The Clustal Omega Multiple Alignment Package

Oxidation of α-hydroxy acids by D-2-hydroxyglutarate dehydrogenase enzymes

α-Hydroxy acids are naturally occurring organic molecules with various medical and industrial applications. However, some α-hydroxy acids, like D-2-hydroxyglutarate (D2HG), have been implicated in cancers and neurometabolic disorders such as D2HG aciduria. Several studies on the D2HG oxidizing enzyme D-2-hydroxyglutarate dehydrogenase (D2HGDH) from various eukaryotic and prokaryotic sources focus on the use and application of the enzyme as biosensors for detecting D2HG. A recent gene knockout study on the bacterial D2HGDH homologs from Pseudomonas stutzeri and Pseudomonas aeruginosa identified the D2HGDH to be essential for bacterial survival by driving l-serine biosynthesis. Thus, D2HGDH is a good candidate for a therapeutic target against the multidrug-resistant P. aeruginosa. However, there is no consensus on the D2HGDH catalytic mechanism, and several D2HGDH homologs have not been characterized in their structural properties, which are two crucial features for therapeutic design. P. aeruginosa D2HGDH, the most extensively studied D2HGDH homolog, is emerging as a paradigm for D2HGDH and flavoproteins with metal ions in their active site. In this review, we have explored the structures of all published D2HGDH homologs from 12 species using AlphaFold 3 and highlighted the fully conserved structure and active site topologies of all D2HGDH homologs. Additionally, evolutionary and functional studies coupled with analyses of enzymatic activities reveal that prokaryotic and eukaryotic D2HGDH homologs, diverging from two distinct ancestors, may have differentially evolved to specialize in their α-hydroxy acid catalysis. Additionally, this review identifies all D2HGDH homologs as metal and FAD-dependent enzymes that employ a metal-triggered FAD reduction in their catalysis. Elucidation of the D2HGDH mechanism will allow designing antibiotics that target these enzymes as potential therapeutics against pathogenic bacteria like P. aeruginosa in addition to the application of D2HGDH homologs as biosensors.

Discovery and Characterization of CcrSult1: A Novel Flavonoid Sulfotransferase from the Red Alga Chondrus crispus

Sulfated flavonoids, prevalent in various plants, possess enhanced bioavailability due to the introduction of sulfonate groups, a process catalyzed by flavonoid sulfotransferases (SULTs). These enzymes serve as invaluable tools for exploring the structure-function relationships of sulfated flavonoids and for the preparation of biologically active derivatives. Despite their significance, flavonoid SULTs remain largely unexplored especially for those from marine environment. In this study, we report the discovery of CcrSULT1, the first flavonoid SULT from the red algaChondrus crispus. Substrate specificity tests revealed that CcrSULT1 exhibits a pronounced chemical selectivity preference for phenolic compounds, particularly flavonoids. More importantly, we discovered that CcrSULT1 may have unique regional selectivity toward mono phenolic hydroxyl groups (e.g., the 4'-OH of kaempferol, a flavonoid aglycone widely distributed in algae and various plants) in substrates, potentially leading to the specific production of monosulfated products. This hypothesis is further supported by the construction of a complex structural model. This study paves the way for the discovery of unknown algal sulfotransferases and provides a biological basis for understanding algal sulfation metabolism and biomass conversion.

Generative Deep Learning Design of Single-Domain Antibodies Against Venezuelan Equine Encephalitis Virus

BACKGROUND/OBJECTIVES

Venezuelan equine encephalitis virus (VEEV) represents a significant biothreat with no FDA-approved vaccine currently available, highlighting the need for alternative therapeutic strategies. Single-domain antibodies (sdAbs) present a potential alternative to conventional antibodies, due to their small size and ability to recognize cryptic epitopes.

METHODS

This research describes the development and preliminary evaluation of VEEV-binding sdAbs generated using a generative artificial intelligence (AI) platform. Using a dataset of known alphavirus-binding sdAbs, the AI model produced sequences with predicted affinity for the E2 glycoprotein of VEEV. These candidate sdAbs were expressed in a bacterial periplasmic system and purified for initial assessment.

RESULTS

Enzyme-linked immunosorbent assays (ELISAs) indicated binding activity of the sdAbs to VEEV antigens. In vitro neutralization tests suggested inhibition of VEEV infection in cultured cells for some of the candidates.

CONCLUSIONS

This study demonstrates how generative AI can expedite antiviral therapeutic development and establishes a framework for quick responses to emerging viral threats when extensive example databases are unavailable. Additional refinement and validation of AI-generated sdAbs could establish effective VEEV therapeutics.

LSDVvac: An immunoinformatics database for vaccine design against lumpy skin disease virus

Development of an effective vaccine against Lumpy Skin Disease Virus (LSDV) is crucial for protecting livestock. The current study outlines a web-based platform developed to aid the scientific community in designing effective peptide-based vaccines against LSDV. First, we generated all possible overlapping (K-mer value 9 and 15) peptides from the proteins of 73 LSDV strains. Second, after removing redundancy, the obtained peptides were utilized for predicting B-cell and T-cell epitopes. Third, the predicted B-cell and T-cell epitopes were screened for immunogenicity, allergenicity, and toxicity. Finally, the LSDV candidate vaccine database was developed utilizing 3913 unique B-cell (Linear 3344 and conformational 569) and 6473 unique T-cell (MHC-I 3200 and MHC-II 3273) epitopes. The three-dimensional structure of 156 LSDV proteins from reference (AF325528.1) LSDV genome was predicted using I-TASSER software and implemented in the database. Additionally, tools for genome analysis like DotPlot, Gblocks, BLAST, and gRNA designing were incorporated into the database. In summary, LSDVvac has been developed, which integrates information about predicted potential vaccine candidates along with useful computational tools. LSDVvac database is available at http://45.248.163.59/bic/lsdb/.

NNKcat: deep neural network to predict catalytic constants (Kcat) by integrating protein sequence and substrate structure with enhanced data imbalance handling

Catalytic constant (Kcat) is to describe the efficiency of catalyzing reactions. The Kcat value of an enzyme-substrate pair indicates the rate an enzyme converts saturated substrates into product during the catalytic process. However, it is challenging to construct robust prediction models for this important property. Most of the existing models, including the one recently published by Nature Catalysis (Li et al.), are suffering from the overfitting issue. In this study, we proposed a novel protocol to construct Kcat prediction models, introducing an intermedia step to separately develop substrate and protein processors. The substrate processor leverages analyzing Simplified Molecular Input Line Entry System (SMILES) strings using a graph neural network model, attentive FP, while the protein processor abstracts protein sequence information utilizing long short-term memory architecture. This protocol not only mitigates the impact of data imbalance in the original dataset but also provides greater flexibility in customizing the general-purpose Kcat prediction model to enhance the prediction accuracy for specific enzyme classes. Our general-purpose Kcat prediction model demonstrates significantly enhanced stability and slightly better accuracy (R2 value of 0.54 versus 0.50) in comparison with Li et al.'s model using the same dataset. Additionally, our modeling protocol enables personalization of fine-tuning the general-purpose Kcat model for specific enzyme categories through focused learning. Using Cytochrome P450 (CYP450) enzymes as a case study, we achieved the best R2 value of 0.64 for the focused model. The high-quality performance and expandability of the model guarantee its broad applications in enzyme engineering and drug research & development.

Understanding the role of oxylipins in Cannabis to enhance cannabinoid production

Phytocannabinoids are medically important specialized defense compounds that are sparsely distributed among plants, yet Cannabis sativa can synthesize unprecedented amounts of these compounds within highly specialized surface cell factories known as glandular trichomes. The control mechanisms that allow for this high level of productivity are poorly understood at the molecular level, although increasing evidence supports the role of oxylipin metabolism in phytocannabinoid production. Oxylipins are a large class of lipid-based oxygenated biological signaling molecules. Although some oxylipins are known to participate in plant defense, roles for the majority of the ca. 600 plant oxylipins are largely unknown. In this review, we examine oxylipin gene expression within glandular trichomes and identify key oxylipin genes that determine the fate of common lipid precursors. Mechanisms by which oxylipins may be interacting with phytocannabinoid metabolism, as well as specialized plant metabolism more broadly, are discussed and a model summarizing these contributions proposed.

Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq

While the production of a draft genome has become more accessible due to long-read sequencing, the annotation of these new genomes has not been developed at the same pace. Long-read RNA sequencing offers a promising solution for enhancing gene annotation. In this study, we explore how sequencing platforms, Oxford Nanopore R9.4.1 chemistry or Pacific Biosciences (PacBio) Sequel II CCS, and data processing methods influence evidence-driven genome annotation using long reads. Incorporating PacBio transcripts into our annotation pipeline significantly outperformed traditional methods, such as ab initio predictions and short-read-based annotations. We applied this strategy to a nonmodel species, the Florida manatee, and compared our results to existing short-read-based annotation. At the loci level, both annotations were highly concordant, with 90% agreement. However, at the transcript level, the agreement was only 35%. We identified 4906 novel loci, represented by 5707 isoforms, with 64% of these isoforms matching known sequences in other mammalian species. Overall, our findings underscore the importance of using high-quality curated transcript models in combination with ab initio methods for effective genome annotation.

Isolation and Characterization of a Bacillus amyloliquefaciens Bacteriophage JBA6 and Its Endolysin PlyJBA6

Bacillus amyloliquefaciens is a Gram-positive, aerobic, spore-forming bacteria usually found in soil. Despite its probiotic potential, B. amyloliquefaciens has been identified as a cause of food spoilage, including the development of off-odors, rope formation, and the production of viscous substances in a wide range of foods. To control B. amyloliquefaciens, we isolated three B. amyloliquefaciens bacteriophages TBA3, JBA3, JBA6, and characterized one representative JBA6 endolysin, PlyJBA6. Transmission electron microscopy and genomic analysis demonstrated that all three phages belong to the Salasmaviridae family, characterized by short, non-contractile tails with linear dsDNA genomes ranging from 18.7 to 19.1 kb. PlyJBA6 contains a glycoside hydrolase family 24 domain (PF00959) at the N-terminus and two LysM domains (PF04176) at the C-terminus. While JBA6 has a narrow host range, infecting only 7 out of 9 tested strains of B. amyloliquefaciens, PlyJBA6 exhibits extended lytic range beyond the Bacillus genus. Interestingly, PlyJBA6 lyses Gram-negative bacteria such as Escherichia coli, Yersinia enterocolitica and Cronobacter sakazakii without other additives to destabilize bacterial outer membrane. We assume that JBA6 might be a useful component for a phage cocktail to control B. amyloliquefaciens and that PlyJBA6 can provide insights into the development of novel biocontrol agents against various food-borne pathogens.

Origins and Distribution of Panicum Mosaic Virus and Sugarcane Mosaic Virus on Stenotaphrum secundatum in Australia

Stenotaphrum secundatum is a premium turf grass in warm temperate and subtropical regions of the world and is the most important turf species in Australia based on the value of its production. A new disease called buffalo grass yellows (BGY) has become a problem on turf farms in Australia. We surveyed turf farms in New South Wales, Queensland, and Western Australia to determine whether panicum mosaic virus (PMV) and sugarcane mosaic virus (SCMV) were associated with BGY. PMV was only found on three farms, two located in the Hawkesbury Valley near Sydney and a third at Echuca, about 800 km to the southwest of the former location. SCMV was more prevalent, present in all major cultivars and states surveyed. We analyzed phylogenetic relationships for SCMV and found that isolates infecting S. secundatum in Australia belonged to three clades. The first included Australian isolates typical of the population of viruses circulating in Digitaria didactyla. The second included a single New South Wales isolate from S. secundatum 'SS100' that grouped with otherwise American isolates of SCMV recorded in S. secundatum and Saccharum officinale from Florida and Zea mays from Ohio. Finally, an isolate of SCMV from S. secundatum originating from a turf farm in South East Queensland grouped with viruses mostly infecting maize; this record is potentially the first maize-adapted strain of SCMV in Australia. Our study sheds light on the etiology of the BGY disease syndrome and invasion history of PMV and SCMV in Australia.

An alternative adaptation strategy of the CCA-adding enzyme to accept noncanonical tRNA substrates in Ascaris suum

Playing a central role in translation, tRNAs act as an essential adapter linking the correct amino acid to the corresponding mRNA codon in translation. Due to this function, all tRNAs exhibit a typical secondary and tertiary structure to be recognized by the tRNA maturation enzymes as well as many components of the translation machinery. Yet, there is growing evidence for structurally deviating tRNAs in metazoan mitochondria, requiring a coevolution and adaptation of these enzymes to the unusual structures of their substrates. Here, it is shown that the CCA-adding enzyme of Ascaris suum carries such a specific adaptation in form of a C-terminal extension. The corresponding enzymes of other nematodes also carry such extensions, and many of them have an additional adaptation in a small region of their N-terminal catalytic core. Thus, the presented data indicate that these enzymes evolved two distinct strategies to tolerate noncanonical tRNAs as substrates for CCA incorporation. The identified C-terminal extension represents a surprising case of convergent evolution in tRNA substrate adaptation, as the nematode mitochondrial translation factor EF-Tu1 carries a similar extension that is essential for efficient binding to such structurally deviating tRNAs.

Sludge amended soil induced multidrug and heavy metal resistance in endophytic Exiguobacterium sp. E21L: genomics evidences

The emergence of multidrug-resistant bacteria in agro-environments poses serious risks to public health and ecological balance. In this study, Exiguobacterium sp. E21L, an endophytic strain, was isolated from carrot leaves cultivated in soil amended with sewage treatment plant-derived sludge. The strain exhibited resistance to clinically relevant antibiotics, including beta-lactams, fluoroquinolones, aminoglycosides, and macrolides, with a high Multi-Antibiotic Resistance Index of 0.88. Whole-genome sequencing revealed a genome of 3.06 Mb, encoding 3894 protein-coding genes, including antimicrobial resistance genes (ARGs) such as blaNDM, ermF, tetW, and sul1, along with heavy metal resistance genes (HMRGs) like czcD, copB, and nikA. Genomic islands carrying ARGs and stress-related genes suggested potential horizontal gene transfer. The strain demonstrated robust biofilm formation, high cell hydrophobicity (> 80%), and significant auto-aggregation (90% at 48 h), correlating with genes associated with motility, quorum sensing, and stress adaptation. Notably, phenotypic assays confirmed survival under simulated gastrointestinal conditions, emphasizing its resilience in host-associated environments. Comparative genomics positioned Exiguobacterium sp. E21L near Exiguobacterium chiriqhucha RW-2, with a core genome of 2716 conserved genes. Functional annotations revealed genes involved in xenobiotic degradation, multidrug efflux pumps, and ABC-type transporters, indicating versatile resistance mechanisms and metabolic capabilities. The presence of ARGs, HMRGs, and MGEs (mobile genetic elements) highlights the potential role of Exiguobacterium sp. E21L as a reservoir for resistance determinants in agricultural ecosystems. These findings emphasized the need for stringent regulations on sludge-based fertilizers and advanced sludge treatment strategies to mitigate AMR risks in agro-environments.

Isolation, Molecular, and Metabolic Profiling of Benzene-Remediating Bacteria Inhabiting the Tannery Industry Soil

Benzene is a pervasive contaminant and human carcinogen. Its remediation from environmental resources using conventional procedures has always been challenging due to high cost and incomplete benzene degradation. The present study was designed to explore highly efficient bacteria with benzene degrading potential from tannery industry soil, which might be used as an alternative to these conventional benzene removal remedies. Bacterial isolation was performed using benzene (80 μl/1,000 ml) supplemented with minimal salt media (MSM). Characterization of isolates was carried out by performing growth curve analysis, Gram staining, biochemical characterization via Remel RapID™ NF PLUS System (Thermo Scientific™, Thermo Fisher Scientific, Inc., USA), antibiotic sensitivity profiling, 16S rRNA gene sequencing, benzene removal efficiency estimation assay, FTIR, and GC-MS profiling. Five bacteria isolated in the present study were identified as Paracoccus aestuarii PUB1, Bacillus tropicus PUB2, Bacillus albus PUB3, Bacillus subtilis PUB4, and Bacillus cereus PUB6. All of these fast-growing bacteria were Gram-positive except P. aestuarii PUB1. Maximum benzene removal efficiency (30 mg/l per 25 h) was found in B. tropicus PUB2. Comparing the FTIR spectra of bacterial culture supernatant versus control revealed the peaks shifting corresponding to benzene ring bonds breaking. GC-MS analysis identified the metabolic intermediates from benzoate methylation and benzaldehyde pathways. These bacteria can be employed for benzene degradation via enzyme-based nanoparticle synthesis or cloning of relevant genes in eco-friendly expression systems.

Psychrobacter saeujeotis sp. nov., a novel halophilic bacterium isolated from salted shrimp jeotgal

A novel bacterial species, designated FBL11T, was isolated from salted shrimp jeotgal, a traditional Korean fermented food sampled in the Republic of Korea. This strain showed the highest 16S rRNA gene sequence similarity to Psychrobacter halodurans strain F2608T (NR_181578.1) at 98.3%. The genome size of strain FBL11T was 3,294,493 bp with a G+C content of 42.5 mol%. Computation of relatedness indicates that strain FBL11T shares the highest relatedness of 78.5% with Psychrobacter fulvigenes strain KC-40T (NZ_CAJGZP01) and 25.2% with Psychrobacter piechaudii strain CIP110854T (NZ_FUGE01), with values clearly below the cut-offs for species distinction. Polyphasic characterization using biochemical tests and matrix-assisted laser desorption/ionization time-of-flight MS analysis confirmed these findings. Strain FBL11T grew at 10-30 °C (optimum, 20-30 °C) with 0-15% NaCl (w/v; optimum, 3-6%). Analysis of biosynthetic gene clusters responsible for secondary metabolite production revealed that strain FBL11T generates unique products such as beta-lactone and redox-cofactors within this genus. Based on the genomic and phenotypic data obtained, we propose that strain FBL11T represents a novel species, for which we propose the name Psychrobacter saeujeotis sp. nov. (type strain FBL11T=KACC 23745T=KCTC 8655T=JCM 37231T).

Structural basis for complement receptor engagement and virus neutralization through Epstein-Barr virus gp350

Epstein-Barr virus (EBV) causes infectious mononucleosis and is associated with malignancies in humans. Viral infection of B cells is initiated by the viral glycoprotein 350 (gp350) binding to complement receptor 2 (CR2). Despite decades of effort, no vaccines or curative agents have been developed, partly due to lack of atomic-level understanding of the virus-host interface. Here, we determined the 1.7 Å structure of gp350 in complex with CR2. CR2 binding of gp350 utilized the same set of Arg residues required for recognition of its natural ligand, complement C3d. We further determined the structures of gp350 in complex with three potently neutralizing antibodies (nAbs) obtained from vaccinated macaques and EBV-infected individuals. Like the CR2 interaction, these nAbs targeted the acidic pocket within the CR2-binding site on gp350 using Arg residues. Our results illustrate two axes of molecular mimicry-gp350 versus C3d and CR2 versus EBV nAbs-offering insights for EBV vaccines and therapeutics development.

Single-stranded DNA binding to the transcription factor PafBC triggers the mycobacterial DNA damage response

The DNA damage response in mycobacteria is controlled by the heterodimeric transcription factor PafBC, a member of the WYL domain-containing protein family. It has been shown that PafBC induces transcription of its regulon by reprogramming the housekeeping RNA polymerase holoenzyme to recognize PafBC-dependent promoters through sigma adaptation. However, the mechanism by which DNA damage is sensed and translated into PafBC activation has remained unclear. Here, we demonstrate that the binding of single-stranded DNA (ssDNA) to the WYL domains of PafBC activates the transcription factor. Our cryo-electron microscopy structure of full-length PafBC in its active conformation, bound to the transcription initiation complex, reveals a previously unknown mode of interaction between the ssDNA and the WYL domains. Using biochemical experiments, we show that short ssDNA fragments bind to PafBC dynamically, resulting in deactivation as ssDNA levels decrease postrepair. Our findings shed light on the mechanism linking DNA damage to PafBC activation and expand our understanding of WYL domain-containing proteins.

An Inversion Polymorphism Under Balancing Selection, Involving Giant Mobile Elements, in an Invasive Fungal Pathogen

Recombination suppression can evolve in sex or mating-type chromosomes, or in autosomal supergenes, with different haplotypes being maintained by balancing selection. In the invasive chestnut blight fungus Cryphonectria parasitica, a genomic region was suggested to lack recombination and to be partially physically linked to the mating-type (MAT) locus based on segregation analyses. Using hundreds of available C. parasitica genomes and generating new high-quality genome assemblies, we show that a ca. 1.2 Mb genomic region proximal to the mating-type locus lacks recombination, with the segregation of two highly differentiated haplotypes in balanced proportions in invasive populations. High-quality genome assemblies further revealed an inversion in one of the haplotypes in the invaded range. The two haplotypes were estimated to have diverged 1.5 million years ago, and each harboured specific genes, some of which likely belonging to Starships. These are large transposable elements, mobilized by tyrosine recombinases, able to move accessory genes, and involved in adaptation in multiple fungi. The MAT-proximal region carried genes upregulated under virus infection or vegetative incompatibility reaction. In the native range, the MAT-proximal region also appeared to have a different evolutionary history than the rest of the genome. In all continents, the MAT-Proximal region was enriched in nonsynonymous substitutions, in gene presence/absence polymorphism, in tyrosine recombinases and in transposable elements. This study thus sheds light on a case of a large nonrecombining region partially linked to a mating compatibility locus, likely maintained by balancing selection on differentiated haplotypes, possibly involved in adaptation in a devastating tree pathogen.

A CACTA-like transposon in the Anthocyanidin synthase 1 (Ans-1) gene is responsible for apricot fruit colour in the raspberry (Rubus idaeus) cultivar 'Varnes'

Cultivated raspberries (Rubus idaeus L.) most commonly bear small, red, highly aromatic fruits. Their colour is derived predominantly from anthocyanins, water soluble polyphenolic pigments, but as well as red forms, there exist cultivars that display yellow- and apricot-coloured fruits. In this investigation, we used a multi-omics approach to elucidate the genetic basis of the apricot fruit colour in raspberry. Using metabolomics, we quantified anthocyanins in red and apricot raspberry fruits and demonstrated that, in contrast to red-fruited raspberries, fruits of the apricot cultivar 'Varnes' contain low concentrations of only a small number of anthocyanin compounds. By performing RNASeq, we revealed differential expression patterns in the apricot-fruited 'Varnes' for genes in the anthocyanin biosynthesis pathway and following whole genome sequencing using long-read Oxford Nanopore Technologies sequencing, we identified a CACTA-like transposable element (TE) in the second exon of the Anthocyanidin synthase (Ans) gene that caused a truncated predicted ANS protein. PCR confirmed the presence in heterozygous form of the transposon in an unrelated, red-fruited cultivar 'Veten', indicating apricot fruit colour is recessive to red and that it may be widespread in raspberry germplasm, potentially explaining why apricot forms appear at regular intervals in modern raspberry breeding populations.

Molecular Prediction and Correlation of the Structure and Function of Universal Stress Protein A (UspA) from Salmonella Typhimurium

Salmonella Typhimurium (ST) is a zoonotic pathogen that can cause gastroenteritis in humans when they consume contaminated food or water. When exposed to various stressors, both from living organisms (biotic) and the environment (abiotic), Salmonella Typhimurium produces Universal Stress Proteins (USPs). These proteins are gaining recognition for their crucial role in bacterial stress resistance and the ability to enter a prolonged state of growth arrest. Additionally, USPs exhibit diverse structures due to the fusion of the USP domain with different catalytic motifs, enabling them to participate in various reactions and cellular activities during stressful conditions. In this particular study, researchers cloned and analyzed the uspA gene obtained from poultry-derived strains of Salmonella Typhimurium. The gene comprises 435 base pairs, encoding a USP family protein consisting of 144 amino acids. Phylogenetic analysis demonstrated a close relationship between the uspA genes of Salmonella Typhimurium and those found in other bacterial species. We used molecular dynamics simulations and 3D structure prediction to ensure that the USPA protein was stable. Furthermore, we also carried out motif search and network analysis of protein-protein interactions. The findings from this study offer valuable insights for the development of inhibitors targeted against Salmonella Typhimurium.

Molecular Characterization of the Infectious Laryngotracheitis Virus (ILTV) Involved in Poultry Outbreaks Reveals the Virus Origin and Estimated Spreading Route

Infectious laryngotracheitis outbreaks have been observed in a short period of time in broiler, layer, and broiler breeder flocks, resulting in clinical signs and high mortality. The affected farms are located in the same geographical area, which is a high-density poultry region of Brazil. To estimate the potential origin of the virus or viruses that caused the outbreaks, the ILTVs detected at six companies were molecularly characterized by sequencing two fragments of the ICP4 gene and then compared with previous field and vaccine viruses detected in the country. The sequencing results revealed that all farms investigated were infected with a nonvaccine-origin virus. Phylogenetic analysis revealed that all farms were infected by the same virus classified as genotype VI. In addition, the ILTV detected in the present study was compared with that of viruses previously detected in egg-layer poultry regions in the country. The viruses detected in the recent outbreaks were indistinguishable, with one of them (VI-4) suggesting a possible route of transmission. This study describes for the first time severe ILT outbreaks in meat-type poultry in Brazil that spread quickly, and the phylogenetic analysis suggests the potential origin of the virus and route of transmission.

Binding and cleavage of pro-urokinase by a tegument extract of Fasciola hepatica newly excysted juveniles activate the host fibrinolytic system

Plasmin, the final product of fibrinolysis, is a broad-spectrum serine protease that degrades extracellular matrix (ECM) components, a function exploited by multiple pathogens for dissemination purposes. The trematode Fasciola hepatica is the leading cause of fasciolosis, a major disease of livestock and an emerging zoonosis in humans. Infection success depends on the ability of F. hepatica newly excysted juveniles (FhNEJ) to penetrate the host intestinal wall, a process that remains incompletely understood. We have previously shown that FhNEJ are capable of binding plasminogen (PLG), the zymogen of plasmin, on their tegument surface, which leads to plasmin generation in the presence of host-derived PLG activators and subsequent degradation of laminin, a major component of the intestinal ECM. Here, we describe the interaction between a tegument extract of FhNEJ and the precursor of the urokinase-type PLG activator (pro-u-PA). We found that F. hepatica cathepsins B3, L3, enolase and glutathione S-transferase mediate this interaction, suggesting a multifactorial or moonlighting role for these proteins. Additionally, our results revealed that the tegument of FhNEJ contains a protease that is capable of cleaving and activating pro-u-PA into its catalytically active form, which positively impacts the capacity of the parasites to generate plasmin from the host PLG. Collectively, our findings indicate that FhNEJ interact with the host fibrinolytic system at multiple levels, reinforcing the potential of targeting this interaction as a strategy to prevent FhNEJ trans-intestinal migration and infection success.

myh9b is a critical non-muscle myosin II encoding gene that interacts with myh9a and myh10 during zebrafish development in both compensatory and redundant pathways

Non-muscle myosin (NMII) motor proteins have diverse developmental functions due to their roles in cell shape changes, cell migration, and cell adhesion. Zebrafish are an ideal vertebrate model system to study the NMII encoding myh genes and proteins due to high sequence homology, established gene editing tools, and rapid ex utero development. In humans, mutations in the NMII encoding MYH genes can lead to abnormal developmental processes and disease. This study utilized zebrafish myh9a, myh9b, and myh10 null mutants to examine potential genetic interactions and roles for each gene in development. It was determined that the myh9b gene is the most critical NMII encoding gene, as myh9b mutants develop pericardial edema and have a partially penetrant lethal phenotype, which was not observed in the other myh mutants. This study also established that genetic interactions occur between the zebrafish myh9a, myh9b, and myh10 genes where myh9b is required for the expression of both myh9a and myh10, and myh10 is required for the expression of myh9b. Additionally, protein analyses suggested that enhanced NMII protein stability in some mutant backgrounds may play a role in compensation. Finally, double mutant studies revealed different and more severe phenotypes at earlier time points than single mutants, suggesting roles for tissue specific genetic redundancy, and in some genotypes, haploinsufficiency. These mutants are the first in vivo models allowing for the study of complete loss of the NMIIA and NMIIB proteins, establishing them as valuable tools to elucidate the role of NMII encoding myh genes in development and disease.

Phylogenetic analysis, metabolic profiling, and environmental adaptation of strain LCG007: a novel Rhodobacteraceae isolated from the East China Sea intertidal zone

Strain LCG007, isolated from Lu Chao Harbor's intertidal water, phylogenetically represents a novel genus within the family Rhodobacteraceae. Metabolically, it possesses a wide array of amino acid metabolic genes that enable it to thrive on both amino acids or peptides. Also, it could hydrolyze peptides containing D-amino acids, highlighting its potential role in the cycling of refractory organic matter. Moreover, strain LCG007 could utilize various carbohydrates, including mannopine and D-apiose-compounds primarily derived from terrestrial plants-demonstrating its capacity to degrade terrestrial organic matter. It could assimilate ammonia, nitrate and nitrite, and utilizes organic nitrogen sources such as polyamines, along with diverse organic and inorganic phosphorus and sulfur sources. Importantly, unlike very limited Sulfitobacter species that possess photosynthetic genes, the genomes of strain LCG007-affiliated genus and all Roseobacter species harbor photosynthetic gene clusters. This conservation was further supported by the significant impact of light on the growth and cell aggregation of strain LCG007, suggesting that acquirement of photosynthetic genes could play a crucial role in the speciation of their common ancestor. In terms of environmental adaptability, the genes that encode for DNA photolyase, heat and cold shock proteins, and enzymes responsible for scavenging reactive oxygen species, along with those involved in the uptake and biosynthesis of osmoprotectants such as betaine, γ-aminobutyric acid (GABA), and trehalose collectively enable strain LCG007 to survive in the dynamic and complex intertidal zone environment. Besides, the capacity in biofilm formation is crucial for its survival under conditions of oligotrophy or high salinity. This study enhances our comprehension of the microbial taxonomy within the Roseobacter clade affiliated cluster, their survival strategies in intertidal ecosystems, and underscores the significance of their role in nutrient cycling. It also highlights the crucial importance of photosynthetic metabolism for the speciation of marine bacteria and their ecological resilience.

Crystal structure of F10 core protein from Mpox virus reveals its potential inhibitors

Mpox virus (MPXV), a member of Poxviridae family, causes a rare zoonotic disease. According to the most recent data, over 15,600 cases and 537 deaths of human mpox have been reported. The MPXV complete RNA polymerase (RNAP), which is responsible for the entire early transcriptional cycle, comprises the RNAP core enzyme and essential factors including viral early transcription factor (VETF), nucleoside triphosphate phosphohydrolase I (NPH-I), RNA polymerase-associated protein (Rap94), and F10 core protein. The dimeric F10 core protein stabilizes the N-terminal region of Rap94, and the C-terminal domain of NPH-I, functioning as a structural clamp that enhances the stability of the RNAP complex. Here, we determined the crystal structure of the F10 core protein at a high resolution of 1.5 Å, and identified a cavity between the F10 core protein and NPH-I through superimposition of the MPXV F10 core protein and the vaccinia virus (VACV) RNAP. We further conducted a virtual screening based on this cavity, and identified 28 compounds as potential MPXV inhibitors. To the best of our knowledge, this is the first study to screen for inhibitors targeting MPXV RNAP. Our study may facilitate the development of novel ways for the discovery of anti-MPXV compounds against emerging pathogens.

Insect-specific RNA viruses detection in Field-Caught Aedes aegypti mosquitoes from Argentina using NGS technology

Mosquitoes are the primary vectors of arthropod-borne pathogens. Aedes aegypti is one of the most widespread mosquito species worldwide, responsible for transmitting diseases such as Dengue, Zika, and Chikungunya, among other medically significant viruses. Characterizing the array of viruses circulating in mosquitoes, particularly in Aedes aegypti, is a crucial tool for detecting and developing novel strategies to prevent arbovirus outbreaks. In this study, we address the implementation of a sequencing and analysis pipeline based on the Oxford Nanopore Technologies MinION Mk1b system, for arboviral detection in field-caught mosquitoes from Argentina. Full genome of Humaita Tubiacanga Virus (HTV), Phasi Charoen-like Phasivirus (PCLV), Aedes aegypti totivirus (AaeTV) has been sequenced in three distinct regions of Argentina comprising Buenos Aires province, Santa Fe province and the northern province of Salta. Viral sequences enriched by SISPA and coupled with Nanopore sequencing can be a useful tool for viral surveillance, not only for detecting viruses that have a high impact on human and animal health, but also for detecting insect-specific viruses that could promote the transmission of arboviruses.

RsNRAMP5, a major metal transporter, promotes cadmium influx and ROS accumulation in radish (Raphanus sativus L.)

Arable soil contamination with heavy metals (HMs) poses a great potential threat to vegetable crops and human health. Radish (Raphanus sativus L.), an economical and popular root vegetable crop, is easily absorbed HMs by its taproot. Although the Natural Resistance-Associated Macrophage Proteins (NRAMPs) were participated in transporting a number of HMs in plants, whether and how the NRAMP genes involved in cadmium (Cd) uptake and transport remains elusive in radish. In this study, a total of nine RsNRAMP gene members were identified, which were classified into three subgroups and dispersed on six radish chromosomes. Three RsNRAMPs (RsNRAMP3, RsNRAMP4 and RsNRAMP5) displayed high expression in the vascular cambium, and they exhibited obviously Cd-induced expression, among which the expression of RsNRAMP4 and RsNRAMP5 reached to the highest level at 24h. Moreover, the RsNRAMP5 was localized to the plasma membrane and its promoter activity was dramatically induced by Cd exposure. Heterologous expression analysis indicated that over-expression of RsNRAMP5 significantly promoted the uptake of Cd, lead (Pb), iron (Fe) and manganese (Mn) in yeast cells. In addition, the transient over-expression of RsNRAMP5 promoted Cd uptake and enhanced ROS (reactive oxygen species) accumulation in radish cotyledons. These findings would expedite unraveling the molecular mechanism underlying RsNRAMP5-mediated Cd uptake and transport in radish.

Recombination Analysis of Geminiviruses Using Recombination Detection Program (RDP)

Geminiviruses are recombination-prone, and characterizing this evolutionary process within their genomes is a frequent goal of researchers. RDP is a stand-alone Windows program combining many algorithms that detect and characterize recombination. It has been widely used by the geminivirus community (and beyond). Here we describe the use of RDP4 and RDP5 for analysis of geminiviral nucleotide sequences including: (i) obtaining a reasonable dataset for analysis, (ii) making a credible multiple sequence alignment and (iii) analyzing an alignment with RDP on that alignment. RDP to both characterize recombination events and to produce statistically recombination-free datasets for other molecular evolution analyses.

Centromere Landscapes Resolved from Hundreds of Human Genomes

High-fidelity (HiFi) sequencing has facilitated the assembly and analysis of the most repetitive region of the genome, the centromere. Nevertheless, our current understanding of human centromeres is based on a relatively small number of telomere-to-telomere assemblies, which have not yet captured its full diversity. In this study, we investigated the genomic diversity of human centromere higher order repeats (HORs) via both HiFi reads and haplotype-resolved assemblies from hundreds of samples drawn from ongoing pangenome-sequencing projects and reprocessed them via a novel HOR annotation pipeline, HiCAT-human. We used this wealth of data to provide a global survey of the centromeric HOR landscape; in particular, we found that 23 HORs presented significant copy number variability between populations. We detected three centromere genotypes with unbalanced population frequencies on chromosomes 5, 8, and 17. An inter-assembly comparison of HOR loci further revealed that while HOR array structures are diverse, they nevertheless tend to form a number of specific landscapes, each exhibiting different levels of HOR subunit expansion and possibly reflecting a cyclical evolutionary transition from homogeneous to nested structures and back.

EF-P and its paralog EfpL (YeiP) differentially control translation of proline-containing sequences

Polyproline sequences are deleterious to cells because they stall ribosomes. In bacteria, EF-P plays an important role in overcoming such polyproline sequence-induced ribosome stalling. Additionally, numerous bacteria possess an EF-P paralog called EfpL (also known as YeiP) of unknown function. Here, we functionally and structurally characterize EfpL from Escherichia coli and demonstrate its role in the translational stress response. Through ribosome profiling, we analyze the EfpL arrest motif spectrum and find additional sequences beyond the canonical polyproline motifs that both EF-P and EfpL can resolve. Notably, the two factors can also induce pauses. We further report that EfpL can sense the metabolic state of the cell via lysine acylation. Overall, our work characterizes the role of EfpL in ribosome rescue at proline-containing sequences, and provides evidence that co-occurrence of EF-P and EfpL is an evolutionary driver for higher bacterial growth rates.

Distinct profiles of plant immune resilience revealed by natural variation in warm temperature-modulated disease resistance among Arabidopsis accessions

Elevated temperature suppresses the plant defence hormone salicylic acid (SA) by downregulating the expression of master immune regulatory genes CALMODULIN BINDING PROTEIN 60-LIKE G (CBP60g) and SYSTEMIC ACQUIRED RESISTANCE DEFICIENT1 (SARD1). However, previous studies in Arabidopsis thaliana plants have primarily focused on the accession Columbia-0 (Col-0), while the genetic determinants of intraspecific variation in Arabidopsis immunity under elevated temperature remain unknown. Here we show that BASIC HELIX LOOP HELIX 059 (bHLH059), a thermosensitive SA regulator at nonstress temperatures, does not regulate immune suppression under warmer temperatures. In agreement, temperature-resilient and -sensitive Arabidopsis accessions based on disease resistance to the bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000 did not correlate with bHLH059 polymorphisms. Instead, we found that temperature-resilient accessions exhibit varying CBP60g and SARD1 expression profiles, potentially revealing CBP60g/SARD1-dependent and independent mechanisms of immune resilience to warming temperature. We identified thermoresilient accessions that exhibited either temperature-sensitive or -insensitive induction of the SA biosynthetic gene ICS1 (direct target gene of CBP60g and SARD1) and SA hormone levels. Collectively, this study has unveiled the intraspecific diversity of Arabidopsis immune responses under warm temperatures, which could aid in predicting plant responses to climate change and provide foundational knowledge for climate-resilient crop engineering.

The Soybean Cyst Nematode Effector Cysteine Protease 1 (CPR1) Targets a Mitochondrial Soybean Branched-Chain Amino Acid Aminotransferase (GmBCAT1)

The soybean cyst nematode (SCN; Heterodera glycines) facilitates infection by secreting a repertoire of effector proteins into host cells to establish a permanent feeding site composed of a syncytium of root cells. Among the diverse proteins secreted by the nematode, we were specifically interested in identifying proteases to pursue our goal of engineering decoy substrates that elicit an immune response when cleaved by an SCN protease. We identified a cysteine protease that we named Cysteine Protease 1 (CPR1), which was predicted to be a secreted effector based on transcriptomic data obtained from SCN esophageal gland cells, the presence of a signal peptide, and the lack of transmembrane domains. CPR1 is conserved in all isolates of SCN sequenced to date, suggesting it is critical for virulence. Transient expression of CPR1 in Nicotiana benthamiana leaves suppressed cell death induced by a constitutively active nucleotide binding leucine-rich repeat protein, RPS5, indicating that CPR1 inhibits effector-triggered immunity. CPR1 localizes in part to the mitochondria when expressed in planta. Proximity-based labeling in transgenic soybean roots, co-immunoprecipitation, and cleavage assays identified a branched-chain amino acid aminotransferase from soybean (GmBCAT1) as a substrate of CPR1. Consistent with this, GmBCAT1 also localizes to mitochondria. Silencing of the CPR1 transcript in the nematode reduced penetration frequency in soybean roots, while the expression of CPR1 in soybean roots enhanced susceptibility. Our data demonstrates that CPR1 is a conserved effector protease with a direct target in soybean roots, highlighting it as a promising candidate for decoy engineering. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

The metabolic characteristics and environmental adaptations of the intertidal bacterium Palleronia sp. LCG004

The intertidal zone, a dynamic interface of marine, atmospheric, and terrestrial ecosystems, exposes microorganisms to rapid shifts in temperature, salinity, and oxidative stress. Strain LCG004, representing a novel Palleronia species, was isolated from the Lu Chao Harbor's intertidal seawater in the Western Pacific Ocean. The genome of the organism reveals its metabolic versatility, enabling the utilization of various organic substrates-ranging from organic acids, amino acids, to sugars, and encompassing complex carbohydrates-as well as adept handling of inorganic nutrients, thereby highlighting its significant role in the cycling of nutrients. The strain is equipped with multiple osmoprotectant transporters, deoxyribodipyrimidine photo-lyase, and a comprehensive antioxidant defense system, featuring with multiple catalases, peroxidases, and superoxide dismutases, enabling it to withstand ever-changing environmental conditions, UV radiation, and oxidative challenges. Notably, LCG004 exhibited enhanced growth and cell aggregation under oligotrophic conditions, promoted by light exposure, underscoring the significant influence of light on its morphological and physiological attributes. This study elucidates strain LCG004's metabolic characteristics and ecological potential, and offers insights into its contributions to biogeochemical cycles and survival strategies in one of nature's most fluctuating environments.

Microbial communities on microplastics from seawater and mussels: Insights from the northern Adriatic Sea

Microplastics, synthetic solid particles of different sizes (< 5 mm), pose a major challenge to marine ecosystems. Introducing microplastics into the marine environment leads to the formation of complex microbial communities, a topic of growing interest in environmental research. For this study, we selected an area in the northern Adriatic Sea, less affected by human activities, to understand how pristine environmental conditions influence microbial colonization of microplastics. Samples of coastal seawater and Mediterranean mussels (Mytilus galloprovincialis) were collected in a mussel farm near Debeli rtič of the Slovenian coast. Microplastics were isolated, visually and chemically analyzed and DNA was extracted for metagenomics. In the marine water column, 12.7 microplastics per m3 water column and 0.58 microplastics per individual mussel were found. Sufficient DNA was available to analyze six particles, five originating from seawater, and one from a mussel. This was the first-ever sequenced microplastic particle from a mussel. Genera of Pseudomonas and Serratia were identified in all samples. In one of the samples, the most abundant was a marine genus Pseudoalteromonas, while in another sample Campylobacter was present with >30 % abundance. The microbiomes of the mussel- and seawater-isolated particles were similar, suggesting a common microbial colonization pattern, which may have implications for the transfer of microplastic-associated microbes, including potential pathogens, through the food web to the consumers. Microplastic pollution is a complex issue requiring further research, especially regarding microbial biofilms, pathogen colonization and the potential of pathogen transmission via microplastic particles. Our findings enhance the understanding of microplastic pollution in the Adriatic Sea and stress the necessity for comprehensive strategies to mitigate the impact on marine ecosystems.

CRISPR/Cas9-Mediated fech Knockout Zebrafish: Unraveling the Pathogenesis of Erythropoietic Protoporphyria and Facilitating Drug Screening

Erythropoietic protoporphyria (EPP1) results in painful photosensitivity and severe liver damage in humans due to the accumulation of fluorescent protoporphyrin IX (PPIX). While zebrafish (Danio rerio) models for porphyria exist, the utility of ferrochelatase (fech) knockout zebrafish, which exhibit EPP, for therapeutic screening and biological studies remains unexplored. This study investigated the use of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-mediated fech-knockout zebrafish larvae as a model of EPP1 for drug screening. CRISPR/Cas9 was employed to generate fech-knockout zebrafish larvae exhibiting morphological defects without lethality prior to 9 days post-fertilization (dpf). To assess the suitability of this model for drug screening, ursodeoxycholic acid (UDCA), a common treatment for cholestatic liver disease, was employed. This treatment significantly reduced PPIX fluorescence and enhanced bile-secretion-related gene expression (abcb11a and abcc2), indicating the release of PPIX. Acridine orange staining and quantitative reverse transcription polymerase chain reaction analysis of the bax/bcl2 ratio revealed apoptosis in fech-/- larvae, and this was reduced by UDCA treatment, indicating suppression of the intrinsic apoptosis pathway. Neutral red and Sudan black staining revealed increased macrophage and neutrophil production, potentially in response to PPIX-induced cell damage. UDCA treatment effectively reduced macrophage and neutrophil production, suggesting its potential to alleviate cell damage and liver injury in EPP1. In conclusion, CRISPR/Cas9-mediated fech-/- zebrafish larvae represent a promising model for screening drugs against EPP1.

Biochemical characterization of Prokineticin 2 binding to Prokineticin receptor 1 in zebrafish

Prokineticin 2 (PK2) binds to prokineticin receptor 1 and prokineticin receptor 2 (PKR1 and PKR2, respectively), two G protein-coupled receptors (GPCRs) that can mediate multiple signalling pathways by promoting the elevation of intracellular calcium and cAMP levels, phosphorylation of Akt and activation of ERK and STAT3. This work aims to evidence the conservation of protein sequence and the mechanism of PK2 binding to PKR1 to use the zebrafish model for the identification of new drugs as targets of prokineticin receptors. To this end, we first demonstrated that the zebrafish genes pk2 and pkr1 are phylogenetically related to orthologous mammalian genes by constructing evolutionary trees and performing syntenic analyses. Subsequently, by comparing the amino acid sequences, we showed that the interaction sites with PK2 are conserved in the zPKR1. Using GST pull-down and cross-linking experiments, we demonstrated the crucial role of the N-terminal region of zPKR1 for binding to the PK2. Finally, by expressing zPKR1 in CHO cells, we demonstrated the ability of zPKR1 to induce the activation of ERK and STAT3.

Biallelic RXFP2 variants lead to congenital bilateral cryptorchidism and male infertility, supporting a role of RXFP2 in spermatogenesis

STUDY QUESTION

Does RXFP2 disruption impair male fertility?

SUMMARY ANSWER

We identified biallelic variants in RXFP2 in patients with male infertility due to spermatogenic arrest at the spermatid stage, supporting a role of RXFP2 in human spermatogenesis, specifically in germ cell maturation.

WHAT IS KNOWN ALREADY

Since RXFP2, the receptor for INSL3, plays a crucial role in testicular descent during prenatal development, biallelic variants lead to bilateral cryptorchidism, as described in four families to date. While animal models have also suggested a function in spermatogenesis, the postnatal functions of RXFP2 and its ligand INSL3, produced in large amounts by the testes from puberty throughout adulthood, are largely unknown.

STUDY DESIGN, SIZE, DURATION

A family with two male members affected by impaired fertility due to spermatogenic maturation arrest and a history of bilateral cryptorchidism underwent clinical, endocrinological, histological, genomic, in vitro cellular, and in silico investigations.

PARTICIPANTS/MATERIALS, SETTING, METHODS

The endocrinological and histological findings were correlated with publicly available single-cell RNA sequencing (scRNA-seq) data. The genomic defects have been characterized using long-read sequencing and validated with in silico modeling and an in vitro cyclic AMP reporter gene assay.

MAIN RESULTS AND THE ROLE OF CHANCE

An intragenic deletion of exon 1-5 of RXFP2 (NM_130806.5) was detected in trans with a hemizygous missense variant c.229G>A, p.(Glu77Lys). The p.(Glu77Lys) variant caused no clear change in cell surface expression or ability to bind INSL3, but displayed absence of a cAMP signal in response to INSL3, indicating a loss-of-function. Testicular biopsy in the proband showed a maturation arrest at the spermatid stage, corresponding to the highest level of RXFP2 expression in scRNA-seq data, thereby providing a potential explanation for the impaired fertility.

LIMITATIONS, REASONS FOR CAUTION

Although this is so far the only study of human cases that supports the role of RXFP2 in spermatogenic maturation, this is corroborated by several animal studies that have already demonstrated a postnatal function of INSL3 and RXFP2 in spermatogenesis.

WIDER IMPLICATIONS OF THE FINDINGS

This study corroborates RXFP2 as gene implicated in autosomal recessive congenital bilateral cryptorchidism due to biallelic variants, rather than autosomal-dominant cryptorchidism due to monoallelic RXFP2 variants. Our findings also support that RXFP2 is essential in human spermatogenesis, specifically in germ cell maturation, and that biallelic disruption can cause male infertility through spermatogenic arrest at the spermatid stage.

STUDY FUNDING/COMPETING INTEREST(S)

Funding was provided by the Bellux Society for Pediatric Endocrinology and Diabetology (BELSPEED) and supported by a Research Foundation Flanders (FWO) senior clinical investigator grant (E.D.B., 1802220N) and a Ghent University Hospital Special Research Fund grant (M.C., FIKO-IV institutional fund). The authors declare no conflict of interest.

TRIAL REGISTRATION NUMBER

N/A.

Transposition with Tn3-family elements occurs through interaction with the host β-sliding clamp processivity factor

Tn3 family transposons are a widespread group of replicative transposons, notorious for contributing to the dissemination of antibiotic resistance, particularly the global prevalence of carbapenem resistance. The transposase (TnpA) of these elements catalyzes DNA breakage and rejoining reactions required for transposition. However, the molecular mechanism for target site selection with these elements remains unclear. Here, we identify a QLxxLR motif in N-terminal of Tn3 TnpAs and demonstrate that this motif allows interaction between TnpA of Tn3 family transposon Tn1721 and the host β-sliding clamp (DnaN), the major processivity factor of the DNA replication machinery. The TnpA-DnaN interaction is essential for Tn1721 transposition. Our work unveils a mechanism whereby Tn3 family transposons can bias transposition into certain replisomes through an interaction with the host replication machinery. This study further expands the diversity of mobile elements that use interaction with the host replication machinery to bias integration.

Graph-based analysis of DNA sequence comparison in closed cotton species: A generalized method to unveil genetic connections

Graph theory provides a systematic method for modeling and analysing complicated biological data as an effective bioinformatics tool. Based on current trends, the number of DNA sequences in the DNA database is growing quickly. To determine the origin of a species and identify homologous sequences, it is crucial to detect similarities in DNA sequences. Alignment-free techniques are required for accurate measures of sequence similarity, which has been one of the main issues facing computational biologists. The current study provides a mathematical technique for comparing DNA sequences that are constructed in graph theory. The sequences of each DNA were divided into pairs of nucleotides, from which weighted loop digraphs and corresponding weighted vectors were computed. To check the sequence similarity, distance measures like Cosine, Correlation, and Jaccard were employed. To verify the method, DNA segments from the genomes of ten species of cotton were tested. Furthermore, to evaluate the efficacy of the proposed methodology, a K-means clustering method was performed. This study proposes a proof-of-model that utilises a distance matrix approach that promises impressive outcomes with future optimisations to be made to the suggested solution to get the hundred percent accurate result. In the realm of bioinformatics, this paper highlights the use of graph theory as an effective tool for biological data study and sequence comparison. It's expected that further optimization in the proposed solution can bring remarkable results, as this paper presents a proof-of-concept implementation for a given set of data using the proposed distance matrix technique.

Fission yeast Duc1 links to ER-PM contact sites and influences PM lipid composition and cytokinetic ring anchoring

Cytokinesis is the final stage of the cell cycle that results in the physical separation of daughter cells. To accomplish cytokinesis, many organisms build an actin- and myosin-based cytokinetic ring (CR) that is anchored to the plasma membrane (PM). Defects in CR-PM anchoring can arise when the PM lipid phosphatidylinositol (4,5)-bisphosphate [PI(4,5)P2] is depleted. In Schizosaccharomyces pombe, reduced PM PI(4,5)P2 results in a CR that cannot maintain a medial position and slides toward one cell end, resulting in two differently sized daughter cells. S. pombe PM PI(4,5)P2 is synthesized by the phosphatidylinositol 4-phosphate 5-kinase (PI5-kinase) Its3, but what regulates this enzyme to maintain appropriate PM PI(4,5)P2 levels in S. pombe is not known. To identify Its3 regulators, we used proximity-based biotinylation, and the uncharacterized protein Duc1 was specifically detected. We discovered that Duc1 decorates the PM except at the cell division site and that its unique localization pattern is dictated by binding to the endoplasmic reticulum (ER)-PM contact site proteins Scs2 and Scs22. Our evidence suggests that Duc1 also binds PI(4,5)P2 and helps enrich Its3 at the lateral PM, thereby promoting PM PI(4,5)P2 synthesis and robust CR-PM anchoring.

Decrypting the phylogenetics history of EGF-CFC proteins Cripto and Cryptic

EGF-CFC proteins are obligate coreceptors for Nodal signaling and are thus required for gastrulation and left-right patterning. Species with multiple family members show evidence of specialization. For example, mouse Cripto is required for gastrulation, whereas Cryptic is involved in left-right patterning. However, the members of the family across model organisms have little sequence conservation beyond the EGF-CFC domain, posing challenges for determining their evolutionary history and functional conservation. In this study we outline the evolutionary history of the EGF-CFC family of proteins. We traced the EGF-CFC gene family from a single gene in the deuterostome ancestor through its expansion and functional specialization in tetrapods, and subsequent gene loss and translocation in eutherian mammals. Mouse Cripto and Cryptic, zebrafish Tdgf1, and all three Xenopus EGF-CFC genes (Tdgf1, Tdgf1.2 and Cripto.3) and are all descendants of the ancestral Tdgf1 gene. We propose that subsequent to the family expansion in tetrapods, Tdgf1B (Xenopus Tdgf1.2) acquired specialization in the left-right patterning cascade, and after its translocation in eutherians to a different chromosomal location, Cfc1/Cryptic has maintained that specialization.

Molecular evolution of Hokkaido virus, a genotype of Orthohantavirus puumalaense, among Myodes rodents

Viruses in the genus Orthohantavirus within the family Hantaviridae cause human hantavirus infections and represent a threat to public health. Hokkaido virus (HOKV), a genotype of Orthohantavirus puumalaense (Puumala virus; PUUV), was first identified in Tobetsu, Hokkaido, Japan. Although it is genetically related to the prototype of PUUV, the evolutionary pathway of HOKV is unclear. We conducted a field survey in a forest in Tobetsu in 2022 and captured 44 rodents. Complete coding genome sequences of HOKVs were obtained from five viral-RNA-positive rodents (four Myodes rufocanus bedfordiae and one Apodemus speciosus). Phylogenetic analysis revealed a close relationship between the phylogenies and geographical origins of M. rufocanus-related orthohantaviruses. Comparison of the phylogenetic trees of the S segments of orthohantaviruses and the cytochrome b genes of Myodes species suggested that Myodes-related orthohantaviruses evolved in Myodes rodent species as a result of genetic isolation and host switching.

Functional analysis of ESRP1/2 gene variants and CTNND1 isoforms in orofacial cleft pathogenesis

Orofacial cleft (OFC) is a common human congenital anomaly. Epithelial-specific RNA splicing regulators ESRP1 and ESRP2 regulate craniofacial morphogenesis and their disruption result in OFC in zebrafish, mouse and humans. Using esrp1/2 mutant zebrafish and murine Py2T cell line models, we functionally tested the pathogenicity of human ESRP1/2 gene variants. We found that many variants predicted by in silico methods to be pathogenic were functionally benign. Esrp1 also regulates the alternative splicing of Ctnnd1 and these genes are co-expressed in the embryonic and oral epithelium. In fact, over-expression of ctnnd1 is sufficient to rescue morphogenesis of epithelial-derived structures in esrp1/2 zebrafish mutants. Additionally, we identified 13 CTNND1 variants from genome sequencing of OFC cohorts, confirming CTNND1 as a key gene in human OFC. This work highlights the importance of functional assessment of human gene variants and demonstrates the critical requirement of Esrp-Ctnnd1 acting in the embryonic epithelium to regulate palatogenesis.

Dissecting structure and function of the monovalent cation/H+ antiporters Mdm38 and Ylh47 in Saccharomyces cerevisiae

Saccharomyces cerevisiae Mdm38 and Ylh47 are homologs of the Ca2+/H+ antiporter Letm1, a candidate gene for seizures associated with Wolf-Hirschhorn syndrome in humans. Mdm38 is important for K+/H+ exchange across the inner mitochondrial membrane and contributes to membrane potential formation and mitochondrial protein translation. Ylh47 also localizes to the inner mitochondrial membrane. However, knowledge of the structures and detailed transport activities of Mdm38 and Ylh47 is limited. In this study, we conducted characterization of the ion transport activities and related structural properties of Mdm38 and Ylh47. Growth tests using Na+/H+ antiporter-deficient Escherichia coli strain TO114 showed that Mdm38 and Ylh47 had Na+ efflux activity. Measurement of transport activity across E. coli-inverted membranes showed that Mdm38 and Ylh47 had K+/H+, Na+/H+, and Li+/H+ antiport activity, but unlike Letm1, they lacked Ca2+/H+ antiport activity. Deletion of the ribosome-binding domain resulted in decreased Na+ efflux activity in Mdm38. Structural models of Mdm38 and Ylh47 identified a highly conserved glutamic acid in the pore-forming membrane-spanning region. Replacement of this glutamic acid with alanine, a non-polar amino acid, significantly impaired the ability of Mdm38 and Ylh47 to complement the salt sensitivity of E. coli TO114. These findings not only provide important insights into the structure and function of the Letm1-Mdm38-Ylh47 antiporter family but by revealing their distinctive properties also shed light on the physiological roles of these transporters in yeast and animals.

IMPORTANCE

The inner membrane of mitochondria contains numerous ion transporters, including those facilitating H+ transport by the electron transport chain and ATP synthase to maintain membrane potential. Letm1 in the inner membrane of mitochondria in animals functions as a Ca2+/H+ antiporter. However, this study reveals that homologous antiporters in mitochondria of yeast, Mdm38 and Ylh47, do not transport Ca2+ but instead are selective for K+ and Na+. Additionally, the identification of conserved amino acids crucial for antiporter activity further expanded our understanding of the structure and function of the Letm1-Mdm38-Ylh47 antiporter family.

Genomic and physiological properties of Anoxybacterium hadale gen. nov. sp. nov. reveal the important role of dissolved organic sulfur in microbial metabolism in hadal ecosystems

Hadal zones account for the deepest 45% of the oceanic depth range and play an important role in ocean biogeochemical cycles. As the least-explored aquatic habitat on earth, hadal ecosystems contain a vast diversity of so far uncultured microorganisms that cannot be grown on conventional laboratory culture media. Therefore, it has been difficult to gain a true understanding of the detailed metabolic characteristics and ecological functions of those difficult-to-culture microorganisms in hadal environments. In this study, a novel anaerobic bacterial strain, MT110T, was isolated from a hadal sediment-water interface sample of the Mariana Trench at 10,890 m. The level of 16S rRNA gene sequence similarity and percentage of conserved proteins between strain MT110T and the closest relatives, Anaerovorax odorimutans DSM 5092T (94.9 and 46.6%) and Aminipila butyrica DSM 103574T (94.4 and 46.7%), indicated that strain MT110T exhibits sufficient molecular differences for genus-level delineation. Phylogenetic analyses based on both 16S rRNA gene and genome sequences showed that strain MT110T formed an independent monophyletic branch within the family Anaerovoracaceae. The combined evidence showed that strain MT110T represents a novel species of a novel genus, proposed as Anoxybacterium hadale gen. nov. sp. nov. (type strain MT110T = KCTC 15922T = MCCC 1K04061T), which represents a previously uncultured lineage of the class Clostridia. Physiologically, no tested organic matter could be used as sole carbon source by strain MT110T. Genomic analysis showed that MT110T had the potential capacity of utilizing various carbon sources, but the pathways of sulfur reduction were largely incomplete. Our experiments further revealed that cysteine is one of the essential nutrients for the survival of strain MT110T, and cannot be replaced by sulfite, leucine, or taurine. This result suggests that organic sulfur compounds might play an important role in metabolism and growth of the family Anaerovoracaceae and could be one of the key factors affecting the cultivation of the uncultured microbes. Our study brings a new perspective to the role of dissolved organic sulfur in hadal ecosystems and also provides valuable information for optimizing the conditions of isolating related microbial taxa from the hadal environment.

Wastewater Surveillance of SARS-CoV-2 in Zambia: An Early Warning Tool

Wastewater-based surveillance has emerged as an important method for monitoring the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). This study investigated the presence of SARS-CoV-2 in wastewater in Zambia. We conducted a longitudinal study in the Copperbelt and Eastern provinces of Zambia from October 2023 to December 2023 during which 155 wastewater samples were collected. The samples were subjected to three different concentration methods, namely bag-mediated filtration, skimmed milk flocculation, and polythene glycol-based concentration assays. Molecular detection of SARS-CoV-2 nucleic acid was conducted using real-time Polymerase Chain Reaction (PCR). Whole genome sequencing was conducted using Illumina COVIDSEQ assay. Of the 155 wastewater samples, 62 (40%) tested positive for SARS-CoV-2. Of these, 13 sequences of sufficient length to determine SARS-CoV-2 lineages were obtained and 2 sequences were phylogenetically analyzed. Various Omicron subvariants were detected in wastewater including BA.5, XBB.1.45, BA.2.86, and JN.1. Some of these subvariants have been detected in clinical cases in Zambia. Interestingly, phylogenetic analysis positioned a sequence from the Copperbelt Province in the B.1.1.529 clade, suggesting that earlier Omicron variants detected in late 2021 could still be circulating and may not have been wholly replaced by newer subvariants. This study stresses the need for integrating wastewater surveillance of SARS-CoV-2 into mainstream strategies for monitoring SARS-CoV-2 circulation in Zambia.

Bioinformatic, Enzymatic, and Structural Characterization of Trichuris suis Hexosaminidase HEX-2

Hexosaminidases are key enzymes in glycoconjugate metabolism and occur in all kingdoms of life. Here, we have investigated the phylogeny of the GH20 glycosyl hydrolase family in nematodes and identified a β-hexosaminidase subclade present only in the Dorylaimia. We have expressed one of these, HEX-2 from Trichuris suis, a porcine parasite, and shown that it prefers an aryl β-N-acetylgalactosaminide in vitro. HEX-2 has an almost neutral pH optimum and is best inhibited by GalNAc-isofagomine. Toward N-glycan substrates, it displays a preference for the removal of GalNAc residues from LacdiNAc motifs as well as the GlcNAc attached to the α1,3-linked core mannose. Therefore, it has a broader specificity than insect fused lobe (FDL) hexosaminidases but one narrower than distant homologues from plants. Its X-ray crystal structure, the first of any subfamily 1 GH20 hexosaminidase to be determined, is closest to Streptococcus pneumoniae GH20C and the active site is predicted to be compatible with accommodating both GalNAc and GlcNAc. The new structure extends our knowledge about this large enzyme family, particularly as T. suis HEX-2 also possesses the key glutamate residue found in human hexosaminidases of either GH20 subfamily, including HEXD whose biological function remains elusive.

Use of Nonhuman Sera as a Highly Cost-Effective Internal Standard for Quantitation of Multiple Human Proteins Using Species-Specific Tryptic Peptides: Applicability in Clinical LC-MS Analyses

Quantitation of proteins using liquid chromatography-tandem mass spectrometry (LC-MS/MS) is complex, with a multiplicity of options ranging from label-free techniques to chemically and metabolically labeling proteins. Increasingly, for clinically relevant analyses, stable isotope-labeled (SIL) internal standards (ISs) represent the "gold standard" for quantitation due to their similar physiochemical properties to the analyte, wide availability, and ability to multiplex to several peptides. However, the purchase of SIL-ISs is a resource-intensive step in terms of cost and time, particularly for screening putative biomarker panels of hundreds of proteins. We demonstrate an alternative strategy utilizing nonhuman sera as the IS for quantitation of multiple human proteins. We demonstrate the effectiveness of this strategy using two high abundance clinically relevant analytes, vitamin D binding protein [Gc globulin] (DBP) and albumin (ALB). We extend this to three putative risk markers for cardiovascular disease: plasma protease C1 inhibitor (SERPING1), annexin A1 (ANXA1), and protein kinase, DNA-activated catalytic subunit (PRKDC). The results show highly specific, reproducible, and linear measurement of the proteins of interest with comparable precision and accuracy to the gold standard SIL-IS technique. This approach may not be applicable to every protein, but for many proteins it can offer a cost-effective solution to LC-MS/MS protein quantitation.

The core spindle pole body scaffold Ppc89 links the pericentrin orthologue Pcp1 to the fission yeast spindle pole body via an evolutionarily conserved interface

Centrosomes and spindle pole bodies (SPBs) are important for mitotic spindle formation and serve as cellular signaling platforms. Although centrosomes and SPBs differ in morphology, many mechanistic insights into centrosome function have been gleaned from SPB studies. In the fission yeast Schizosaccharomyces pombe, the α-helical protein Ppc89, identified based on its interaction with the septation initiation network scaffold Sid4, comprises the SPB core. High-resolution imaging has suggested that SPB proteins assemble on the Ppc89 core during SPB duplication, but such interactions are undefined. Here, we define a connection between Ppc89 and the essential pericentrin Pcp1. Specifically, we found that a predicted third helix within Ppc89 binds the Pcp1 pericentrin-AKAP450 centrosomal targeting (PACT) domain complexed with calmodulin. Ppc89 helix 3 contains similarity to present in the N-terminus of Cep57 (PINC) motifs found in the centrosomal proteins fly SAS-6 and human Cep57 and also to the S. cerevisiae SPB protein Spc42. These motifs bind pericentrin-calmodulin complexes and AlphaFold2 models suggest a homologous complex assembles in all four organisms. Mutational analysis of the S. pombe complex supports the importance of Ppc89-Pcp1 binding interface in vivo. Our studies provide insight into the core architecture of the S. pombe SPB and suggest an evolutionarily conserved mechanism of scaffolding pericentrin-calmodulin complexes for mitotic spindle formation.

PrgE: an OB-fold protein from plasmid pCF10 with striking differences to prototypical bacterial SSBs

A major pathway for horizontal gene transfer is the transmission of DNA from donor to recipient cells via plasmid-encoded type IV secretion systems (T4SSs). Many conjugative plasmids encode for a single-stranded DNA-binding protein (SSB) together with their T4SS. Some of these SSBs have been suggested to aid in establishing the plasmid in the recipient cell, but for many, their function remains unclear. Here, we characterize PrgE, a proposed SSB from the Enterococcus faecalis plasmid pCF10. We show that PrgE is not essential for conjugation. Structurally, it has the characteristic OB-fold of SSBs, but it has very unusual DNA-binding properties. Our DNA-bound structure shows that PrgE binds ssDNA like beads on a string supported by its N-terminal tail. In vitro studies highlight the plasticity of PrgE oligomerization and confirm the importance of the N-terminus. Unlike other SSBs, PrgE binds both double- and single-stranded DNA equally well. This shows that PrgE has a quaternary assembly and DNA-binding properties that are very different from the prototypical bacterial SSB, but also different from eukaryotic SSBs.

Transient PP2A SIP complex localization to mitotic SPBs for SIN inhibition is mediated solely by the Csc1 FHA domain

Many organisms utilize an actin- and myosin-based cytokinetic ring (CR) to help complete cytokinesis. In Schizosaccharomyces pombe, the Septation Initiation Network (SIN) promotes proper CR function and stability. The SIN is a conserved and essential signaling network consisting of a GTPase and a cascade of kinases assembled at the spindle pole body (SPB). The PP2A SIN inhibitory phosphatase (SIP) complex related to the STRIPAK phosphatase complex is one inhibitor of SIN signaling. The SIP consists of Csc1, Csc2, Csc3, Csc4, Paa1, and the phosphatase subunit Ppa3. Here, we determine that the SIP is anchored at the SPB via the Csc1 FHA domain and that constitutive SPB localization of the SIP is lethal due to persistent SIN inhibition. Disrupting SIP docking at the SPB with a point mutation within the FHA domain or eliminating phosphatase activity by introducing a point mutation within Ppa3 resulted in intact SIP complexes without SIN inhibitory function. Lastly, we defined the unique features of Ppa3 that allow it, but not two other PP2A catalytic subunits, to incorporate into the SIP. Overall, we provide insight into how the SIP complex assembles, localizes, and functions to counteract the SIN with spatiotemporal precision during cytokinesis.

Evolutionarily conserved enhancer-associated features within the MYEOV locus suggest a regulatory role for this non-coding DNA region in cancer

The myeloma overexpressed gene (MYEOV) has been proposed to be a proto-oncogene due to high RNA transcript levels found in multiple cancers, including myeloma, breast, lung, pancreas and esophageal cancer. The presence of an open reading frame (ORF) in humans and other primates suggests protein-coding potential. Yet, we still lack evidence of a functional MYEOV protein. It remains undetermined how MYEOV overexpression affects cancerous tissues. In this work, we show that MYEOV has likely originated and may still function as an enhancer, regulating CCND1 and LTO1. Firstly, MYEOV 3' enhancer activity was confirmed in humans using publicly available ATAC-STARR-seq data, performed on B-cell-derived GM12878 cells. We detected enhancer histone marks H3K4me1 and H3K27ac overlapping MYEOV in multiple healthy human tissues, which include B cells, liver and lung tissue. The analysis of 3D genome datasets revealed chromatin interactions between a MYEOV-3'-putative enhancer and the proto-oncogene CCND1. BLAST searches and multi-sequence alignment results showed that DNA sequence from this human enhancer element is conserved from the amphibians/amniotes divergence, with a 273 bp conserved region also found in all mammals, and even in chickens, where it is consistently located near the corresponding CCND1 orthologues. Furthermore, we observed conservation of an active enhancer state in the MYEOV orthologues of four non-human primates, dogs, rats, and mice. When studying this homologous region in mice, where the ORF of MYEOV is absent, we not only observed an enhancer chromatin state but also found interactions between the mouse enhancer homolog and Ccnd1 using 3D-genome interaction data. This is similar to the interaction observed in humans and, interestingly, coincides with CTCF binding sites in both species. Taken together, this suggests that MYEOV is a primate-specific gene with a de novo ORF that originated at an evolutionarily older enhancer region. This deeply conserved putative enhancer element could regulate CCND1 in both humans and mice, opening the possibility of studying MYEOV regulatory functions in cancer using non-primate animal models.