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

Genome-wide identification and analysis of the NF-Y transcription factor family reveal its potential roles in tobacco (Nicotiana tabacum L.)

Nuclear Factor Y (NF-Y) represents a group of transcription factors commonly present in higher eukaryotes, typically consisting of three subunits: NF-YA, NF-YB, and NF-YC. They play crucial roles in the embryonic development, photosynthesis, flowering, abiotic stress responses, and other essential processes in plants. To better understand the genome-wide NF-Y domain-containing proteins, the protein physicochemical properties, chromosomal localization, synteny, phylogenetic relationships, genomic structure, promoter cis-elements, and protein interaction network of NtNF-Ys in tobacco (Nicotiana tabacum L.) were systematically analyzed. In this study, we identified 58 NtNF-Ys in tobacco, respectively, and divided into three subfamilies corresponding to their phylogenetic relationships. Their tissue specificity and expression pattern analyses for leaf development, drought and saline-alkali stress, and ABA response were carried out using RNA-seq or qRT-PCR. These findings illuminate the role of NtNF-Ys in regulating plant leaf development, drought and saline-alkali stress tolerance, and ABA response. This study offers new insights to enhance our understanding of the roles of NtNF-Ys and identify potential genes involved in leaf development, as well as drought and saline-alkali stress tolerance of plants.

Protein targeting to Starch 2 and the plastidial phosphorylase 1 revealed protein-protein interactions with photosynthesis proteins in yeast two-hybrid screenings

Starch metabolism in plants involves a complex network of interacting proteins that work together to ensure the efficient synthesis and degradation of starch. These interactions are crucial for regulating the balance between energy storage and release, adapting to the plant's developmental stage and environmental conditions. Several studies have been performed to investigate protein-protein interactions (PPIs) in starch metabolism complexes, yet it remains impossible to unveil all of the PPIs in this highly regulated process. This study uses yeast-two-hybrid (Y2H) screening against the Arabidopsis leaf cDNA library to explore PPIs, focusing on the starch-granule-initiating protein named Protein Targeting to Starch 2 (PTST2, At1g27070) and the protein involved in starch and maltodextrin metabolism, namely, plastidial phosphorylase 1 (PHS1, EC 2.4.1.1). More than 100 positive interactions were sequenced, and we found chloroplastidial proteins to be putative interacting partners of PTST2 and PHS1. Among them, photosynthetic proteins were discovered. These novel interactions could reveal new roles of PTST2 and PHS1 in the connection between starch metabolism and photosynthesis. This dynamic interplay between starch metabolism and other chloroplast functions highlights the importance of starch as both an energy reservoir and a regulatory component in the broader context of plant physiology and adaptation.

New freshwater Ceratomyxa species, Ceratomyxa schwanefeldii n. sp. (Myxozoa: Ceratomyxidae) from the gall bladder of tinfoil barb, Barbonymus schwanefeldii (Cyprinidae, Cypriniformes) in Malaysia

Genus Ceratomyxa comprises coelozoic parasites of mainly marine and brackish water fish. This study describes a new Ceratomyxa species, Ceratomyxa schwanefeldii n. sp. which parasitizes the gall bladder of Barbonymus schwanefeldii collected from Sungai Tong in Setiu, Terengganu, Malaysia. The new species was described using morphological characteristics, and on nucleotide sequences of small subunit ribosomal DNA (SSU rDNA) and large subunit ribosomal DNA (LSU rDNA). Ceratomyxa schwanefeldii n. sp. exhibited vermiform shape plasmodia with slow undulatory motility, measuring 151.6 ± 86.0 (43.0-271.0) μm in length and 15.1 ± 4.8 (9.3-22.7) μm in width, with blunt poles at both ends. The mature spores were crescent-shaped, strongly arched in frontal view, with a sutural line between the two valves tapering to blunt ends. Formalin-fixed spores were 3.0 ± 0.4 (2.4-3.9) μm in length, 12.6 ± 1.2 (10.8-15.4) μm in thickness, with a concave posterior angle, 104.8° ± 10.2° (73.4-123.8). Two equal-sized spheroid polar capsules measured 1.5 ± 0.2 (1.2-1.8) μm in length and 1.3 ± 0.2 (0.9-1.7) μm in width. Phylogenetic analyses by Maximum likelihood and Bayesian Inference algorithms positioned C. schwanefeldii n. sp. as a sister species to Unicapsulocaudum mugilum and clustered within the clade of Amazonian freshwater Ceratomyxa species. The LSU rDNA phylogeny revealed that C. schwanefeldii n. sp. clusters within the marine Ceratomyxa clade and forms a sister relationship with C. leatherjacketi. This study represents the first description of a freshwater Ceratomyxa in Malaysia and the fourth recorded detection in the Asian region.

Origin and diversification of Dicrocoeliidae (Neodermata, Trematoda) with the description of a new species of Euparadistomum, a parasite of Tropidurus torquatus (Squamata, Tropiduridae) in South America

A new digenean trematode species, Euparadistomum cisalpinai sp. n., is described parasitizing the gallbladder of Tropidurus torquatus from Brazil. A set of morphological features, including ovary shape, the oral/ventral sucker ratio, and the presence of cuticular papillae, distinguish the new species from other Euparadistomum species. Phylogenetic inferences using 28S rDNA sequences confirmed its placement within the family Dicrocoeliidae. Although some morphological variability was observed, COI sequences support conspecificity among the specimens. The origin of Dicrocoeliidae is estimated to date back to the Late Jurassic, a period marked by the fragmentation of Pangaea, the greatest radiation of insects, and the emergence of modern birds. These paleogeographic events, combined with the ecological traits of the hosts, likely served as key drivers of dicrocoeliid diversification. Additionaly, the opening of the North Atlantic, the dispersal of yangochiropteran bats, and the spread of Turdus birds significantly influenced the evolution of genera such as Lyperosomum, Anenterotrema, Metadelphis, and Lutztrema. This research provides key insights into the evolutionary and biogeographic history of Dicrocoeliidae, highlighting the pivotal role of host-parasite interactions and geographic events in shaping the diversification of these trematodes.

A conserved role for centriolar satellites in translation of centrosomal and ciliary proteins

Centriolar satellites are cytoplasmic particles found in the vicinity of centrosomes and cilia whose specific functional contribution has long been unclear. Here, we identify Combover as the Drosophila ortholog of the main scaffolding component of satellites, PCM1. Like PCM1, Combover localizes to cytoplasmic foci containing centrosomal proteins and its depletion or mutation results in centrosomal and ciliary phenotypes. Strikingly, however, the concentration of satellites near centrosomes and cilia is not a conserved feature, nor do Combover foci display directed movement. Proximity interaction analysis revealed not only centrosomal and ciliary proteins, but also RNA-binding proteins and proteins involved in quality control. Further work in Drosophila and vertebrate cells found satellites to be associated with centrosomal and ciliary mRNAs, as well as evidence for protein synthesis occurring directly at satellites. Given that PCM1 depletion does not affect overall protein levels, we propose that satellites instead promote the coordinate synthesis of centrosomal and ciliary proteins, thereby facilitating the formation of protein complexes.

Psychrophilic insights into petroleum degradation: Gene abundance dynamics

Petroleum degradation by psychrophiles can be enhanced on the basis of omics analyses, which offer better sensitivity than traditional biochemical methods do. A metagenomic analysis focusing on gene abundance comparisons may provide new guidance to optimize soil decontamination under cold environmental conditions. The soil used in this study was sampled from Dalian, from which an indigenous consortium was isolated. The degradative soil systems, initially categorized into control (DLC) and experimental (DLD) groups, were kept at room temperature (20 ± 5 °C) for six weeks. The DLD group was subsequently transferred to a low-temperature environment (5-10 °C) for 90 days and renamed DDL. A petroleum removal rate of 74.59 % was achieved in the process from DLD to DDL groups. Each soil sample was subjected to analysis and metagenomic sequencing. The abundance of genes of interest was compared between pathways to determine trends. The findings demonstrate that psychrophilic degradation is more effective than natural remediation is. The soil microbial community structure displayed site specificity, with 802 genes in DDL associated with 249 pathways, indicating greater abundance of psychrophilic genes in DDL than in DLC. The abundance of key genes was at different orders of magnitude but showed similar trends. The abundance of genes associated with hydrocarbon-related metabolism surpassed that of genes associated with sphingolipid, fatty acid, or benzene metabolism. This study provides valuable insights into psychrophilic microbe-driven petroleum degradation and indicates the need for precise supplementation of biosurfactants to improve remediation efficiency.

Grain protein function prediction based on improved FCN and bidirectional LSTM

With the development of high-throughput sequencing technologies, predicting grain protein function from amino acid sequences based on intelligent model has become one of the significant tasks in bioinformatics. The soybean, maize, indica, and japonica are selected as grain dataset from the UniProtKB. Aiming at the problem of neglecting the sequence order of amino acids and the long-term dependence between amino acids, the PBiLSTM-FCN model is proposed for predicting grain protein function in this paper. The sequence of amino acid sequences is considered in the Fully Convolutional Networks (FCN), and the long-term dependence between amino acids is addressed by the bidirectional Long Short-Term Memory network (BiLSTM). The experimental results show that the PBiLSTM-FCN model is superior to existing models, and can predict more accurately by solving the problem of capturing long-range dependencies and the order of amino acid sequences. Finally, the interpretability analyses are performed by the actual protein function compared with the predicted protein function which proves the effectiveness of the PBiLSTM-FCN model in predicting grain protein function.

PILOT: Deep Siamese network with hybrid attention improves prediction of mutation impact on protein stability

Evaluating the mutation impact on protein stability (ΔΔG) is essential in the study of protein engineering and understanding molecular mechanisms of disease-associated mutations. Here, we propose a novel deep learning framework, PILOT, for improved prediction of ΔΔG using a Siamese network with hybrid attention mechanism. The PILOT framework leverages multiple attention modules to effectively extract representations for amino acids, atoms, and protein sequences, respectively. This approach significantly ensures the deep fusion of structural information at both residue and atom levels, the seamless integration of structural and sequence representations, and the effective capture of both long-range and short-range dependencies among amino acids. Our extensive evaluations demonstrate that PILOT greatly outperforms other state-of-the-art methods. We also showcase that PILOT identifies exceptional patterns for different mutation types. Moreover, we illustrate the clinical applicability of PILOT in highlighting pathogenic variants from benign variants and VUS (variants of uncertain significance), and distinguishing de novo mutations in disease cases and controls. In summary, PILOT presents a robust deep learning tool that could offer significant insights into drug design, medical applications, and protein engineering studies.

A comprehensive review of computational methods for Protein-DNA binding site prediction

Accurately identifying protein-DNA binding sites is essential for understanding the molecular mechanisms underlying biological processes, which in turn facilitates advancements in drug discovery and design. While biochemical experiments provide the most accurate way to locate DNA-binding sites, they are generally time-consuming, resource-intensive, and expensive. There is a pressing need to develop computational methods that are both efficient and accurate for DNA-binding site prediction. This study thoroughly reviews and categorizes major computational approaches for predicting DNA-binding sites, including template detection, statistical machine learning, and deep learning-based methods. The 14 state-of-the-art DNA-binding site prediction models have been benchmarked on 136 non-redundant proteins, where the deep learning-based, especially pre-trained large language model-based, methods achieve superior performance over the other two categories. Applications of these DNA-binding site prediction methods are also involved.

Molecular epidemiological investigation and identification of Mycoplasma gallisepticum in large-scale duck farms

Mycoplasma gallisepticum (MG) can infect a wide range of birds, seriously jeopardizing the development of the poultry industry. A nested-PCR method was constructed based on mgc2 gene for evaluating the prevalence of MG in duck flocks. A total of 1002 samples were detected from Shandong and Inner Mongolia by this method. The total positive rate of MG was 22.75 % (228/1002), with the highest prevalence in commercial laying ducks (34.83 %), the lowest in dead duck embryos (6.67 %), and a proportionate prevalence of 17.33 % in commercial meat ducks. Genetic evolutionary analysis by mgc2 gene showed that the homology among the wild strains of duck derived MG was 73.3 %-99.8 %, which revealed genetic diversity, and the homology with the international chicken-derived MG reference strain was ranged 68.4 %-98.4 %, indicating that some duck-derived MG strains had an independent origin. Duck embryo pathogenicity tests showed only the mortality rate of duck embryos infected by strain 1-9 reached 60 %. To clarify the genetic background of strain 1-9, the data of whole genome sequencing showed that the full length of 1-9 was 962,503 bp, and the GC content was 31 %. Among the predicted 1576 genes, a total of 599 genes were functionally classified, and the virulence genes were distributed in 21 virulence factors. Phylogenetic tree based on 16S rRNA and single copy gene set were confirmed that there was a far genetic evolutionary distance between the isolate 1-9 and the chicken-derived reference strains. Our findings provided a scientific basis for the research on the pathogenicity and exploring functional genes of duck-derived MG.

Gut microbiota dysbiosis triggered by salinity stress enhances systemic inflammation in spotted scat (Scatophagus argus)

As an ecological disturbance, salinity changes substantially impact aquatic organism health. Gut microbiota plays a pivotal role in host health and exhibits heightened sensitivity to environmental salinity stress; however, the potential correlative mechanisms between gut microbiota dysbiosis triggered by salinity changes and host health remain unclear. The present study conducted a 4-week stress experiment to investigate the precise impact of gut microbiota on the inflammatory response in Scatophagus argus under different salinities (0 ‰ [hyposaline group, HO], 25 ‰ [control group, CT], and 40 ‰ [hypersaline group, HE]). Our results revealed that both HO and HE stress significantly changed the relative abundances of Gram-negative bacteria and the impairment of intestinal barrier function. Subsequently, the levels of lipopolysaccharide (LPS) in the serum exhibited a significant increase, and the expression levels of genes (tlrs, myd88, irak1, irak4, and traf6) involving TLRs/MyD88/NF-κB signaling pathway and pro-inflammatory cytokines (il-6, il-8, il-1β, and tnf-α) in the representative immune organs were significantly upregulated. Conversely, the abundance of the anti-inflammatory gene (tgf-β1) and its protein contents in serum were decreased. Transplantation of the gut microbiota from S. argus exposed to varying salinities into germ-free Oryzias latipes resulted in an enhanced inflammatory response. Our results suggested that both HO and HE stress increased the presence of Gram-negative bacteria and disrupted the intestinal barrier, leading to elevated serum LPS and subsequent systemic inflammation in fish. These findings provide innovative insights into the influence of salinity manipulation strategies on the health of aquatic organisms, contributing to the mariculture management in coastal areas.

Pseudomonas syringae exacerbates apple replant disease caused by Fusarium

Apple replant disease (ARD) causes significant economic losses globally, including in China. Analyzing the causes of this replant disease from the perspective of rhizosphere microecology is therefore essential. In this study, we examined rhizosphere soils from apple trees subjected to continuous cropping. The mechanisms underlying ARD were elucidated through high-throughput sequencing of the soil microbiome, co-occurrence network analysis using NetShift, and correlation analyses. Core bacterial microbes were isolated, and their roles in altering the microecological environment were verified through reinoculation experiments. The results indicated that the disease indices for apple seedlings cultivated increased in continuously cropped soils. Bacterial diversity decreased in continuously cropped apple orchards for 10 years (R10) and 15 years (R15), but the relative abundance of Pseudomonas increased. In contrast, fungal diversity increased, with the relative abundance of Fusarium also increasing. As a dominant genus, Pseudomonas exhibited significant network variation after 10 years of consecutive cultivation, suggesting that this microorganism may play a key role in the occurrence of ARD. Moreover, the correlation analysis revealed, for the first time, that Pseudomonas is negatively correlated with bacterial diversity but positively correlated with the relative abundance of Fusarium, indicating a close relationship between Pseudomonas and Fusarium in continuously cropped soil. Four key Pseudomonas amplicon sequence variants (ASVs) strains were isolated from the continuously cropped rhizosphere soil of apple trees, and reinoculation experiments verified that introducing Pseudomonas exacerbated the occurrence of replant diseases in both strawberry and apple, with significantly higher disease indices compared to single Fusarium inoculation. The findings of this study provide new and timely insights into the mechanism underlying the occurrence of ARD.

Strictly screening of HTLV-1/2 peptides can drive the development of rapid point-of-care tests

The Human T-cell lymphotropic virus (HTLV-1/2) cause neglected infections that drives life-threatening diseases and the numbers of infected people around the world are underestimated. Point-of-care tests (POCT) are useful to identifying carriers, to controlling the infection's spread with timely and cost-effectiveness, to include the most affected areas and susceptible populations, and the establishment of public health policies, including the control of vertical transmission. After in silico analysis of Env, Gag and Tax proteins of HTLV-1 and HTLV-2, we synthetized and characterized peptides to screening antibodies anti-HTLV-1/2 with high sensitivity and specificity. The 173 peptides chosen were screened by immunoblot, and by indirect in-house ELISA. Peptides that had best performed in recognize both, HTLV-1 or HTLV-2 sera from infected individual, were Gag-HTLV-1 and Gag-HTLV-2 showing to be very good candidates for screening tests. Peptides of Tax-HTLV-1, and Env-HTLV-2 had discriminated sera from HTLV-1 and HTLV-2 with high sensitivity and specificity. The screening of HTLV-1/2 peptides showed here, including the use of sera from HIV-infected individuals along with seronegative ones were crucial to avoid the use of peptides with unspecific reaction in the final pilot tests, and to reach the Point-of-care test that is under registration at regulatory Brazilian agency.

Unified Aedes aegypti Protein Resource Database (UAAPRD): An Integrated High-Throughput In Silico Platform for Comprehensive Protein Structure Modeling and Functional Target Analysis to Enhance Vector Control Strategies

A comprehensive examination of Aedes aegypti's proteome to detect key proteins that can be targeted with small molecules can disrupt blood feeding and disease transmission. However, research currently only focuses on finding repellent-like compounds, limiting studies on identifying unexplored proteins in its proteome. High-throughput analysis generates vast amounts of data, raising concerns about accessibility and usability. Establishing a dedicated database is a solution, centralizing information on identified proteins, functions, and modeled structures for easy access and research. This study focuses on scrutinizing key proteins in A. aegypti, modeling their structures using RaptorX standalone tool, identification of druggable binding sites using BiteNet, validating the models via Ramachandran plot studies and refining them via 50-ns molecular dynamic simulations using Schrodinger Maestro. By analyzing ~ 18 k proteins in the proteome of A. aegypti in our previous studies, all proteins involved in the light and dark circadian rhythm of the mosquito, inclusive of proteins in blood feeding, metabolism, etc. were chosen for the current study. The outcome is UAAPRD, a unique repository housing information on hundreds of previously unmodeled and un-simulated mosquito proteins. This robust MYSQL database ( https://uaaprd.onrender.com/user ) houses data on 309 modeled & simulated proteins of A. aegypti. It allows users to obtain protein data, view evolutionary analysis data of the protein categories, visualize proteins of interest, and send request to screen against the pharmacophore models present in UAAPRD against ligand of interest. This study offers crucial insights for developing targeted studies, which will ultimately contribute to more effective vector control strategies.

Genomic analysis and metabolic pathway mining of Phallus cremeo-ochraceus

Phallus cremeo-ochraceus is a nutritious edible mushroom. In this study, after tissue isolation, 33 strains were obtained, among which one strain PC7 with rapid mycelial growth and stable passage was obtained. Here, after quality control and assembly, a sequence of 410,647,36 bp was obtained, with 20,218 contigs. 23,184 genes were predicted, 8,092 were repetitive sequences, and 165 were non-coding RNA (ncRNA), which was obtained by the Illumina platform. NCBI Blast+ was used to compare the protein sequences of the genes with several databases, such as NR, KOG, GO, KEGG, CAzy, etc. The NR database annotated 18,159 genes, KOG annotated 6752 genes, GO annotated 5872 genes, and KEGG annotated 3820 genes. Exploration of the terpenoid synthesis pathway of strain PC7 by KEGG, the results revealed that the genome of PC7 has a more complete metabolic pathway regarding terpenoid synthesis. The analysis of amino acid metabolic pathways shows that Phallus cremeo-ochraceus contains 18 genes related to amino acid metabolic pathways. Combined with carbohydrate enzyme annotation and KEGG annotation, the genes related to carbon source, nitrogen source, sulfur source and growth factor of Phallus cremeo-ochraceus were analyzed, which enriched the related genomic research of Phallus cremeo-ochraceus.

Manure input propagated antibiotic resistance genes and virulence factors in soils by regulating microbial carbon metabolism

Antibiotic resistance genes (ARGs) and virulence factors (VFs) in soils represent a significant threat to ecological security and human health. The carbon-rich soil formed by manure fertilization provides an energy source for soil microbes. However, we still know little about how microbial-dominated carbon metabolism affects ARGs and VFs proliferation in soils subjected to long-term fertilization and irrigation practices in wheat-maize system. Here, we investigated soil microbial carbon metabolism, ARGs and VFs distribution, and microbial composition in soils under 9-year of different fertilization and irrigation managements during wheat growing period. Results showed that manure (M) increased total abundance of soil ARGs by 5.9 %-8.0 % and 2.1 %-4.8 % and VFs by 5.4 %-7.5 % and 2.0 %-4.9 % compared to no fertilizer (CK) and NPK fertilizer (C), respectively, regardless of irrigation. M enriched more number of ARGs and VFs types, and increased abundance of host microbes involved in carbon fixation and carbon degradation, such as Streptomyces, Lysobacter and Agromyces. M increased abundance of carbohydrate-active enzymes (CAZymes) and carbon cycle functional pathways, as well as microbial carbon metabolism capacity. Partial least squares path modeling and correlation analysis showed that microbial diversity, CAZymes, carbon cycle functional pathways (particularly carbon fixation and degradation) and microbial carbon metabolism capacity of microbial community had direct positive effects on the proliferation and spread of ARGs and VFs. In conclusion, our results highlight the importance of microbial mediated carbon metabolism in driving the dissemination of ARGs and VFs in soils under long-term manure application.

Whole-genome sequence of Salmonella Typhimurium E-5591 and its methionine sulfoxide reductase (msr) gene deletion mutant strains

Salmonella Typhimurium is one of the leading causes of foodborne illness in humans. Poultry products are the main source of infection for humans. Here we report the whole-genome sequences of Salmonella Typhimurium strain E-5591 (a field poultry isolate) and its mutant strains lacking the various methionine sulfoxide reductase genes.

A PCR primer design method for identifying spider mite species using k-mer counting

Using PCR to distinguish closely related species can be difficult because they may have very similar genomes. Advances in bioinformatics make it possible to design PCR primers that are species-specific. In this study, we developed a bioinformatics method for extracting species-specific primer candidate sequences (i.e., unpaired primers that were specific to a single species) from RNA-Seq data sets of 19 species of spider mites (Acari, Tetranychidae). Using k-mer counting, we obtained between 257 and 48,621 species-specific unpaired primer candidates for the 19 species. We then manually obtained a second primer that was also species-specific. The primer pairs were then confirmed to work in the target species and not to work in the non-target species. Finally, species-specific primer pairs were obtained for 17 of the 19 species tested. Such species-specific primers may be used for practical species discrimination by optimizing multiplex PCR. Our primer design method is expected to be applicable to other taxa.

Lysosomal TPC2 channels disrupt Ca2+ entry and dopaminergic function in models of LRRK2-Parkinson's disease

Parkinson's disease results from degeneration of dopaminergic neurons in the midbrain, but the underlying mechanisms are unclear. Here, we identify novel crosstalk between depolarization-induced entry of Ca2+ and lysosomal cation release in maintaining dopaminergic neuronal function. The common disease-causing G2019S mutation in LRRK2 selectively exaggerated Ca2+ entry in vitro. Chemical and molecular strategies inhibiting the lysosomal ion channel TPC2 reversed this. Using Drosophila, which lack TPCs, we show that the expression of human TPC2 phenocopied LRRK2 G2019S in perturbing dopaminergic-dependent vision and movement in vivo. Mechanistically, dysfunction required an intact pore, correct subcellular targeting and Rab interactivity of TPC2. Reducing Ca2+ permeability with a novel biased TPC2 agonist corrected deviant Ca2+ entry and behavioral defects. Thus, both inhibition and select activation of TPC2 are beneficial. Functional coupling between lysosomal cation release and Ca2+ influx emerges as a potential druggable node in Parkinson's disease.

Unearthing limestone fungal diversity: Description of seven novel species from Portugal

Stone-built heritages are found worldwide, and despite stony surfaces being considered a stressful environment with challenging conditions to overcome, research has demonstrated that it can support diverse fungal communities, fostering a unique array of peculiar yet crucial species. These species exhibit a dual nature, being both foe and friend. While these fungi play a considerable role in the deterioration of cultural heritage, their mechanisms of adaptation to unfavourable environments hold great promise for biotechnology. Despite their importance, there is limited information available about these stone dwellers in Portugal. During an experimental survey aimed at isolating fungal species thriving in a deteriorated limestone funerary art piece at the Lemos Pantheon, a national monument located in Águeda, Portugal, several fungal specimens were isolated that could not be identified as any currently known species. Through morphological characteristics and multilocus phylogenetic analyses, seven new species (Aspergillus albicolor sp. nov., Banksiophoma dissensa sp. nov., Knufia lusitanica sp. nov., Microascus lausatensis sp. nov., Neodevriesia saximollicula sp. nov., Paramicrodochium filiforme sp. nov. and Talaromyces benedictus sp. nov.) are here proposed, illustrated, and compared to closely related species. These newly discovered fungal taxa form distinct lineages independent of other previously described species and are classified into seven families across six orders within the phylum Ascomycota. This paper also provides additional evidence that stone heritages harbour a diverse range of new species, deserving additional focus in the future. Citation: Paiva DS, Fernandes L, Pereira E, Mesquita N, Tiago I, Trovão J, Portugal A (2025). Unearthing limestone fungal diversity: Description of seven novel species from Portugal Fungal Systematics and Evolution 15: 47-77. doi: 10.3114/fuse.2025.15.02.

Construction of the super pan-genome for the genus Actinidia reveals structural variations linked to phenotypic diversity

Kiwifruits, belonging to the genus Actinidia, are acknowledged as one of the most successfully domesticated fruits in the twentieth century. Despite the rich wild resources and diverse phenotypes within this genus, insights into the genomic changes are still limited. Here, we conducted whole-genome sequencing on seven representative materials from highly diversified sections of Actinidia, leading to the assembly and annotation of 14 haplotype genomes with sizes spanning from 602.0 to 699.6 Mb. By compiling these haplotype genomes, we constructed a super pan-genome for the genus. We identified numerous structural variations (SVs, including variations in gene copy number) and highly diverged regions in these genomes. Notably, significant SV variability was observed within the intronic regions of the MED25 and TTG1 genes across different materials, suggesting their potential roles in influencing fruit size and trichome formation. Intriguingly, our findings indicated a high genetic divergence between two haplotype genomes, with one individual, tentatively named Actinidia × leiocacarpae, from sect. Leiocacarpae. This likely hybrid with a heterozygous genome exhibited notable genetic adaptations related to resistance against bacterial canker, particularly through the upregulation of the RPM1 gene, which contains a specific SV, after infection by Pseudomonas syringae pv. actinidiae. In addition, we also discussed the interlineage hybridizations and taxonomic treatments of the genus Actinidia. Overall, the comprehensive pan-genome constructed here, along with our findings, lays a foundation for examining genetic compositions and markers, particularly those related to SVs, to facilitate hybrid breeding aimed at developing desired phenotypes in kiwifruits.

ProtCB-bind: Protein-carbohydrate binding site prediction using an ensemble of classifiers

Proteins and carbohydrates are fundamental biomolecules that play crucial roles in life processes. The interactions between these molecules are essential for various biological functions, including immune response, cell activation, and energy storage. Therefore, understanding and identifying protein-carbohydrate binding regions is of significant importance. In this study, we propose ProtCB-Bind, a computational model for predicting protein-carbohydrate interactions. ProtCB-Bind leverages an ensemble of machine learning classifiers and utilizes a common averaging approach to form predictions. The proposed model is trained using a combination of sequence-based and evolutionary-based features of protein sequences, as well as the physicochemical properties of amino acids. To enhance predictive performance, ProtCB-Bind incorporates features derived from recent advancements in transformer-based Natural Language Processing (NLP) for proteins. ProtCB-Bind was designed by systematically identifying the best combination of classifiers and features, and was evaluated using a state-of-the-art benchmark dataset. Its performance was compared against established predictors, including SPRINT-CBH, StackCB-Pred, and StackCB-Embed. ProtCB-Bind outperformed these state-of-the-art predictors, achieving an approximate 3 % improvement in overall performance on benchmark dataset. The sources code for ProtCB-Bind is available at https://github.com/Divnesh/ProtCB-Bind.

Mixed, not stirred: Genomic data confirm the first case of interspecific hybridization in planarian triclads (Platyhelminthes: Tricladida) and raise questions about a possibly novel form of hybrid speciation

Speciation is a complex process where many evolutionary forces interplay. The Mediterranean is acknowledged as one of the most relevant biodiverse areas in the Palearctic region and researchers have long studied the species inhabiting it to pursue the goals of evolutionary biology. Here, we study a complex of freshwater flatworm species of the genus Dugesia from Corsica and Sardinia using restriction site-associated DNA sequencing (specifically, 3RAD) data to unravel their evolutionary history and tackle the processes driving it. We assess the phylogenetic relationships and population structure within the group and evaluate new species boundaries using multispecies coalescent approaches. Furthermore, we offer insights into the environmental niche model of the group and use said model to guide our sampling efforts and collect and present molecular evidence for the first time of Dugesia leporii specimens, endemic from Sardinia last spotted in 1999. Our results indicate that paleoclimatic conditions rather than microplate tectonic dynamics were likely an important driver of diversification for the Corso-Sardinian group. Furthermore, our results warrant the taxonomic re-evaluation of the group as eight primary species candidates are established based on molecular data. Our study also reveals the first case of interspecific natural hybridization reported in Dugesiidae and, to our knowledge, in Tricladida. Finally, we discuss how this hybridization might constitute a new form of hybrid speciation.

The food application of a novel Staphylococcus aureus bacteriophage vB_SA_STAP152 and its endolysin LysP152 with high enzymatic activity under cold temperature

Staphylococcus aureus, a foodborne bacterial pathogen, poses a serious challenge due to antibiotic resistance, highlighting the urgent need for effective and alternative antimicrobial agents. Undoubtedly, bacteriophages and bacteriophage-encoded antibacterial proteins have been considered effective biopreservatives. Herein, we report the isolation and characterization of a novel lytic bacteriophage, vB_SA_STAP152, along with its endolysin LysP152. Morphological and genomic analysis revealed that vB_SA_STAP152 could be considered as a new species in the Rosenblumvirus genus. Stability tests demonstrated that vB_SA_STAP152 can withstand a range of temperatures (∼65 °C) and pH values (4-11). Moreover, we successfully cloned and expressed the bacteriophage-encoded protein, endolysin LysP152, which exhibited optimal activity at temperatures between 4 and 35 °C and within a broad pH range (4-11). The antibacterial spectrum experiments revealed that phage vB_SA_STAP152 effectively targeted 76.15% of S. aureus strains across 14 different sequence types (STs), particularly including community-associated methicillin-resistant S. aureus (CA-MRSA) ST59. Furthermore, endolysin LysP152 demonstrated complete lysis all tested S. aureus strains spanning 17 STs. Subsequently, the efficacy of vB_SA_STAP152 and LysP152 against MRSA in pork was evaluated, revealing a significant reduction of bacterial counts by 4.27-4.42 log10 CFU/mL with phage vB_SA_STAP152 at room temperature and by 3.31 log10 CFU/mL with endolysin LysP152 at refrigerator temperature. Overall, the in-vitro studies and favorable physical and chemical properties suggested that phage vB_SA_STAP152 and endolysin LysP152 have the potential to be developed as antimicrobial agents against S. aureus in the food industry.

Phylogenetic Diversity and Geographic Distribution of Atlantic Salmon Calicivirus in Major Salmon Farming Regions

Salovirus is a genus within the family Caliciviridae, which contains a single member species, Salovirus nordlandense, also known as Atlantic salmon calicivirus (ASCV). While previous work has shown that ASCV can replicate in fish cell lines and establish systemic infection in vivo, its exact role in disease remains unclear and very little is known about its geographic distribution and evolution among Atlantic salmon. To expand the phylogenetic range of ASCV and better understand its potential role in disease, we screened publicly available transcriptomes for ASCV-like sequences. Notably, we detected ASCV in sequencing projects of Atlantic salmon (Salmo salar) (n = 40) and wild common whitefish (Coregonus lavaretus) (n = 1), across Chile, Scotland and Norway. Our phylogenetic analysis identified two viral species, which we provisionally name Salovirus nordlandense 1 and 2, each containing distinct genotypes. Both viral species were found in all three countries, with no clear geographic pattern, indicating that saloviruses have spread through the Atlantic salmon trade. It was notable that 88% of these transcriptomes were generated for the study of other pathogens, including infectious salmon anaemia virus, piscine myocarditis virus and Piscirickettsia salmonis, suggesting that saloviruses might be frequently associated with co-infections. Overall, this study indicates that viruses, like ASCV, can silently spread through aquacultural practices, potentially contributing to a variety of fish diseases.

Prevalence, risk factors, and phylogeny of Toxascaris leonina in stray dogs and cats in Tashkent region, Uzbekistan, with a note on co-infection with Toxocara canis and Toxocara cati

Toxascaris leonina is a significant parasitic agent, affecting domestic carnivores, with implications for public health. This study investigates the prevalence, risk factors, and phylogenetic relationships of T. leonina in stray dogs and cats in Tashkent, Uzbekistan, while also examining co-infection rates with Toxocara canis and Toxocara cati. A cross-sectional study was conducted in the Tashkent Region of Uzbekistan, focusing on stray dogs and cats. From February 2023 to September 2024, 180 dog and 84 cat necropsies were collected for analysis. Parasitological examinations were performed to identify T. leonina, T. canis, and T. cati. Epidemiological data, including species, sex, age group, and collection location, were recorded. Molecular analysis was conducted on selected T. leonina specimens to assess genetic variations, and a phylogenetic analysis was performed. The study revealed a high prevalence of T. leonina in stray dogs (95 %) and cats (63.1 %), with significantly different co-infection patterns identified: 78.89 % of dogs were co-infected with T. canis, while 28.57 % of cats had co-infections with T. cati. Notably, in dogs, the infection rate of T. leonina among different age groups was statistically significant. Genetic analysis revealed 100 % nucleotide identity among local T. leonina isolates. The phylogenetic analysis indicated four distinct clusters within the T. leonina group, with our isolates exclusively forming a cluster, which is genetically close to an isolate infecting a dog from Australia. The findings highlight the urgent need for monitoring and control strategies for T. leonina and its co-infections in stray carnivores in Tashkent, Uzbekistan. Understanding the genetic diversity and risk factors associated with these infections will aid in developing effective public health interventions and inform future research in the region.

Alphanudiviral segments found in transcriptomes of the two-spotted spider mite, Tetranychus urticae (Acari: Tetranychidae)

Nudiviruses (family Nudiviridae) are a diverse group of enveloped, rod-shaped viruses with double-stranded DNA genomes that infect a wide range of insects and crustaceans. These viruses are of significance both as biological control agents in agriculture and as agents of disease in aquaculture and insect rearing. In this work, we found four segments of a novel and divergent nudivirus identified through RNA-seq data from the two-spotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae). The sequences of this virus were detected only in a subset of mite transcriptomes. The assembled segments covered a total of 100,780 bp, with 122 annotated ORFs, including all the 28 conserved nudiviral core genes. Phylogenetic analysis based on the predicted amino acid sequences of 17 selected nudiviral core genes placed the virus within the Alphanudivirus genus, in a clade containing nudiviruses identified from flea transcriptomes. This placement was confirmed by phylogenies of segment-specific concatenated core gene alignments. Indeed, the virus was designated as Tetranychus urticae alphanudivirus (TuNV). Transcriptional profiling revealed variable levels of transcriptional activity among genomic segments and viral genes. Arthropod gene homologs were found interspersed among nudiviral genes across all segments along with several unique genes. This genomic and phylogenetic characterization enhances our understanding of nudivirus diversity and evolution within arthropod hosts.

Microbial Rumen proteome analysis suggests Firmicutes and Bacteroidetes as key producers of lignocellulolytic enzymes and carbohydrate-binding modules

Lignocellulosic biomass, rich in cellulose, hemicellulose, and lignin, offers a sustainable source for biofuels and and production of other materials such as polymers, paper, fabrics, bioplastics and biofertilizers. However, its complex structure hinders efficient conversion. Chemical, enzymatic, and microbial methods aim to unlock the trapped sugars and phenols. The rumen microbiome, a fascinating ecosystem within ruminant animals, holds particular promise. The Hungate 1000 project sequenced 410 microbial genomes from the rumen, enabling in silico screening for lignocellulolytic enzymes. This approach saves time and resources, supporting the development of sustainable bioconversion technologies aligned with the UN's 2030 agenda goals. Analysis of these 410 predicted proteomes revealed diverse carbohydrate-active enzymes (CAZymes) and carbohydrate-binding modules (CBMs) across various microorganisms. Notably, Firmicutes and Bacteroidetes dominated CAZyme and CBM production, suggesting collaborative efforts among different phyla during degradation. The presence of CBM50 and chitinases hints at the ability to utilize chitin from fungal cell walls. Interestingly, the absence of ligninolytic auxiliary activity enzymes reaffirms the rumen microbiome's incapability of directly degrading lignin. However, enzymes facilitating the loosening of the cell wall by cleaving lignin-hemicellulose linkages were identified. This suggests a strategy for making cellulose more accessible to hydrolytic enzymes. This study highlights the intricate relationship between rumen microbes, contributing necessary enzymes for plant cell wall deconstruction in this unique environment. Additionally, it underlines the power of in silico techniques for analyzing big data, paving the way for advancements in sustainable bioconversion.

AcrDB update: Predicted 3D structures of anti-CRISPRs in human gut viromes

Anti-CRISPR (Acr) proteins play a key role in phage-host interactions and hold great promise for advancing genome-editing technologies. However, finding new Acrs has been challenging due to their low sequence similarity. Recent advances in protein structure prediction have opened new pathways for Acr discovery by using 3D structure similarity. This study presents an updated AcrDB, with the following new features not available in other databases: (1) predicted Acrs from human gut virome databases, (2) Acr structures predicted by AlphaFold2, (3) a structural similarity search function to allow users to submit new sequences and structures to search against 3D structures of experimentally known Acrs. The updated AcrDB contains predicted 3D structures of 795 candidate Acrs with structural similarity (TM-score ≥0.7) to known Acrs supported by at least two of the three non-sequence similarity-based tools (TM-Vec, Foldseek, AcrPred). Among these candidate Acrs, 121 are supported by all three tools. AcrDB also includes 3D structures of 122 experimentally characterized Acr proteins. The 121 most confident candidate Acrs were combined with the 122 known Acrs and clustered into 163 sequence similarity-based Acr families. The 163 families were further subject to a structure similarity-based hierarchical clustering, revealing structural similarity between 44 candidate Acr (cAcr) families and 119 known Acr families. The bacterial hosts of these 163 Acr families are mainly from Bacillota, Pseudomonadota, and Bacteroidota, which are all dominant gut bacterial phyla. Many of these 163 Acr families are also co-localized in Acr operons. All the data and visualization are provided on our website: https://pro.unl.edu/AcrDB.

High pressure induced in situ orderly encapsulation of apoferritin and its application in protecting non-acylated anthocyanin

Anthocyanins are important natural plant pigments with many physiological activities. However, because of their highly reactive nature, anthocyanins are unstable, a new approach was established in this study to encapsulate cyanidin 3-β-D-glucoside (C3G) into the inner cavity of recombinant H-2 of soybean seed apoferritin (rH-2) using high pressure processing (HPP) to improve its stability. At the optimal conditions (500 MPa/20 min, C3G/rH-2 mass ratio of 1 to 1), 15 C3G molecules could be encapsulated by per protein cage, which is comparable with pH shift method with stirring, and much higher than urea method. Moreover, the antioxidant capacity of C3G was improved by rH-2 and such interaction and encapsulation increased the stability of C3G at different temperatures and against metal ions. Multi-spectroscopy methods and molecular dynamics simulation revealed that HPP induced significant conformational changes in ferritin, disturbing the highly ordered α-helix structure and increasing the overall flexibility, which allowed the diffusion of C3G into the nanocage via emerging gaps. Furthermore, HPP encapsulation was applied in C3G enriched plant-based beverage and pudding, showing high retention of C3G. The findings of this study suggest that HPP encapsulation is a novel and green approach for in situ orderly encapsulation of heat-sensitive bioactive hydrophilic phytochemicals. Moreover, this approach has been successfully used for non-acylated anthocyanins stabilization in the real plant-based foods for the first time.

Testing the Effectiveness of a Commercially Sold Probiotic on Restoring the Gut Microbiota of Honey Bees: a Field Study

Antibiotic use in apiculture is often necessary to ensure the survival of honey bee colonies. However, beekeepers are faced with the dilemma of needing to combat bacterial brood infections while also knowing that antibiotics kill beneficial bacteria important for bee health. In recent years, bee probiotics have become increasingly purchased by beekeepers because of product claims like being able to "replenish the microbes lost due to agricultural modifications of honey bees' environment" or "promote optimal gut health." Unfortunately, these products have little scientific evidence to support their efficacy, and previous lab experiments have refuted some of their claims. Here, we performed hive-level field experiments to test the effectiveness of SuperDFM-HoneyBee™ - the most commonly purchased honey bee probiotic in the United States - on restoring the honey bee gut microbiota after antibiotic treatment. We found slight but significant changes in the microbiota composition of bees following oxytetracycline (TerraPro) treatment and no difference between the microbiota of antibiotic treated bees with or without subsequent probiotic supplementation. Moreover, the microorganisms in the probiotic supplement were never found in the guts of the worker bee samples. These results highlight that more research is needed to test the efficacy and outcomes of currently available commercial honey bee probiotic supplements.

Fungi Matter: Aphanoascella galapagosensis Associated with Carapace Lesions in Free-Living Galapagos Tortoises

Galapagos giant tortoises are among the most iconic reptile species on earth; however, an increase in anthropogenic activities has created new challenges for their health and well-being. The presence of whitish lesions on the carapace of Galapagos tortoises (Chelonoidis spp.) was previously described, potentially due to fungal growths, but its etiology remained unexplored. Aiming to close this gap, we analyzed carapace scrapes from six different species of free-living giant tortoises of Santa Cruz, Isabela, San Cristobal, and Española islands. In total, we tested 145 fresh and frozen carapace scrapes from 145 individuals with carapace whitish lesions (W-L, n = 80) and without them (W-O, n = 65), using panfungal endpoint PCRs for the ITS and D1-D2 regions. Aphanoascella galapagosensis was detected in W-L samples from all tortoise species and in none of the W-O samples. Four A. galapagosensis nucleotide sequence types (ST) obtained by using the D1-D2 protocol were identified in these tortoises; ST1 was detected on Santa Cruz, Isabela, and Española Islands whereas ST2 and ST3 were only detected on Isabela, and ST4 on San Cristobal. Neodevriesia spp. and Elsinoe spp. were the most common microorganisms found in W-O samples. These results suggest that A. galapagosensis is the etiological agent of whitish lesions in tortoise carapace contributing to baseline data on carapace fungi in giant Galapagos tortoises. Further research is needed to assess the prevalence and potential pathogenicity of A. galapagosensis and its impact for the conservation of these endangered species.

Investigating the antimicrobial and anticancer potential of culturable fungal endophytes isolated from the stems of Kirkia acuminata Oliv

Background

Fungal endophytes produce various structurally and chemically diverse bioactive secondary metabolites including those that are similar to their host plants. However, fungal endophytes from South African medicinal plants are relatively under-explored. The medicinal plant, Kirkia acuminata Oliv., is on the decline in the natural environment due to overharvesting. This necessitates the search for novel alternatives to sustainably obtain the plant’s bioactive metabolites. Thus, fungal endophytes may serve as suitable candidates as they can produce host-similar bioactive compounds.

Results

Eighteen morphologically distinct fungal endophytes were isolated from the surface-sterilised stems of K. acuminata Oliv. Sequencing of the internal transcribed spacer (ITS) region revealed that the isolates were distributed among three genera, namely Diaporthe , Neofusicoccum and Pseudofusicoccum . The broth micro-dilution assay showed that 17 of the 18 ethyl acetate crude extracts exhibited inhibitory activity with minimum inhibitory concentration (MIC) values ranging from 0.31 to 2.5 mg/mL and 1.25 to 2.5 mg/mL against bacterial pathogens and Candida albicans , respectively. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay revealed that most of the crude extracts had dose-dependent cytotoxicity against non-cancerous human embryonic kidney (HEK-293) cells, with the crude extracts of the N . parvum KaS-3, D. macadamiae KaS-4, P . olivaceum KaS-5 and D . neotheicola KaS-6 isolates demonstrating safety against the non-cancerous cells. The alamarBlue assay revealed that the four non-cytotoxic crude extracts had moderate anticancer activity against cervical cancer ME-180 and melanoma A375 cancerous cell lines. Moreover, mycochemical analysis of the non-cytotoxic crude extracts using colourimetric quantification methods revealed that the observed cytotoxic effect could be attributed to the high total phenolic content in the crude extracts.

Conclusion

The study highlights that the fungal endophytes inhabiting the stems of K. acuminata Oliv. produce secondary metabolites that may serve as leads for novel antimicrobial and non-toxic anticancer agents.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-025-03964-y.

De novo assembly of plasmodium interspersed repeat (pir) genes from Plasmodium vivax RNAseq data suggests geographic conservation of sub-family transcription

BACKGROUND

The plasmodium interspersed repeats (pir) multigene family is found across malaria parasite genomes, first discovered in the human-infecting species Plasmodium vivax, where they were initially named the virs. Their function remains unknown, although studies have suggested a role in virulence of the asexual blood stages. Sub-families of the P. vivax pir/virs have been identified, and are found in isolates from across the world, however their transcription at different localities and in different stages of the life cycle have not been quantified. Multiple transcriptomic studies of the parasite have been conducted, but many map the pir reads to existing reference genomes (as part of standard bioinformatic practice), which may miss members of the multigene family due to its inherent variability. This obscures our understanding of how the pir sub-families in P. vivax may be contributing to human/vector infection.

RESULTS

To overcome the issue of hidden pir diversity from utilising a reference genome, we employed de novo transcriptome assembly to construct the pir 'reference' of different parasite isolates from published and novel RNAseq datasets. For this purpose, a pipeline was written in Nextflow, and first tested on data from the rodent-infecting P. c. chabaudi parasite to ascertain its efficacy on a sample with a full, genome-based set of pir gene sequences. The pipeline assembled hundreds of pirs from the studies included. By performing BLAST sequence identity comparisons with reference genome pirs (including P. vivax and related species) we found a clustered network of transcripts which corresponded well with prior sub-family annotations, albeit requiring some updated nomenclature. Mapping the RNAseq datasets to the de novo transcriptome references revealed that the transcription of these updated pir gene sub-families is generally consistent across the different geographical regions. From this transcriptional quantification, a time course of mosquito bloodmeals (after feeding on an infected patient) highlighted the first evidence of ookinete stage pir transcription in a human-infective malaria parasite.

CONCLUSIONS

De novo transcriptome assembly is a valuable tool for understanding highly variable multigene families from Plasmodium spp., and with pipeline software these can be applied more easily and at scale. Despite a global distribution, P. vivax has a conserved pir sub-family structure-both in terms of genome copy number and transcription. We suggest that this indicates important roles of the distinct sub-families, or a genetic mechanism maintaining their preservation. Furthermore, a burst of pir transcription in the mosquito stages of development is the first glint of ookinete pir expression for a human-infective malaria parasite, suggesting a role for the gene family at a new stage of the lifecycle.

Characterization of the NRPS operon homolog for surfactin A and surfactin C synthesis in Bacillus spp

Surfactin is a cyclic lipopeptide produced by Bacillus spp., consisting of a β-hydroxy fatty acid and a heptapeptide synthesized by non-ribosomal peptide synthetases. Surfactin congeners (A, B, and C) differ in amino acid substitutions, with Leu7 in surfactin A replaced by Val in B and Ile in C. Our LC-MS analysis revealed that the elution profiles of surfactin-producing strains could be classified into two distinct patterns under identical culture conditions, corresponding to surfactin A and C production. This suggests that endogenous factors influence surfactin production. Therefore, we aimed to identify the genetic factor that regulates surfactin congener production. The srfA operon for surfactin A biosynthesis in B. subtilis, composed of four open reading frames (ORFs), is srfAABCD. Comparative genomic analysis between the B. subtilis JCM 1465 srfA operon and the TUA12 surfactin biosynthesis genes examined in this study revealed that the operon responsible for surfactin A biosynthesis is distinct, exhibiting 68.7%, 69.2%, 84.7%, and 67.4% homology with the four ORFs, respectively. Similarly, the operon for Ptrs2 surfactin C biosynthesis showed 68.7%, 69.2%, 64.4%, and 67.1% homology. These differences indicate that the identified surfactin A and C biosynthetic operons are novel genetic variants. Further analysis identified the adenylation domain responsible for selecting Ile7 in surfactin C via domain substitution in a surfactin A-producing strain. Average nucleotide identity analysis showed that the surfactin A and C operons were found in B. velezensis and B. amyloliquefaciens, respectively. Our findings suggest that surfactin congener production is species-dependent, with the srf operon specifically distributed in Bacillus spp.

Extensive N4 cytosine methylation is essential for Marchantia sperm function

N4-methylcytosine (4mC) is an important DNA modification in prokaryotes, but its relevance and even its presence in eukaryotes have been mysterious. Here we show that spermatogenesis in the liverwort Marchantia polymorpha involves two waves of extensive DNA methylation reprogramming. First, 5-methylcytosine (5mC) expands from transposons to the entire genome. Notably, the second wave installs 4mC throughout genic regions, covering over 50% of CG sites in sperm. 4mC requires a methyltransferase (MpDN4MT1a) that is specifically expressed during late spermiogenesis. Deletion of MpDN4MT1a alters the sperm transcriptome, causes sperm swimming and fertility defects, and impairs post-fertilization development. Our results reveal extensive 4mC in a eukaryote, identify a family of eukaryotic methyltransferases, and elucidate the biological functions of 4mC in reproductive development, thereby expanding the repertoire of functional eukaryotic DNA modifications.

Evolutionary and functional analyses reveal a role for the RHIM in tuning RIPK3 activity across vertebrates

Receptor interacting protein kinases (RIPK) RIPK1 and RIPK3 play important roles in diverse innate immune pathways. Despite this, some RIPK1/3-associated proteins are absent in specific vertebrate lineages, suggesting that some RIPK1/3 functions are conserved, while others are more evolutionarily labile. Here, we perform comparative evolutionary analyses of RIPK1-5 and associated proteins in vertebrates to identify lineage-specific rapid evolution of RIPK3 and RIPK1 and recurrent loss of RIPK3-associated proteins. Despite this, diverse vertebrate RIPK3 proteins are able to activate NF-κB and cell death in human cells. Additional analyses revealed a striking conservation of the RIP homotypic interaction motif (RHIM) in RIPK3, as well as other human RHIM-containing proteins. Interestingly, diversity in the RIPK3 RHIM can tune activation of NF-κB while retaining the ability to activate cell death. Altogether, these data suggest that NF-κB activation is a core, conserved function of RIPK3, and the RHIM can tailor RIPK3 function to specific needs within and between species.

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

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

Evolutionary-conserved RLF, a cytochrome b5-like heme-binding protein, regulates organ development in Marchantia polymorpha

In Arabidopsis thaliana, REDUCED LATERAL ROOT FORMATION (RLF), a cytochrome b5-like heme-binding domain (Cytb5-HBD) protein, is necessary for proper lateral root (LR) formation. Whereas the other Cytb5-HBD proteins in A. thaliana regulate different metabolic reactions, RLF is unique as it specifically regulates organ development. However, it remains unknown whether heme binding to RLF is necessary for its function and whether RLF orthologs in different plant species also regulate organ development. We demonstrate that RLF binds to heme in vitro and that two histidine residues, which are conserved among Cytb5-HBD, are crucial for both heme binding and its biological function in A. thaliana. In addition, we show that MpRLF, a RLF ortholog in the bryophyte Marchantia polymorpha, also binds to heme in vitro and that MpRLF rescues the LR formation phenotype of the A. thaliana rlf mutant. Mprlfge, the loss-of-function mutation in MpRLF, resulted in delayed thallus growth and inhibited both gemma cup and reproductive organ formation. Our findings indicate that MpRLF is essential for proper vegetative and reproductive development in M. polymorpha. This suggests that RLF-dependent redox reaction systems are conserved across diverse plant species and were independently co-opted for organ development in bryophyte and seed plant evolution.

Exploiting taxonomic information from metagenomes to infer bacterial bioindicators and environmental quality at salmon aquaculture installations

Environmental DNA (eDNA) metabarcoding has emerged as a powerful method for assessing the environmental impacts of marine Atlantic salmon aquaculture by identifying bacterial bioindicators and inferring biotic indices. However, because this approach relies on the PCR amplification of 16S rRNA gene fragments, it may introduce errors that compromise bioindicator reliability. In contrast, metagenomic analysis which captures the complete set of genetic material directly extracted from environmental samples circumvents biases inherent to PCR amplification. We hypothesized that metagenomic data could offer superior assessments of benthic environmental impacts associated with salmon aquaculture compared to metabarcoding. To test this, we compared bacterial community structures derived from both metabarcoding and metagenomic analyses of 68 sediment samples obtained from aquaculture installation sites characterized by varying degrees of benthic impact as determined by macroinvertebrate inventories. Bacterial bioindicators were identified from each dataset, and Random Forest models were used to predict the degrees of benthic impacts. Metagenomics identified a greater number of bioindicators at both the family and individual sequence variant levels, resulting in higher predictive accuracy for impact assessments. Notably, only a few bioindicators were common to both methods, suggesting that methodological limitations and distorted abundance patterns in metabarcoding data may lead to spurious indicators. These findings highlight both the challenges and potential advantages of employing metagenomics for reliable environmental impact assessments.

Structure of AcMNPV nucleocapsid reveals DNA portal organization and packaging apparatus of circular dsDNA baculovirus

Baculoviruses are large DNA viruses found in nature propagating amongst insects and lepidoptera in particular. They have been studied for decades and are nowadays considered as invaluable biotechnology tools used as biopesticides, recombinant expression systems or delivery vehicle for gene therapy. However, little is known about the baculovirus nucleocapsid assembly at a molecular level. Here, we solve the whole structure of the Autographa californica multiple nucleopolyhedrovirus (AcMNPV) nucleocapsid by applying cryo-electron microscopy (CryoEM) combined with de novo modelling and Alphafold predictions. Our structure completes prior observations and elucidates the intricate architecture of the apical cap, unravelling the organization of a DNA portal featuring intriguing symmetry mismatches between its core and vertex. The core, closing the capsid at the apex, holds two DNA helices of the viral genome tethered to Ac54 proteins. Different symmetry components at the apical cap and basal structure are constituted of the same building block, made of Ac101/Ac144, proving the versatility of this modular pair. The crown forming the portal vertex displays a C21 symmetry and contains, amongst others, the motor-like protein Ac66. Our findings support the viral portal to be involved in DNA packaging, probably in conjunction with other parts of a larger DNA packaging apparatus.

RNA-Seq uncovers endogenous NO-induced hormone signal transduction and carbon metabolism in response to PEG stress in alfalfa

BACKGROUND

Alfalfa (Medicago sativa L.) has the benefits of high yield and nutritional value as a sustainable forage. However, the water deficit significantly limits its growth and yield performance. Nitric oxide (NO) is a signal molecule that can enhance plant tolerance. The majority of previous studies focus on the role of exogenous NO in plant tolerance. However, the underlying mechanism of endogenous NO in alfalfa drought tolerance remains largely unexplored.

RESULTS

To explore the mechanism of the endogenous NO-mediated water deficit resistance in the alfalfa, seedlings were exposed to polyethylene glycol 6000 (PEG) and NO scavenger (cPTIO). Results showed that PEG treatment significantly augmented alfalfa endogenous NO, MDA, O2·-, and H2O2 levels. In parallel, eliminating endogenous NO under PEG stress (PEG-NO) significantly diminished NO level, exacerbated MDA and reactive oxygen species accumulation, and decreased the activities of key enzymes involved in carbon fixation and TCA cycle, such as Rubisco, FBA, PDH, α-KGDH, and SDH, as well as reduced ABA and IAA content in alfalfa leaves. RNA-Seq and bioinformatics analysis suggested that endogenous NO-responsive DEGs primarily relate to carbon metabolism and hormone signal transduction. In further studies of these DEGs, we speculated that GH3, SAUR, SnRK2, and ABF genes and FBA, GAPDH, SBP, and CS are critical genes in response to endogenous NO under PEG stress.

CONCLUSIONS

In summary, our study innovatively proposes a mechanism model of how endogenous NO enhances alfalfa tolerance to water deficiency at the physiological and molecular levels. The novel candidate genes can give genetic resources for the subsequent molecular-assisted breeding of drought-resistant alfalfa crops.

Targeting HER2 with DNA Aptamers for Efficient Anticancer Drug Delivery: A Combined Experimental and Computational Study

Targeted delivery of cytostatic drugs is a powerful approach to achieving tumor tissue selectivity, reducing systemic toxicity, and ultimately improving the efficacy of anticancer chemotherapy. Targeting can be achieved using a wide range of molecular ligands, with DNA aptamers being a promising representative. In this work, we employed flow cytometry, a AuNP-aptasensor, and atomic-scale computer modeling to assess the affinity of several DNA aptamers (Anti-HER2, HB5, Apt-6, HeA2_1, and HeA2_3) for human epidermal growth factor receptor 2 (HER2), which is known to be one of the factors that promote the growth of breast cancer cells. Flow cytometry showed that short aptamers (HeA2_1 and HeA2_3) had a higher affinity for HER2 on MDAMB453 cancer cells than longer aptamers (HB5, Apt-6). HER2-negative MDA-MB-231 cells served as the negative control. The HeA2_3 aptamer has a high average affinity (HeA2_3:23.6, HeA2_1:13.1, Apt-6:3.6; HB5:3.5; Anti-HER2:3.2) and a nearly Gaussian distribution across the cells, while HeA2_1 forms a fraction of cells with a relatively high fluorescence signal intensity (HeA2_1:11.6; HeA2_3:5.9; Apt-6:3.4; HB5:3.1; Anti-HER2:2.1). Most of the findings for cancer cells also hold for the HER2-positive small extracellular vesicles studied using the AuNP-aptasensor. Computer simulations confirmed that short aptamers are characterized by stronger binding to the extracellular domain of HER2. A detailed analysis of the free energy allowed us to show for the first time that tight binding to HER2 correlates with well-separated hot and cold spots on the protein surface. For the aptamers that meet these criteria (HeA2_1, HeA2_3, and Anti-HER2), favorable interactions with HER2 are driven by the local attraction of nucleotides to arginine and lysine residues of HER2 and possibly stabilized by intermolecular hydrogen bonds. For longer aptamers (Apt-6 and HB5), hot and cold spots on the HER2 surface overlap and the aptamers show much weaker binding. Overall, our findings show that binding of DNA aptamers to HER2 cannot be characterized merely by the dissociation equilibrium constant. A more sophisticated approach that combines experimental and computational methods allowed us to unlock the molecular mechanisms behind the aptamer-HER2 bindings. The results of our study also suggest that computer modeling has become a reliable and accurate tool for aptamer prescreening prior to laboratory experiments.

Mitogenome of Endemic Species of Flying Squirrel, Trogopterus xanthipes (Rodentia, Mammalia) and Phylogeny of the Sciuridae

Trogopterus xanthipes (Sciuridae, Rodentia) is a medium-sized flying squirrel species in the monotypic genus Trogopterus, and is endemic to China. It is distinguishable from other squirrels by the long black hairs on the inner and outer sides at the base of the ears and numerous ridges on the crowns of the upper and lower cheek teeth. Mitogenomes have been widely used in phylogenetic studies. We described T. xanthipes morphological features and successfully sequenced its mitogenome for the first time. The T. xanthipes mitogenome was conserved in number and order of genes. We analyzed codon usage patterns, evolutionary mutation rates, K2P distance, and genetic diversity of protein-coding genes. We reconstructed the phylogeny of Sciuridae (94 species and 21 genera in 4 subfamilies). All phylogenetic trees shared the same topologies and consistently supported the monophyly of Sciuridae, and the supported subfamilies relationship as follows: ((Xerinae + Callosciurinae) + Sciurinae) + Ratufinae. The relationship within the Sciurinae clade was ((Glaucomys + Hylopetes) + ((Trogopterus+Pteromys) + Petaurista) + Sciurus). The relationship within the Callosciurinae clade was Exilisciurus + ((Tamiops + Dremomys) + ((Lariscus+Sundasciurus) + Callosciurus)). The relationship within the Xerinae clade was Sciurotamias + (Tamias + (Callospermophilus + (Marmota + (Spermophilus + (Urocitellus + (Ictidomys + Cynomys)))))). The phylogenetic position among different subfamilies of Sciuridae was consistently recovered with high support across different datasets (PCGRNA and PCG12RNA) and supported the monophyletic lineage of each genus of Sciuridae. Trogopterus xanthipes was sister species to Pteromys volans. Species within the genus formed different minor clades, suggesting relatively high interspecific divergences. The tribe Pteromyini was sister taxon of the tribe Sciurini, which was not supported by the traditional division of Sciuridae into subfamilies Pteromyinae and Sciurinae. Hence, our data supported a division of the Sciuridae into five subfamilies.

Engineered β-Carotene Hydroxylase with Excellent Thermostability Promotes Zeaxanthin Production in Yeast

Zeaxanthin, as an important natural pigment and nutrient, is applied in food and cosmetics industries. Zeaxanthin is converted from β-carotenoid by the β-carotene hydroxylase (CrtZ). Limited by the thermostability of CrtZ, zeaxanthin and its derivatives tend to be fermented in Saccharomyces cerevisiae at low temperatures. In this study, CrtZ mutants with improved thermostability and catalytic efficiency were designed via the position-specific scoring matrix (PSSM), and the beneficial mutants were verified in vitro. Moreover, molecular dynamics simulations revealed the thermostability mechanisms of the mutants. Subsequently, CrtZ mutant M83L was introduced into the S. cerevisiae chassis, and the zeaxanthin titer increased by 121.2% compared with that of the CrtZ, reaching 156.8 mg/L in shake flask fermentation at 30 °C. Furthermore, the oxidoreductase RFNR/FD3 system was introduced to match the overexpressed M83L, and the zeaxanthin titer further increased by 138.9% (reaching 374.6 mg/L). Ultimately, 814.6 mg/L zeaxanthin was produced in S. cerevisiae in 5.0 L fed-batch fermentation at 30 °C, which is the highest reported titer in S. cerevisiae. This study not only provides a useful strategy to increase the thermostability of key enzymes but also describes an efficient platform for the biosynthesis of zeaxanthin and its high-value derivatives.

The genetic basis of replicated bullseye pattern reduction across the Hibiscus trionum complex

Colorful petal patterns fulfill important functions and constitute excellent systems to illuminate the evolutionary processes that generate morphological diversity or instead support the repetitive emergence of similar forms. Here, we combined phylogenomic approaches, genetic manipulations, molecular techniques, and bee behavioral experiments to (i) solve the species relationships across the Trionum complex, a small Hibiscus clade that displays bullseye petal patterns varying in size, hue, and composition, (ii) identify key genes involved in the production of bullseye pigmentation, and (iii) reveal molecular events underpinning pattern variation during the evolution of the group. We found that epidermal cell shape, texture, and pigmentation are genetically distinct and that pigmentation is the most labile feature across the group. We demonstrate that repetitive bullseye reduction events primarily occur through independent modifications of a single genetic locus encoding BERRY1, an R2R3 MYB (myeloblastosis) that regulates anthocyanin pigment production in petals. We also found that buff-tailed bumblebees discriminate against flowers with smaller bullseye sizes, suggesting that changing bullseye proportions impact plant-pollinator interactions. Our results demonstrate how repeated mutations in a single locus led to morphological variation in petal patterning, a trait shown to impact plant fitness in other species and contribute to angiosperm reproductive isolation and speciation.

Modulation of host ATP levels by secreted bacterial effectors

Adenosine 5'-triphosphate (ATP) is the currency of energy in cells; it plays essential roles in virtually all cellular processes, ranging from basic metabolism to signaling in development and disease. The opportunistic bacterial pathogen Legionella pneumophila utilizes the Dot/Icm type IV secretion system to deliver over 300 effectors into host cells, some of which utilize ATP to perform biochemical reactions catalyzed by their unique enzymatic activities. However, whether L. pneumophila directly regulates ATP level in host cells is unknown. Here, we discover that the Dot/Icm substrate Ceg14 (Lpg0437, a.k.a. SidL) is an ATP/dATPase, which after being activated by the host protein actin, efficiently converts ATP and dATP into adenosine and deoxyadenosine monophosphate, respectively by a mechanism that requires its S-HxxxE (x, any amino acid) motif. The activity of Ceg14 is regulated by its metaeffector AnkJ (Lpg0436, a.k.a. LegA11), which inhibits its ATPase activity via direct protein-protein interactions. Ceg14 and AnkJ impose temporal regulation of ATP levels in L. pneumophila-infected cells. Our results demonstrate that L. pneumophila modulates the energy level of host cells to create an environment permissive for its growth.

Extracting Residue Solvent Exposure from Covalent Labeling Data with Machine Learning: A Hybrid Approach for Protein Structure Prediction

Hydroxyl radical protein footprinting (HRPF) coupled with mass spectrometry yields information about residue solvent exposure and protein topology. However, data from these experiments are sparse and require computational interpretation to generate useful structural insight. We previously implemented a Rosetta algorithm that uses experimental HRPF data to improve protein structure prediction. Modern structure prediction methods, such as AlphaFold2 (AF2), use machine learning (ML) to generate their predictions. Implementation of an HRPF-guided version of AF2 is challenging due to the substantial amount of training data required and the inherently abstract nature of ML networks. Thus, here we present a hybrid method that uses a light gradient boosting machine to predict residue solvent accessibility from experimental HRPF data. These predictions were subsequently used to improve Rosetta structure prediction. Our hybrid approach identified models with atomic-level detail for all four proteins in our benchmark set. These results illustrate that it is possible to successfully use ML in combination with HRPF data to accurately predict protein structures.

In silico bioprospecting of the Neotropical Plant Mandacaru (Cereus) for antimicrobial properties

The mandacaru is a cactus species complex widely known in Brazil, with extensive applications in medicinal, food, and agricultural fields. Although it is used medicinally by traditional populations, to treat several diseases, knowledge about its biomolecules of biotechnological potential is still limited, specifically regarding antimicrobial and healing properties. The bacterial resistance to conventional antibiotics presents a significant challenge in modern medicine. In light of this scenario, bioprospecting mandacaru for biotechnological applications as an antimicrobial has emerged as a new and promising research area. In this study, transcriptomic data from three Cereus species (C. fernambucensis, C. hildmannianus, and C. jamacaru) were combined with bioinformatic approaches, including protein modeling, molecular docking, and molecular dynamics simulations, to identify proteins with therapeutic potential for treating wound infections. Our findings highlighted peptides as particularly promising antimicrobial agents, demonstrating efficacy against a range of pathogens, including Gram-positive and Gram-negative bacteria, as well as fungi. Those peptides showed strong interactions with the streptolydigin and sodium ligands, with the streptolydigin ligand emerging as the most promising for enhancing antimicrobial activity. Molecular dynamics revealed that while CF15 exhibited limited stability, CF267, CF48, CH167, and CH176 displayed superior stability, positioning them as the most promising candidates for further investigation. Future work will focus on synthesizing these peptides and evaluating their antimicrobial properties through in vitro and in vivo analyses, to develop them into potent therapeutic agents.

The knockout of ClaCSLH1 induced dwarfing in watermelon

In agriculture, selecting ideal plant types with desirable traits, such as dwarfing and upright stem structures, significantly enhances crop yield and quality by optimizing light absorption, spatial efficiency, and nutrient utilization. Developing new varieties of dwarf watermelon is a crucial objective in watermelon breeding. In this study, we constructed an F2 population using the wild-type V063 as the paternal parent and the dwarf variety dw-n as the maternal parent. The dwarfing trait was found to be governed by a pair of recessive alleles. Through bulk segregant analysis sequencing (BSA-seq) and RNA sequencing (RNA-seq), we identified the gene Cla97C02G035450, which encodes cellulose synthase-like H1 (CSLH1), as a candidate gene associated with the dwarfing phenotype. ClaCLSH1 belongs to the ClaCESA/CSLs family, which is involved in the cell wall formation by regulating the synthesis of cellulose and hemicellulose. Microscopic analyses revealed that dw-n exhibited shorter internode cells, thicker cell walls, and elevated hemicellulose content compared to V063. Subcellular localization studies demonstrated that the CLACSLH1 protein is primarily localized in the nucleus and the cell membrane/wall. Notably, the overexpression of CLACSLH1 in the dw-n background rescued its dwarf phenotype. Furthermore, experiments indicated that knockdown of CLACSLH1 resulted in excessive hemicellulose synthesis, inhibited internode cell elongation, and ultimately led to the stunted phenotype observed in dw-n. This research provides innovative insights into the development of superior dwarf watermelon varieties and advances our understanding of the molecular mechanisms underlying watermelon dwarfism.