrafast, mild and enable absolute m6A quantification from one to two orders of magnitude less than the RNA starting material: GLORI 2.0 is compatible with RNA from ~10,000 cells and enhances sensitivity for both transcriptome-wide and locus-specific m6A detection; GLORI 3.0 further utilizes a reverse transcription-silent carrier RNA to achieve m6A quantification from as low as 500-1,000 cells. Using limited RNA from mouse dorsal hippocampus, we reveal a high modification level in synapse-related gene sets. We envision that the updated GLORI methods will greatly expand the applicability of absolute quantification of m6A in biology.

Development of universal PCR primers for the environmental DNA metabarcoding of cephalopod (Mollusca) diversity

Cephalopods play crucial roles in marine ecosystems, acting as both predators and prey for apex predators, thereby contributing to the distribution of energy and nutrients across the food web. Traditional net capture methods are often ineffective for studying cephalopods owing to their wide distribution in marine environments, necessitating the development of simple and efficient surveying techniques to assess cephalopod diversity. Therefore, in this study, we aimed to establish universal polymerase chain reaction primers specifically targeting mitochondrial 16S rRNA genes for environmental DNA metabarcoding in cephalopods. Two primer sets, Cep16S_D and Cep16S_O, were designed for squids and octopuses, respectively. Taxonomic specificity, resolution, and coverage of these primers were evaluated via in silico and in vitro analyses. Additionally, efficiency of these primer sets was assessed using tissue samples and mock communities. Finally, their applicability and performance were tested at various depths. The developed primers exhibited a relatively large amplification size with mixed bases that enhanced their amplification efficiency and sensitivity for cephalopod detection. We successfully identified cephalopod species with different body sizes, from small species, such as Heteroteuthis dagamensis, to large species, such as Architeuthis dux, at varying water depths. Overall, the primer sets established in this study serve as powerful tools to study cephalopod diversity and exhibit great potential for barcoding and genetic diversity investigations.

Type 4 plant metallothioneins - players in zinc biofortification?

Food security is defined as uninterrupted access to food that meets people's dietary needs. One essential trace element of a complete diet is zinc, which is vital for various processes, including growth, development, and the immune response. The estimated global prevalence of zinc deficiency is around 30%. Meat and meat products provide an abundant and also bioavailable source of zinc. However, in developing countries, access to meat is restricted, and in developed countries, meat consumption has declined for ethical and environmental reasons. The potential for zinc deficiency arises from (i) low concentrations of this element in plant-based diets, (ii) poor zinc absorption from plant-based food in the human intestine, and (iii) the risk of uptake of toxic metals together with essential ones. This review summarises the current knowledge concerning type 4 metallothioneins, which represent promising targets for zinc biofortification. We describe their place in the zinc route from soil to seed, their expression patterns, their role in plants, and their three-dimensional protein structure and how this affects their selectivity towards zinc. This review aims to provide a comprehensive theoretical basis for the potential use of type 4 plant metallothioneins to create zinc-biofortified crops.

Genomic surveillance of SARS-CoV-2 variants in Guangzhou, China, from April 2023 to March 2024

BACKGROUND

After the relaxation of stringent control measures, nationwide large-scale SARS-CoV-2 surveillance was gradually phased out post-2023, transitioning to focused monitoring of Influenza-like Illness (ILI) through sentinel hospitals and laboratory networks. Nationally, surveillance of respiratory pathogens was performed via random sampling, resulting in a lack of microbial monitoring results in Guangzhou China. A crucial area of scientific inquiry is whether the current cases are attributable to the emergence of a novel SARS-CoV-2 variant.

METHODS

Throat swab samples were obtained from 1478 outpatients and 337 hospitalized patients with fever (temperature ≥ 38 °C) and cough or sore throat to detect SARS-CoV-2. The positive samples were subjected to viral whole-genome sequencing and phylogenetic analysis. Respiratory pathogen multiplex PCR tests were performed on stratified random samples.

RESULTS

SARS-CoV-2 was detected in 517 (28.48 %) patients. There were higher rates of SARS-CoV-2 infection among women, older patients and those who were hospitalized. A total of 299 high-quality SARS-CoV-2 sequences were obtained, including 12 clades and 71 pango lineages. The advantageous clades evolved over three peak periods of infection, from BA.5 (April 2023) to XBB (June to July 2023) and then to JN.1 (February 2024). A total of 590 distinct amino acid mutations were identified across the sequences. The highest prevalence of mutations was observed for spike protein mutations, with more than 50 % of the three epidemic peaks detected. Epidemiological profiles of interactions between SARS-CoV-2 and other respiratory pathogens exhibit considerable variation across different seasons, with a tendency toward suppression within each.

CONCLUSION

Surveillance by Guangzhou Eighth People's Hospital provides a snapshot of the epidemic in Guangzhou, which is consistent with the national epidemic and offers important data for understanding the spread of SARS-CoV-2 in southern China.

Sorbate induces lysine sorbylation through noncanonical activities of class I HDACs to regulate the expression of inflammation genes

Environmental factors may affect gene expression through epigenetic modifications of histones and transcription factors. Here, we report that cellular uptake of sorbate, a common food preservative, induces lysine sorbylation (Ksor) in mammalian cells and tissue mediated by the noncanonical activities of class I histone deacetylases (HDAC1-3). We demonstrated that HDAC1-3 catalyze sorbylation upon sorbate uptake and desorbylation in the absence of sorbate both in vitro and in cells. Sorbate uptake in mice livers significantly induced histone Ksor, correlating with decreased expressions of inflammation-response genes. Accordingly, sorbate treatment in macrophage RAW264.7 cells upon lipopolysaccharide (LPS) stimulation dose-dependently down-regulated proinflammatory gene expressions and nitric oxide production. Proteomic profiling identified RelA, a component of the NF-κB complex, and its interacting proteins as bona fide Ksor targets and sorbate treatment significantly decreased NF-κB transcriptional activities in response to LPS stimulation in RAW264.7 cells. Together, our study demonstrated a noncanonical mechanism of sorbate uptake in regulating epigenetic histone modifications and inflammatory gene expression.

Evolutionary insights into Interleukin-12 family targets across 405 species

The Interleukin-12 (IL-12) family ligand subunits (IL-12s) and receptor subunits (IL-12Rs) constitute pivotal regulators of immune homeostasis, with direct implications in autoimmune pathologies and oncogenesis. Through phylogenetic reconstruction, synteny analysis, and sequence alignment across 400+ animal species, we delineated the evolutionary trajectories and functional diversification of these immune mediators. Phylogenetic analysis revealed IL-12Rs originated prior to the mollusk era (514-686.2 million years ago, Mya), while ligand subunits p19/p28 emerged during the mammalian and avian epoch (180-225 Mya). Structural characterization identified three evolutionarily invariant signature motifs within the fibronectin type III (fn3) domain essential for receptor-ligand interface stability. Furthermore, phylogenetically ultra-conserved residue and motif configurations were mapped, revealing candidate therapeutic epitopes. These findings establish an evolutionary framework explaining functional conservation/divergence in IL-12 signaling components. The identified ancient receptor architectures coupled with derived ligand innovations provide a blueprint for cross-species immunotherapy design targeting conserved interaction interfaces. The conserved molecular signatures offer dual utility in developing precision therapies and interspecies disease management strategies, particularly for translational applications across human medicine, agriculture, and aquaculture.

A point mutation in PsbW disrupts thylakoid membrane organization and causes aberrant starch granule formation

Chloroplast thylakoid membranes are the sites of the light reactions of photosynthesis. They are also thought to influence starch granule biogenesis via the thylakoid anchored protein MAR-BINDING FILAMENT-LIKE PROTEIN 1 (MFP1), but mechanistic understanding is scarce. Here we report an Arabidopsis mutant affected in PsbW, an integral thylakoid membrane protein associated with photosynthetic complexes of PSII. This mutant (psbw-2) was identified in a large-scale mutant screen designed to find proteins that regulate starch granule shape and size because it produces an excessive number of small, irregularly shaped starch granules. The mutation in psbw-2 causes a glycine-to-arginine substitution in PsbW's transmembrane helix. The resulting PsbWG107R protein remains membrane-associated but has lost its ability to stabilize PSII supercomplexes. In addition, the transgenic expression of this mutated version results in abnormal thylakoid membranes that have drastically enlarged luminal spaces and no longer form distinct grana stacks, leading to reduced plant growth and impaired photosynthesis. These effects increase with PsbWG107R expression levels but are not observed in the psbw knockout mutant, suggesting that PsbWG107R has acquired an aberrant function. We analyzed psbw-2 mutants also lacking either MFP1 or STARCH SYNTHASE 4, a key factor involved in granule initiation and growth. These data suggest that thylakoid distortion is caused by the membrane insertion of PsbWG107R, which in turn affects the initiation and growth of starch granules. Our results reaffirm the link between thylakoid membrane system and starch formation and highlight the importance of proper thylakoid architecture for plant fitness.

Dancing molecules: group A bZIPs and PEBPs at the heart of plant development and stress responses

Group A basic leucine zipper (bZIP) transcription factors play critical roles in abscisic acid (ABA) signaling and plant development. In Arabidopsis thaliana, these factors are defined by a highly conserved core bZIP domain, and four conserved domains throughout their length: three at the N-terminus (C1-C3) and a phosphorylatable C-terminal SAP motif located at the C4 domain. Initially, members such as ABI5 and ABFs were studied for their roles in ABA signaling during seed germination or stress responses. Later, a sub-clade of group A bZIPs, including FD, was found to play important roles in floral induction by interacting with the florigen FLOWERING LOCUS T (FT) at the shoot apical meristem. Recent research has expanded our understanding of these transcription factors by identifying intriguing parallels between those involved in ABA signaling and those promoting floral induction, and revealing dynamic interactions with FT and other phosphatidylethanolamine-binding proteins (PEBPs) such as TERMINAL FLOWER 1. Studies in crop plants and non-model species demonstrate broader roles, functions, and molecular targets of group A bZIPs. This review highlights common features of group A bZIPs and their post-translational regulation in enabling the activation of gene regulatory networks with important functions in plant development and stress responses.

High Throughput Meta-analysis of Antimicrobial Peptides for Characterizing Class Specific Therapeutic Candidates: An In Silico Approach

The increasing incidence of antimicrobial resistance is becoming a serious concern worldwide and requires newer drugs. Recent evidence has shown growing interest in peptide-based therapeutics. Here, we performed a meta-analysis of nearly 867,000 predicted antimicrobial peptides and assessed their antibacterial (ABPs), antifungal (AFPs), and antiviral (AVPs) activity. We created high-quality, class-specific datasets and performed several computational analyses. Composition analysis revealed enrichment of aliphatic (V, A, I, and L) and positively charged (K and R) amino acids in ABPs: aliphatic (G, I), basic (K and R), and aromatic amino acids (F) in AFPs and sulfur containing (M) and aliphatic amino acids (V, I, and L) in AVPs. We observed significant differences in the molecular weight, charge, isoelectric point, and instability index of the peptides among three classes. We observed AFPs possessing the highest molecular weight and ABPs showing the highest charge and isoelectric point, whereas instability index was found to be comparable among the three classes. Motif analysis shows enrichment of unique motifs such as "VRVR" and "AKKPA" in ABPs, "DFFAI" and "FFAI" in AFPs, and "VVV" and "IM" in AVPs. We further developed seven distinct machine learning models to predict peptide activity where ExtraTree model achieved the highest AUROC of 0.98 in classifying ABPs and non-ABPs, 0.99 for classifying AFPs and non-AFPs, and 0.99 for classifying AVPs and non-AVPs on an independent dataset. To assist scientific community, we have provided the dataset and models at our GitHub page ( https://github.com/agrawalpiyush-srm/AMP_MetaAnalysis ). Subsequent filtering of peptides based on moonlighting properties (toxicity, allergenicity, cell-penetrating ability, half-life, and secondary structure) yielded a list of peptides that exhibit substantial therapeutic potential. We further selected the top ten peptides in each class, predicted their 3D structures using ColabFold embedded in ChimeraX1.8 software and performed molecular docking analysis with a pathogenic protein selected from an organism in each class using HDOCK webserver. Docking studies demonstrated strong interaction between peptides and the proteins. Lastly, we proposed list of peptides with high therapeutic potential in each class.

An interbacterial cysteine protease toxin inhibits cell growth by targeting type II DNA topoisomerases GyrB and ParE

Bacteria deploy a diverse arsenal of toxic effectors to antagonize competitors, profoundly influencing the composition of microbial communities. Previous studies have identified an interbacterial toxin predicted to exhibit proteolytic activity that is broadly distributed among gram-negative bacteria. However, the precise mechanism of intoxication remains unresolved. Here, we demonstrate that one such protease toxin from Escherichia coli, Cpe1, disrupts DNA replication and chromosome segregation by cleaving conserved sequences within the ATPase domain of type II DNA topoisomerases GyrB and ParE. This cleavage effectively inhibits topoisomerase-mediated relaxation of supercoiled DNA, resulting in impaired bacterial growth. Cpe1 belongs to the papain-like cysteine protease family and is associated with toxin delivery pathways, including the type VI secretion system and contact-dependent growth inhibition. The structure of Cpe1 in complex with its immunity protein reveals a neutralization mechanism involving competitive substrate binding rather than active site occlusion, distinguishing it from previously characterized effector-immunity pairs. Our findings unveil a unique mode of interbacterial intoxication and provide insights into how bacteria protect themselves from self-poisoning by protease toxins.

Derivatization of pBACpAK entrapment vectors for enhanced mobile genetic element transposition detection in multidrug-resistant Escherichia coli

Aim. Antimicrobial resistance poses a critical global health threat, driven by the dissemination of resistance genes via mobile genetic elements (MGEs). This study aims to enhance the detection of MGE insertions in multidrug-resistant Escherichia coli by derivatizing the pBACpAK entrapment vector. Methods and results. Three derivatives were constructed with additional nucleotides upstream of the cI repressor gene, based on conserved regions identified from GenBank sequences containing known IS26 and IS1 insertions. Using colony PCR, intracellular transposition screening was performed on 194 tetracycline-resistant colonies from four E. coli ESI123 strains carrying different pBACpAK constructs. The derivatives showed increased MGE capture rates (10.7-73.1 %) compared to the WT vector (3.75%), identifying multiple MGEs, including the novel composite transposon Tn7824. Tn7824 harbours the bla OXA-181 carbapenem resistance gene and the qnrS1 quinolone resistance gene, highlighting the clinical relevance of these findings. Long-read sequencing of transposants confirmed the accuracy of MGE identification and structural characterization, which also revealed chromosomal integration events of the pBACpAK derivatives mediated by flanking insertion sequences. Conclusions. The modifications introduced in the pBACpAK derivatives could increase the detection of transposition events by alleviating spatial constraints, allowing for more robust MGE detection.

Improved DNA binding to a type IV minor pilin increases natural transformation

Bacteria take up environmental DNA using dynamic appendages called type IV pili (T4P) to elicit horizontal gene transfer in a process called natural transformation. Natural transformation is widespread amongst bacteria yet the parameters that enhance or limit this process across species are poorly understood. We show that the most naturally transformable species known, Acinetobacter baylyi, owes this property to uniquely high levels of DNA binding by its orphan minor pilin, FimT. Expression of A. baylyi FimT in a closely related Acinetobacter pathogen substantially improves its capacity for natural transformation, showing that the acquisition of a single gene is sufficient to increase rates of horizontal gene transfer. We show that, compared with its homologs, A. baylyi FimT contains multiple regions of positively charged residues that additively promote DNA binding efficiency. These results demonstrate the importance of T4P-DNA binding in establishing natural transformation rates and provide a basis for improving or limiting this mechanism of horizontal gene transfer in different species.

Prediction of lipase-specific foldase-dependence in bacterial lipase subfamilies I.1 and I.2

BACKGROUND

Most bacterial lipases in subfamily I.1/I.2 depend on a specific chaperone protein, lipase-specific foldase (Lif), for folding into their active form. In contrast, several Lif-independent lipases have been reported in subfamily I.1. Lif-independent lipases have the potential to be industrially useful owing to their ease of heterologous expression; however, no method has been reported to predict Lif-dependence for an arbitrary lipase. In this study, we comprehensively estimated the Lif-dependence of subfamily I.1/I.2.

RESULTS

To estimate Lif-dependence, we comprehensively analyzed the presence or absence of Lif genes in the genomes of bacteria from which the lipases were derived and integrated the results with those of phylogenetic analysis. We identified a range of lipases from the Pseudomonas fragi/Proteus vulgaris clade, which contained all known Lif-independent lipases and were enriched for lipases that did not coexist with Lif. Sequences and structural features conserved in the P. fragi/P. vulgaris clade and other lipases were identified, and the residues involved in Lif-dependence were inferred. Furthermore, we identified the Pseudoalteromonas shioyasakiensis clade, which is phylogenetically distinct from the P. fragi/P. vulgaris clade, as having no Lif in the genome of the bacterium from which the lipase was derived. The P. shioyasakiensis clade lipase, PliLip, was heterologously expressed in Escherichia coli in an active form, independent of Lif.

CONCLUSIONS

In this study, we developed a method to predict Lif-dependence in any lipase belonging to subfamily I.1/I.2 and comprehensively extracted putative Lif-independent lipases from public databases. This study contributes to expand the diversity of industrially available Lif-independent lipases and provides fundamental insights into the evolution of lipases and Lif.

West African-South American pandemic Vibrio cholerae encodes multiple distinct phage defence systems

Our understanding of the factors underlying the evolutionary success of different lineages of pandemic Vibrio cholerae remains incomplete. The West African-South American (WASA) lineage of V. cholerae, responsible for the 1991-2001 Latin American cholera epidemic, is defined by two unique genetic signatures. Here we show that these signatures encode multiple distinct anti-phage defence systems. Firstly, the WASA-1 prophage encodes an abortive-infection system, WonAB, that renders the lineage resistant to the major predatory vibriophage ICP1, which, alongside other phages, is thought to restrict cholera epidemics. Secondly, a unique set of genes on the Vibrio seventh pandemic island II encodes an unusual modification-dependent restriction system targeting phages with modified genomes, and a previously undescribed member of the Shedu defence family that defends against vibriophage X29. We propose that these anti-phage defence systems likely contributed to the success of a major epidemic lineage of the ongoing seventh cholera pandemic.

A distinct class of ferredoxin:NADP+ oxidoreductase enzymes driving thermophilic ethanol production

Biofuel production from lignocellulosic biomass offers a transformative solution to reduce global fossil fuel dependency. Certain thermophilic anaerobes, including Clostridium thermocellum, show promise for renewable ethanol production due to their ability to break down plant material at high temperatures. However, achieving commercially viable ethanol yields has proven challenging despite extensive engineering efforts. Here, we characterized 27 ferredoxin:NADP+ oxidoreductase (Fnor) enzymes for their enzyme activity, nicotinamide cofactor specificity, thermotolerance, and functional expression in C. thermocellum. We identified a subset of ten of these enzymes as a novel class of Fnor enzymes suited for metabolic pathways aimed at high-titer ethanol production. When expressed in engineered C. thermocellum, these enzymes increased ethanol production up to 2.2-fold. These findings establish a novel ethanol pathway and provide insights into physiological roles and biotechnological applications of this new class of Fnor enzymes.

Unravelling the role of key amino acid residues of the parainfluenza fusion peptide in membrane fusion

Parainfluenza viruses enter host cells by fusing their envelope with the cell membrane. In this process mediated by the fusion glycoprotein, the fusion peptide plays an essential role in membrane binding and triggering fusion. Previously, we demonstrated that the parainfluenza fusion peptide (PIFP) oligomerizes into porelike structures within the membrane, leading to membrane perturbations, fusion, and leakage. Additionally, we identified two key amino acid residues in the PIFP, F103 and Q120, which are important in inducing lipid tail protrusion and maintaining peptide-peptide interactions, respectively. Here, we seek to elucidate the role of these two residues in the PIFP function by studying the impact of F103A and Q120A substitutions on peptide activity. We compared the substituted peptides with the native peptide using biophysical experiments and molecular dynamics (MD) simulations. Our results show that the F103A substitution significantly impairs PIFP's interaction with the membrane and its ability to induce lipid mixing and membrane leakage in experimental assays. Moreover, a decrease in lipid perturbation and water flux through the membrane was observed in the MD simulations. In contrast, the Q120A substitution appears to have minimal impact on membrane interaction and PIFP-induced membrane leakage. Interestingly, a pronounced change in the interpeptide interactions within the membrane of the substituted peptides was observed in the MD simulations. These findings provide crucial insights into the potential role of F103 and Q120 in PIFP activity: the N-terminal phenylalanine (F103) is pivotal for membrane insertion and fusion, while the Q120 is crucial for regulating peptide oligomerization and pore formation.

GPR15LG binds CXCR4 and synergistically modulates CXCL12-induced cell signaling and migration

BACKGROUND

GPR15LG, a chemokine-like ligand for the G-protein coupled receptor 15 (GPR15), is abundantly expressed in the gastrointestinal mucosa and inflamed skin. Emerging evidence suggests its involvement in inflammatory disorders and cancers. C-X-C chemokine receptor type 4 (CXCR4) plays a critical role in immune cell trafficking and cancer metastasis. Recent evidence suggests a connection between GPR15LG and CXCR4 signaling, which has not been investigated so far.

METHODS

We investigated the effects of GPR15LG on CXCR4 signaling and downstream functions. Binding assays and computational modeling were performed to assess the interaction between GPR15LG and CXCR4. Functional assays, including wound healing and cell migration assays, were conducted across various cell types, including CD4⁺ T cells and cancer cells, to evaluate the impact of GPR15LG on CXCL12-mediated CXCR4 signaling.

RESULTS

The results demonstrate that GPR15LG binds to the orthosteric site of CXCR4, modulating downstream signaling in a context-dependent manner. Specifically, GPR15LG enhances CXCL12-mediated CXCR4 signaling synergistically, promoting wound healing and cell migration across various cell types, including CD4 + T cells and cancer cells.

CONCLUSIONS

These findings underscore the role of GPR15LG in inflammation and metastasis, offering potential therapeutic avenues for CXCR4-mediated diseases.

Structural basis for OAS2 regulation and its antiviral function

Oligoadenylate synthetase (OAS) proteins are immune sensors for double-stranded RNA and are critical for restricting viruses. OAS2 comprises two OAS domains, only one of which can synthesize 2'-5'-oligoadenylates for RNase L activation. Existing structures of OAS1 provide a model for enzyme activation, but they do not explain how multiple OAS domains discriminate RNA length. Here, we discover that human OAS2 exists in an auto-inhibited state as a zinc-mediated dimer and present a mechanism for RNA length discrimination: the catalytically deficient domain acts as a molecular ruler that prevents autoreactivity to short RNAs. We demonstrate that dimerization and myristoylation localize OAS2 to Golgi membranes and that this is required for OAS2 activation and the restriction of viruses that exploit the endomembrane system for replication, e.g., coronaviruses. Finally, our results highlight the non-redundant role of OAS proteins and emphasize the clinical relevance of OAS2 by identifying a patient with a loss-of-function mutation associated with autoimmune disease.

Comprehensive genomic and evolutionary analysis of biofilm matrix clusters and proteins in the Vibrio genus

Vibrio cholerae pathogens cause cholera, an acute diarrheal disease resulting in significant morbidity and mortality worldwide. Biofilms in vibrios enhance their survival in natural ecosystems and facilitate transmission during cholera outbreaks. Critical components of the biofilm matrix include the Vibrio polysaccharides produced by the vps-1 and vps-2 gene clusters and the biofilm matrix proteins encoded in the rbm gene cluster, together comprising the biofilm matrix cluster. However, the biofilm matrix clusters and their evolutionary patterns in other Vibrio species remain underexplored. In this study, we systematically investigated the distribution, diversity, and evolution of biofilm matrix clusters and proteins across the Vibrio genus. Our findings reveal that these gene clusters are sporadically distributed throughout the genus, even appearing in species phylogenetically distant from Vibrio cholerae. Evolutionary analysis of the major biofilm matrix proteins RbmC and Bap1 shows that they are structurally and sequentially related, having undergone structural domain and modular alterations. Additionally, a novel loop-less Bap1 variant was identified, predominantly represented in two phylogenetically distant V. cholerae subspecies clades that share specific gene groups associated with the presence or absence of the protein. Furthermore, our analysis revealed that rbmB, a gene involved in biofilm dispersal, shares a recent common ancestor with Vibriophage tail proteins, suggesting that phages may mimic host functions to evade biofilm-associated defenses. Our study offers a foundational understanding of the diversity and evolution of biofilm matrix clusters in vibrios, laying the groundwork for future biofilm engineering through genetic modification.

IMPORTANCE

Biofilms help vibrios survive in nature and spread cholera. However, the genes that control biofilm formation in vibrios other than Vibrio cholerae are not well understood. In this study, we analyzed the biofilm matrix gene clusters and proteins across diverse Vibrio species to explore their patterns and evolution. We discovered that these genes are spread across different Vibrio species, including those not closely related to V. cholerae. We also found various forms of key biofilm proteins with different structures. Additionally, we identified genes involved in biofilm dispersal that are related to vibriophage genes, highlighting the role of phages in biofilm development. This study not only provides a foundational understanding of biofilm diversity and evolution in vibrios but also leads to new strategies for engineering biofilms through genetic modification, which is crucial for managing cholera outbreaks and improving the environmental resilience of these bacteria.

An Alkaliphilic Chitinase Unveils Environment-Dependent Variation in the Canonical Catalytic Machinery of Family-18 Glycoside Hydrolases

Chitinases belonging to glycoside hydrolase family-18 (GH18) employ substrate-assisted catalysis and typically have neutral/acidic pH-optima. We describe the structural and functional analysis of CaChiA, a chitinase from the anaerobic alkaliphilic bacterium Chitinivibrio alkaliphilus with an alkaline pH optimum (8.8) and unique active site features, including a noncanonical catalytic HxxExDxE motif, which is DxxDxDxE in other chitinases. Propka calculations indicated a significantly higher pKa for the catalytic acid/base, Glu148, in CaGH18, compared to other GH18 enzymes, aligning with its alkaline pH optimum. Both Propka calculations and functional studies of enzyme variants with mutations in the catalytic center suggested that not the change in the catalytic motif, but rather a unique glutamine, Gln57, modulating the properties of this motif, enables activity at alkaline pH. Further characterization of CaChiA unveiled additional peculiar enzyme properties, such as a unique ability to convert chitin to chitotriose. Thus, CaChiA adds novel catalytic capabilities to the widespread family of GH18 chitinases, made possible by adaptation of an intricate catalytic center.

Expansion of the genus Bevemovirus: Novel genome discovery and evidence for virus-host co-segregation

The genus Bevemovirus (family Potyviridae) currently comprises one recognized species, bellflower veinal mottle virus (BVMoV), and one putative member, Striga-associated poty-like virus 1 (SaPlV1). To investigate the hidden diversity of this genus, we mined publicly available plant transcriptome datasets, yielding nine bevemovirus genome sequences from diverse host species, including five Oreocharis species, Campanula takesimana, Ariocarpus retusus, Maihueniopsis conoidea, and Pachycereus pringlei. Phylogenetic analysis of large polyprotein sequences placed all novel viruses within a well-supported Bevemovirus clade, distinct from other Potyviridae genera. Conserved proteolytic cleavage sites inferred from the polyproteins revealed sequence motifs similar to those of Macluravirus and Bymovirus, although several sites exhibited genus-specific features. All genomes encoded the P3N-PIPO protein via a conserved GA6 transcriptional slippage motif. The resulting PIPO peptides displayed conserved N-terminal regions and variable C-termini. Notably, the virus phylogeny was topologically congruent with that of their host plants, suggesting co-segregation and vertical transmission rather than the horizontal transmission typical of many potyviruses. These findings expand the known diversity of Bevemovirus, provide insights into its conserved genomic features, and suggest a persistent virus-host relationship. Our results underscore the utility of plant transcriptome data for virus discovery and for inferring evolutionary processes in RNA virus lineages.

Physiological roles of an Acinetobacter-specific σ factor

The Gram-negative pathogen Acinetobacter baumannii is considered an "urgent threat" to human health due to its propensity to become antibiotic resistant. Understanding the distinct regulatory paradigms used by A. baumannii to mitigate cellular stresses may uncover new therapeutic targets. Many γ-proteobacteria use the extracytoplasmic function (ECF) σ factor, RpoE, to invoke envelope homeostasis networks in response to stress. Acinetobacter species contain the poorly characterized ECF "SigAb"; however, it is unclear if SigAb has the same physiological role as RpoE. Here, we show that SigAb is a metal stress-responsive ECF that appears unique to Acinetobacter species and distinct from RpoE-like ECFs. We combine promoter mutagenesis, motif scanning, and chromatin immunoprecipitation-sequencing (ChIP-seq) to define the direct SigAb regulon, which consists of genes encoding SigAb itself, the stringent response mediator, RelA, and the uncharacterized small RNA, "SabS." However, RNA-seq of strains overexpressing SigAb revealed a large, indirect regulon containing hundreds of genes. Metal resistance genes are key elements of the indirect regulon, as CRISPRi knockdown of sigAb or sabS resulted in increased copper sensitivity and excess copper-induced SigAb-dependent transcription. Furthermore, we found that two uncharacterized genes in the sigAb operon, "aabA" and "aabB," have anti-SigAb activity. Finally, employing a targeted Tn-seq approach that uses CRISPR-associated transposons, we show that sigAb, aabA, and aabB are important for fitness even during optimal growth conditions. Our work reveals new physiological roles for SigAb and SabS, provides a novel approach for assessing gene fitness, and highlights the distinct regulatory architecture of A. baumannii.

IMPORTANCE

Acinetobacter baumannii is a hospital-acquired pathogen, and many strains are resistant to multiple antibiotics. Understanding how A. baumannii senses and responds to stress may uncover novel routes to treat infections. Here, we examine how the Acinetobacter-specific transcription factor, SigAb, mitigates stress. We find that SigAb directly regulates only a small number of genes, but indirectly controls hundreds of genes that have substantial impacts on cell physiology. We show that SigAb is required for maximal growth, even during optimal conditions, and is acutely required during growth in the presence of elevated copper. Given that copper toxicity plays roles in pathogenesis and on copper-containing surfaces in hospitals, we speculate that SigAb function may be important in clinically relevant contexts.

Evolution and classification of Ser/Thr phosphatase PP2C family in bacteria: Sequence conservation, structures, domain distribution

Serine/threonine kinases (STKs) and serine/threonine phosphatases (STPs) are widely present across various organisms and play crucial roles in regulating cellular processes such as growth, proliferation, signal transduction, and other physiological functions. Recent research has increasingly focused on the regulation of STKs and STPs in bacteria. STKs have been well studied, identified and characterized in a variety of bacterial species. However, the role of STPs in bacteria remains less understood, and the number of proteins characterized is limited. It has been found that most of the STPs characterized in bacteria were Mg2+/Mn2+ dependent 2C protein phosphatases (PP2Cs), but the evolutionary relationship and taxonomic distribution of bacterial PP2C phosphatases were still not fully elucidated. In this study, we utilized bacterial PP2C phosphatase sequences from the InterPro database to perform a phylogenetic analysis, categorizing the family into five groups. Based on this classification, we examined the evolutionary relationships, species distribution, sequence and structural variations, and domain distribution characteristics of bacterial PP2C phosphatases. Our analysis uncovered evidence of a common evolutionary origin for bacterial PP2C phosphatases. These findings advance the understanding of PP2C phosphatases, offering valuable insights for future functional studies of bacterial serine/threonine phosphatases and aiding in the design of targeted therapeutics for pathogenic bacteria.

An integrated multiscale computational framework deciphers SARS-CoV-2 resistance to sotrovimab

The emergence of resistance mutations in the SARS-CoV-2 spike (S) protein presents a challenge for monoclonal antibody treatments like sotrovimab. Understanding the structural, dynamic, and molecular features of these mutations is essential for therapeutic advancements. However, the intricate landscape of potential mutations and critical residues conferring resistance to mAbs like sotrovimab remains elusive. This study introduces an integrated framework that combines interface protein design, machine learning, hybrid quantum mechanics/molecular mechanics methodologies, all-atom and coarse-grained molecular dynamics simulations, and correlation analysis. Beginning with the interface-based design and analysis, this framework elucidates the interaction between sotrovimab and the S-protein, identifying pivotal residues and plausible resistance mutations. Machine learning algorithms then facilitate the identification of potential resistance mutations using structural-sequence-binding affinity-energetics features. The hybrid quantum mechanics/molecular mechanics approach subsequently evaluates the role of mutational residues as quantum regions, assessing their impact on stabilizing the macromolecular complex. To gain a deeper understanding of the dynamic behavior of these mutations, multiscale simulations comprising all-atom and coarse-grained molecular dynamics simulations were performed, revealing their structural, biophysical and energetic impacts. These simulations complemented the static predictions, capturing the conformational dynamics and stability of the mutants in presence of glycan in the S-protein. The accuracy of the predictions is validated by correlating identified resistance mutations with clinical-sequencing data and empirical evidence from sotrovimab-treated patients. Notably, two residues, E340 at the S-protein-sotrovimab interface and Y508 distal from it, and their designs, align with clinically observed resistance mutations. Furthermore, machine learning approaches predict novel S-protein sequences with enhanced/reduced affinity for sotrovimab, validated structurally using AlphaFold. This integrated framework showcases its effectiveness in identifying potential resistance mutations, corroborated with clinical insights and offering a multidimensional strategy for decoding resistance mutations in SARS-CoV-2. Its translational relevance extends to understanding resistance mechanisms and designing novel antibody therapeutics in other systems.

Biases from Oxford Nanopore library preparation kits and their effects on microbiome and genome analysis

BACKGROUND

Oxford Nanopore sequencing is a long-read sequencing technology that does not rely on a polymerase to generate sequence data. Sequencing library preparation methods used in Oxford Nanopore sequencing rely on the addition of a motor protein bound to an adapter sequence, which is added either using ligation-based methods (ligation sequencing kit), or transposase-based methods (rapid sequencing kit). However, these methods have enzymatic steps that may be susceptible to motif bias, including the underrepresentation of adenine-thymine (AT) sequences due to ligation and biases from transposases. This study aimed to compare the recognition motif and relative interaction frequencies of these library preparation methods and assess their effects on relative sequencing coverage, microbiome, and methylation profiles. The impacts of DNA extraction kits and basecalling models on microbiome analysis were also investigated.

RESULTS

By using sequencing data generated by the ligation and rapid library kits, we identified the recognition motif (5'-TATGA-3') consistent with MuA transposase in the rapid kit and low frequencies of AT in the sequence terminus of the ligation kit. The rapid kit showed reduced yield in regions with 40-70% guanine-cytosine (GC) contents, while the ligation kit showed relatively even coverage distribution in areas with various GC contents. Due to longer reads, ligation kits showed increased taxonomic classification efficiency compared to the rapid protocols. Rumen microbial profile at different taxonomic levels and mock community profile showed significant variation due to the library preparation method used. The ligation kit outperformed the rapid kit in subsequent bacterial DNA methylation statistics, although there were no significant differences.

CONCLUSIONS

Our findings indicated that careful and consistent library preparation method selection is essential for quantitative methods such as bovine-related microbiome analysis due to the systematic bias induced by the enzymatic reactions in Oxford Nanopore library preparation.

Vacuolar Proteases of Candida auris from Clades III and IV and Their Relationship with Autophagy

Candida auris is a multidrug-resistant pathogen with a high mortality rate and widespread distribution. Additionally, it can persist on inert surfaces for extended periods, facilitating its transmissibility in hospital settings. Autophagy is a crucial cellular mechanism that enables fungal survival under adverse conditions. A fundamental part of this process is mediated by vacuolar proteases, which play an essential role in the degradation and recycling of cellular components. The present work explores the relationship between C. auris vacuolar peptidases and autophagy, aiming to establish a precedent for understanding the survival mechanisms of this emerging fungus. Thus, eight genes encoding putative vacuolar peptidases in the C. auris genomes were identified: PEP4, PRB1, PRC1, ATG42, CPS, LAP4, APE3, and DAP2. Analysis of the protein domains and their phylogenetic relationships suggests that these enzymes are orthologs of Saccharomyces cerevisiae vacuolar peptidases. Notably, both vacuolar protease gene expression and the proteolytic activity of cell-free extracts increased under nutritional stress and rapamycin. An increase in the expression of the ATG8 gene and the presence of autophagic bodies were also observed. These results suggest that proteases could play a role in yeast autophagy and survival during starvation conditions.

IL-1 Superfamily Across 400+ Species: Therapeutic Targets and Disease Implications

An important area of interest for therapeutic development is the IL-1 superfamily, a critical group of immune regulators with profound implications in a variety of disorders. This study clarifies the evolutionary patterns of IL-1 family members by thoroughly analyzing more than 400 animal species, demonstrating their ancient roots that extend back to the earliest vertebrates. Important results show that, although IL-1 ligands expanded significantly over the evolution of mammals, their corresponding receptors remained remarkably structurally conserved. Identifying both lineage-specific adaptations and evolutionarily conserved residues provides vital information for treatment design. These findings point to the possibility of two different therapeutic strategies: addressing species-specific variants may allow for more targeted interventions, whereas focusing on conserved motifs may result in broad-acting treatments. The study also identified less well-known species as useful models for comprehending early immune systems. In addition to advancing our knowledge of the function of the IL-1 family in autoimmune, inflammatory, and carcinogenic illnesses, this research lays the groundwork for the development of more potent targeted therapeutics by creating an evolutionary framework for the IL-1 family.

Utilization of Native CRISPR-Cas9 System for Expression of Glucagon-like Peptide-1 in Lacticaseibacillus paracasei

Type 2 diabetes is one of the main causes of cardiovascular diseases, kidney diseases, and visual impairments, posing a global healthcare challenge. The current treatment of this disease, involving glucagon-like peptide-1 (GLP-1), is faced with problems such as frequent injections and plasmid instability. In this study, we used the native clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9 (CRISPR-Cas9) system of Lacticaseibacillus paracasei to develop a novel, genetically stable, and orally administrable strain expressing human GLP-1. Integration and subsequent expression of glp-1 gene were confirmed by genomic sequencing, qPCR, and Nano LC-MS. The engineered strain demonstrated stable genomic integration and sustained high-level expression of GLP-1 over multiple generations. This innovative approach provides a promising strategy for the oral delivery of therapeutic peptides, potentially enhancing patient compliance and improving the treatment of diabetes and other chronic diseases requiring peptide-based therapies.

tRNA pseudouridine synthase D (TruD) from Thermus thermophilus modifies U13 in tRNAAsp, tRNAGlu, and tRNAGln and U35 in tRNATyr

Pseudouridine is a modified nucleoside found in various RNA species, including tRNA, rRNA, mRNA, and other noncoding RNAs. Pseudouridine is synthesized from uridine by pseudouridine synthases. While the landscape of pseudouridines in RNA has been extensively studied, much less is known about substrate RNA recognition mechanisms of pseudouridine synthases. Herein, we investigate the tRNA pseudouridine synthase D (TruD), which catalyzes the formation of pseudouridine at position 13 in tRNAAsp in Thermus thermophilus, a thermophilic eubacterium. To identify the tRNA substrates of TruD, we compared results of next-generation sequencing experiments combined with bisulfite probing of pseudouridine in tRNAs from both wild-type and a truD gene disruption mutant. Our data reveal that TruD recognizes tRNAAsp, tRNAGlu, and tRNAGln as substrate tRNAs. In addition, we discover that TruD modifies U35 in tRNATyr, which has previously been reported as a substrate of RluF in Escherichia coli These findings were validated through in vitro assays with recombinant TruD, which further demonstrated that TruD can act on other RNAs, including a CDC8 mRNA fragment, a known substrate of Pus7, the eukaryotic counterpart of TruD. Systematic mutational analysis of CDC8 transcripts reveals that TruD preferentially pseudouridylates the UNUAR sequence in tRNA substrates (N = any nucleotide, R = purine, U = target site). Finally, we identify over 600 mRNA fragments containing this recognition sequence in T. thermophilus ORFs and demonstrate the ability of TruD to act on these potential mRNA substrates. Our findings suggest the possibility that many other RNAs are modified by TruD in vivo.

Insufficiency of 40S ribosomal proteins, RPS26 and RPS25, negatively affects biosynthesis of polyglycine-containing proteins in fragile-X associated conditions

Expansion of CGG repeats (CGGexp) in the 5' untranslated region (5'UTR) of the FMR1 gene underlies the fragile X premutation-associated conditions including tremor/ataxia syndrome, a late-onset neurodegenerative disease and fragile X-associated primary ovarian insufficiency. One common pathomechanism of these conditions is the repeat-associated non-AUG-initiated (RAN) translation of CGG repeats of mutant FMR1 mRNA, resulting in production of FMRpolyG, a toxic protein containing long polyglycine tract. To identify novel modifiers of RAN translation we used an RNA-tagging system and mass spectrometry-based screening. It revealed proteins enriched on CGGexp-containing FMR1 RNA in cellulo, including a ribosomal protein RPS26, a component of the 40 S subunit. We demonstrated that depletion of RPS26 and its chaperone TSR2, modulates FMRpolyG production and its toxicity. We also found that the RPS26 insufficiency impacted translation of limited number of proteins, and 5'UTRs of mRNAs encoding these proteins were short and guanosine and cytosine-rich. Moreover, the silencing of another component of the 40 S subunit, the ribosomal protein RPS25, also induced repression of FMRpolyG biosynthesis. Results of this study suggest that the two 40 S ribosomal proteins and chaperone TSR2 play an important role in noncanonical CGGexp-related RAN translation.

Molecular Basis for Vacuolar Iron Transport by OsVIT2, a Target for Iron Biofortification in Rice

Iron deficiency is the prevalent and most widespread nutritional shortfall for humans, affecting over 30% of the global population and leading to anemia, particularly among preschool-aged children and pregnant women in developing countries. Simultaneously, while half of the world's population depends on rice (Oryza sativa L.) as a staple food, this cereal does not provide a sufficient amount of that micronutrient to meet these people's nutritional needs: even when iron is readily available in the soil, it does not accumulate in the consumed portion of the grain, namely, the starchy endosperm, being instead retained in the aleurone layer, in the pericarp and in the embryo. In this context, the present work applies computational biology tools-such as normal mode analysis and molecular dynamics simulations-to elucidate the behavior and transport mechanism of the Vacuolar Iron Transporter 2 (OsVIT2), a central protein for iron homeostasis in rice, with the objective of laying the foundations for future OsVIT2 engineering projects that could be articulated with ongoing efforts to promote iron biofortification in rice. We shed light on the interplay between protonation state, configuration and hydration of OsVIT2's pore; on the mechanics of its opening and on the ever-shifting hydrogen bond network contained within it. We also explore the potential contribution of the "flexible arms" to the iron-capturing function performed by the cytoplasmic domain.