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

Integrative structural analysis of NF45-NF90 heterodimers reveals architectural rearrangements and oligomerization on binding dsRNA

Complexes of nuclear factors 45 and 90 (NF45-NF90) play a multitude of roles in co- and post-transcriptional RNA processing, including regulating adenosine-to-inosine editing, cassette exon and back splicing, and splicing fidelity. NF45-NF90 complexes recognize double-stranded RNA (dsRNA) and, in human cells, primarily interact with Alu inverted repeats (AluIRs) that are commonly inserted into introns and other non-coding RNA regions. Intronic AluIRs of ∼300 bp can regulate splicing outcomes, such as generation of circular RNAs. We examined domain reorganization of NF45-NF90 domains on dsRNAs exceeding 50 bp to gain insight into its RNA recognition properties on longer dsRNAs. Using a combination of phylogenetic analysis, solution methods (including small angle X-ray scattering and quantitative cross-linking mass spectrometry), machine learning, and negative stain electron microscopy, we generated a model of NF45-NF90 complex formation on dsRNA. Our data reveal that different interactions of NF45-NF90 complexes allow these proteins to coat long stretches of dsRNA. This property of the NF45-NF90 complex has important implications for how long, nuclear dsRNAs are recognized in the nucleus and how this might promote (co)-regulation of specific RNA splicing and editing events that shape the mammalian transcriptome.

Architecture remodeling activates the HerA-DUF anti-phage defense system

Leveraging AlphaFold models and integrated experiments, we characterized the HerA-DUF4297 (DUF) anti-phage defense system, focusing on DUF's undefined biochemical functions. Guided by structure-based genomic analyses, we found DUF homologs to be universally distributed across diverse bacterial immune systems. Notably, one such homolog, Cap4, is a nuclease. Inspired by this evolutionary clue, we tested DUF's nuclease activity and observed that DUF cleaves DNA substrates only when bound to its partner protein HerA. To dissect the mechanism of DUF activation, we determined the structures of DUF and HerA-DUF. Although DUF forms large oligomeric assemblies both alone and with HerA, oligomerization alone was insufficient to elicit nuclease activity. Instead, HerA binding induces a profound architecture remodeling that propagates throughout the complex. This remodeling reconfigures DUF into an active nuclease capable of robust DNA cleavage. Together, we highlight an architecture remodeling-driven mechanism that may inform the activation of other immune systems.

Exploring the Antimicrobial, Antioxidant and Extracellular Enzymatic Activities of Culturable Endophytic Fungi Isolated from the Leaves of Kirkia acuminata Oliv

Fungal endophytes of medicinal plants produce diverse secondary metabolites and extracellular enzymes with therapeutic and biotechnological potential. However, the biological and biotechnological potential of fungal endophytes from South African medicinal plants remain relatively underexplored. In this study, the antimicrobial, antioxidant, anti-inflammatory and extracellular enzymatic capabilities of five fungal endophytes previously isolated from the leaves of Kirkia acuminata Oliv. were investigated. Sequencing of the internal transcribed spacer (ITS) regions revealed that the isolates belonged to the genera Setosphaeria, Diaporthe and Corynespora. The broth micro-dilution assay and the Folin-Ciocalteau reagent method were used to assess the antibacterial activity and the total phenolic content (TPC) of the fungal endophytes' ethyl acetate crude extracts (CEs), respectively. The antioxidant activity was assessed using the ferric reducing antioxidant power (FRAP) and 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging assays. The influence of the CE of the Setosphaeria rostrata KaL-4 on the viability and LPS-induced interleukin-6 (IL-6) production in Raw 264.7 macrophages was assessed using a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and an ELISA, respectively. The ability of the isolates to produce extracellular proteases, laccases and peroxidases was also determined. The CEs displayed antimicrobial activity with MICs ranging from 0.63 to 1.25 mg/mL and reducing power and scavenging activity ranging from 40% to 18% and from 60% to 48%, respectively. The S. rostrata KaL-4 CE possessed the highest TPC and demonstrated dose-dependent cytotoxicity. The CE further demonstrated a significant reduction in IL-6 production at a concentration of 0.75 µg/mL. Only one isolate demonstrated the ability to produce proteases with an enzymatic index (EI) of 0.66, while laccases (EI range of 0.14 to 1.15) and peroxidases were produced by all of the isolates. These findings suggest that fungal endophytes from South African medicinal plants are promising sources of bioactive compounds and industry-significant extracellular enzymes.

Insights into a Novel and Efficient Microbial Nest System for Treating Pig Farm Wastewater

A microbial nest system (MNS) represents a novel and efficient approach to treating solid-liquid mixtures from pig farming instead of the conventional method, which separates the solid and liquid at first using centrifugation before treating the solid and liquid. However, the key environmental factors influencing the efficiency of this system and the microbial structure are still not clear. This study aimed to elucidate the changes in an MNS considering physicochemical properties, spectral analysis, and correlations between microbial community structures and environmental factors during the treatment. The results showed that the MNS underwent three temperature stages during the treatment process of piggery slurry: a warming period, a high-temperature period, and a cooling period. In the high-temperature period, the most abundant bacterium was Bacillus, with a relative abundance of 22.16%, and Chaetomium dominated the fungal community with a relative abundance of 11.40%. Moreover, the moisture content, pH value, and electrical conductivity (EC) exhibited an increasing trend, whereas the carbon-to-nitrogen (C/N) ratio and the ratio of ammonia nitrogen to nitrate nitrogen (NH4+-N/NO3--N) showed a decreasing trend. The accumulation of humic acid and fulvic acid suggested that the humification process of organic matter was occurring. The moisture content and C/N ratio were identified as crucial factors influencing the bacterial and fungal community structures, respectively. This study provides a theoretical basis for enhancing the efficiency of piggery slurry treatment using an MNS and rational optimisation of the associated processes.

Gelling and reducing agents are potential carbon and energy sources in culturing of anaerobic microorganisms

The majority of microorganisms in the environment have yet to be isolated in pure cultures, and the reasons behind this phenomenon remain elusive. In this study, we investigated the possibility of the commonly used gelling agent including agar and gellan gum as a source of carbon and energy in anaerobic roll-tube cultivation from one mangrove sediment sample and two high-temperature oilfield samples. Based on growth tests and genomic evidence, anaerobic gellan degraders were retrieved from genera of Clostridium, Lacrimispora, and lineages from the rarely cultivated phylum Atribacterota. Anaerobic agarolytic microorganisms were found to be members of Bacillus and Clostridium. We also proved the role of carbon and energy sources of L-cysteine, a routine agent used to make culture media anoxic/anaerobic in both enrichment cultures and isolated strains representing Acetomicrobium, Thermodesulfovibrio, Lacrimispora, Clostridium, Bacillus, Coprothermobacter, Citrobacter, and Enterobacter. Furthermore, the isolates and enriched microbial communities utilizing L-cysteine under anaerobic conditions were mainly through L-cysteine desulfuration to pyruvate, ammonia, and sulfide. This study demonstrates that the widely used gelling and reducing agents in the basal medium can serve as carbon and energy sources for anaerobic microorganisms and thus may bias the enrichment and isolation.

IMPORTANCE

Most microbial species inhabiting natural environments have not been isolated in pure cultures using conventional media and laboratory conditions, but the reason behind this is unclear. Here, we provided a new explanation for the phenomenon, in that both the gelling agents, like agar and gellan gum, and reducing agent L-cysteine-HCl in the media provide extra carbon and energy sources to microorganisms and therefore decrease the chance in isolation specifically for the supplemented substrate which is supposed to be the sole source of carbon and energy. This result demonstrated that further improvement in the effectiveness of isolation of targeted microorganisms will be facilitated by subtracting the overlooked organic ingredients in the medium and more innovations.

Identification and Characterization of Copper-Responsive miRNAs and Their Target Genes in Jerusalem Artichoke

microRNAs (miRNAs) are key regulators of gene expression in plants, significantly contributing to various biological processes and stress responses. While their roles have been extensively studied in Arabidopsis thaliana and other model plants, the response of miRNAs to copper (Cu) stress in Jerusalem artichoke remains unknown. This study addresses this gap by investigating Cu-responsive miRNAs and their regulatory roles in Jerusalem artichoke under Cu stress. Through small RNA library analysis, six miRNA families-miR168, miR394, miR397, miR398, miR408, and miR858-were identified in Cu-stressed and control plants of the Jerusalem artichoke cv. NY1. These miRNAs possess characteristic stem-loop precursor structures and detectable miRNA* sequences, with miR858 having unusually long precursors (1524-6448 nt). This study outlines a framework for miRNA-mediated Cu stress responses in Jerusalem artichoke, highlighting the roles of both well-established Cu-responsive miRNAs (miR397, miR398, and miR408) and other conserved miRNAs (miR168, miR394, and miR858). These miRNAs are suggested to influence Cu stress adaptation by modulating target genes involved in essential metabolic, physiological, and morphological processes, offering new insights into miRNA-mediated stress regulation in plants.

Chromosome-scale assembly of the Xenocypris davidi using PacBio HiFi reads and Hi-C technologies

Xenocypris davidi is a benthic fish species widely distributed in the water systems south of the Yellow River in China, playing a significant role in aquatic ecosystems. Despite its ecological and economic importance, genomic resources for X. davidi are limited, hindering a comprehensive understanding of its evolutionary adaptations and genetic improvements. This study presents the first chromosome-level genome assembly of X. davidi, utilizing PacBio long-reads, Illumina short reads, and Hi-C sequencing data. The genome assembly spans 1.05 Gb with a scaffold N50 length of 33.99 Mb, and 95.12% of the genome sequence was successfully anchored onto 24 pseudochromosomes. We identified 27,360 protein-coding genes, of which 26,672 were functionally annotated. This genome sequence provides a valuable resource for exploring the molecular basis of agronomic traits in X. davidi and will facilitate its genetic enhancement.

Unraveling the molecular mechanism of polysaccharide lyases for efficient alginate degradation

Alginate lyases (ALs) catalyze the depolymerization of brown macroalgae alginates, widely used naturally occurring polysaccharides. Their molecular reaction mechanism remains elusive due to the lack of catalytically competent Michaelis-Menten-like complex structures. Here, we provide structural snapshots and dissect the mechanism of mannuronan-specific ALs from family 7 polysaccharide lyases (PL7), employing time-resolved NMR, X-ray, neutron crystallography, and QM/MM simulations. We reveal the protonation state of critical active site residues, enabling atomic-level analysis of the reaction coordinate. Our approach reveals an endolytic and asynchronous syn β-elimination reaction, with Tyr serving as both Brønsted base and acid, involving a carbanion-type transition state. This study not only reconciles previous structural and kinetic discrepancies, but also establishes a comprehensive PL reaction mechanism which is most likely applicable across all enzymes of the PL7 family as well as other PL families.

Type IV pili-associated secretion of a biofilm matrix protein from Clostridium perfringens that forms intermolecular isopeptide bonds

Clostridium perfringens is a Gram-positive, anaerobic, spore-forming, bacterial pathogen of humans and animals. C. perfringens also produces type IV pili (T4P) and has two complete sets of T4P-associated genes, one of which has been shown to produce surface pili needed for cell adherence. One hypothesis about the second set of T4P genes is that they comprise a system analogous to the type II secretion systems (TTSS) found in Gram-negative bacteria, which is used to export folded proteins from the periplasm through the outer membrane to the extracellular environment. Gram-positive bacteria have a similar secretion barrier in the thick peptidoglycan (PG) layer, which blocks secretion of folded proteins >25 kD. To determine if the T4P-associated genes comprise a Gram-positive TTSS, the secretome of mutants lacking type IV pilins were examined and a single protein, a von Willebrand A domain containing protein, BsaC (CPE0517), was identified as being dependent on pilin PilA3 for secretion. The bsaC gene is in an operon with genes encoding a SipW signal peptidase and two putative biofilm matrix proteins BsaA and BsaB, both of which have remote homology to Bacillus subtilis biofilm protein TasA. Since BsaA forms long oligomers that are secreted, we analyzed BsaA monomer interactions with de novo modeling. These models projected that the monomers formed isopeptide bonds as part of a donor strand exchange process, in which an N-terminal disordered loop of one monomer intercalates into a beta sheet structure of an adjacent monomer and reforms into a beta sheet with subsequent isopeptide bond formation. Mutations in residues predicted to form the isopeptide bonds led to loss of oligomerization, supporting an exchange and lock mechanism. Phylogenetic analysis showed the BsaA family of proteins are widespread among bacteria and archaea but only a subset is predicted to form isopeptide bonds.

SpudDB: a database for accessing potato genomic data

Potato is a key food crop with a complex, polyploid genome. Advancements in sequencing technologies coupled with improvements in genome assembly algorithms have enabled generation of phased, chromosome-scale genome assemblies for cultivated tetraploid potato. The SpudDB database houses potato genome sequence and annotation, with the doubled monoploid DM 1-3 516 R44 (hereafter DM) genome serving as the reference genome and haplotype. Diverse annotation data types for DM genes are provided through a suite of Gene Report Pages including gene expression profiles across 438 potato samples. To further annotate potato genes based on expression, 65 gene co-expression modules were constructed that permit the identification of tightly co-regulated genes within DM across development and responses to wounding, abiotic stress, and biotic stress. Genome browser views of DM and 28 other potato genomes are provided along with a download page for genome sequence and annotation. To link syntenic genes within and between haplotypes, syntelogs were identified across 25 cultivated potato genomes. Through access to potato genome sequences and associated annotations, SpudDB can enable potato biologists, geneticists, and breeders to continue to improve this key food crop.

Metatranscriptomic profiling reveals pathogen and host response signatures of pediatric acute sinusitis and upper respiratory infection

BACKGROUND

Acute sinusitis (AS) is a frequent cause of antibiotic prescriptions in children. Distinguishing bacterial AS from common viral upper respiratory infections (URIs) is crucial to prevent unnecessary antibiotic use but is challenging with current diagnostic methods. Despite its speed and cost, untargeted RNA sequencing of clinical samples from children with suspected AS has the potential to overcome several limitations of other methods. In addition, RNA-seq may reveal novel host-response biomarkers for development of future diagnostic assays that distinguish bacterial from viral infections. There are however no available RNA-seq datasets of pediatric AS that provide a comprehensive view of both pathogen etiology and host immune response.

METHODS

Here, we performed untargeted RNA-seq (metatranscriptomics) of nasopharyngeal samples from 221 children with AS and performed a comprehensive analysis of pathogen etiology and the impact of bacterial and viral infections on host immune responses. Accuracy of RNA-seq-based pathogen detection was evaluated by comparison with culture tests for three common bacterial pathogens and qRT-PCR tests for 12 respiratory viruses. Host gene expression patterns were explored to identify potential host responses that distinguish bacterial from viral infections.

RESULTS

RNA-seq-based pathogen detection showed high concordance with culture or qRT-PCR, showing 87%/81% sensitivity (sens) / specificity (spec) for detecting three AS-associated bacterial pathogens, and 86%/92% (sens/spec) for detecting 12 URI-associated viruses, respectively. RNA-seq also detected an additional 22 pathogens not tested for clinically and identified plausible pathogens in 11/19 (58%) of cases where no organism was detected by culture or qRT-PCR. We reconstructed genomes of 196 viruses across the samples including novel strains of coronaviruses, respiratory syncytial virus, and enterovirus D68, which provide useful genomic data for ongoing pathogen surveillance programs. By analyzing host gene expression, we identified host-response signatures that differentiate bacterial and viral infections, revealing hundreds of candidate gene biomarkers for future diagnostic assays.

CONCLUSIONS

Our study provides a one-of-kind dataset that profiles the interplay between pathogen infection and host responses in pediatric AS and URI. It reveals bacterial and viral-specific host responses that could enable new diagnostic approaches and demonstrates the potential of untargeted RNA-seq in diagnostic analysis of AS and URI.

Evolutionary adaptations of doublet microtubules in trypanosomatid parasites

The movement and pathogenicity of trypanosomatid species, the causative agents of trypanosomiasis and leishmaniasis, are dependent on a flagellum that contains an axoneme of dynein-bound doublet microtubules (DMTs). In this work, we present cryo-electron microscopy structures of DMTs from two trypanosomatid species, Leishmania tarentolae and Crithidia fasciculata, at resolutions up to 2.7 angstrom. The structures revealed 27 trypanosomatid-specific microtubule inner proteins, a specialized dynein-docking complex, and the presence of paralogous proteins that enable higher-order periodicities or proximal-distal patterning. Leveraging the genetic tractability of trypanosomatid species, we quantified the location and contribution of each structure-identified protein to swimming behavior. Our study shows that proper B-tubule closure is critical for flagellar motility, exemplifying how integrating structural identification with systematic gene deletion can dissect individual protein contributions to flagellar motility.

Island geography drives evolution of rattan palms in tropical Asian rainforests

Distributed across two continents and thousands of islands, the Asian tropics are among the most species-rich areas on Earth. The origins of this diversity, however, remain poorly understood. Here, we reveal and classify contributions of individual tropical Asian regions to their overall diversity by leveraging species-level phylogenomic data and new fossils from the most species-rich Asian palm lineage, the rattans and relatives (Arecaceae, Calamoideae). Radiators (Borneo) generate and distribute diversity, incubators (Indochina, New Guinea, and Sulawesi) produce diversity in isolation, corridors (Java, Maluku, Sumatra, and the Thai-Malay Peninsula) connect neighboring regions, and accumulators (Australia, India, Palawan, and the Philippines) acquire diversity generated elsewhere. These contrasting contributions can be explained by differences in region size and isolation, elucidating how the unique island-dominated geography of the Asian tropics drives their outstanding biodiversity.

A Chlorinated Diketopiperazine Antibiotic Targets Mycobacterium Tuberculosis DNA Gyrase

We describe a novel macrocyclic peptide, speirobactin, produced by Photorhabdus that selectively kills Mycobacterium tuberculosis . A non-ribosomal peptide synthase (NRPS) containing two linear modules codes for the synthesis of speirobactin. The biosynthetic operon contains a pentapeptide-repeat protein as a resistance gene. Genomic analysis of speirobactin-resistant mutants of M. tuberculosis led to identification of DNA gyrase as the molecular target. The mutations were recreated by allelic replacement and show that DNA gyrase is the only target. Transcriptome analysis of M. tuberculosis treated with antibiotics shows that speirobactin clusters close to fluoroquinolones, supporting its action against the DNA gyrase.

A comparative genomic analysis at the chromosomal-level reveals evolutionary patterns of aphid chromosomes

Genomic rearrangements are primary drivers of evolution, promoting biodiversity. Aphids, an agricultural pest with high species diversity, exhibit rapid chromosomal evolution and diverse karyotypes. These variations have been attributed to their unique holocentric chromosomes and parthenogenesis, though this hypothesis has faced scrutiny. In this study, we generated a chromosomal-level reference genome assembly of the celery aphid (Semiaphis heraclei) and conducted comparative genomic analysis, revealing varying chromosomal evolution rates among aphid lineages, positively correlating with species diversity. Aphid X chromosomes have undergone frequent intra-chromosomal recombination, while autosomes show accelerated inter-chromosomal recombination. Moreover, considering both inter- and intra-chromosomal rearrangements, the increased autosomal rearrangement rates may be common across the Aphidomorpha. We identified that the expansion of DNA transposable elements and short interspersed nuclear elements (SINEs), coupled with gene loss and duplication associated with karyotypic instability (such as RIF1, BRD8, DMC1, and TERT), may play crucial roles in aphid chromosomal evolution. Additionally, our analysis revealed that the mutation and expansion of detoxification gene families in S. heraclei may be a key factor in adapting to host plant chemical defenses. Our results provide new insights into chromosomal evolutionary patterns and detoxification gene families evolution in aphids, aiding the understanding of species diversity and adaptive evolution.

Identification and Characterization of Histone Modification Gene Families and Their Expression Patterns During Pod and Seed Development in Peanut

Histone methylation and acetylation play potential roles in plant growth and development through various histone modification (HM) genes. However, studies of HM genes are still limited in peanut (Arachis hypogaea L.), a globally important oilseed crop. Here, comprehensive identification and investigation of HM genes were performed using the whole genome of peanut, and a total of 207 AhHMs encoding 108 histone methyltransferases, 51 histone demethylases, 16 histone acetylases, and 32 histone deacetylases were identified. Detailed analysis of these AhHMs, including chromosome locations, gene structures, protein motifs, and protein-protein interactions, was performed. Tandem, segmental, transposed, dispersed, and whole-genome duplications were involved in the evolution and expansion of the HM gene families in peanut. Ka/Ks analysis indicated that the AhHMs underwent purifying selection. The expression profiles of the 207 AhHMs were investigated during the pod and seed development stages on the basis of the transcriptome sequencing results. Quantitative real-time PCR confirmed that eight AhHMs were differentially expressed during pod and seed development. These results provide data support for further studying the epigenetic mechanism of peanut histones, deepen the understanding of seed development, and provide a new direction for the cultivation of more high-yield and high-quality peanut varieties.

Total tocopherol levels in maize grain depend on chlorophyll biosynthesis within the embryo

BACKGROUND

Tocopherols are a class of lipid-soluble compounds that have multiple functional roles in plants and exhibit vitamin E activity, an essential nutrient for human and animal health. The tocopherol biosynthetic pathway is conserved across the plant kingdom, but source of the key tocopherol pathway precursor, phytol, is unclear. Two protochlorophyllide reductases (POR1 and POR2) were previously identified as loci controlling the natural variation of total tocopherols in maize grain, a non-photosynthetic tissue. POR1 and POR2 are key genes in chlorophyll biosynthesis yet the contribution of the chlorophyll biosynthetic pathway to tocopherol biosynthesis is still not understood.

RESULTS

We took two approaches to alter the activity of these two POR genes within kernel tissue, physiological treatments and CRISPR/Cas9-mediated knockouts, to determine the role of chlorophyll biosynthesis for tocopherol content. Since light is required for POR enzymatic activity, we imposed a dark treatment on developing kernels, which reduced chlorophyll a and tocopherols levels in embryo tissue by 92-99% and 87-90%, respectively, compared to the light treatment. In CRISPR/Cas9-mediated knockouts, the levels of chlorophyll a and tocopherols in embryos of the por1 por2 double homozygous mutant were reduced by 98-100% and 76-83%, respectively, compared to WT.

CONCLUSION

These findings demonstrate that tocopherol synthesis in maize grain depends almost entirely on phytol derived from chlorophyll biosynthesis within the embryo. POR1 and POR2 activity play crucial roles in chlorophyll biosynthesis, underscoring the importance of POR alleles and their activity in the biofortification of vitamin E levels in non-photosynthetic grain of maize.

Phage reprogramming of Pseudomonas aeruginosa amino acid metabolism drives efficient phage replication

Phages have been shown to use diverse strategies to commandeer bacterial host cell metabolism during infection. However, for many of the physiological changes in bacteria during infection, it is often unclear if they are part of a bacterial response to infection or if they are actively driven by the phage itself. Here, we identify two phage proteins that promote efficient phage replication by reprogramming host amino acid metabolism. These proteins, Eht1 and Eht2, are expressed early in the infection cycle and increase the levels of key amino acids and the arginine-derived polyamine putrescine. This provides a fitness advantage as these metabolites are important for phage replication and are often depleted during infection. We provide evidence that Eht1 and Eht2 alter the expression of bacterial host metabolic genes, and their activities may impinge on metabolism-related signaling processes. This work provides new insight into how phages ensure access to essential host resources during infection and the competitive advantage this provides.IMPORTANCEBacterial viruses, known as phages, are abundant in all environments that are inhabited by bacteria. During the infection process, phages exploit bacterial resources, resulting in notable changes to bacterial metabolism. However, precise mechanisms underlying these changes, and if they are driven by the phage or are a generalized bacterial response to infection, remain poorly understood. We characterized two proteins in Pseudomonas aeruginosa phage JBD44 whose activities alter bacterial host metabolism to optimize phage replication. Our work provides insight into how phages control bacterial processes to ensure access to essential host resources during infection.

Description of Cytobacillus Mangrovibacter sp. nov., and Cytobacillus Spartinae sp. nov., Isolated from Mangrove Sediment

Two Gram-stain-positive, aerobic, rod-shaped, and motile strains FJAT-53684 T and FJAT-54145 T were isolated from the mangrove sediment. They optimally grew at pH 8.0 and could tolerate NaCl up to 5% (w/v). The optimum temperature for growth of strains FJAT-53684 T and FJAT-54145 T were 35 and 40 ºC, respectively. The 16S rRNA gene sequence similarity between FJAT-53684 T and FJAT-54145 T was 97.1%. Both strains showed the highest 16S rRNA gene sequence similarity to the Cytobacillus species. Menaquinone-7 was the only respiratory quinone present in both strains. The major fatty acids (≥ 10%) in strain FJAT-53684 T were iso-C14:0, anteiso-C15:0, iso-C15:0, and iso-C19:0, while strain FJAT-54145 T consist of iso-C14:0, iso-C15:0, iso-C19:0, iso-C16:0, and C16:1 ω7c alcohol. The polar lipids present in both strains were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified lipid, unidentified phospholipid, and phosphatidylinositol. Their average nucleotide identity and digital DNA-DNA hybridization values were below the threshold values (95% and 70%, respectively) for species delineation. Based on the above results, strains FJAT-53684 T and FJAT-54145 T represent two novel species of the genus Cytobacillus, for which the names Cytobacillus mangrovibacter sp. nov., and Cytobacillus spartinae sp. nov., are proposed. The type strains are FJAT-53684 T (= JCM 35618 T = GDMCC 1.3071 T), and FJAT-54145 T (= JCM 35621 T = GDMCC 1.3079 T).

The genome of Aspergillus niger strain melanoliber

Aspergillus niger strain melanoliber was isolated from the coastal region of Mumbai, Maharashtra, India. This strain secretes water-soluble melanin attached to peptides possessing metal-chelation properties. Here, we report the whole-genome sequence of Aspergillus niger strain melanoliber. The genome was sequenced using Illumina Novaseq6000 giving a total size of 3.86 Mb.

Predicting protein-protein interactions in microbes associated with cardiovascular diseases using deep denoising autoencoders and evolutionary information

Introduction

Protein-protein interactions (PPIs) are critical for understanding the molecular mechanisms underlying various biological processes, particularly in microbes associated with cardiovascular disease. Traditional experimental methods for detecting PPIs are often time-consuming and costly, leading to an urgent need for reliable computational approaches.

Methods

In this study, we present a novel model, the deep denoising autoencoder for protein-protein interaction (DAEPPI), which leverages the denoising autoencoder and the CatBoost algorithm to predict PPIs from the evolutionary information of protein sequences.

Results

Our extensive experiments demonstrate the effectiveness of the DAEPPI model, achieving average prediction accuracies of 97.85% and 98.49% on yeast and human datasets, respectively. Comparative analyses with existing effective methods further validate the robustness and reliability of our model in predicting PPIs.

Discussion

Additionally, we explore the application of DAEPPI in the context of cardiovascular disease, showcasing its potential to uncover significant interactions that could contribute to the understanding of disease mechanisms. Our findings indicate that DAEPPI is a powerful tool for advancing research in proteomics and could play a pivotal role in the identification of novel therapeutic targets in cardiovascular disease.

Complete genome sequence of Parvimonas parva: first isolate of a human clinical specimen from Japan

Parvimonas parva is a bacterium belonging to the Peptoniphilaceae family, which was first classified in 2021. Herein, we report the complete genome sequence of P. parva (GAI15033) isolated from a clinical sample in Japan. The genome comprises a 1,447,534 bp circular chromosome.

DeepEpiIL13: Deep Learning for Rapid and Accurate Prediction of IL-13-Inducing Epitopes Using Pretrained Language Models and Multiwindow Convolutional Neural Networks

Accurate prediction of interleukin-13 (IL-13)-inducing epitopes is crucial for advancing targeted therapies against allergic inflammation, the cytokine storm associated with severe COVID-19, and related disorders. Current epitope prediction methods, however, often exhibit limitations in efficiency and accuracy. To address this, we introduce DeepEpilL13, a novel deep learning framework that uniquely synergizes pretrained language models with multiwindow convolutional neural networks (CNNs) for the rapid and accurate identification of IL-13-inducing epitopes from protein sequences. DeepEpilL13 leverages high-dimensional embeddings generated by the pretrained language model, which capture rich contextual information from protein sequences. These embeddings are then processed by a multiwindow CNN architecture, enabling the effective exploration of both local and global sequence patterns pertinent to IL-13 induction. The proposed DeepEpilL13 approach underwent rigorous evaluation using both benchmark data sets and an independent SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) data set. Results demonstrate that DeepEpilL13 achieves superior performance compared with traditional methods. On the benchmark data set, DeepEpilL13 attained a Matthews correlation coefficient (MCC) of 0.52 and an area under the receiver operating characteristic curve (AUC) of 0.86. Notably, when assessed on the independent SARS-CoV-2 data set, DeepEpilL13 exhibited remarkable robustness, achieving an MCC of 0.63 and an AUC of 0.92. These metrics underscore the enhanced predictive capability and robust applicability of DeepEpilL13, particularly within the context of the COVID-19 research and related viral infections. This study presents DeepEpilL13 as a powerful and efficient deep learning framework for accurate epitope prediction. By offering significant improvement in performance and robustness, DeepEpilL13 provides new and promising avenues for the development of epitope-based vaccines and immunotherapies specifically targeting IL-13-mediated disorders. The successful and rapid identification of IL-13-inducing epitopes using DeepEpilL13 paves the way for novel therapeutic interventions against a range of conditions, including allergic diseases, inflammatory conditions, and severe viral infections such as COVID-19, with potential for a significant impact on public health outcomes.

Decoding Solubility Signatures from Amyloid Monomer Energy Landscapes

This study investigates the energy landscapes of amyloid monomers, which are crucial for understanding protein misfolding mechanisms in Alzheimer's disease. While proteins possess inherent thermodynamic stability, environmental factors can induce deviations from native folding pathways, leading to misfolding and aggregation, phenomena closely linked to solubility. Using the UNOPTIM program, which integrates the UNRES potential into the Cambridge energy landscape framework, we conducted single-ended transition state searches and employed discrete path sampling to compute kinetic transition networks starting from PDB structures. These kinetic transition networks consist of local energy minima and the transition states that connect them, which quantify the energy landscapes of the amyloid monomers. We defined clusters within each landscape using energy thresholds and selected their lowest-energy structures for the structural analysis. Applying graph convolutional networks, we identified solubility trends and correlated them with structural features. Our findings identify specific minima with low solubility, characteristic of aggregation-prone states, highlighting the key residues that drive reduced solubility. Notably, the exposure of the hydrophobic residue Phe19 to the solvent triggers a structural collapse by disrupting the neighboring helix. Additionally, we investigated selected minima to determine the first passage times between states, thereby elucidating the kinetics of these energy landscapes. This comprehensive approach provides valuable insights into the thermodynamics and kinetics of Aβ monomers. By integration of multiple analytical techniques to explore the energy landscapes, our study investigates structural features associated with reduced solubility. These insights have the potential to inform future therapeutic strategies aimed at addressing protein misfolding and aggregation in neurodegenerative diseases.

In Silico Functional Annotation and Structural Characterization of Hypothetical Proteins in Bacillus paralicheniformis and Bacillus subtilis Isolated from Honey

Bacillus species are ubiquitous and survive in competitive microbial communities under adverse environmental conditions. Bacillus paralicheniformis and Bacillus subtilis obtained from honey revealed a significant proportion of proteins within their genomes as uncharacterized hypothetical proteins (HPs). A total of 1007 HP sequences were evaluated, resulting in the successful annotation of 56 HPs by assigning specific functions to them. A systematic in silico approach, integrating a range of bioinformatics tools and databases to annotate functions, characterize physicochemical properties, determine subcellular localization, and study protein-protein interactions, was used. Homology and de novo models were generated for the HPs, coupled with iterative remodeling and molecular dynamics (MD) simulations. HPs having significant roles in sporulation, biofilm formation, motility, ion transportation, regulation of metabolic processes, DNA repair, replication, and transcription were identified. Classical MD simulations of globular and transducer membrane proteins, along with postprocessing analyses, refined our structural predictions and provided deeper insights into the stability and functional dynamics of the protein structures under physiological conditions. Moreover, we observed a correlation between the percentage of α helix, β sheet, and coil structures in globular proteins and transducer membrane proteins. The integration of iterative loop modeling, MD simulations, and Dictionary of Secondary Structure in Proteins analysis further validated our predicted models and facilitated the identification of regions critical for protein function, thereby enhancing the overall reliability and robustness of our functional annotations. Furthermore, annotation of these hypothetical proteins aids in identifying novel proteins within bacterial cells, ultimately contributing to a deeper understanding of bacterial cell biology and their use for biotechnological purposes.

Differential growth and flowering capacity of tulip bulbs and the potential involvement of PHOSPHATIDYLETHANOLAMINE-BINDING PROTEINS (PEBPs)

BACKGROUND

Tulipa gesneriana reproduces vegetatively by the development of bulb clusters from axillary meristems in the scales of a mother bulb. While part of the daughter bulbs in a cluster develop into large, flowering bulbs, others stay small and vegetative under the same environmental conditions. This study aims to investigate how these different developmental fates are orchestrated.

RESULTS

RNA-seq analysis revealed that the overall transcriptomic landscape of the two types of daughter bulbs does not differ substantially, but follows a similar trajectory over time. Nonetheless, the expression levels of genes related to proliferation already differ at early development stages. Surprisingly, at a later stage, transcriptomic changes related to flower induction are detectable in flowering as well as non-flowering bulbs, with some quantitative differences. However, genes linked with floral organ development are differentially expressed, as well as negative regulators of flowering and more basal metabolic processes. In search for the molecular determinants of daughter bulb size and developmental fate, we investigated members of the PHOSPHATIDYLETHANOLAMINE-BINDING PROTEIN (PEBP) gene family as candidates. Tulip FLOWERING LOCUS T1 (TgFT1), TgFT2, and TgFT3 are expressed in leaves and leaf-like organs of the mother plant, and their encoded proteins interact with the TCP transcription factor TEOSINTE BRANCHED1 (TgTB1). Therefore, we suggest that these three genes act as 'bulbigens', meaning regulators of axillary meristem outgrowth and hence, daughter bulb size. Furthermore, we found that TgFT2 and TgFT4 could constitute the main florigens in tulips, because of their expression pattern and the binding of their encoding proteins to the bZIP transcription factor FD (TgFD). Moreover, Arabidopsis lines ectopically expressing TgFT2 or TgFT4 flower significantly earlier than the wild type.

CONCLUSIONS

Differences in the developmental fate of tulip daughter bulbs are established early during development and are linked with differences in cell division and metabolism. The activity of members of the PEBP family, known for their role in flowering and storage organ formation in geophytes, appeared to be associated with the transcriptional switches observed during daughter bulb development. This points towards a functional role of these proteins in governing developmental trajectories underlying the mode of reproduction.

Lower termite (Coptotermes heimi) gut fibrolytic bacterial consortium: Isolation, phylogenetic characterization, fibre degradation potential and in vitro digestibility

Lower termites produce wide array of fibrolytic enzymes and serves as prospective microbial enzymes source for enhancing biodegradability of recalcitrant ligno-cellulosic fibrous feeds. The present study was aimed to isolate and characterize anaerobic fibrolytic bacteria from gut of termite Coptotermes heimi for screening promising isolates to improve fiber digestibility in ruminants. A total of 141 isolates were obtained from 97 termite gut samples, and 24 isolates (TM1 to TM24) were selected and characterized as fibrolytic. All isolates were obligatory anaerobes and catalase negative except, TM8, TM9, TM14 and TM22 which were facultative anaerobes and catalase positive. Overall fibrolytic enzyme activity was highest in isolate TM23, TM6 and TM22. Highest FPase activity was observed in isolate TM5 (12.05 U/ml) while, lowest in TM19 (6.41 U/ml). The phylogenetic analysis of the isolates depicted four major families, i.e., Clostridiales, Bacillales, Lactobacillales and Enterobacterales under phyla Firmicutes and Proteobacteria. The in vitro dry matter digestibility of the substrate was increased by 9.4 to 36.0% with the inoculation of isolated bacterial strains. Among the screened isolates, TM6 exhibited highest ability to improve the in vitro dry matter digestibility. The findings of the present study revealed that the fibrolytic bacteria isolated from - termite gut can be used for commercial enzyme production or in rumen biotechnological application for enhancing utilization of fibrous feed in ruminants.

From Sea to Freshwater: Shared and Unique Microbial Traits in Sponge Associated Prokaryotic Communities

Despite their ecological significance and biotechnological potential, freshwater sponges remain relatively understudied compared to their marine counterparts. In special, the prokaryotic communities of species from isolated yet highly diverse ecosystems, such as the Amazon Rainforest, remain unknown, leaving an important part of the Porifera microbiome underexplored. Using high-throughput sequencing of the 16S rRNA gene, we unraveled the structure of the microbiota associated to the freshwater sponges Heteromeyenia cristalina and Metania reticulata for the first time. Their microbiome was compared with that of the haplosclerid marine sponges Amphimedon viridis and Haliclona melana; and the tetractinellid Cinachyrella alloclada. Our findings reveal not only a shared core microbiome between the freshwater and marine environments but also indicate functional redundancy in their communities, suggesting that certain microbial metabolic functions are conserved across diverse habitats. Comparisons between ecosystems also revealed that microbiomes of freshwater sponges can be richer and more diverse than those of marine species. Moreover, we compared the microbiome of adults and asexual reproduction structures (buds and gemmules) of sponges from both habitats, revealing a remarkable similarity between adults and their respective offsprings, indicating an important role of vertical transmission in this mode of reproduction. Our observations emphasize the dynamic interactions and the adaptability of the sponge-associated microbiota, providing insights into how these symbiotic associations were affected during the colonization of freshwater environments and shedding light into how symbiotic relationships are maintained throughout generations.

Heterogeneity of rock-hosted microbial communities in a serpentinizing aquifer of the Coast Range Ophiolite

The movement of groundwater through fractured bedrock provides favorable conditions for subsurface microbial life, characterized by constrained flow pathways and distinctive local environmental conditions. In this study, we examined a subsurface microbial ecosystem associated with serpentinized rocks recovered from the Coast Range Ophiolite in northern California, USA. The distribution and diversity of microbial communities at various depths within two separate cores reaching up to 45 m below the land surface were investigated with microbiological and geochemical approaches. Core samples contained low total organic carbon content, low DNA yields, and low copy numbers of 16S rRNA genes, yet some samples still yielded amplifiable DNA sequences. The microbial community composition of rock cores was distinct from groundwater, and source tracking of DNA sequences indicated that groundwater is not a significant source of DNA into basement rocks. In contrast, the microbial community of some rock core samples shared similarities with overlying soil samples, which could indicate potential contamination, weathering of shallow serpentinites, or a combination of both. Individual DNA sequences of archaea and bacteria predicted to be endemic to the basement rocks were identified by differential abundance analyses. Core-enriched sequences were distinct from those in groundwater or in the overlying soils and included OTUs related to Serpentinimonas as well as putatively anaerobic, deep subsurface-associated taxa such as methanogens and Bathyarchaeia. Stable isotope analyses of organic and inorganic carbon did not reveal a chemoautotrophic signal and were instead consistent with a primarily surface vegetation source of organic carbon into the basement. This census of archaeal and bacterial DNA sequences associated with altered ultramafic rocks provides a useful resource for further research into the potential for deep subsurface microbial activity fueled by geochemical reactions associated with serpentinization.

A Broad Genome Survey Reveals Widespread Presence of Secretoglobin Genes in Squamate and Archosaur Reptiles that Flowered into Diversity in Mammals

Secretoglobins (SCGBs) are a superfamily of small, dimeric, cytokine-like proteins found originally in the reproductive tracts and airways of mammals. Most SCGB research has focused on respiratory diseases in humans and laboratory animal models but knowledge of their biological functions is sparse. We report here a broad survey of Scgbs, the genes that encode SCGBs, in animal genomes. We tested the view that they are uniquely mammalian in origin and distribution, hoping that understanding their distribution would shed light on their evolutionary history and perhaps point to putative biological functions. Rather than being uniquely mammalian, we found many different SCGBs in turtles, crocodilians, lizards, and birds, suggesting they existed in the Carboniferous Period (∼320 MYA) when the sauropsids evolved in the amniote lineage. We identified no SCGBs in amphibians or fishes, suggesting that this characteristic originated in an amniote ancestor. Amniotes include sauropsid and synapsid lineages, and three subfamilies of SCGBs (SCGB2A, SCGB3A, and SCGB1C) are found in both sauropsid and synapsid lineages. Uteroglobin (SCGB1A), the first identified SCGB protein, is uniquely mammalian, having appeared in monotremes. The SCGB subfamilies including androgen-binding proteins (SCGB1B and SCGB2B) are first seen in metatherians. This complex distribution suggests that there is an as-yet-undiscovered basic function of SCGBs shared by all amniotes.

The RNA helicase HrpA rescues collided ribosomes in E. coli

Although many antibiotics inhibit bacterial ribosomes, the loss of known factors that rescue stalled ribosomes does not lead to robust antibiotic sensitivity in E. coli, suggesting the existence of additional mechanisms. Here, we show that the RNA helicase HrpA rescues stalled ribosomes in E. coli. Acting selectively on ribosomes that have collided, HrpA uses ATP hydrolysis to split stalled ribosomes into subunits. Cryoelectron microscopy (cryo-EM) structures reveal how HrpA simultaneously binds to two collided ribosomes, explaining its selectivity, and how its helicase module engages downstream mRNA such that, by exerting a pulling force on the mRNA, it would destabilize the stalled ribosome. These studies show that ribosome splitting is a conserved mechanism that allows proteobacteria to tolerate ribosome-targeting antibiotics.

The hidden bacterial microproteome

Microproteins encoded by small open reading frames comprise the "dark matter" of proteomes. Although microproteins have been detected in diverse organisms from all three domains of life, many more remain to be identified, and only a few have been functionally characterized. In this comprehensive study of intergenic small open reading frames (ismORFs, 15-70 codons) in 5,668 bacterial genomes of the family Enterobacteriaceae, we identify 67,297 clusters of ismORFs subject to purifying selection. Expression of tagged Escherichia coli microproteins is detected for 11 of the 16 tested, validating the predictions. Although the ismORFs mainly code for hydrophobic, potentially transmembrane, unstructured, or minimally structured microproteins, some globular folds, oligomeric structures, and possible interactions with proteins encoded by neighboring genes are predicted. Complete information on the predicted microprotein families, including evidence of transcription and translation, and structure predictions are available as an easily searchable resource for investigation of microprotein functions.

A fast approach for structural and evolutionary analysis based on energetic profile protein comparison

In structural bioinformatics, the efficiency of predicting protein similarity, function, and evolutionary relationships is crucial. Our approach proposed herein leverages protein energy profiles derived from a knowledge-based potential, deviating from traditional methods relying on structural alignment or atomic distances. This method assigns unique energy profiles to individual proteins, facilitating rapid comparative analysis for both structural similarities and evolutionary relationships across various hierarchical levels. Our study demonstrates that energy profiles contain substantial information about protein structure at class, fold, superfamily, and family levels. Notably, these profiles accurately distinguish proteins across species, illustrated by the classification of coronavirus spike glycoproteins and bacteriocin proteins. Introducing a separation measure based on energy profile similarity, our method shows significant correlation with a network-based approach, emphasizing the potential of energy profiles as efficient predictors for drug combinations with faster computational requirements. Our key insight is that the sequence-based energy profile strongly correlates with structure-derived energy, enabling rapid and efficient protein comparisons based solely on sequences.

Widespread and Convergent Evolution of Cone Monochromacy in Galeomorph Sharks

Color vision is widespread in marine vertebrates but is notably lacking in whales, dolphins, seals, and apparently also sharks. All sharks studied to date possess only a single spectral class of cone and are thus potentially totally color blind. The reason why sharks lack color vision is unclear, but as the visual pigments of only a handful of this large and ecologically diverse taxon have been studied, more data are required to address this question. Here, we assembled the retinal transcriptomes of 9 species from 7 families and 3 orders within the superorder Galeomorphii to screen for visual opsin and phototransduction genes. We reveal that cone monochromacy is widespread in galeomorph sharks, but the type of cone opsin expressed varies, with lamniform and orectolobiform sharks expressing a long-wavelength-sensitive (LWS) opsin, and carcharhiniform and heterodontiform sharks expressing a rhodopsin-like 2 (RH2) opsin. Cone monochromacy has evolved from a dichromatic ancestral state at least 4 times, implying strong selection pressure to prioritize achromatic over chromatic vision. While all species express the GRK1A and GRK7 isoforms of G protein-coupled receptor kinase, only sharks with the LWS cone opsin express the GRK1B isoform, which suggests that nonspectral functions of photoreception may have influenced, or result from, the opsin complement in the shark retina. Finally, we show that the shark rod (RH1) opsin gene shows evidence of positive selection at sites known to influence pigment kinetics (i.e. metarhodopsin II stability) and that the rate of retinal release likely differs substantially between species in ways that reflect their physiology and ecology.

Decoding Pecan's Fungal Foe: A Genomic Insight into Colletotrichum plurivorum Isolate W-6

Pecan (Carya illinoinensis) is a world-renowned nut crop that is highly favored by consumers for its high content of healthy nutrients. For a long time, anthracnose has severely threatened the yield and quality of pecan, causing significant economic losses to the global pecan industry. Here, we report the 54.57-Mb gapless chromosome-level assembly of the pathogenic ascomycetes Colletotrichum plurivorum isolate W-6 from pecan plantations in Southeast China. Six of 12 chromosomes contain, at least, telomeric repeats (CCCTAA)n or (TTAGGG)n at one end. A total of 14,343 protein-coding genes were predicted. Pathogenicity- and virulence-related annotations revealed 137 to 4558 genes associated with the TCDB, PHI, Cyt_P450, DFVF, effector, and secretome databases, respectively. A comparative analysis of isolate W-6, together with 51 other Colletotrichum strains, reveled 13 genes unique to the Orchidearum complex to which isolate W-6 belongs, highlighting the major facilitator superfamily transporters. The detailed analyses of MFS transporters associated with secondary metabolite gene clusters in isolate W-6 led to the identification and protein structure analyses of two key virulence factor candidates in DHA1 subclass, prlG and azaK, which were reported as efflux transporters of antibiotics in other pathogenic fungi. The assembly and further functional investigation of two pathogenic genes identified here potentially provide important resources for better understanding the biology and lifestyle of Colletotrichum and pave the way for designing more efficient strategies to control anthracnose in pecan plantations.

Lineage-Specific Class-A GPCR Dynamics Reflect Diverse Chemosensory Adaptations in Lophotrochozoa

Sensing external chemosensory cues via Class-A G protein-coupled receptors (GPCRs) is crucial for a multitude of behavioral and biological functions, influencing animal evolution and ecological adaptations. While extensively studied in vertebrates and echinoderms, the role of GPCR-mediated chemoreception in major protostome clades like Lophotrochozoa remains obscure despite their remarkable ecological adaptations across diverse aquatic and terrestrial environments. Utilizing 238 lophotrochozoan genomes across eight phyla, we conducted a large-scale comparative genomics analysis to identify lineage-specific expansions of Class-A GPCR subsets that are likely adapted for chemoreception. Using phylogeny and orthology-inference-based clustering, we distinguished these expansions from conserved orthogroups of prospective endogenous ligand-binding Class-A GPCR subsets. Across phyla, lineage-specific expansions correlated with adaptations to various habitats, ecological niches, and lifestyles, while the influence of whole-genome duplications in driving these lineage-specific expansions appeared to be less significant. Species adapted to various coastal, freshwater, and terrestrial habitats across several classes of Mollusca, Annelida, and other analyzed phyla exhibit large and diverse lineage-specific expansions, while adaptations to extreme deep-sea environments, parasitic lifestyles, sessile behaviors, or alternative chemosensory mechanisms consistently exhibit reductions. Sequence heterogeneity, signatures of positive selection, and conformational flexibility in ligand-binding pockets further highlighted adaptations to environmental signals. In summary, the evolutionary dynamics of Class-A GPCRs in lophotrochozoans reveal a widespread pattern of lineage-specific expansions driven by adaptations for chemoreception across diverse environmental niches, mirroring the trends and prominent roles seen in deuterostome lineages. The comprehensive datasets spanning numerous genomes offer a valuable foundation for advancing GPCR-mediated chemoreception studies in Lophotrochozoa.

Genome-Wide Identification and Expression Analysis of CrRLK1-like Gene Family in Potatoes (Solanum tuberosum L.) and Its Role in PAMP-Triggered Immunity

BACKGROUND

The Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) subfamily, a specialized group within receptor-like kinases (RLKs), was initially identified in C. roseus cell cultures. CrRLK1L plays an important role in the growth, development and stress response of plants. Although CrRLK1L genes have been characterized across multiple plant species, their biological and genetic functions in potatoes (Solanum tuberosum) remains poorly elucidated.

METHODS

a genome-wide investigation, phylogenetic analysis, chromosome localization, exon-intron structure, conserved motifs, stress-responsive cis-elements, tissue-specific expression patterns, and their effects on pathogen associated molecular patterns (PAMPs) induced reactive oxygen species (ROS) production were analyzed.

RESULTS

A total of 29 CrRLK1L genes were identified in the S. tuberosum genome, unevenly distributed across 10 chromosomes and divided into three groups. Tissue-specific expression analysis revealed seven genes highly expressed in all tissues, while CrRLK1L13 was specific to stamens and flowers. Under stress conditions (mannitol, salt, hormone, and heat), StCrRLK1L genes exhibited diverse expression patterns. Functional characterization in Nicotiana benthamiana identified seven ROS suppressors and four ROS enhancers, implicating their roles in PAMP-triggered immunity.

CONCLUSIONS

This study provides valuable insights into the StCrRLK1L gene family, enhancing our understanding of its functions, particularly in plant innate immunity.

Isolation and characterization of fMGyn-Pae01, a phiKZ-like jumbo phage infecting Pseudomonas aeruginosa

BACKGROUND

Pseudomonas aeruginosa is an opportunistic pathogen that causes a wide variety of infections, and belongs to the group of ESKAPE pathogens that are the leading cause of healthcare-associated infections and have high level of antibiotic resistance. The treatment of infections caused by antibiotic-resistant P. aeruginosa is challenging, which makes it a common target for phage therapy. The successful utilization of phage therapy requires a collection of well characterized phages.

METHODS

Phage fMGyn-Pae01 was isolated from a commercial phage therapy cocktail. The phage morphology was studied by transmission electron microscopy and the host range was analyzed with a liquid culture method. The phage genome was sequenced and characterized, and the genome was compared to closest phage genomes. Phage resistant bacterial mutants were isolated and whole genome sequencing and motility, phage adsorption and biofilm formation assays were performed to the mutants and host bacterium.

RESULTS

The genomic analysis revealed that fMGyn-Pae01 is a lytic, phiKZ-like jumbo phage with genome size of 277.8 kb. No genes associated with lysogeny, bacterial virulence, or antibiotic resistance were identified. Phage fMGyn-Pae01 did not reduce biofilm formation of P. aeruginosa, suggesting that it may not be an optimal phage to be used in monophage therapy in conditions where biofilm formation is expected. Host range screening revealed that fMGyn-Pae01 has a wide host range among P. aeruginosa strains and its infection was not dependent on O-serotype. Whole genome sequencing of the host bacterium and phage resistant mutants revealed that the mutations had inactivated either a flagellar or rpoN gene, thereby preventing the biosynthesis of a functional flagellum. The lack of functional flagella was confirmed in motility assays. Additionally, fMGyn-Pae01 failed to adsorb on non-motile mutants indicating that the bacterial flagellum is the phage-binding receptor.

CONCLUSION

fMGyn-Pae01 is a phiKZ-like jumbo phage infecting P. aeruginosa. fMGyn-Pae01 uses the flagellum as its phage-binding receptor, supporting earlier suggestions that flagellum might be utilized by phiKZ but differs from some other previous findings showing that phiKZ-like phages use the type-IV pili as the phage-binding receptor.

Genomic configuration of Bacillus subtilis (NMB01) unveils its antiviral activity against Orthotospovirus arachinecrosis infecting tomato

Orthotospovirus arachinecrosis (groundnut bud necrosis virus, GBNV) infecting tomato is a devastating viral pathogen responsible for severe yield losses of up to 100%. Considering the significance of the plant growth-promoting bacteria to induce innate immunity, attempts were made to evaluate the antiviral efficacy of Bacillus subtilis NMB01 against GBNV in cowpea and tomato. Foliar application of B. subtilis NMB01 at 1.5% onto the leaves of cowpea and tomato followed by challenge inoculation with GBNV significantly reduced the incidence of GBNV from 80% to 90% in response to the untreated inoculated control. Hence, we had a quest to understand if any genes were contributing toward the suppression of GBNV in assay hosts. To unveil the secrecy, whole-genome sequencing of B. subtilis NMB01 was carried out. The genome sequence of NMB01 revealed the presence of secondary metabolite biosynthetic gene clusters, including non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) which also encoded bacteriocins and antimicrobial peptides. The pan-genome analysis identified 1,640 core genes, 4,885 dispensable genes, and 60 unique genes, including MAMP genes that induce host immune responses. Comparative genome and proteome analysis with other genomes of B. subtilis strains in a public domain through OrthoVenn analysis revealed the presence of 4,241 proteins, 3,695 clusters, and 655 singletons in our study isolate. Furthermore, the NMB01-treated tomato plants increased the levels of defense-related genes (MAPKK1, WRKY33, PR1, PAL, and NPR1), enhancing immune system priming against GBNV infection. These findings suggest that B. subtilis NMB01 can be used as a promising biological control agent for managing plant viral disease sustainably.

Regularly updated benchmark sets for statistically correct evaluations of AlphaFold applications

AlphaFold2 changed structural biology by providing high-quality structure predictions for all possible proteins. Since its inception, a plethora of applications were built on AlphaFold2, expediting discoveries in virtually all areas related to protein science. In many cases, however, optimism seems to have made scientists forget about data leakage, a serious issue that needs to be addressed when evaluating machine learning methods. Here we provide a rigorous benchmark set that can be used in a broad range of applications built around AlphaFold2/3.

Characterization and Genome Analysis of Fusarium oxysporum Provides Insights into the Pathogenic Mechanisms of the Pokkah Boeng Disease in China

Pokkah Boeng Disease (PBD) is a severe and devastating disease that causes significant damage and yield losses in China. The pathogenic fungus Fusarium oxysporum is responsible for the rapid onset of top rot symptoms in sugarcane. In this study, we selected a representative strain, BS2-6, to perform morphological observations of colonies and determine pathogenicity. We examined the effects of BS2-6 infestation on the ultrastructure of sugarcane leaves. Moreover, we sequenced the whole genome of BS2-6 and examined the effects of various nitrogen sources and chemical reagents on its growth and pathogenicity. Our results indicate that sugarcane leaves inoculated with BS2-6 quickly succumb to heart leaf and growing rot. Ultrastructural analysis revealed that the surface tissues of the diseased leaves were destroyed with mycelium, and conidia blocked leaf stomata, which ultimately led to the degradation of leaf tissues. Ammoniacal nitrogen significantly promoted mycelial growth, pigment secretion, and the expression of genes related to secondary metabolite synthesis, thereby accelerating the development of PBD. In addition, we found that carbendazim effectively inhibited the growth of BS2-6 at various concentrations. These findings provide important insights for the effective prevention and control of PBD during sugarcane production.

Effects of Oral Administration of the Probiotic Lactobacillus rhamnosus GG on the Proteomic Profiles of Cerebrospinal Fluid and Immunoregulatory Signaling in the Hippocampus of Adult Male Rats

INTRODUCTION

The microbiome-gut-brain axis, by modulating bidirectional immune, metabolic, and neural signaling pathways in the host, has emerged as a target for the prevention and treatment of psychiatric and neurological disorders. Oral administration of the probiotic bacterium Lactobacillus rhamnosus GG (LGG; ATCC 53103) exhibits anti-inflammatory effects, although the precise mechanisms by which LGG benefits host physiology and behavior are not known. The goal of this study was to explore the general effects of LGG on the cerebrospinal fluid (CSF) proteome and a biological signature of anti-inflammatory signaling in the central nervous system (CNS) of undisturbed, adult male rats.

METHODS

Liquid chromatography-tandem mass spectrometry-based proteomics were conducted using CSF samples collected after 21 days of oral treatment with live LGG (3.34 × 107 colony-forming units (CFU)/mL in the drinking water (resulting in an estimated delivery of ∼1.17 × 109 CFU/day/rat) or water vehicle. Gene enrichment analysis (using DAVID, v. 6.8) and protein-protein interactions (using STRING, v. 11) were used to explore physiological network changes in CSF. Real-time reverse transcription polymerase chain reaction (real-time RT-PCR) was performed to assess gene expression changes of anti-inflammatory cytokines in the hippocampus. Genes associated with anti-inflammatory signaling that were analyzed included Il10, Tgfb1, Il4, and IL-4-responsive genes, Cd200, Cd200r1, and Mrc1 (Cd206).

RESULTS

Oral LGG administration altered the abundance of CSF proteins, increasing the abundance of five proteins (cochlin, NPTXR, reelin, Sez6l, and VPS13C) and decreasing the abundance of two proteins (CPQ, IGFBP-7) in the CSF. Simultaneously, LGG increased the expression of Il10 mRNA, encoding the anti-inflammatory cytokine interleukin 10, in the hippocampus.

CONCLUSION

Oral LGG altered the abundance of CSF proteins associated with extracellular scaffolding, synaptic plasticity, and glutamatergic signaling. These data are consistent with the hypothesis that oral administration of LGG improves memory and cognition, and promotes a physiological resilience to neurodegenerative disease, by increasing glutamatergic signaling and promoting an anti-inflammatory environment in the brain.

Prediction of Plant Resistance Proteins Using Alignment-Based and Alignment-Free Approaches

Plant disease resistance (PDR) proteins are critical in identifying plant pathogens. Predicting PDR protein is essential for understanding plant-pathogen interactions and developing strategies for crop protection. This study proposes a hybrid model for predicting and designing PDR proteins against plant-invading pathogens. Initially, we tried alignment-based approaches, such as Basic Local Alignment Search Tool (BLAST) for similarity search and MERCI for motif search. These alignment-based approaches exhibit very poor coverage or sensitivity. To overcome these limitations, we developed alignment-free or machine learning (ML)-based methods using compositional features of proteins. Our ML-based model, developed using compositional features of proteins, achieved a maximum performance area under the receiver operating characteristic curve (AUROC) of 0.91. The performance of our model improved significantly from AUROC of 0.91-0.95 when we used evolutionary information instead of protein sequence. Finally, we developed a hybrid or ensemble model that combined our best ML model with BLAST and obtained the highest AUROC of 0.98 on the validation dataset. We trained and tested our models on a training dataset and evaluated them on a validation dataset. None of the proteins in our validation dataset are more than 40% similar to proteins in the training dataset. One of the objectives of this study is to facilitate the scientific community working in plant biology. Thus, we developed an online platform for predicting and designing plant resistance proteins, "PlantDRPpred" (https://webs.iiitd.edu.in/raghava/plantdrppred).

Loss of Pleiotropic Regulatory Functions in Tannin1, the Sorghum Ortholog of Arabidopsis Master Regulator TTG1

Transcriptional master regulators are often targeted to improve plant traits, but antagonistic pleiotropic effects of these regulators can hamper this approach. The Myb-bHLH-WDR (MBW) complex is a broadly conserved transcriptional regulator affecting pigmentation, biotic stress resistance, and abiotic stress tolerance. We investigated the function of sorghum grain pigmentation regulator Tannin1, the ortholog of Arabidopsis pleiotropic WD40 regulator TTG1, to test for conserved pleiotropic regulatory effects and to better understand the evolution of the MBW complex in Poaceae. We characterized genome-wide differential expression of leaf tissue using RNA sequencing in near-isogenic lines (NILs) that contrasted wildtype Tan1 and loss-of-function tan1-b alleles, under optimal temperature and chilling stress. Notably, Gene Ontology analyses revealed no pathways with differential expression between Tan1 and tan1-b NILs, suggesting that, in contrast to Arabidopsis TTG1, Tannin1 has no pleiotropic regulatory role in leaves. Further, NILs had no visible difference in anthocyanin pigmentation, and no genes with known or expected function in flavonoid synthesis were differentially expressed. Genome-wide, only 18 total genes were differentially expressed between NILs, with six of these genes located inside the NIL introgression region, an observation most parsimoniously explained by cis-regulatory effects unrelated to Tannin1 regulation. Comparing our findings with known function of TTG1 orthologs in maize, rice, and Arabidopsis, we conclude that pleiotropic regulatory function in leaf tissue was likely lost in panicoid grass evolution before the sorghum-maize split. These findings inform future molecular breeding of MBW regulated traits and highlight the benefit of subfunctionalization to relieve pleiotropic constraints.

The TRAPPC8/TRS85 subunit of the Arabidopsis TRAPPIII tethering complex regulates endoplasmic reticulum function and autophagy

Transport protein particle (TRAPP) tethering complexes are known for their function as Rab GTPase exchange factors. Two versions of the complex are considered functionally separate: TRAPPII, an activator of the Rab11 family (RabA in plants) GTPases that function in post-Golgi sorting, and TRAPPIII, activating Rab1 family (RabD in plants) members that regulate endoplasmic reticulum (ER)-to-Golgi trafficking and autophagy. In Arabidopsis (Arabidopsis thaliana), the TRAPPIII complex has been identified and its subunit composition established, but little is known about its functions. Here, we found that binary subunit interactions of the plant TRAPPIII complex are analogous to those of metazoan TRAPPIII, with the 2 large subunits TRAPPC8 and TRAPPC11 linking the TRAPP core and the small C12 to C13 dimer. To gain insight into the functions of TRAPPIII in plants, we characterized 2 A. thaliana trappc8 mutants. These mutants display abnormalities in plant morphology, particularly in flower and seed development. They also exhibit autophagic defects, a constitutive ER stress response, and elevated levels of the ER lipid dolichol (Dol), which is an indispensable cofactor in protein glycosylation. These results indicate that plant TRAPPC8 is involved in multiple cellular trafficking events and suggest a link between ER stress responses and Dol levels.

Fine mapping of stripe rust resistance gene YrAn1589 in common wheat using Wheat660K SNP array and BSR-Seq

KEY MESSAGE

A new stripe rust resistance gene YrAn1589 in Chinese wheat Annong1589 was mapped to a 160.9-166.6 kb interval on chromosome arm 3BL and co-segregated with a marker CAPS9 developed from candidate gene TraesCS3B03G1054600.  Stripe rust, caused by Puccinia. striiformis f. sp. tritici (Pst), is a devastating fungal disease that can significantly reduce wheat yield. The Chinese wheat cultivar Annong1589 demonstrates high resistance against the predominant Pst races in the Huang-Huai valley wheat region. The present study aimed to identify the stripe rust resistance gene in Annong1589. Genetic analysis indicated that the resistance in Annong1589 was conferred by a single dominant gene, provisionally designated YrAn1589. Using Wheat660K SNP array, bulked segregant RNA sequencing and new molecular markers developed, the resistance gene was mapped to a 160.9-166.6 kb region between CAPS8 and CAPS10 on chromosome 3BL based on IWGSC CS RefSeq v2.1 and eight other reference genome sequences, including eight high-confidence annotated genes. Transcriptome and qRT-PCR analyses revealed significantly upregulated expression of TraesCS3B03G1054600 in resistant plants following CYR32 inoculation, suggesting it is a potential candidate gene for YrAn1589. A functional marker CAPS9 developed from a A/G polymorphic SNP in the candidate co-segregated with YrAn1589 in the F2 population. Subcellular localization experiments showed that TraesCS3B03G1054600 protein was localized in the cytoplasm and nucleus, implying its role in immune response and resistance. Our findings establish YrAn1589 as a new stripe rust resistance gene, providing valuable gene resource and molecular markers for improvement of stripe rust resistance in wheat.

Pigment-dispersing factor neuropeptides act as multifunctional hormones and modulators in tardigrades

Pigment-dispersing factors (PDFs) are neuropeptides that play key roles in controlling the circadian rhythms in various insects, whereas their function remains elusive in other protostomes including tardigrades (water bears). Here we show that the three PDFs of the tardigrade Hypsibius exemplaris are co-localized in two pairs of inner lobe cells in the brain, whereas only one PDF occurs in four additional cerebral and two extracerebral cells. The axons of the inner lobe cells pass through the contralateral brain hemisphere, descend to the ventral nerve cord and terminate in two pairs of potential release sites in the posteriormost trunk ganglion. Using in vitro assays, we demonstrate that all three PDFs and their deorphanized receptor (PDFR) are functional. Widespread localization of PDFR suggests that tardigrade PDFs may act as multifunctional hormones and neuromodulators that control major functions including light detection, neural processing, locomotion, feeding, digestion, osmoregulation, growth, embryonic development and oogenesis/reproduction.

High intra-laboratory reproducibility of nanopore sequencing in bacterial species underscores advances in its accuracy

Nanopore sequencing is a third-generation technology known for its portability, real-time analysis and ability to generate long reads. It has great potential for use in clinical diagnostics, but thorough validation is required to address accuracy concerns and ensure reliable and reproducible results. In this study, we automated an open-source workflow (freely available at https://gitlab.com/FLI_Bioinfo/nanobacta) for the assembly of Oxford Nanopore sequencing data and used it to investigate the reproducibility of assembly results under consistent conditions. We used a benchmark dataset of five bacterial reference strains and generated eight technical sequencing replicates of the same DNA using the Ligation and Rapid Barcoding kits together with the Flongle and MinION flow cells. We assessed reproducibility by measuring discrepancies such as substitution and insertion/deletion errors, analysing plasmid recovery results and examining genetic markers and clustering information. We compared the results of genome assemblies with and without short-read polishing. Our results show an average reproducibility accuracy of 99.999955% for nanopore-only assemblies and 99.999996% when the short reads were used for polishing. The genomic analysis results were highly reproducible for the nanopore-only assemblies without short read in the following areas: identification of genetic markers for antimicrobial resistance and virulence, classical MLST, taxonomic classification, genome completeness and contamination analysis. Interestingly, the clustering information results from the core genome SNP and core genome MLST analyses were also highly reproducible for the nanopore-only assemblies, with pairwise differences of up to two allele differences in core genome MLST and two SNPs in core genome SNP across replicates. After polishing the assemblies with short reads, the pairwise differences for cgMLST were 0 and for cgSNP were 0-1 SNP across replicates. These results highlight the advances in sequencing accuracy of nanopore data without the use of short reads.

Overcoming cross-reactivity of antibodies against human lactate dehydrogenase

Lactate dehydrogenase subunit A (LD-A) plays an important role in cancer regulation and therapy. We attempted to develop an enzyme-linked immune-solvent assay (ELISA) for LD-A in human serum. However, commercial antibodies against LD-A exhibited cross-reactivity with an unknown protein. The unknown protein was purified and characterized by protein sequencing and Western blotting. In addition, we attempted to prepare a specific antibody for the ELISA using partially synthesized peptides of LD-A as immunogens. The epitope position in LD-A was carefully selected based on bioinformatics analysis. Peptide sequencer elucidated a ten amino acid sequence of the purified protein at the N-terminal. A BLAST search revealed that this sequence perfectly matched that at the N-terminus of the IgG heavy chain (H-chain). Furthermore, we demonstrated that twelve commercially available antibodies targeting LD-A or LD-B (subunit B) primarily cross-reacted with IgG or its H-chain, with only one specific antibody for each subunit. As the specific antibody against LD-A is no longer commercially accessible, we successfully produced two kinds of specific antibodies using partially synthesized LD-A peptides as immunogens. In conclusion, we have successfully produced specific antibodies against LD-A. Moreover, our findings underscore the utility of bioinformatics tools for determining the optimal positions of immunizing peptides.

Presence of polyketide synthases and nonribosomal peptide synthetase in culturable bacteria associated with Aplysina fulva and Aplysina caissara (Porifera)

Culture-dependent and -independent studies have provided access to symbiont genes and the functions they play for host sponges. Thus, this work investigates the diversity, presence of genes of pharmacological interest, biological activities and metabolome of the bacteria isolated from the sponges Aplysina caissara and Aplysina fulva collected on the southwestern Atlantic Coast. The genes for Polyketide Synthases types I and II and Nonribosomal Peptide Synthetases were screened in more than 200 bacterial strains obtained, from which around 40% were putatively novel. Twenty-two were positive for at least one of the genes screened. Among them, 12 exhibited antimicrobial activities and one inhibited the proliferation of cancer cells. The metabolic profiles of the 22 strains were analyzed by liquid chromatography with tandem mass spectrometry and molecular network. The Global Natural Products Social Molecular Networking MolNetEnhancer workflow provided a more comprehensive understanding of the metabolic profiles. The results revealed the existence of a wide range of metabolites, however more than half of the compounds could not be identified. It was further observed that the metabolic diversity among the strains varied primarily due to the cultivation medium used. Together the results obtained here revealed the pharmacological potential of the bacteria isolated from Aplysina species.