Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

Assessing Structural Classification Using AlphaFold2 Models Through ECOD-Based Comparative Analysis

Identifying homologous proteins is a fundamental task in structural bioinformatics. While AlphaFold2 has revolutionized protein structure prediction, the extent to which structure comparison of its models can reliably detect homologs remains unclear. In this study, we evaluate the feasibility of homology detection using AlphaFold2-predicted structures through structural comparisons. We considered the classification of the ECOD database for experimental structures as the correct standard and obtained their corresponding predicted models from AlphaFoldDB. To ensure blind assessment, we divided the structures into test and train sets according to their release date. Predicted and experimental 3D structures in the test and train sets were compared using 3D structure comparisons (MATRAS, Dali, and Foldseek) and sequence comparisons (BLAST and HHsearch). The results were evaluated based on the homology annotations in the ECOD database. For top-1 accuracy, the performance of structural comparisons was comparable to that of HHsearch. However, when considering metrics that included all structural pairs, including more remote homology, structural comparisons outperformed HHsearch. No significant differences were observed between comparisons of experimental versus experimental, predicted versus experimental, and predicted versus predicted structures with pLDDT (prediction confidence) values greater than 60. We also demonstrate that predicted protein structures, determined by NMR, had lower pLDDT values and contained fewer coils than their experimental counterparts. These findings highlight the potential of AlphaFold2 models in structural classification and suggest that 3D structural searches should be conducted not only against the PDB but also against AlphaFoldDB to identify more potential homologs.

Phylogenetic and ecological drivers of the avian lung mycobiome and its potentially pathogenic component

Vertebrate lungs contain diverse microbial communities, but little is known about the drivers of community composition or consequences for health. Microbiome assembly by processes such as dispersal, coevolution, and host-switching can be probed with comparative surveys; however, few studies exist for lung microbiomes, particularly for the fungal component, the mycobiome. Distinguishing among fungal taxa that are generalist or specialist symbionts, potential pathogens, or incidentally inhaled spores is urgent because of potential for emerging diseases. Here, we characterize the avian lung mycobiome and test the relative influences of environment, phylogeny, and functional traits. We used metabarcoding and culturing from 195 lung samples representing 32 bird species across 20 families. We identified 526 fungal taxa as estimated by distinct sequence types (zOTUs) including many opportunistic pathogens. These were predominantly from the phylum Ascomycota (79%) followed by Basidiomycota (16%) and Mucoromycota (5%). Yeast and yeast-like taxa (Malassezia, Filobasidium, Saccharomyces, Meyerozyma, and Aureobasidium) and filamentous fungi (Cladosporium, Alternaria, Neurospora, Fusarium, and Aspergillus) were abundant. Lung mycobiomes were strongly shaped by environmental exposure, and further modulated by host identity, traits, and phylogenetic affinities. Our results implicate migratory bird species as potential vectors for long-distance dispersal of opportunistically pathogenic fungi.

Identification of EppR, a Second Repressor of Error-Prone DNA Polymerase Genes in Acinetobacter baumannii

Acinetobacter baumannii is an opportunistic pathogen causing several infections that are increasingly difficult to treat due to its ability to rapidly gain antibiotic resistances. These resistances can arise due to mutations through the activity of error-prone DNA polymerases, such as DNA polymerase V (DNA Pol V) in response to DNA damage. The regulation of the DNA damage response (DDR) in A. baumannii is not completely understood; the regulation of genes encoding multiple copies of DNA Pol V is not fully characterized. Through genome-wide mutagenesis, we have identified a novel TetR-like family regulator of the umuDC and umuC genes, which we have named Error-prone polymerase regulator (EppR). We have found that EppR represses the expression of the genes encoding DNA Pol V and itself through direct binding to an EppR motif in their promoters. Lastly, we show that EppR also regulates UmuDAb, previously identified as a regulator of genes encoding DNA Pol V. These two gene products are functionally required to ensure regulation of the expression of the two umuDC, the two umuC genes as well as the regulators umuDAb and eppR genes. With these results, we propose a model in which multiple transcription factors regulate the expression of all these genes.

Fungal Infections Resulting From Prolonged Use of Personal Protective Equipment

This study is the first to investigate fungal infections resulting from prolonged use of personal protective equipment (PPE) among healthcare workers at Kütahya Health Sciences University Evliya Çelebi Training and Research Hospital, during the COVID-19 pandemic. The research aimed to isolate, molecularly type, and assess the antifungal susceptibility of superficial fungal infection agents associated with PPE use. Additionally, the relationship between these fungi and PPE use was evaluated through a questionnaire. Samples were collected from 100 healthcare workers experiencing skin issues. Among them, all N95/FFP2 mask users, 44.3% of glove users, 36.1% of surgical mask users, and 22.9% of hair cap users reported skin reactions, with acne (n = 34) being the most common. Identified fungal isolates included Trametes hirsuta, Penicillium chrysogenum, Aspergillus fumigatus, Rhodotorula sp., Candida sp., Pichia fermentans, and the dermatophyte Microsporum ferrugineum. Antifungal susceptibility tests revealed 47.6% resistance to fluconazole and 76.2% resistance to voriconazole (n = 16). This study provides the first institutional data on PPE-associated fungal infections and antifungal resistance in healthcare settings. These findings highlight the dermatological risks of prolonged PPE use. To mitigate these effects, healthcare institutions should prioritize high-quality materials, establish optimal usage guidelines, and provide continuous training on self-protection.

Identification of a conserved cryptic epitope with cross-immunoreactivity in outer membrane protein K (OmpK) from Vibrio species

Outer membrane protein K (OmpK) has been proven to be an ideal vaccine candidate for broad-spectrum cross-prevention against Vibriosis. However, due to the extensive biological and genetic diversity of Vibrio species, current OmpK subunit vaccines can only target different strains of the same bacterial species or closely related species and have difficulty providing promising cross-immunoprotection against more diverse Vibrio infections. In recent years, the development of epitope-focused vaccines has been described as the latest stage in the development of vaccine formulations, providing new ideas for the development of broad-spectrum Vibrio vaccines. Interestingly, a cryptic epitope (K7) was identified in OmpK from Vibrio species, which is itself immunogenic but is not involved in the immune response to intact OmpK. Epitope K7 is a 15-residue hairpin structure in OmpK predicted to contain a 6-residue extracellular turn region. Interestingly, unlike other highly variable extracellular long loops, epitope K7 is the only conserved extracellular short turn in OmpK, with a similarity of 33 % to 93 %. K7 homologous peptides stimulated the production of specific antibodies, confirming their high immunogenicity. Cross-immunoreactivity between K7 homologous and K7-induced antibodies was evaluated by peptide-based ELISA, western blot, and cell-based ELISA. Flow cytometry and immunofluorescence assay further confirmed that the native epitope K7 in OmpK is surface-exposed and therefore an extracellular target that binds to antibodies. Moreover, an antibody-dependent and complement-mediated serum bactericidal assay suggested that epitope K7-induced antibodies have vibriocidal activity. In conclusion, we identified a conserved cryptic epitope with cross-immunoreactivity in OmpK from Vibrio species. Our results suggest that epitope K7 could be an ideal candidate for the design of epitope-focused vaccines against diverse Vibrio infections.

In vitro VS in vivo transcriptional approach provides new insight on temporal cold response which works without root system in tea plant (Camellia sinensis (L.) Kuntze)

Low temperature stress is the main constraint for the stable yield and production of many crops. The differences of the short- and long-term- cold responses remains unclear. In this study, in vitro VS in vivo transcriptome analysis was used to reveal the shared and specific responsive pathways under cold stress. The core responsive pathways were downregulation of photosynthesis, plant-pathogen interaction, DNA replication and repair, pyruvate metabolism; upregulation of phenylpropanoid biosynthesis; secondary metabolism and sugar metabolism and were enriched during the whole experiment. The significant differences between the short- and long-term cold responses were also observed. The circadian clock, MAPK- and hormonal signaling pathways were upregulated, while fatty acid biosynthesis was downregulated under the short-term cold. Under the long-term cold, response to high light, endocytosis and spliceosome were upregulated, while MAPK- and hormonal signaling were downregulated; amino acids biosynthesis was also enriched. The key differentially expressed genes (DEGs) and crosstalk between the secondary metabolism and the other core pathways were revealed in this study. Particularly, several DEGs (polygalacturonase inhibitor, chitinases, disease resistance proteins, uridine 5'-monophosphate synthase, F-box protein CPR1-like, fatty acid amide hydrolase et al.) which connect plant-pathogen interaction, signaling and secondary metabolism were revealed. The obtained results further clarify the key molecular responses to short- and long-term- cold and highlights the possible role of the roots in the cold-tolerance of evergreen tree crops.

Bacterial pathogen deploys the iminosugar glycosyrin to manipulate plant glycobiology

The extracellular space (apoplast) in plants is a key battleground during microbial infections. To avoid recognition, the bacterial model phytopathogen Pseudomonas syringae pv. tomato DC3000 produces glycosyrin. Glycosyrin inhibits the plant-secreted β-galactosidase BGAL1, which would otherwise initiate the release of immunogenic peptides from bacterial flagellin. Here, we report the structure, biosynthesis, and multifunctional roles of glycosyrin. High-resolution cryo-electron microscopy and chemical synthesis revealed that glycosyrin is an iminosugar with a five-membered pyrrolidine ring and a hydrated aldehyde that mimics monosaccharides. Glycosyrin biosynthesis was controlled by virulence regulators, and its production is common in bacteria and prevents flagellin recognition and alters the extracellular glycoproteome and metabolome of infected plants. These findings highlight a potentially wider role for glycobiology manipulation by plant pathogens across the plant kingdom.

Zygotic activation of transposable elements during zebrafish early embryogenesis

Although previous studies have shown that transposable elements (TEs) are conservatively activated to play key roles during early embryonic development, the details of zygotic TE activation (ZTA) remain poorly understood. Here, we employ long-read sequencing to precisely identify that only a small subset of TE loci are activated among numerous copies, allowing us to map their hierarchical transcriptional cascades at the single-locus and single-transcript level. Despite the heterogeneity of ZTA across family, subfamily, locus, and transcript levels, our findings reveal that ZTA follows a markedly different pattern from conventional zygotic gene activation (ZGA): ZTA occurs significantly later than ZGA and shows a pronounced bias for nuclear localization of TE transcripts. This study advances our understanding of TE activation by providing a high-resolution view of TE copies and creating a comprehensive catalog of thousands of previously unannotated transcripts and genes that are activated during early zebrafish embryogenesis. Among these genes, we highlight two that are essential for zebrafish development.

A geranylgeranyl reductase homolog required for cholesterol production in Myxococcota

Myxococcota is a phylum of sterol-producing bacteria. They exhibit a clade depth for sterol biosynthesis unparalleled in the bacterial domain and produce sterols of a biosynthetic complexity that rivals eukaryotes. Additionally, the sterol biosynthesis pathways found in this phylum have been proposed as a potential source for sterol biosynthesis in the last eukaryotic common ancestor, lending evolutionary importance to our understanding of this pathway in Myxococcota. However, sterol production has only been characterized in a few species, and outstanding questions about the evolutionary history of this pathway remain. Here, we identify two myxobacteria, Minicystis rosea and Sandaracinus amylolyticus, capable of cholesterol biosynthesis. These two myxobacteria possess a cholesterol biosynthesis pathway that differs in both the ordering and enzymes involved in biosynthesis compared with Enhygromyxa salina, a myxobacterium previously demonstrated to produce cholesterol, as well as the canonical pathways found in eukaryotes. We characterize an alternative bacterial reductase responsible for performing C-24 reduction, further delineating bacterial cholesterol production from eukaryotes. Finally, we examine the distribution and phylogenetic relationships of sterol biosynthesis proteins across both cultured and uncultured Myxococcota species, providing evidence for multiple acquisition events and instances of both horizontal and vertical transfer at the family level. Altogether, this work further demonstrates the capacity of myxobacteria to synthesize eukaryotic sterols but with an underlying diversity in the biochemical reactions that govern sterol synthesis, suggesting a complex evolutionary history and refining our understanding of how myxobacterial cholesterol production relates to their eukaryotic counterparts.

IMPORTANCE

Sterols are essential and ubiquitous lipids in eukaryotes, but their significance in bacteria is less understood. Sterol production in Myxococcota, a phylum of developmentally complex predatory bacteria, has provided insight into novel sterol biochemistry and prompted discussion regarding the evolution of this pathway within both the eukaryotic and bacterial domains. Here, we characterize cholesterol biosynthesis in two myxobacteria, providing evidence for distinct pathway organization and identifying a unique protein responsible for C-24 reduction. We couple these results with the phylogenomic analysis of sterol biosynthesis within Myxococcota, revealing a complicated evolutionary history marked by vertical and horizontal transfer. This suggests a mosaic acquisition of this pathway in Myxococcota and highlights the complex role myxobacteria may have had in sterol transfer to eukaryotes.

Biochemical and structural characterization of a family-9 glycoside hydrolase bioprospected from the termite Syntermes wheeleri gut bacteria metagenome

Glycosyl hydrolases (GH) are enzymes involved in the degradation of plant biomass. They are important for biorefineries that aim at the sustainable utilization of lignocellulosic residues to generate value-added products. The termite Syntermes wheeleri gut microbiota showed an abundance of bacteria from the phylum Firmicutes, a phylum with enzymes capable of breaking down cellulose and degrading lignin, facilitating the use of plant materials as a food source for termites. Using bioinformatics techniques, cellobiohydrolases were searched for in the gut metagenome of the termite Syntermes wheeleri, endemic to the Cerrado. After selecting sequences of the target enzymes, termite gut microbiome metatranscriptome data were used as the criteria to choose the GH9 enzyme sequence Exo8574. Here we present the biochemical and structural characterization of Exo8574, a GH9 enzyme that showed activity with the substrate p-nitrophenyl-D-cellobioside (pNPC), consistent with cellobiohydrolase activity. Bioinformatics tools were used to perform phylogeny studies of Exo8574 and to identify conserved families and domains. Exo8574 showed 48.8 % homology to a protein from a bacterium belonging to the phylum Firmicutes. The high-quality three-dimensional (3D) model of Exo8574 was obtained by protein structure prediction AlphaFold 2, a neural network-based method. After the heterologous expression of Exo8574 and its purification, biochemical experiments showed that the optimal activity of the enzyme was at a temperature of 55 ºC and pH 6.0, which was enhanced in the presence of metal ions, especially Fe2 +. The estimated kinetic parameters of Exo8574 using the synthetic substrate p-nithrophenyl-beta-D-cellobioside (pNPC) were: Vmax = 9.14 ± 0.2 x10-5 μmol/min and Km = 248.27 ± 26.35 μmol/L. The thermostability test showed a 50 % loss of activity after 1 h incubation at 55 °C. The secondary structure contents of Exo8574 evaluated by Circular Dichroism were pH dependent, with greater structuring of protein in β-antiparallel and α-helices at pH 6.0. The similarity between the CD results and the Ramachandran plot of the 3D model suggests that a reliable model has been obtained. Altogether, the results of the biochemical and structural characterization showed that Exo8574 is capable of acting on p-nithrophenyl-beta-D-cellobioside (pNPC), a substrate that mimics bonds cleaved by cellobiohydrolases. These findings have significant implications for advancing in the field of biomass conversion while also contributing to efforts aimed at overcoming challenges in developing more efficient cellulase cocktails.

Bioinformatics Analysis Identifies Sequence Determinants of Enzymatic Activity for the PHARC-Associated Lipase ABHD12

In humans, PHARC (polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, and cataract) is an early onset autosomal recessive neurological disorder caused by deleterious mutations to ABHD12 (α/β-hydrolase domain protein # 12). Biochemically, ABHD12 functions as a lipase and catalyzes the hydrolysis of lysophosphatidylserine (lyso-PS) (lyso-PS lipase). By doing so, it controls the concentrations and signaling pathways regulated by this potent signaling lysophospholipid in the mammalian brain. While genetic mapping efforts have identified over 30 mutations in ABHD12 from human PHARC subjects, the biochemical activity of these pathogenic mutants remains unknown. To understand this, here, we performed an exhaustive bioinformatics survey and collated ABHD12 protein sequences from various organisms across evolution. Next, based on sequence alignments and structural modeling, we identified functionally relevant conserved residues in the ABHD12 protein sequence that are potentially important for its enzymatic activity. To validate these in silico findings, we generated numerous mutants of murine ABHD12, including those associated with human PHARC subjects, and assayed them for their enzymatic activity. Taken together, these complementary in silico and biochemical studies provide the first thorough sequence-function relationship for mammalian ABHD12, especially relevant in the context of PHARC. Finally, our evolutionary analysis identified CG15111 as an ABHD12 ortholog in the fruit fly (Drosophila melanogaster), and enzymatic assays indeed confirmed that recombinant CG15111 has robust lyso-PS lipase activity. Flies serve as an excellent animal system to model various human neurological diseases, and the identification of CG15111 as a Drosophila melanogaster ABHD12 ortholog opens new avenues to study PHARC in fly models.

Statistical factorial design for optimum reduction of tellurite and production of tellurium nanostructure by a novel strain Phytobacter diazotrophicus Te1

A tellurite-reducing isolate (Te1) was recovered from a soil sample receiving industrial effluents from Ismailia Canal, Egypt. The isolate exhibited dark black colonies when grown on solid medium containing potassium tellurite, which indicated the reduction of tellurite to black tellurium. The isolate was identified using 16S rRNA gene sequencing and was submitted to GenBank as Phytobacter diazotrophicus strain Te1 (PP724698). The tellurite reduction percentage was 96.5% ± 0.354%. Moreover, energy-dispersive X-ray (EDX) analysis confirmed the presence of tellurium nanostructure, with a 3.7 keV absorption peak along with phosphorus, sulfur, and oxygen, revealing a complex biogenic nature. Fourier-transform infrared (FTIR) spectroscopy identified distinct absorption peaks within the 400-4000 cm-1 range, corresponding to various vibrational modes of chemical bonds, including those of lipids, proteins, polysaccharides, and free radicals. X-ray diffraction (XRD) analysis highlighted the nanoscale crystalline structure of the material, with broad peaks confirming limited crystallite size and structural disorder, and revealed tellurium peaks on a hexagonal phase at 2-theta values of 27.36°, 38.19° and 40.20°. According to the results of the response optimizer and the subsequent validation experiments, complete reduction of tellurium was achieved at a medium pH of 6.8, incubation temperature of 33.5 °C, tellurite concentration of 1375 μM, and agitation speed of 110 rpm for 96 h. Black Te nanostructure was visible intracellularly and extracellularly upon examination using the transmission electron microscope. To the best of the authors' knowledge, this is the first report of tellurite reduction by Phytobacter diazotrophicus.

Development of the breastfed infant oral microbiome over the first two years of life in the BLOSOM Cohort

Background

Acquisition and development of the oral microbiome are dynamic processes that occur over early life. This study aimed to characterize the temporal development of the oral microbiome of predominantly breastfed infants during the first two years of life.

Methods

Infant oral samples (n=667) were collected at ten time points from the first week to year two of life from 84 infants. Bacterial DNA profiles were analyzed using full-length 16S rRNA gene sequencing.

Results

The oral microbiome was dominated by Streptococcus mitis, Gemella haemolysans, and Rothia mucilaginosa. Bacterial richness decreased from 1 to 2 months (P = 0.043) and increased from 12 to 24 months (P = 0.038). Shannon diversity increased from 1 week to 1 month and again from 6 to 9 months and 9 to 12 months (all P ≤ 0.04). The composition of the infant oral microbiome was associated with multiple factors, including early pacifier use, intrapartum antibiotic prophylaxis, maternal allergy, pre-pregnancy body mass index, siblings, delivery mode, maternal age, pets at home, and birth season (all P < 0.01). Introduction of solid foods was a significant milestone in oral microbiome development, triggering an increase in bacterial diversity (richness P = 0.0004; Shannon diversity P = 0.0007), a shift in the abundance of seven species, and a change in beta diversity (P = 0.001).

Conclusion

These findings underscore the importance of multiple factors, particularly the introduction of solid foods, in shaping the oral microbiome of breastfed infants during early life.

Insights into Octopus maya cathepsins from metatranscriptome and genome: structure evolutionary relationships and functional role prediction in digestive processes

Physiological response to feeding is crucial for various production factors such as feed catabolism and growth. Despite growing significance in red Octopus maya aquaculture, large-scale commercial production is limited by not sufficiently knowing their nutritional needs, especially their digestive physiology. Since this species is carnivorous, one of the main feeding aspects is directed to protein digestion, but its enzymatic digestive repertoire has not been studied yet at genomic and transcriptomic levels. This study searched for protease enzymes encoded in O. maya genome and expressed in the transcriptome, allowing an initial annotation of genes involved in protein catabolism; 117 amino acid sequences related to 'octopus digestive enzymes' were retrieved from 66 available-species' genomes in the NCBI database, coding for cathepsins, papilins, and metalloproteases. Homology analysis identified 36 homologous sequences from O. maya transcriptome and three from its genome. Phylogenetic analysis grouped 37 of 39 sequences into 11 of 14 main clades, offering new insights into the evolutionary relationships and functional roles of these proteases. Phylogenetic and motif analyses resulted in selecting 19 amino acid O. maya sequences using multiple sequence alignment that were used to generate three-dimensional protein models. The obtained models revealed a diverse structural architecture among 16 modelled cathepsins; however, their catalytic potential to fully clarify their role in protein hydrolysis and cellular processes remains to be determined. Foundational data provides insights into biochemistry and physiology behind O. maya protein digestion. Further complementation of these results with enzymatic characterization of the identified proteases should allow for improved diet formulation in order to foster this species aquaculture.

DeepMFFGO: A Protein Function Prediction Method for Large-Scale Multifeature Fusion

Protein functional studies are crucial in the fields of drug target discovery and drug design. However, the existing methods have significant bottlenecks in utilizing multisource data fusion and Gene Ontology (GO) hierarchy. To this end, this study innovatively proposes the DeepMFFGO model designed for protein function prediction under large-scale multifeature fusion. A fine-tuning strategy using intermediate-level feature selection is proposed to reduce redundancy in protein sequences and mitigate distortion of the top-level features. A hierarchical progressive fusion structure is designed to explore feature connections, optimize complementarity through dynamic weight allocation, and reduce redundant interference. On the CAFA3 data set, the Fmax values of the DeepMFFGO model on the MF, BP, and CC ontologies reach 0.702, 0.599, and 0.704, respectively, which are improved by 4.2%, 2.4%, and 0.07%, respectively, compared with state-of-the-art multisource methods.

Vesicular and non-vesicular extracellular small RNAs direct gene silencing in a plant-interacting bacterium

Extracellular plant small RNAs (sRNAs) and/or double-stranded RNA (dsRNA) precursors act as triggers of RNAi in interacting filamentous pathogens. However, whether any of these extracellular RNA species direct gene silencing in plant-interacting bacteria remains unknown. Here, we show that Arabidopsis transgenic plants expressing sRNAs directed against virulence factors of a Pseudomonas syringae strain, reduce its pathogenesis. This Antibacterial Gene Silencing (AGS) phenomenon is directed by Dicer-Like (DCL)-dependent antibacterial sRNAs, but not cognate dsRNA precursors. Three populations of active extracellular sRNAs were recovered in the apoplast of these transgenic plants. The first one is mainly non-vesicular and associated with proteins, whereas the second one is located inside Extracellular Vesicles (EVs). Intriguingly, the third population is unbound to proteins and in a dsRNA form, unraveling functional extracellular free sRNAs (efsRNAs). Both Arabidopsis transgene- and genome-derived efsRNAs were retrieved inside bacterial cells. Finally, we show that salicylic acid (SA) promotes AGS, and that a substantial set of endogenous efsRNAs exhibits predicted bacterial targets that are down-regulated by SA biogenesis and/or signaling during infection. This study thus unveils an unexpected AGS phenomenon, which may have wider implications in the understanding of how plants regulate microbial transcriptome, microbial community composition and genome evolution of associated bacteria.

Genome-wide identification and gene expression pattern analysis of the carotenoid cleavage oxygenase gene family in Fagopyrum tataricum

BACKGROUND

Carotenoid cleavage oxygenases (CCOs) convert carotenoids into volatile aromatic compounds implicated in plant growth and development. They affect the synthesis of hormones, including abscisic acid (ABA) and strigolactone (SL). However, the CCO family in Tartary buckwheat remains unelucidated.

RESULTS

We identified the FtCCO gene family based on Tartary buckwheat genomic data and analyzed the biological function of the FtCCO genes using bioinformatics methods and the expression pattern of the gene using fluorescence quantitative PCR. Three pairs of fragment duplication genes were found in FtCCOs, and the motifs were highly conserved within the same subfamily. FtCCO genes are closely related to the dicotyledonous Arabidopsis thaliana, which has the highest number of co-linear genes. The qRT-PCR showed that among the tissue-specific expression patterns of Tartary buckwheat CCO genes, the expression of the FtCCOs was higher in the leaves. In Tartary buckwheat grain development, the relative expression of most FtCCOs was higher at the later stage. The relative expression of many genes was higher in the stems under cold, dark, NaCl, and abiotic stress conditions. However, under the hormone and plant growth regulator treatments, the expression of the nine FtCCOs was relatively low in the stems. Notably, the relative expression of FtNCED4 was extremely high under abiotic stress and hormone induction, indicating that FtNCED4 may be involved in the growth and development of Tartary buckwheat. In this study, the FtCCO family genes of Tartary buckwheat were identified at the genome-wide level, and the gene expression pattern of the FtCCO gene family in different tissues or treatments was determined. This study provides a theoretical basis for further analysis of the functions of theFtCCO family, which is of great significance for the mining of resistance genes and trait improvement.

Deep learning tools predict variants in disordered regions with lower sensitivity

BACKGROUND

The recent AI breakthrough of AlphaFold2 has revolutionized 3D protein structural modeling, proving crucial for protein design and variant effects prediction. However, intrinsically disordered regions-known for their lack of well-defined structure and lower sequence conservation-often yield low-confidence models. The latest Variant Effect Predictor (VEP), AlphaMissense, leverages AlphaFold2 models, achieving over 90% sensitivity and specificity in predicting variant effects. However, the effectiveness of tools for variants in disordered regions, which account for 30% of the human proteome, remains unclear.

RESULTS

In this study, we found that predicting pathogenicity for variants in disordered regions is less accurate than in ordered regions, particularly for mutations at the first N-Methionine site. Investigations into the efficacy of variant effect predictors on intrinsically disordered regions (IDRs) indicated that mutations in IDRs are predicted with lower sensitivity and the gap between sensitivity and specificity is largest in disordered regions, especially for AlphaMissense and VARITY.

CONCLUSIONS

The prevalence of IDRs within the human proteome, coupled with the increasing repertoire of biological functions they are known to perform, necessitated an investigation into the efficacy of state-of-the-art VEPs on such regions. This analysis revealed their consistently reduced sensitivity and differing prediction performance profile to ordered regions, indicating that new IDR-specific features and paradigms are needed to accurately classify disease mutations within those regions.

Developing a crop- wild-reservoir pathogen system to understand pathogen evolution and emergence

Crop pathogens reduce yield and contribute to global malnourishment. Surveillance not only detects presence/absence but also reveals genetic diversity, which can inform our understanding of rapid adaptation and control measures. An often neglected aspect is that pathogens may also use crop wild relatives as alternative hosts. This study develops the beet (Beta vulgaris) rust (Uromyces beticola) system to explore how crop pathogens evolve to evade resistance using a wild reservoir. We test predictions that crop selection will drive virulence gene differentiation and affect rates of sex between crop- and wild-host rust populations. We sequenced, assembled, and annotated the 588 Mb beet rust genome, developed a novel leaf peel pathogen DNA extraction protocol, and analysed genetic diversity in 42 wild and crop isolates. We found evidence for two populations: one containing exclusively wild-host isolates; the other containing all crop-host isolates, plus five wild isolates. Effectors showed greater diversity in the exclusively wild population and greater differentiation between populations. Preliminary evidence suggests the rates of sexual reproduction may differ between populations. This study highlights how differences in pathogen populations might be used to identify genes important for survival on crops and how reproduction might impact adaptation. These findings are relevant to all crop-reservoir systems and will remain unnoticed without comparison to wild reservoirs.

Control of morphogenesis during the Staphylococcus aureus cell cycle

Bacterial cell division is a complex, multistage process requiring septum development while maintaining cell wall integrity. A dynamic, macromolecular protein complex, the divisome, tightly controls morphogenesis both spatially and temporally, but the mechanisms that tune septal progression are largely unknown. By studying conditional mutants of genes encoding DivIB, DivIC, and FtsL, an essential trimeric complex central to cell division in bacteria, we demonstrate that FtsL and DivIB play independent, hierarchical roles coordinating peptidoglycan synthesis across specific septal developmental checkpoints. They are required for the localization of downstream divisome components and the redistribution of peptidoglycan synthesis from the cell periphery to the septum. This is achieved by positive regulation of septum production and negative regulation of peripheral cell wall synthesis. Our analysis has led to a model for the coordination of cell division in Staphylococcus aureus, forming a framework for understanding how protein localization and function are integrated with cell wall structural dynamics across the bacteria.

Characterization of the Orphan Cytochrome P450 CYP135B1 from Mycobacterium tuberculosis: Involvement in Metabolism but Not in the Antibacterial Activity of the Antitubercular Drug SQ109

The rise of multidrug-resistant tuberculosis (TB) has increased the need for new antitubercular (anti-TB) drugs and the identification of novel drug targets. One promising target is Mycobacterium tuberculosis (Mtb) cytochrome P450 enzymes (P450s). This study focuses on the characterization of CYP135B1, a prevalent Mtb P450. Using a combination of microbiology, genomics, bioinformatics, docking, spectroscopy, and mass spectrometry, researchers successfully expressed, purified, and characterized CYP135B1. A 3D model was built with AlphaFold 3. The enzyme displayed typical features of P450 proteins and showed strong binding to imidazole derivatives. Notably, CYP135B1 metabolized the anti-TB drug SQ109 by inserting oxygen into its geranyl moiety in a manner distinct from CYP124A1. However, genetic studies using a ΔCYP135B1 mutant strain revealed that CYP135B1 is not required for SQ109's antibacterial activity, as its deletion did not affect drug efficacy despite CYP135B1 metabolizes SQ109.

Biogenesis of Cytochromes c and c1 in the Electron Transport Chain of Malaria Parasites

Plasmodium malaria parasites retain an essential mitochondrional electron transport chain (ETC) that is critical for growth within humans and mosquitoes and is a key antimalarial drug target. ETC function requires cytochromes c and c1, which are unusual among heme proteins due to their covalent binding to heme via conserved CXXCH sequence motifs. Heme attachment to these proteins in most eukaryotes requires the mitochondrial enzyme holocytochrome c synthase (HCCS) that binds heme and the apo cytochrome to facilitate the biogenesis of the mature cytochrome c or c1. Although humans encode a single bifunctional HCCS that attaches heme to both proteins, Plasmodium parasites are like yeast and encode two separate HCCS homologues thought to be specific for heme attachment to cyt c (HCCS) or cyt c1 (HCC1S). To test the function and specificity of Plasmodium falciparum HCCS and HCC1S, we used CRISPR/Cas9 to tag both genes for conditional expression. HCC1S knockdown selectively impaired cyt c1 biogenesis and caused lethal ETC dysfunction that was not reversed by the overexpression of HCCS. Knockdown of HCCS caused a more modest growth defect but strongly sensitized parasites to mitochondrial depolarization by proguanil, revealing key defects in ETC function. These results and prior heterologous studies in Escherichia coli of cyt c hemylation by P. falciparum HCCS and HCC1S strongly suggest that both homologues are essential for mitochondrial ETC function and have distinct specificities for the biogenesis of cyt c and c1, respectively, in parasites. This study lays a foundation to develop novel strategies to selectively block ETC function in malaria parasites.

Telomere-to-telomere gapless genome assembly of Triplophysa yaopeizhii

The genus Triplophysa exhibits remarkable adaptability to the unique environment found at the Qinghai-Tibet Plateau (QTP). Higher quality genomes are helpful to the study of the adaptability to the extreme environment in the plateau. This study utilized PacBio HiFi, Ultra-long ONT, and Hi-C sequencing of Triplophysa yaopeizhii to construct the first telomere-to-telomere (T2T) gapless genome assembly of the genus Triplophysa. The genome size is 671.58 Mb, with a contig N50 length of 26.04 Mb. The sequences were anchored onto 25 chromosomes with all centromeres and telomeres. Furthermore, 293.98 Mb (43.77%) of repetitive sequences and 26,487 protein-coding genes were identified. Comparative analyses with the genomes of closely related species demonstrated high completeness, continuity, and accuracy of the genome. The genomic quality was further substantiated by the QV of 31.82 with 96.60% of BUSCO. This study provides a valuable genetic resource of the genus Triplophysa and serves as an essential reference for elucidating the adaptive genetic mechanisms of plateau fish to the high altitude.

Application of a replicative targetable vector system for difficult-to-manipulate streptomycetes

The low frequency of homologous recombination together with poor efficiency in introducing DNA into the cell are the main factors hampering genetic manipulation of some bacterial strains. We faced this problem when trying to construct mutants of Streptomyces iranensis DSM 41954, a strain in which conjugation is particularly inefficient, and suicidal vectors had failed to yield any exconjugants. In this work, we report the construction and application of a conjugative replicative vector, pDS0007, which allows selection of exconjugants even with poor conjugation efficiency. The persistence of the construct inside the cell for as long as required facilitates the homologous recombination events leading to single and double crossovers. While it was confirmed that the vector is frequently lost without selection, the recognition sequence for the I-SceI endonuclease was included in the backbone of pDS0007. The presence of a I-SceI recognition sequence would allow to force the loss of the vector and the appearance of double crossover recombinants by introducing a second construct (e.g. pIJ12742) that expresses a Streptomyces codon-optimised gene encoding the I-SceI endonuclease. To facilitate screening for vector-free clones, the construct also carries a Streptomyces codon-optimised gusA gene encoding the β-glucuronidase expressed from a constitutive promoter. We prove the usefulness of this vector and strategy with the strain S. iranensis DSM 41954, in which we could readily delete an essential gene of a newly discovered biosynthetic pathway for a phosphonate-containing natural product, which led to loss of phosphonate production according to 31P NMR spectroscopy. KEY POINTS: • pDS0007 is a new vector for gene-targeting in difficult-to-manipulate streptomycetes. • pDS0007 is self-replicative but easy to cure, targetable and allows visual screening. • pDS0007 was used to prove the discovery of a novel phosphonate biosynthetic pathway.

PLM-ATG: Identification of Autophagy Proteins by Integrating Protein Language Model Embeddings with PSSM-Based Features

Autophagy critically regulates cellular development while maintaining pathophysiological homeostasis. Since the autophagic process is tightly regulated by the coordination of autophagy-related proteins (ATGs), precise identification of these proteins is essential. Although current computational approaches have addressed experimental recognition's costly and time-consuming challenges, they still have room for improvement since handcrafted features inadequately capture the intricate patterns and relationships hidden in sequences. In this study, we propose PLM-ATG, a novel computational model that integrates support vector machines with the fusion of protein language model (PLM) embeddings and position-specific scoring matrix (PSSM)-based features for the ATG identification. First, we extracted sequence-based features and PSSM-based features as the inputs of six classifiers to establish baseline models. Among these, the combination of the SVM classifier and the AADP-PSSM feature set achieved the best prediction accuracy. Second, two popular PLM embeddings, i.e., ESM-2 and ProtT5, were fused with the AADP-PSSM features to further improve the prediction of ATGs. Third, we selected the optimal feature subset from the combination of the ESM-2 embeddings and AADP-PSSM features to train the final SVM model. The proposed PLM-ATG achieved an accuracy of 99.5% and an MCC of 0.990, which are nearly 5% and 0.1 higher than those of the state-of-the-art model EnsembleDL-ATG, respectively.

Penton blooming, a conserved mechanism of genome delivery used by disparate microviruses

Microviruses are single-stranded DNA viruses infecting bacteria, characterized by T = 1 shells made of single jelly-roll capsid proteins. To understand how microviruses infect their host cells, we have isolated and studied an unusually large microvirus, Ebor. Ebor belongs to the proposed "Tainavirinae" subfamily of Microviridae and infects the model Alphaproteobacterium Rhodobacter capsulatus. Using cryogenic electron microscopy, we show that the enlarged capsid of Ebor is the result of an extended C-terminus of the major capsid protein. The extra packaging space accommodates genes encoding a lytic enzyme and putative methylase, both absent in microviruses with shorter genomes. The capsid is decorated with protrusions at its 3-fold axes, which we show to recognize lipopolysaccharides on the host surface. Cryogenic electron tomography shows that during infection, Ebor attaches to the host cell via five such protrusions. This attachment brings a single pentameric capsomer into close contact with the cell membrane, creating a special vertex through which the genome is ejected. Both subtomogram averaging and single particle analysis identified two intermediates of capsid opening, showing that the interacting penton opens from its center via the separation of individual capsomer subunits. Structural comparison with the model Bullavirinae phage phiX174 suggests that this genome delivery mechanism may be widely present across Microviridae.

IMPORTANCE

Tailless Microviridae bacteriophages are major components of the global virosphere. Notably, microviruses are prominent members of the mammalian gut virome, and certain compositions have been linked to serious health disorders; however, a molecular understanding of how they initiate infection of their host remains poorly characterized. We demonstrate that trimeric protrusions located at the corners of a single microvirus capsomer mediate host cell attachment. This interaction triggers opening of the capsomer, driven by separation of subunits from its center, much like flower petals open during blooming. This extensive opening explains how the genome translocation apparatus, along with the genome itself, is able to exit the capsid. "Penton blooming" likely represents a conserved mechanism shared by diverse viruses possessing similar capsid architectures.

Physiological and molecular insights into alternate bearing in mango using next-generation sequencing approaches

The productivity of the mango crop in India is hindered by many factors, one of the most important factors is our limited understanding of the genomic complexities behind the regular versus alternate bearing habit of fruit. In this study, we quantified carbohydrate fractions, protein content, and macro- and micronutrient storage pools together with their transportation and contributions to a regular bearing variety, Totapuri, and to an alternate-bearer, Bombay Green during the 'off' year. RNA-sequencing was used to assess gene expression dynamics between buds and flowers of these varieties. Differential pathway analysis showed the greatest number of differentially expressed genes in metabolic processes, followed by oxidoreductase, hormone, oxidative stress, starvation, alternate bearing, flowering, meristem, and cellular component pathways. Bioinformatics analysis showed that, among 15 highly differentially expressed genes between varieties representing alternate bearing, hormone, and carbohydrate metabolism pathways, 12 were up-regulated in Totapuri and 3 in Bombay Green, and this was confirmed by qRT-PCR. In addition, 202 single-nucleotide polymorphisms were identified in 32 genes related to alternate bearing. Our results confirmed the strong ability of reproductive buds to import sugars, proteins, and starch in the regular-bearer variety, thereby enhancing flowering and fruiting during 'off' years. Thus, our study shows a potential role for the mineral nutrient and biochemical constituents of buds and leaves in determining the regular versus alternate bearing fruiting habit in mango.

Rational Design Principles for De Novo α-Helical Peptide Barrels with Dynamic Conductive Channels

Despite advances in peptide and protein design, the rational design of membrane-spanning peptides that form conducting channels remains challenging due to our imperfect understanding of the sequence-to-structure relationships that drive membrane insertion, assembly, and conductance. Here, we describe the design and computational and experimental characterization of a series of coiled coil-based peptides that form transmembrane α-helical barrels with conductive channels. Through a combination of rational and computational design, we obtain barrels with 5 to 7 helices, as characterized in detergent micelles. In lipid bilayers, these peptide assemblies exhibit two conductance states with relative populations dependent on the applied potential: (i) low-conductance states that correlate with variations in the designed amino-acid sequences and modeled coiled-coil barrel geometries, indicating stable transmembrane α-helical barrels; and (ii) high-conductance states in which single channels change size in discrete steps. Notably, the high-conductance states are similar for all peptides in contrast to the low-conductance states. This indicates the formation of large, dynamic channels, as observed in natural barrel-stave peptide channels. These findings establish rational routes to design and tune functional membrane-spanning peptide channels with specific conductance and geometry.

Pangenome Analysis of Clostridium scindens: A Collection of Diverse Bile Acid- and Steroid-Metabolizing Commensal Gut Bacterial Strains

Clostridium scindens is a commensal gut bacterium capable of forming the secondary bile acids as well as converting glucocorticoids to androgens. Historically, only two strains, C. scindens ATCC 35704 and C. scindens VPI 12708, have been characterized to any significant extent. The formation of secondary bile acids is important in the etiology of cancers of the GI tract and in the prevention of Clostridioides difficile infection. We determined the presence and absence of bile acid inducible (bai) and steroid-17,20-desmolase (des) genes among C. scindens strains and the features of the pangenome of 34 cultured strains of C. scindens and a set of 200 metagenome-assembled genomes (MAGs) to understand the variability among strains. The results indicate that the C. scindens cultivars have an open pangenome with 12,720 orthologous gene groups and a core genome with 1630 gene families, in addition to 7051 and 4039 gene families in the accessory and unique (i.e., strain-exclusive) genomes, respectively. The pangenome profile including the MAGs also proved to be open. Our analyses reveal that C. scindens strains are distributed into two clades, indicating the possible onset of C. scindens separation into two species, as suggested by gene content, phylogenomic, and average nucleotide identity (ANI) analyses. This study provides insight into the structure and function of the C. scindens pangenome, offering a genetic foundation of significance for many aspects of research on the intestinal microbiota and bile acid metabolism.

Identification of glyoxalase A in group B Streptococcus and its contribution to methylglyoxal tolerance and virulence

Group B Streptococcus (GBS) is a Gram-positive pathobiont that commonly colonizes the gastrointestinal and lower female genital tracts but can cause sepsis and pneumonia in newborns and is a leading cause of neonatal meningitis. Despite the resulting disease severity, the pathogenesis of GBS is not completely understood, especially during the early phases of infection. To investigate GBS factors necessary for bloodstream survival, we performed a transposon (Tn) mutant screen in our bacteremia infection model using a GBS mariner transposon mutant library previously developed by our group. We identified significantly underrepresented mutations in 623 genes that contribute to survival in the blood, including those encoding known virulence factors such as capsule, the β-hemolysin, and inorganic metal ion transport systems. Most of the underrepresented genes have not been previously characterized or studied in GBS, including gloA and gloB, which are homologs for genes involved in methylglyoxal (MG) detoxification. MG is a byproduct of glycolysis and a highly reactive toxic aldehyde that is elevated in immune cells during infection. Here, we observed MG sensitivity across multiple GBS isolates and confirmed that gloA contributes to MG tolerance and invasive GBS infection. We show specifically that gloA contributes to GBS survival in the presence of neutrophils and depleting neutrophils in mice abrogates the decreased survival and infection of the gloA mutant. The requirement of the glyoxalase pathway during GBS infection suggests that MG detoxification is important for bacterial survival during host-pathogen interactions.IMPORTANCEA transposon-mutant screen of group B Streptococcus (GBS) in a bacteremia mouse model of infection revealed virulence factors known to be important for GBS survival such as the capsule, β-hemolysin/cytolysin, and genes involved in metal homeostasis. Many uncharacterized factors were also identified including genes that are part of the metabolic pathway that breaks down methylglyoxal (MG). The glyoxalase pathway is the most ubiquitous metabolic pathway for MG breakdown and is only a two-step process using glyoxalase A (gloA) and B (gloB) enzymes. MG is a highly reactive byproduct of glycolysis and is made by most cells. Here, we show that in GBS, the first enzyme in the glyoxalase pathway, encoded by gloA, contributes to MG resistance and blood survival. We further demonstrate that GloA contributes to GBS survival against neutrophils in vitro and in vivo and, therefore, is an important virulence factor required for invasive infection.

Harnessing killer yeast system: from molecular insight to real world biocontrol solution

The biocontrol mechanisms of yeasts are gaining global attention as a vital response to the rising threat of antimicrobial resistance in emerging pathogens. With their diverse genetic traits, yeasts present potent antagonistic capabilities that have extensive applications across various sectors. This review examines the fundamental mechanisms and molecular bases of yeast antagonism, emphasizing innovative screening techniques for identifying effective strains. Key molecular methods, including gene identification, sequence analysis, and expression studies, reveal insights into their modes of action, such as nutrient competition, mycocin production, and volatile organic compound release. While the potential of antagonistic yeasts spans crop protection, food safety, and disease prevention, their commercial availability remains limited. To foster adoption, there is an urgent need for advanced screening methods and deeper molecular understanding. Future research should prioritize the optimization and commercialization of yeast-based biocontrol products, effectively bridging the gap between scientific discovery and practical application in combating harmful pathogens.

Phylogenetic Analysis and Expression Patterns of Triterpenoid Saponin Biosynthesis Genes in 19 Araliaceae Plants

The Araliaceae family has significant economic and medicinal value. However, the phylogenetic relationships and the expression patterns of key genes of the active triterpenoid substance within this family are still unclear. In this study, we employed comparative transcriptomics to analyze the transcriptomes of 19 species from 11 genera of Araliaceae, aiming to elucidate the evolutionary history of the family and the expression patterns of key genes in the ginsenoside biosynthesis pathway. Our results divide Araliaceae into two subfamilies: Aralioideae and Hydrocotyloideae. Aralioideae is further classified into three groups: the Aralia-Panax group, the Polyscias-Pseudopanax group, and the Asian Palmate group. PhyloNet analysis reveals that the common ancestor of Panax ginseng, Panax quinquefolius, and Panax japonicus was an allopolyploid, likely resulting from hybridization between Panax notoginseng and Panax pseudoginseng. Additionally, all Aralioideae species underwent the pg-β event, which may be critical for ginsenoside biosynthesis. We discovered that Panax species exhibit distinct expression patterns of key enzyme genes (β-AS, DDS, CYP450, UGTs) compared to other Araliaceae species. These enzyme genes show independent evolutionary lineages in gene trees, suggesting unique functional adaptations that enable Panax species to efficiently synthesize ginsenosides. This study provides a theoretical foundation for the conservation and utilization of Araliaceae germplasm resources.

Viral metagenomics reveals diverse viruses in the fecal samples of children with acute respiratory infection

Introduction

Changes in the gut microbiome have been associated with the development of acute respiratory infection (ARI). However, due to methodological limitations, our knowledge of the gut virome in patients with ARIs remains limited.

Methods

In this study, fecal samples from children with ARI were investigated using viral metagenomics.

Results

The fecal virome was analyzed, and several suspected disease-causing viruses were identified. The five viral families with the highest abundance of sequence reads were Podoviridae, Virgaviridae, Siphoviridae, Microviridae, and Myoviridae. Additionally, human adenovirus, human bocavirus, human astrovirus, norovirus, and human rhinovirus were detected. The genome sequences of these viruses were respectively described, and phylogenetic trees were constructed using the gene sequences of the viruses.

Discussion

We characterized the composition of gut virome in children with acute respiratory infections. However, further research is required to elucidate the relationship between acute respiratory infection and gut viruses.

A lateral flow immunoassay-based survey reveals a low-frequency truncated Solenopsis invicta venom 2-like protein and unique Solenopsis invicta venom 2 protein genotypes in Solenopsis invicta

The purpose of this research was to examine the Solenopsis invicta venom 2 protein and transcript among Solenopsis invicta fire ants exhibiting an unusual response to antibody interrogation of this protein. Sequence and phylogenetic analyses combined with Western blotting and lateral flow immunoassay were employed to examine the venom proteins from these fire ants. Genotypic variation was discovered in the Solenopsis invicta venom 2 gene. Many of these unique genotypes exhibited strong identity to the Solenopsis richteri venom 2 ortholog from the congener, Solenopsis richteri. Phylogenetic analysis of these sequences revealed a significant evolutionary relationship with Solenopsis richteri despite being obtained from Solenopsis invicta. A unique, truncated, Solenopsis invicta venom 2-like protein was also discovered in these colonies originating from a unique locus on chromosome 10 where multiple duplication events have apparently copied this gene. These results suggest the possible presence of a cryptic species.

Computational prediction of Homo sapiens-Candida albicans protein-protein interactions reveal key virulence factors using dual RNA-Seq data analysis

A prevalent pathobiont, Candida albicans, accounts for approximately 70% of fungal infections worldwide owing to its virulence traits that culminate in devastating fatalities within healthcare facilities. Protein-protein interactions (PPIs) between Homo sapiens and C. albicans play a pivotal role in infection and disease progression. Additionally, scarcity of information on H. sapiens-C. albicans protein-protein interactions makes it difficult to understand the molecular mechanisms underlying infection and host immune responses. Investigating these PPIs can provide crucial insights into host-pathogen relationships and facilitate the development of novel therapeutic interventions. To address this challenge, we utilized computational techniques based on homology and domain to project 56,515 human-fungal pathogen protein-protein interactions (HF-PPIs) involving 6830 human and 486 C. albicans proteins. We have identified 16 key virulence factors of C. albicans, including SOD1, ERG10, GFA1, and VPS4, as potential therapeutic targets. As evidenced by dual RNA-Seq data acquired at various stages of infection such as 15, 30, 60, 120, and 240 min, these fungal genes interact with down-regulated human immunomodulatory genes specifically, ADRM1, DAXX, RYBP, SGTA, and SRGN. In addition to their intrinsically disordered regions, these human genes are particularly susceptible to fungal manipulation. Through the identification of experimentally validated virulence factors and their interaction partners, this investigation constructs HF-PPI between H. sapiens and C. albicans. Our knowledge of human-fungal pathogen protein-protein interactions will be improved by integrating computational and experimental data in order to facilitate the development of efficient fungal infection prevention and treatment protocols.

Genomic and Epidemiological Investigations Reveal Chromosomal Integration of the Acipenserid Herpesvirus 3 Genome in Lake Sturgeon Acipenser fulvescens

DNA sequence from a new alloherpesvirus named acipenserid herpesvirus 3 (AciHV-3) was found in sturgeon species that are vulnerable to decline globally. A study was undertaken to develop a better understanding of the virus genome and to develop diagnostic tools to support an epidemiological investigation. A 184,426 bp genome was assembled from PacBio HiFi sequences generated with DNA from a Lake Sturgeon Acipenser fulvescens gonad cell line. The AciHV-3 genome was contiguous with host chromosomal DNA and was structured with telomere-like terminal direct repeat regions, five internal direct repeat regions and a U region that included intact open reading frames encoding alloherpesvirus core proteins. Diagnostic testing conducted with a newly developed and analytically validated qPCR assay established the ubiquitous presence and high titer of AciHV-3 DNA in somatic and germline tissues from wild Lake Sturgeon in the Hudson Bay drainage basin. Phylogenetic reconstructions confirm that the monophyletic AciHV-3 lineage shares a common ancestor with AciHV-1 and that AciHV-3 taxa cluster according to their sturgeon host. The same genotype of AciHV-3 is found in disjunctive Lake Sturgeon populations within and among drainage basins. The results support the hypotheses that AciHV-3 has established latency through germline chromosomal integration, is vertically transmitted via a Mendelian pattern of inheritance, is evolving in a manner consistent with a replication competent virus and has co-evolved with its host reaching genetic fixation in Lake Sturgeon populations in central Canada.

Ornithine enhances common bean growth and defense against white mold disease via interfering with SsOAH and diminishing the biosynthesis of oxalic acid in Sclerotinia sclerotiorum

The necrotrophic fungal phytopathogen, Sclerotinia sclerotiorum (Lib.) de Bary, employs a multilayered strategy to infect a wide range of host plants. The current study proposed the diamine L-ornithine, a non-proteinogenic amino acid that promotes the synthesis of other essential amino acids, as an alternative management strategy to boost the molecular, physiological, and biochemical responses of common bean (Phaseolus vulgaris L.) against white mold disease caused by S. sclerotiorum. In vitro experiments showed that L-ornithine significantly inhibited the mycelial growth of S. sclerotiorum in a dose-dependent manner. Moreover, it markedly diminished the white mold severity under greenhouse conditions. Moreover, L-ornithine stimulated the growth of treated plants suggesting that the tested concentration of L-ornithine has no phytotoxicity on treated plants. Additionally, L-ornithine enhanced the non-enzymatic antioxidants (total soluble phenolics and flavonoids), the enzymatic antioxidants (CAT, POX, and PPO), and upregulated the gene expression of three antioxidant-associated genes (PvCAT1, PvSOD, and PvGR). Moreover, in silico analysis showed that the genome of S. sclerotiorum possesses a putative oxaloacetate acetylhydrolase (SsOAH) protein that is highly similar in its functional analysis, conserved domains, and topology with OAH from Aspergillus fijiensis (AfOAH) and Penicillium lagena (PlOAH). Interestingly, the addition of L-ornithine to the potato dextrose broth (PDB) medium significantly down-regulated the gene expression of SsOAH in the mycelium of S. sclerotiorum. Likewise, exogenous application of L-ornithine significantly down-regulated the gene expression of SsOAH in the fungal mycelia collected from treated plants. Finally, L-ornithine application significantly diminished the secretion of oxalic acid in the PDB medium as well as infected leaves. Collectively, L-ornithine plays a pivotal role in maintaining the redox status, in addition to boosting the defense responses of infected plants. The current study provides insights that may lead to innovative eco-friendly approaches for controlling white mold disease and mitigating its impact on common bean cultivation particularly, and other crops in general.

Advancements in one-dimensional protein structure prediction using machine learning and deep learning

The accurate prediction of protein structures remains a cornerstone challenge in structural bioinformatics, essential for understanding the intricate relationship between protein sequence, structure, and function. Recent advancements in Machine Learning (ML) and Deep Learning (DL) have revolutionized this field, offering innovative approaches to tackle one- dimensional (1D) protein structure annotations, including secondary structure, solvent accessibility, and intrinsic disorder. This review highlights the evolution of predictive methodologies, from early machine learning models to sophisticated deep learning frameworks that integrate sequence embeddings and pretrained language models. Key advancements, such as AlphaFold's transformative impact on structure prediction and the rise of protein language models (PLMs), have enabled unprecedented accuracy in capturing sequence-structure relationships. Furthermore, we explore the role of specialized datasets, benchmarking competitions, and multimodal integration in shaping state-of-the-art prediction models. By addressing challenges in data quality, scalability, interpretability, and task-specific optimization, this review underscores the transformative impact of ML, DL, and PLMs on 1D protein prediction while providing insights into emerging trends and future directions in this rapidly evolving field.

Horizontal Transfer of Bacterial Operons into Eukaryote Genomes

In prokaryotes, functionally linked genes are typically clustered into operons, which are transcribed into a single mRNA, providing for the coregulation of the production of the respective proteins, whereas eukaryotes generally lack operons. We explored the possibility that some prokaryotic operons persist in eukaryotic genomes after horizontal gene transfer (HGT) from bacteria. Extensive comparative analysis of prokaryote and eukaryote genomes revealed 33 gene pairs originating from bacterial operons, mostly encoding enzymes of the same metabolic pathways, and represented in distinct clades of fungi or amoebozoa. This amount of HGT is about an order of magnitude less than that observed for the respective individual genes. These operon fragments appear to be relatively recent acquisitions as indicated by their narrow phylogenetic spread and low intron density. In 20 of the 33 horizontally acquired operonic gene pairs, the genes are fused in the respective group of eukaryotes so that the encoded proteins become domains of a multifunctional protein ensuring coregulation and correct stoichiometry. We hypothesize that bacterial operons acquired via HGT initially persist in eukaryotic genomes under a neutral evolution regime and subsequently are either disrupted by genome rearrangement or undergo gene fusion which is then maintained by selection.

The structure of a NEMO construct engineered for screening reveals novel determinants of inhibition

NEMO is an essential component in the activation of the canonical nuclear factor κB (NF-κB) pathway and exerts its function by recruiting the IκB kinases (IKK) to the IKK complex. Inhibition of the NEMO/IKKs interaction is an attractive therapeutic paradigm for diseases related to NF-κB mis-regulation, but a difficult endeavor because of the extensive protein-protein interface. Here we report the design and characterization of novel engineered constructs of the IKK-binding domain of NEMO, programmed to render this difficult protein domain amenable to NMR measurements and crystallization, while preserving its biological function. ZipNEMO binds IKKβ with nanomolar affinity, is amenable to heteronuclear nuclear magnetic resonance (NMR) techniques and structure determination by X-ray crystallography. We show that NMR spectra of zipNEMO allow to detect inhibitor binding in solution and resonance assignment. The crystal structure of zipNEMO reveals a novel ligand binding motif and the adaptability of the binding pocket and inspired the design of new peptide inhibitors.

A Class of Allopolyploidy Showing High Duplicate Retention and Continued Homoeologous Exchanges

We describe four ancient polyploidy events where the descendant taxa retain many more duplicated gene copies than has been seen in other paleopolyploidies of similar ages. Using POInT (the Polyploidy Orthology Inference Tool), we modeled the evolution of these four events, showing that they do not represent recent independent polyploidies despite the rarity of shared gene losses. We find that these events have elevated rates of interlocus gene conversion and that these gene conversion events are spatially clustered in the genomes. Regions of gene conversion also show very low synonymous divergence between the corresponding paralogous genes. We suggest that these genomes have experienced a delay in the return to a diploid state after their polyploidies. Under this hypothesis, homoeologous exchanges between the duplicated regions created by the polyploidy persist to this day, explaining the high rates of duplicate retention. Genomes with these characteristics arguably represent a new class of paleopolyploid taxa because they possess evolutionary patterns distinct from the more common and well-known paradigm of the rapid loss of many of the duplicated pairs created by polyploidy.

Three Novel Bacterial Species, Roseateles flavus sp. nov., Roseateles paludis sp. nov., and Roseateles hydrophilus sp. nov., Isolated from Various Water-Related Environments

A polyphasic study was conducted to determine the taxonomic positions of three bacterial strains, designated as strains 2.12 T, DJS-2-20 T, and UHG3T, isolated from the water of an agricultural water pipe, wetland, and artificial lake, respectively. These strains were Gram-stain-negative, rod-shaped, and oxidase positive. The fatty acid profiles of all three strains revealed that the major fatty acids (> 10%) were C16:0 and summed features 3 (comprising C16:1ω6c and/or C16:1ω7c), with strain UHG3T additionally featuring C16:0 3-OH as its main fatty acid. Phosphatidylethanolamine was the major polar lipid. Ubiquinone 8 (Q-8) was the only respiratory quinone detected. The genomic G + C contents were 68.5% for strain 2.12 T, 68% for strain DJS-2-20 T, and 69% for strain UHG3T. Strains 2.12 T, DJS-2-20 T, and UHG3T had the closest 16S rRNA gene sequence similarity with R. subflavus APW6T (98.5%), R. puraquae CCUG 52769 T (98.2%), and R. puraquae CCUG 52769 T (99.4%), respectively. The pairwise amino acid identity, average nucleotide identity, and digital DNA-DNA hybridization values for strains 2.12 T, DJS-2-20 T, and UHG3T with its closely related type strain of the species were below the species delineation thresholds. The genotypic and phenotypic characteristics observed in this study indicated that strains 2.12 T (= KACC 23730 T = TBRC 19013 T), DJS-2-20 T (= KACC 23731 T = TBRC 19014 T), and UHG3T (= KACC 22636 T = TBRC 16347 T) represent three novel Roseateles species, for which we propose the names Roseateles flavus sp. nov., Roseateles paludis sp. nov., and Roseateles hydrophilus sp. nov., respectively.

Genome mining reveals the biosynthetic potential of a novel Lysinibacillus zambalensis sp. nov., isolated from a hyperalkaline spring

A novel bacterium, designated as strain M3T, was isolated from a hyperalkaline spring in the Philippines and identified as a new species within the genus Lysinibacillus through 16 S rRNA gene sequence and genomic analyses. Although strain M3T shared a high 16 S rRNA gene sequence similarity (> 98.7%) with many Lysinibacillus species, the digital DNA-DNA hybridization and orthologous average nucleotide identity values between strain M3T and its closet relative, Lysinibacillus xylanilyticus DSM 23,493T, were 41.2% and 90.6%, respectively-both below the established threshold for prokaryotic species delineation. Genome mining of the 5.3 Mbp-draft genome of strain M3T revealed eight biosynthetic gene clusters, which shared little sequence similarity with characterized clusters, suggesting the potential for encoding novel specialized metabolites. The cells of strain M3T were Gram-stain-positive, aerobic, rod-shaped, non-motile, and capable of endospore formation. Optimum growth was observed at 30 °C, pH 8.0, and 0.5% (w/v) NaCl. The major respiratory quinone was menaquinone-7, and the predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and two unknown phospholipids. Its fatty acid profile showed an elevated level of iso-C15:0, and the peptidoglycan type was determined to be A4α (L-Lys-D-Asp). This study contributes to the growing database and understanding of the genus and aims to help drive future research on the bioactive potential of the genus. Lysinibacillus zambalensis sp. nov. is proposed with strain M3T as the type strain (= TISTR 10640T = BIOTECH 10973T).

Allogenic grafting induces PI3K-mediated tissue overgrowth in hydrozoan jellyfish Cladonema radiatum medusae

Allorecognition, which is the ability of an organism to discriminate between self and non-self, protects multicellular animals from somatic cell/germline parasitism. We reported and characterised allorecognition in the stolons of colonies of the hydrozoan jellyfish Cladonema radiatum (C. radiatum) in our previous publication. C. radiatum has a free-swimming medusa form besides the sessile colonial form. In this study, we investigated the allorecognition responses in the medusa form of C. radiatum. By using grafting experiments, we observed that while C. radiatum medusae show tolerance to both isogenic and allogenic chimerism, allogenic grafting induces the formation of a form of circular scars-we refer to as "ring-shaped scars"-around the grafts on the host umbrella. Within the scars, overgrowth of tissues occurs with additional gastrovascular canal development. By pharmaceutical experiments, we found that tissue overgrowth is dependent on phosphoinositide 3-kinase (PI3K) and vascular endothelial growth factor (VEGF), showing a resemblance to mammalian neoplasia.

Combination therapy delays antimicrobial resistance after adaptive laboratory evolution of Staphylococcus aureus

Antibiotic resistance, driven by misuse and overuse of antibiotics, is one of the greatest threats against human health. The antimicrobial pressure during prolonged antibiotic treatment of chronic bacterial infections selects for resistance. While antibiotic combinations may reduce resistance emergence, antibiotic-tolerant persister cells can serve as a reservoir for resistance development. Therefore, targeting these cells with anti-persister drugs might provide a novel strategy for resistance prevention. In this study, we conducted 42 days of adaptive laboratory evolution using Staphylococcus aureus exposed to rifampicin, ciprofloxacin, daptomycin, and vancomycin, alone or in combination with the anti-persister drug mitomycin C. We monitored antibiotic susceptibility daily and assessed phenotypic changes in growth and biofilm formation in evolved strains. Whole-genome sequencing revealed mutations linked to antibiotic resistance and phenotypic shifts. Rifampicin resistance developed within a few days, while ciprofloxacin and daptomycin emerged in approximately 3 weeks. Treatments with vancomycin or mitomycin C resulted in minimal changes in susceptibility. While combination therapy delayed resistance, it did not fully prevent it. Notably, the combination of rifampicin with mitomycin C maintained rifampicin susceptibility throughout the long-term evolution experiment. Sub-inhibitory antibiotic treatments selected for both previously characterized and novel mutations, including unprecedented alterations in the nucleotide excision repair system and azoreductase following mitomycin C exposure. The delayed resistance development observed with combination therapy, particularly mitomycin C's ability to suppress rifampicin resistance, suggests potential therapeutic applications. Future studies should evaluate the clinical efficacy of anti-persister drugs in preventing resistance across different bacterial pathogens and infection models.

TargetSeeker-MS: A Bayesian Inference Approach for Drug-Target Discovery Using Protein Fractionation Coupled to Mass Spectrometry

To understand the mechanism of action of a drug and assess its clinical usefulness and viability, it is imperative that its affinity for its putative targets is determined. When coupled to mass spectrometry (MS), energetics-based protein separation (EBPS) techniques, such as a thermal shift assay, have shown great potential to identify the targets of a drug on a proteome scale. Nevertheless, the computational analyses assessing the confidence of drug-target predictions made by these methods have remained tightly tied to the protocol under which the data were produced. To identify drug targets in data sets produced using different EBPS-MS techniques, we have developed a novel flexible Bayesian inference approach named TargetSeeker-MS. We showed that TargetSeeker-MS identifies known and novel drug targets in Caenorhabditis elegans and HEK 293 samples treated with the fungicide benomyl. We also demonstrated that TargetSeeker-MS' drug-target identifications are reproducible in C. elegans samples that were processed using two different EBPS techniques (thermal shift assay and a differential precipitation of proteins, named DiffPOP). In addition, we validated a novel benomyl target by measuring its altered enzymatic activity upon drug treatment in vitro. TargetSeeker-MS, which is available as a web server (https://targetseeker.scripps.edu/), allows for the rapid, versatile, and confident identification of targets of a drug on a proteome scale, thereby providing a better understanding of its mechanisms and facilitating the evaluation of its clinical viability.

ToxDL 2.0: Protein toxicity prediction using a pretrained language model and graph neural networks

Motivation

Assessing the potential toxicity of proteins is crucial for both therapeutic and agricultural applications. Traditional experimental methods for protein toxicity evaluation are time-consuming, expensive, and labor-intensive, highlighting the requirement for efficient computational approaches. Recent advancements in language models and deep learning have significantly improved protein toxicity prediction, yet current models often lack the ability to integrate evolutionary and structural information, which is crucial for accurate toxicity assessment of proteins.

Results

In this study, we present ToxDL 2.0, a novel multimodal deep learning model for protein toxicity prediction that integrates both evolutionary and structural information derived from a pretrained language model and AlphaFold2. ToxDL 2.0 consists of three key modules: (1) a Graph Convolutional Network (GCN) module for generating protein graph embeddings based on AlphaFold2-predicted structures, (2) a domain embedding module for capturing protein domain representations, and (3) a dense module that combines these embeddings to predict the toxicity. After constructing a comprehensive toxicity benchmark dataset, we obtained experimental results on both an original non-redundant test set (comprising pre-2022 protein sequences) and an independent non-redundant test set (a holdout set of post-2022 protein sequences), demonstrating that ToxDL 2.0 outperforms existing state-of-the-art methods. Additionally, we utilized Integrated Gradients to discover known toxic motifs associated with protein toxicity. A web server for ToxDL 2.0 is publicly available at www.csbio.sjtu.edu.cn/bioinf/ToxDL2/.

High temperature-responsive DEAR4 condensation confers thermotolerance through recruiting TOPLESS in Arabidopsis nucleus

Global warming is harmful to plants and threatens crop yields in the world. In contrast to other abiotic stresses, the molecular mechanisms for plant high temperature perception and signaling are still not fully understood. Here, we report that transcription factor DREB AND EAR MOTIF PROTEIN 4 (DEAR4) positively regulates heat tolerance in Arabidopsis thaliana. We further reveal that DEAR4 proteins undergo liquid-liquid phase separation (LLPS) and high temperature could induce DEAR4 condensate formation in the nucleus. Moreover, DEAR4 recruits the transcriptional co-repressor TOPLESS (TPL) into the nuclear speckles under high temperature. The high temperature triggered DEAR4-TPL co-condensates enhance their transcriptional repression activity through modulating histone deacetylation levels of GASA5, which is a reported negative regulator of HEAT SHOCK PROTEINs (HSPs). A genome-wide transcriptional landscape study confirms that DEAR4 induces the expression of multiple HSPs. Taken together, we illustrate a transcriptional repression mechanism mediated by DEAR4 through LLPS to confer plants thermotolerance and open a new avenue for translating this knowledge into crops for improving their heat resistance.

The Biarylitides: Understanding the Structure and Biosynthesis of a Fascinating Class of Cytochrome P450 Modified RiPP Natural Products

The biarylitides are a recently discovered class of RiPP natural products that are fascinating both from the small size of the core peptides as well as the diversity of peptide crosslinking exhibited by the cytochrome P450 enzymes found in these systems. In this review, we address the discovery and biosynthetic diversity of these systems and discuss the methods and challenges of analysing the structures of these constrained cyclic peptides. We also discuss the structures of the P450 enzymes involved in these pathways and address the potential for alternate catalytic outcomes and activities as seen most recently with the inclusion of biarylitide related enzymes within rufomycin biosynthesis.

Salmonella Typhi serine threonine kinase T4519 induces lysosomal membrane permeabilization by manipulating Toll-like receptor 2-Cystatin B-Cathepsin B-NF-κB-reactive oxygen species pathway and promotes survival within human macrophages

Intracellular pathogens of Salmonella spp. survive and replicate within the phagosomes, called Salmonella-containing vacuoles (SCVs) inside macrophages by manipulating phagosomal maturation and phagolysosome formation. While controversies exist about the phagosomal traffic of Salmonella Typhimurium, little studies were carried out with the intracellular survival mechanisms of Salmonella Typhi (S. Typhi). We had previously reported that a eukaryote-like serine/threonine kinase of S. Typhi (T4519) contributes to survival within macrophages and activates host pro-inflammatory signaling pathways regulated by NF-κB. However, neither the mechanisms underlying NF-κB activation nor how it contributes to intracellular survival of S. Typhi were studied. Here we show, by using antibody-mediated blocking and gene knockdown studies that T4519 activates Toll-like receptor 2 (TLR2) signals in the human monocyte-derived macrophages. We computationally predicted the NH2-terminal glycine rich repeat domain of T4519 as the TLR2-binding moiety and confirmed the interaction by co-immunoprecipitation experiment. TLR2-T4519 interaction transcriptionally repressed cystatin B, a cathepsin B inhibitor, leading to the activation of cytosolic cathepsin B, leaked from the lysosomes of the infected cells. Through a series of RT-qPCR, western blotting, gene knockdown, flow cytometry and confocal microscopy experiments, we have shown that active cytosolic cathepsin B cleaves IKB-α, resulting in nuclear translocation of NF-κB and transactivation of its target genes, including reactive oxygen species (ROS), which in turn induces lysosomal membrane permeabilization (LMP). TLR2-dependent targeting of the cystatin B-cathepsin B-NF-κB-ROS pathways by T4519, leading to LMP promotes phagosomal survival of S. Typhi. This study describes a unique mechanism of the exploitation of host NF-κB signaling pathways by bacterial pathogens to promote its own persistence within macrophage cells.