The InterPro protein families and domains database: 20 years on

Inferring gene-pathway associations from consolidated transcriptome datasets: an interactive gene network explorer for Tetrahymena thermophila

Although an established model organism, Tetrahymena thermophila remains comparatively inaccessible to high throughput screens, and alternative bioinformatic approaches still rely on unconnected datasets and outdated algorithms. Here, we report a new approach to consolidating RNA-seq and microarray data based on a systematic exploration of parameters and computational controls, enabling us to infer functional gene associations from their co-expression patterns. To illustrate the power of this approach, we took advantage of new data regarding a previously studied pathway, the biogenesis of a secretory organelle called the mucocyst. Our untargeted clustering approach recovered over 80% of the genes that were previously verified to play a role in mucocyst biogenesis. Furthermore, we tested four new genes that we predicted to be mucocyst-associated based on their co-expression and found that knocking out each of them results in mucocyst secretion defects. We also found that our approach succeeds in clustering genes associated with several other cellular pathways that we evaluated based on prior literature. We present the Tetrahymena Gene Network Explorer (TGNE) as an interactive tool for genetic hypothesis generation and functional annotation in this organism and as a framework for building similar tools for other systems.

Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models

Protein sequence analysis examines the order of amino acids within protein sequences to unlock diverse types of a wealth of knowledge about biological processes and genetic disorders. It helps in forecasting disease susceptibility by finding unique protein signatures, or biomarkers that are linked to particular disease states. Protein Sequence analysis through wet-lab experiments is expensive, time-consuming and error prone. To facilitate large-scale proteomics sequence analysis, the biological community is striving for utilizing AI competence for transitioning from wet-lab to computer aided applications. However, Proteomics and AI are two distinct fields and development of AI-driven protein sequence analysis applications requires knowledge of both domains. To bridge the gap between both fields, various review articles have been written. However, these articles focus revolves around few individual tasks or specific applications rather than providing a comprehensive overview about wide tasks and applications. Following the need of a comprehensive literature that presents a holistic view of wide array of tasks and applications, contributions of this manuscript are manifold: It bridges the gap between Proteomics and AI fields by presenting a comprehensive array of AI-driven applications for 63 distinct protein sequence analysis tasks. It equips AI researchers by facilitating biological foundations of 63 protein sequence analysis tasks. It enhances development of AI-driven protein sequence analysis applications by providing comprehensive details of 68 protein databases. It presents a rich data landscape, encompassing 627 benchmark datasets of 63 diverse protein sequence analysis tasks. It highlights the utilization of 25 unique word embedding methods and 13 language models in AI-driven protein sequence analysis applications. It accelerates the development of AI-driven applications by facilitating current state-of-the-art performances across 63 protein sequence analysis tasks.

Depletion-dependent activity-based protein profiling using SWATH/DIA-MS detects serine hydrolase lipid remodeling in lung adenocarcinoma progression

Systematic inference of enzyme activity in human tumors is key to understanding cancer progression and resistance to therapy. However, standard protein or transcript abundances are blind to the activity status of the measured enzymes, regulated, for example, by active-site amino acid mutations or post-translational protein modifications. Current methods for activity-based proteome profiling (ABPP), which combine mass spectrometry (MS) with chemical probes, quantify the fraction of enzymes that are catalytically active. Here, we describe depletion-dependent ABPP (dd-ABPP) combined with automated SWATH/DIA-MS, which simultaneously determines three molecular layers of studied enzymes: i) catalytically active enzyme fractions, ii) enzyme and background protein abundances, and iii) context-dependent enzyme-protein interactions. We demonstrate the utility of the method in advanced lung adenocarcinoma (LUAD) by monitoring nearly 4000 protein groups and 200 serine hydrolases (SHs) in tumor and adjacent tissue sections routinely collected for patient histopathology. The activity profiles of 23 SHs and the abundance of 59 proteins associated with these enzymes retrospectively classified aggressive LUAD. The molecular signature revealed accelerated lipoprotein depalmitoylation via palmitoyl(protein)hydrolase activities, further confirmed by excess palmitate and its metabolites. The approach is universal and applicable to other enzyme families with available chemical probes, providing clinicians with a biochemical rationale for tumor sample classification.

Horizontal transmission of functionally diverse transposons is a major source of new introns

Since the discovery of spliceosomal introns in eukaryotic genomes, the proximate molecular and evolutionary processes that generate new introns have remained a critical mystery. Specialized transposable elements (TEs), introners, are thought to be one of the major drivers of intron gain in diverse eukaryotes. However, the molecular mechanism(s) and evolutionary processes driving introner propagation within and between lineages remain elusive. Here, we analyze 8,716 genomes, revealing 1,093 introner families in 201 species spanning 1.7 billion years of evolution. Introners are derived from functionally diverse TEs including families of terminal-inverted-repeat DNA TEs, retrotransposons, cryptons, and helitrons as well as mobile elements with unknown molecular mechanisms. We identify eight cases where introners recently transferred between divergent host species and show that giant viruses that integrate into genomes may facilitate introner transfer across lineages. We propose that ongoing intron gain is primarily a consequence of TE activity in eukaryotes, thereby resolving a key mystery of genome structure evolution.

MTPSol: Multimodal Twin Protein Solubility Prediction Architecture Based on Pretrained Models

In the process of mining and de novo designing of new enzymes, the solubility of proteins is one of the key factors determining the efficiency of their functional expression. The development of solubility prediction algorithms is important for reducing experimental costs and enhancing the success of protein engineering. However, only a small number of studies have involved the input of protein structural information, which extremely limited the models' accuracy and generalization. Here, we developed a protein solubility prediction architecture named MTPSol by utilizing pretrained models to extract protein features and process the multimodal input of proteins. To further improve the performance of the architecture, cross-modal twin attention and multiscale feature networks were developed to integrate the multimodal features. Evaluating MTPSol with public benchmark data sets, MTPSol demonstrates that the architecture achieves competitive predictive performance. In the assessment conducted on our constructed and validated transaminase data set, MTPSol outperformed existing state-of-the-art models, further attests the architecture's generalization across different protein families. We firmly believe that MTPSol not only offers a more efficient screening method for the discovery of natural enzymes but also holds significant potential in the field of protein de novo design.

Genomic insights into Neopusillimonas aestuarii sp. nov., a novel estuarine bacterium with adaptations for ectoine biosynthesis and stress tolerance

A novel Gram-stain-negative, aerobic rod-shaped bacterial strain, which was catalase- and oxidase-positive, designated as DMV24BSW_DT, was isolated from the estuarine waters of the Bhavnagar (India) coast of the Arabian Sea. Its 16S rRNA gene exhibited 99.52% similarity with Neopusillimonas maritima 17-4AT, followed by 97.95% similarity with the Pusillimonas caeni strain EBR-8-1 and 97.4% similarity with the P. noertemannii strain BN9T. Phylogenomic analysis using BPGA (14,332 aa) and UBCG (90,261 bp) tools revealed a unique phylogenetic position within the genus Neopusillimonas. The genome exhibited a G + C content of 53.25%. In comparison with N. maritima 17-4AT, the strain demonstrated an average nucleotide identity (ANIb) of 94.47% and a digital DNA-DNA hybridization (dDDH) value of 60.1%, indicating distinct genomic divergence. The genome of DMV24BSW_DT contains several unique metabolic genes that facilitate efficient electron transfer during aerobic respiration. Additionally, it harbours one intact prophage and four defective prophages, indicating ongoing viral interactions. The genome encodes a complete pathway for ectoine biosynthesis and transportation. Strain DMV24BSW_DT tested positive for gelatin hydrolysis and demonstrated the ability to utilize a wide range of carbohydrates, including α-D-glucose, D-melibiose, D-fructose, L-rhamnose, and various organic acids, such as methyl pyruvate and propionic acid, along with tolerance to fluctuating pH (5 to 10) and salinity (0-4% NaCl). The major polar lipids included phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylethanolamine, while fatty acid analysis revealed C12:0, C16:0, C17:0 cyclo, and summed feature 2 (C12:0 aldehyde/unknown) as major components. The respiratory quinones identified were MK-7 and MK-8. These comprehensive phenotypic, chemotaxonomic, and genomic characteristics support the unique taxonomic position of DMV24BSW_DT within the genus Neopusillimonas and the proposal of a novel species of the genus Neopusillimonas, for which the name Neopusillimonas aestuarii sp. nov. (Type strain DMV24BSW_DT = MCC 2506 T = KCTC 72453 T = JCM 34508 T) is proposed.

Metagenome-Derived CRISPR-Cas12a Mining and Characterization

The advent of clustered regularly interspaced short palindromic repeats (CRISPR)-based technologies has revolutionized genome editing, with continued interest in expanding the CRISPR-associated proteins (Cas) toolbox with diverse, efficient, and specific effectors. CRISPR-Cas12a is a potent, programmable RNA-guided dual nickase, broadly used for genome editing. Here, we mined dairy cow microbial metagenomes for CRISPR-Cas systems, unraveling novel Cas12a enzymes. Using in silico pipelines, we characterized and predicted key drivers of CRISPR-Cas12a activity, encompassing guides and protospacer adjacent motifs for five systems. We next assessed their functional potential in cell-free transcription-translation assays with GFP-based fluorescence readouts. Lastly, we determined their genome editing potential in vivo in Escherichia coli by generating 1 kb knockouts. Unexpectedly, we observed natural sequence variation in the bridge-helix domain of the best-performing candidate and used mutagenesis to alter the activity of Cas12a orthologs, resulting in increased gene editing capabilities of a relatively inefficient candidate. This study illustrates the potential of underexplored metagenomic sequence diversity for the development and refinement of genome editing effectors.

Physiological Stress Response to Sulfide Exposure of Freshwater Anaerobic Methanotrophic Archaea

Freshwater wetlands and coastal sediments are becoming hotspots for the emission of the greenhouse gas methane. Eutrophication-induced deposition of organic matter leads to elevated methanogenesis and sulfate reduction, thereby increasing the concentrations of methane and toxic sulfide, respectively. However, the effects of sulfide stress on the anaerobic methanotrophic biofilter have not been well explored. Here, we show how an enrichment culture dominated by the freshwater anaerobic methane-oxidizing archaeon "Candidatus (Ca.) Methanoperedens" responds to short-term and long-term exposure to sulfide in a bioreactor. The methane-oxidizing activity decreased to 45% and 20% but partially recovered to 70% and 30% within 5 days after short- and long-term sulfide exposure, respectively. Metagenomics indicated that "Ca. Methanoperedens" remained dominant in the enrichment throughout the entire experiment. The first short-term sulfide pulse led to increased expression of genes encoding for sulfide detoxification by low abundant community members, whereas long-term exposure resulted in upregulation of "Ca. Methanoperedens" genes encoding sulfite reductases of group III (Dsr-LP). "Ca. Methanoperedens" consumed polyhydroxyalkanoates during long-term sulfide exposure, possibly to aid in stress adaptation. Together, these results provide a valuable baseline for understanding fundamental ecophysiological adaptations to methane cycling in sulfate- and nitrate-rich aquatic ecosystems.

Transcriptome of Taenia solium during in vitro cyst activation and initial growth into the tapeworm stage

The cestode Taenia solium develops as a tapeworm solely in the human intestine, starting from a larva (cyst). Upon maturing, it produces hundreds of thousands of infectious eggs. When ingested by pigs or humans, the eggs develop as cysts that lodge in various tissues, including the brain, leading to neurocysticercosis. Despite advances in understanding cestode biology through genomic and transcriptomic studies, particularly in model organisms, much remains unknown about the activation of T. solium cysts in the human digestive tract and the events that drive the development into adult worms-the stage responsible for dispersing the parasite. We present a transcriptome generated by Next Generation Sequencing from T. solium cysts activated in culture and collected at three different in vitro growth phases, defined by their morphology. Differentially expressed genes and biological processes relevant to activation and growth can be explored with the dataset. The information is valuable for identifying genes that regulate the molecular, metabolic, and cellular events leading to parasite maturation or elements driving its transmission.

Toxins under a Rock: Proteo-transcriptomic analysis reveals the venom composition of the Pseudoscorpion Ammogarypus lawrencei (Pseudoscorpiones: Garypidae)

Pseudoscorpions represent one of the venomous animal groups least investigated with respect to their venom composition. So far, the venom of only a few species of these tiny arachnids has been analyzed, among which only the cosmopolitan species Chelifer cancroides and the Australian Synsphyronus apimelus have been investigated in more detail. Here, we advance the current understanding on pseudoscorpion toxins by unveiling the venom composition of the African species Ammogarypus lawrencei via proteo-transcriptomics-guided venomics. Belonging to the same family as S. apimelus whose venom was analyzed solely by a transcriptomic approach, we found the highest similarities between putative venom compounds in these species. Instead of an enzyme-rich venom predicted for S. apimelus, we found the venom of A. lawrencei to be dominated by Cysteine-rich peptides (CRPs). Many of these peptides show moderate similarity to neurotoxins found primarily in other arachnids, although a large proportion could not be annotated in more detail due to their high sequence disparity. Enzymes are a minor component in the venom of A. lawrencei and classified mostly as peptidases and triacylglycerol lipases, likely fulfilling a predigestive function or acting as spreading factors. Lastly, we identified a range of linear and putatively antimicrobial peptides in the A. lawrencei venom, which seem to be unrelated to the previously identified checacin-type linear peptides identified in the venom of C. cancroides. Our study provides valuable insights into the molecular diversity encoded in pseudoscorpion venom glands and identifies a range of novel biomolecules with putative translational potential.

An updated Gallus gallus genome annotation through multi-tissue transcriptome analysis

This study presents an updated Gallus gallus genome annotation through a comprehensive multi-tissue transcriptome analysis aimed at enhancing the Functional Annotation of Animal Genomes (FAANG) efforts. Generating RNA sequencing data from 20 different chicken tissues and cell types allowed for the identification of 110,930 transcript isoforms, including approximately 37,000 unannotated transcripts. This expanded resource significantly enhances transcript diversity and functional annotation. We analyzed allele-specific expression (ASE) across tissues, revealing 11,530 unique ASE genes. Our findings elucidate the intricate landscape of gene expression patterns and allelic imbalances. Notably, tissue-specific isoforms and differentially expressed genes, particularly in reproductive and muscle tissues, showcase their relevance for traits like fertility and meat quality. The identification of novel lncRNAs and protein-coding genes underscores the necessity of continued genomic improvements. This work contributes valuable resources for breeding strategies focused on disease resistance and productivity enhancement, addressing global agricultural challenges and the evolving needs of poultry science.

Titin-dependent biomechanical feedback tailors sarcomeres to specialized muscle functions in insects

Sarcomeres are the universal contractile units of muscles that enable animals to move. Insect muscles display a remarkable functional diversity: they operate at extremely different contraction frequencies (ranging from ~1 to 1000 hertz) and amplitudes during flying, walking, and crawling. This is puzzling because sarcomeres are built from essentially the same actin-myosin components. Here, we address how functionally different sarcomeres are made. We show that the giant protein titin and the regulation of developmental contractility are key for the sarcomere specializations. I-band titin spans and determines the length of the sarcomeric I-band in a muscle type-specific manner. Unexpectedly, I-band titin also rules the length of the force-generating myosin filament using a feedback mechanism that is modulated by myosin contractility. We propose a model of how sarcomere specializations in insects are tuned, provide evidence for this model, and discuss its validity beyond insects.

Molecular and functional analysis of a putative pyocin S9, with endonuclease activity from P. chlororaphis subsp aurantiaca PB-St2

Pyocins are bacteriocins which are explicitly associated with pseudomonads. In this study, the genome mining and in-depth sequence analysis identified three similar S9-like (a, b, and c), an S3-like (d) and one R-type pyocin systems from P. chlororaphis subsp aurantiaca PB-St2. The phenotypic screening of bacteriocin production by PB-St2 indicated narrow-spectrum bactericidal activity against closely related Pseudomonas species i.e., Pseudomonas aeruginosa PAi, PAc1, PAc3, PAc4; Pseudomonas fluorescens Psi-RS1 and Pseudomonas kilonensis OSRS3. Herein, the proposed pyocin S9c was further selected for molecular and functional characterization. The presumptive N-terminal receptor binding domain of candidate system lacks significant similarity with any characterized HNH-type pyocin S DNases from P. aeruginosa. In contrast, the cytotoxic domain showed 53% sequence similarity with pyocin S8 and 70% to pyocin S9. Thus, pyocin S9c was suggested as an isoform under the Class I DNase (H-N-H) family in pyocin S9 cluster, commonly found in P. chlororaphis subsp. aurantiaca and P. chlororaphis subsp aureofaciens strains. Molecular screening of the pyocin S9c system revealed its presence in 6 out of 7 tested strains of P. chlororaphis subsp. aurantiaca GS1, GS3, GS4, GS6, ARS38, FS2 and one P. chlororaphis RP4 relative strains, isolated from diverse plant hosts. The 1.59 kb fragment consisting of two structural genes of pyocin-immunity operon (S9c) in P. aurantiaca PB-St2 were cloned in pET28a(+) and expressed in Escherichia coli BL21 DE3 (pLysS) strain as a fusion protein with histidine tag. The recombinant cytotoxic protein of pyocin S9c operon was purified with N-term His-tag with a molecular weight of ≈ 50 kDa. The identity of target protein was affirmed by tandem mass spectrometry analysis. The purified cytotoxic protein was active against P. chlororaphis subsp. aurantiaca GS7, with a minimum inhibitory concentration of 12.5 µg/ml. The mechanism of cytotoxicity was affirmed as a metal-dependent endonuclease by evidence of non-specific hydrolysis of pTZ57R plasmid isoforms. These results indicate that pyocin S9c can contribute to the rhizo-competence of this strain in plant-associated natural habitats, occupied by related Pseudomonas strains.

The expanded Bostrychia moritziana genome unveils evolution in the most diverse and complex order of red algae

Red algae are an ancient eukaryotic lineage that were among the first to evolve multicellularity. Although they share a common origin with modern-day plants and display complex multicellular development, comprehensive genome data from the most highly evolved red algal groups remain scarce. Here, we present a chromosome-level genome assembly of Bostrychia moritziana, a complex red seaweed in the Rhodomelaceae family of the Ceramiales-the largest and most diverse order of red algae. Contrary to the view that red algal genomes are typically small, we report significant genome size expansion in Bostrychia and other Ceramiales, which represents one of at least three independent expansion events in red algal evolution. Our analyses suggest that these expansions do not involve polyploidy or ancient whole-genome duplications, but in Bostrychia rather stem from the proliferation of a single lineage of giant Plavaka DNA transposons. Consistent with its enlarged genome, Bostrychia has an increased gene content shaped by de novo gene emergence and amplified gene families in common with other Ceramiales, providing insight into the genetic adaptations underpinning this successful and species-rich order. Finally, our sex-specific assemblies resolve the UV sex chromosomes in Bostrychia, which feature expanded gene-rich sex-linked regions. Notably, each sex chromosome harbors a three amino acid loop extension homeodomain (TALE-HD) transcription factor orthologous to ancient regulators of haploid-diploid transitions in other multicellular lineages. Together, our findings offer a unique perspective of the genomic adaptations driving red algal diversity and demonstrate how this red seaweed lineage can provide insight into the evolutionary origins and universal principles underpinning complex multicellularity.

PRESCOTT: a population aware, epistatic, and structural model accurately predicts missense effects

Predicting the functional impact of point mutations is a critical challenge in genomics. PRESCOTT reconstructs complete mutational landscapes, identifies mutation-sensitive regions, and categorizes missense variants as benign, pathogenic, or variants of uncertain significance. Leveraging protein sequences, structural models, and population-specific allele frequencies, PRESCOTT surpasses existing methods in classifying ClinVar variants, the ACMG dataset, and over 1800 proteins from the Human Protein Dataset. Its online server facilitates mutation effect predictions for any protein and variant, and includes a database of over 19,000 human proteins, ready for population-specific analyses. Open access to residue-specific scores offers transparency and valuable insights for genomic medicine.

Structural insights into thraustochytrid-specific lipases using alphafold to identify the role of GXSXG motif

BACKGROUND

Triacylglycerol lipases (E.C. 3.1.1.3) are serine hydrolases, universally present in animals, plants and microbes and are an integral part of lipid metabolism. They are industrially relevant enzymes that cleave ester bonds of triacylglycerides to release free fatty acids and glycerol. Thraustochytrid Aurantiochytrium limacinum SR21 has previously been reported to utilize 120 g L- 1 of oil substrate. Previously, thraustochytrid specific lipases was reported that allowed the microbe to thrive on oil substrate, however the structural characteristics of these enzymes remain undetermined.

RESULTS

In this study, we identified nearly 30 genes that encode TAG lipases with Lipase_3 domain, allowing the marine microbe to thrive on oil substrate. The lipases were predicted to localize at several subcellular compartments such as extracellular (31293), membrane-bound and cytosolic. Phylogenomic analysis revealed that lipases from thraustochytrids form distinct clades, diverging significantly from the well-characterized lipases from yeast Yarrowia lipolytica. Motif enrichment analysis confirmed the presence of the conserved 'GXSXG' motif in all lipases, where serine serves as the catalytic residue. Notably, histidine (H) or tyrosine (Y) was found at the second position of the motif in A. limacinum SR21 lipases 34357 (cytosolic) and 31293 (extracellular) respectively, suggesting functional differences. Docking analysis with tripalmitoylglycerol (4RF) revealed lower binding energy (ΔG = -5.7 kcal/mol) for cytoplasmic lipase 34357, indicating a stronger ligand interaction compared to ΔG = -3.4 kcal/mol for the extracellular lipase 31293. This suggests that substituting histidine for tyrosine in the active site affects lipase catalytic efficiency and substrate specificity.

CONCLUSIONS

Our study provides novel insights regarding the structure and ligand binding affinities for thraustochytrid specific lipases which are diversified attributed to the heterogeneity within the catalytic triads. In conclusion, we hypothesize that differential localization and higher binding efficiency of thraustochytrid specific lipases allow the microbe to efficiently utilize oil substrates. These thraustochytrid-specific lipases are potential candidates for commercialization as large-scale production of thraustochytrids can be achieved sustainably by cultivating on sustainable substrates and these enzymes are highly efficient and robust.

Genome-wide identification of the regulatory network of mitogen-activated protein kinase signaling cascades gene families in Hevea Brasiliensis

BACKGROUND

The mitogen-activated protein kinase (MPK) cascade pathway represents a highly conserved signal transduction mechanism in plants, playing a crucial role in growth, development, and stress response. Nevertheless, systematic analysis on the MPK cascade genes in rubber trees remains unexplored.

RESULTS

We conducted a comprehensive identification of the MPK cascade gene family of Hevea brasiliensis, identifying a total of 20 HbMPKs, 13 HbMPKKs, and 167 HbMAPKKKs genes. Through phylogenetic analysis and compared to Arabidopsis MPK cascade genes, HbMPKs and HbMPKKs were categorized into categorized four subgroups with no significant expansion or contraction, while the notably expanded HbMAPKKKs were divided into three subgroups: Raf, ZIK, and MEKK. Conserved motifs, gene structure, and motif analysis further bolster the validity of phylogenetic classification. Furthermore, expression profiling analysis based on public transcriptomic data revealed that these genes were differentially expressed in various tissues and differentially regulated in response to different stresses. Among them, the genes highly expressed in latex or the upregulated genes after tapped including HbMPK8, HbMPK12, HbMPK19, HbMPKK6, HbMPKK9, HbMPKKK15, HbMPKKK21 might be related to latex development and natural rubber (NR) yield. Through yeast two-hybrid assays, we successfully pinpointed 34 pairs of HbMPKKK-HbMPKK-HbMPK interaction modules. Integrating the interaction network and gene expression patterns, 12 potential HbMPK cascade signaling modules including HbMPKKK6/41/79-HbMPKK1-HbMPK9/12/15 and HbMPKKK6/14/21/41/79-HbMPKK9-HbMPK9/15 might involve in NR production and stress responses.

CONCLUSIONS

Our study comprehensively unveils the multidimensional characteristics of the MPK cascade gene family in rubber trees and successfully identifies its core signaling cascade module, laying a crucial foundation for future in-depth exploration of the biological functions of the MPK cascade signaling module in rubber trees.

Co-silencing of PhENO1 and PhPPT alters anthocyanin production by reducing phosphoenolpyruvate supply in petunia flower

The shikimate pathway is crucial for the production of aromatic amino acids and various secondary plant products, including anthocyanins. Phosphoenolpyruvate (PEP) is an important source for shikimate production. The pre-chorismate part of the shikimate pathway is confined to plastids. There are three sources of PEP in plastids. PEP can be imported into the plastids from cytoplasm via the PEP/phosphate translocator (PPT), and it can also be generated in plastids via enolase (ENO) and pyruvate orthophosphate dikinase (PPDK) catalysis. A large number of anthocyanins are synthesized in the flowers of most ornamental plants in the coloring stage. However, the source of PEP, the precursor of anthocyanin synthesis, is still unknown. Herein, Petunia hybrida PhENO1, PhPPT and PhPPDK genes were identified and their expression patterns and subcellular localization of encoded proteins were analyzed. Silencing of PhENO1, PhPPT, and PhPPDK alone and co-silencing of PhENO1 and PhPPDK or PhPPT and PhPPDK did not exhibit any visible phenotypic change compared with the control, while co-silencing of PhENO1 and PhPPT resulted in the flower color change from purple to light purple. The content of PEP, shikimate, flavonoids, anthocyanins, and aromatic amino acids were all significantly decreased in PhENO1 and PhPPT co-silenced plants. Co-silencing of PhENO1 and PhPPT did not affect the expression level of key genes in anthocyanin synthesis and shikimate pathways. Furthermore, co-silencing of PhENO1, PhPPT, and PhPPDK resulted in a phenotype similar to the co-silencing of PhENO1 and PhPPT. Altogether, our study suggested that PEP used for anthocyanin synthesis is mainly provided by PhENO1 and PhPPT, rather than PhPPDK.

Cythochrome P450-mediated dinotefuran resistance in onion thrips, Thrips tabaci

Onion thrips, Thrips tabaci, have developed resistance to many insecticides, and over the last decade, resistant populations have spread widely across Japan. The cytochrome P450 (CYP) family, a widely conserved detoxification enzyme that metabolizes xenobiotics such as insecticides and phytochemicals, is believed to play important roles in the development of resistance in T. tabaci. However, CYPs involved in insecticide resistance in T. tabaci remain unclear. To comprehensively identify CYPs in T. tabaci, the genome sequences of the thelytokous T. tabaci (ANO strain) were constructed, and 18,965 genes (protein coding) were predicted. We identified 127 CYP genes in the predicted gene set by manual curation, and 38 of these CYP genes belonged to the CYP3 clan, including genes from the CYP6 family, which is one of the most important CYP families involved in resistance to neonicotinoids in many insect pests. To identify the CYPs involved in resistance to dinotefuran, which is one of the neonicotinoids used to control T. tabaci, RNA sequencing of dinotefuran-resistant and dinotefuran-susceptible strains was performed. Results revealed that, TtCYP3652A1, which belongs to the thrips-specific CYP3652A subfamily in the CYP3 clan, was significantly upregulated in the resistant strain. In vitro CYP metabolism assays using insect cells were conducted for TtCYP3652A1 and five highly expressed CYP6 genes. Only TtCYP3652A1 significantly metabolized dinotefuran, which is considered to contribute to detoxification of dinotefuran. As no amino acid mutations were identified in the known target-site genes of neonicotinoids, TtCYP3652A1 was considered to be the main factor involved in the resistance to dinotefuran.

Pangenomics to understand prophage dynamics in the Pectobacterium genus and the radiating lineages of Pectobacterium brasiliense

Bacterial pathogens of the genus Pectobacterium are responsible for soft-rot and blackleg diseases in a wide range of crops and have a global impact on food production. The emergence of new lineages and their competitive succession is frequently observed in Pectobacterium species, in particular in Pectobacterium brasiliense. With a focus on one such recently emerged P. brasiliense lineage in the Netherlands that causes blackleg in potatoes, we studied genome evolution in this genus using a reference-free graph-based pangenome approach. We clustered 1,977,865 proteins from 454 Pectobacterium spp. genomes into 30,156 homology groups. The Pectobacterium genus pangenome is open, and its growth is mainly contributed by the accessory genome. Bacteriophage genes were enriched in the accessory genome and contributed 16% of the pangenome. Blackleg-causing P. brasiliense isolates had increased genome size with high levels of prophage integration. To study the diversity and dynamics of these prophages across the pangenome, we developed an approach to trace prophages across genomes using pangenome homology group signatures. We identified lineage-specific as well as generalist bacteriophages infecting Pectobacterium species. Our results capture the ongoing dynamics of mobile genetic elements, even in the clonal lineages. The observed lineage-specific prophage dynamics provide mechanistic insights into Pectobacterium pangenome growth and contribution to the radiating lineages of P. brasiliense.

Pan-Genome Analysis Reveals Local Adaptation to Climate Driven by Introgression in Oak Species

The genetic base of local adaptation has been extensively studied in natural populations. However, a comprehensive genome-wide perspective on the contribution of structural variants (SVs) and adaptive introgression to local adaptation remains limited. In this study, we performed de novo assembly and annotation of 22 representative accessions of Quercus variabilis, identifying a total of 543,372 SVs. These SVs play crucial roles in shaping genomic structure and influencing gene expression. By analyzing range-wide genomic data, we identified both SNPs and SVs associated with local adaptation in Q. variabilis and Quercus acutissima. Notably, SV-outliers exhibit selection signals that did not overlap with SNP-outliers, indicating that SNP-based analyses may not detect the same candidate genes associated with SV-outliers. Remarkably, 29%-37% of candidate SNPs were located in a 250 kb region on chromosome 9, referred to as Chr9-ERF. This region contains 8 duplicated ethylene-responsive factor (ERF) genes, which may have contributed to local adaptation of Q. variabilis and Q. acutissima. We also found that a considerable number of candidate SNPs were shared between Q. variabilis and Q. acutissima in the Chr9-ERF region, suggesting a pattern of repeated selection. We further demonstrated that advantageous variants in this region were introgressed from western populations of Q. acutissima into Q. variabilis, providing compelling evidence that introgression facilitates local adaptation. This study offers a valuable genomic resource for future studies on oak species and highlights the importance of pan-genome analysis in understating mechanism driving adaptation and evolution.

Studying sleep orthologs in Epsilonproteobacteria through an evolutionary lens: investigating sleep mysteries through phylogenomics

The current study employed phylogenomic methods to examine sleep-related genes' evolutionary role and significance in Sulfurimonas paralvinellae of the Epsilonproteobacteria class. This has facilitated the identification of conserved sleep orthologs, including DnaK (Hsp70), serine hydroxymethyltransferase (SHMT), and potassium channel family proteins, exhibiting sequence similarities ranging from 39.13% to 61.45%. These findings align with prior research indicating that chaperones and ion channels are conserved during sleep. This was demonstrated by the observation that proteins with fewer domains exhibited more significant conservation than others, such as adenylate kinase (AK). Distinct adaptations in bifunctional protein-serine/threonine kinases and phosphatases were linked to S. paralvinellae, an extremophilic organism adapted to high-pressure and/or high-temperature conditions, indicating functional divergence influenced by the organism's environment. The Gene Ontology study results indicated catalytic activity, potassium channel function, and cellular processes, underscoring the significance of ion channels in regulating the sleep-wake cycle. Furthermore, the categories not recognized as particularly significant for the over-represented genes encompassed metabolic and signal transduction categories, suggesting enhanced functional flexibility within this protein subfamily. The findings emphasize that orthologous interactions are complex and influenced by subfunctionalization and neofunctionalization of ecology and evolution. These findings enhance the existing understanding of the evolution of sleep-related genes and their association with metabolic and environmental changes, providing a foundation for subsequent experimental investigations and cross-taxonomic comparisons.

Comparative genomic analysis of trypanosomatid protists illuminates an extensive change in the nuclear genetic code

Trypanosomatids are among the most extensively studied protists due to their parasitic interactions with insects, vertebrates, and plants. Recently, Blastocrithidia nonstop was found to depart from the canonical genetic code, with all three stop codons reassigned to encode amino acids (UAR for glutamate and UGA for tryptophan), and UAA having dual meaning also as a termination signal (glutamate and stop). To explore features linked to this phenomenon, we analyzed the genomes of four Blastocrithidia and four Obscuromonas species, the latter representing a sister group employing the canonical genetic code. We found that all Blastocrithidia species encode cognate tRNAs for UAR codons, possess a distinct 4 bp anticodon stem tRNATrpCCA decoding UGA, and utilize UAA as the only stop codon. The distribution of in-frame reassigned codons is consistently non-random, suggesting a translational burden avoided in highly expressed genes. Frame-specific enrichment of UAA codons immediately following the genuine UAA stop codon, not observed in Obscuromonas, points to a specific mode of termination. All Blastocrithidia species possess specific mutations in eukaryotic release factor 1 and a unique acidic region following the prion-like N-terminus of eukaryotic release factor 3 that may be associated with stop codon readthrough. We infer that the common ancestor of the genus Blastocrithidia already exhibited a GC-poor genome with the non-canonical genetic code. Our comparative analysis highlights features associated with this extensive stop codon reassignment. This cascade of mutually dependent adaptations, driven by increasing AU-richness in transcripts and frequent emergence of in-frame stops, underscores the dynamic interplay between genome composition and genetic code plasticity to maintain vital functionality.

IMPORTANCE

The genetic code, assigning amino acids to codons, is almost universal, yet an increasing number of its alterations keep emerging, mostly in organelles and unicellular eukaryotes. One such case is the trypanosomatid genus Blastocrithidia, where all three stop codons were reassigned to amino acids, with UAA also serving as a sole termination signal. We conducted a comparative analysis of four Blastocrithidia species, all with the same non-canonical genetic code, and their close relatives of the genus Obscuromonas, which retain the canonical code. This across-genome comparison allowed the identification of key traits associated with genetic code reassignment in Blastocrithidia. This work provides insight into the evolutionary steps, facilitating an extensive departure from the canonical genetic code that occurred independently in several eukaryotic lineages.

HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets

BACKGROUND

Recent years have seen a substantial increase in RNA-seq data production, with this technique becoming the primary approach for gene expression studies across a wide range of non-model organisms. The majority of these organisms lack a well-annotated reference genome to serve as a basis for studying differentially expressed genes (DEGs). As an alternative cost-effective protocol to using a reference genome, the assembly of RNA-seq raw reads is performed to produce what is referred to as a 'de novo transcriptome,' serving as a reference for subsequent DEGs' analysis. This assembly step for conventional DEGs analysis pipelines for non-model organisms is a computationally expensive task. Furthermore, the complexity of the de novo transcriptome assembly workflows poses a challenge for researchers in implementing best-practice techniques and the most recent software versions, particularly when applied to various organisms of interest.

RESULTS

To address computational challenges in transcriptomic analyses of non-model organisms, we present HPC-T-Assembly, a tool for de novo transcriptome assembly from RNA-seq data on high-performance computing (HPC) infrastructures. It is designed for straightforward setup via a Web-oriented interface, allowing analysis configuration for several species. Once configuration data is provided, the entire parallel computing software for assembly is automatically generated and can be launched on a supercomputer with a simple command line. Intermediate and final outputs of the assembly pipeline include additional post-processing steps, such as assembly quality control, ORF prediction, and transcript count matrix construction.

CONCLUSION

HPC-T-Assembly allows users, through a user-friendly Web-oriented interface, to configure a run for simultaneous assemblies of RNA-seq data from multiple species. The parallel pipeline, launched on HPC infrastructures, significantly reduces computational load and execution times, enabling large-scale transcriptomic and meta-transcriptomics analysis projects.

In-depth single-cell transcriptomic exploration of the regenerative dynamics in stony coral

Coral reef ecosystems face escalating threats from anthropogenic global climate challenges, leading to frequent bleaching events. A key issue in coral transplantation is the inability of fragments to rapidly grow to sizes that can resist environmental pressures. The observation of accelerated growth during the early stages of coral regeneration provides new insights for addressing this challenge. To investigate the underlying molecular mechanisms, we study the fast-growing stony coral Acropora muricata. Using single-cell RNA sequencing, bulk RNA sequencing, and high-resolution micro-computed tomography, we identify a critical regeneration phase around 2-4 weeks post-injury. Single-cell transcriptome analysis reveals 11 function-specific cell clusters. Pseudotime analysis indicates epidermal cell differentiation into calicoblasts. Bulk RNA-seq results highlight a temporal limitation in coral's rapid regeneration. Through integrated multi-omics analysis, this study emphasizes the importance of a comprehensive understanding of coral regeneration, providing insights beyond fundamental knowledge and offering potential protective strategies to promote coral growth.

Structure and Functions of NDR1/HIN1-Like (NHL) Proteins in Plant Development and Response to Environmental Stresses

The NON-RACE-SPECIFIC DISEASE RESISTANCE 1/harpin-induced 1-LIKE (NHL) gene family plays pivotal roles, including pathogen resistance, abiotic stress tolerance, and developmental regulation, underscoring their functional versatility in developmental and physiological processes of plants. NHL proteins often localize to the plasma membrane and contain conserved motifs, including the LEA2 and transmembrane domains, enabling dynamic interactions with signalling molecules and transcription factors. The ability of NHL proteins to dimerize and oligomerize further enhances their regulatory potential in signalling pathways. This review explores the structural and functional diversity of NHL proteins including their localizations, interacting proteins, and responses to abiotic and biotic stresses, ion transportation, seed germination, and responses to phytohormones. Future research integrating phylogenetics, and advanced tools including artificial intelligence will unlock the full potential of this gene family for breeding climate-resilient crops and agricultural sustainability.

Identification of a novel phage depolymerase against ST11 K64 carbapenem-resistant Klebsiella pneumoniae and its therapeutic potential

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a clinical pathogen with a high mortality rate, and its clinical management and infection control have become a serious challenge. Phage-encoded depolymerase cleaves the capsular polysaccharide, a major virulence factor of K. pneumoniae. This study aimed to identify a phage depolymerase targeting ST11 K64 CRKP, evaluate its antimicrobial activity and therapeutic efficacy, and provide new alternative therapeutic strategies for K64 CRKP. Phages were screened from untreated hospital sewage using clinically isolated CRKP as the host bacterium. The host range, efficiency of plaque formation, optimal multiplicity of infection, adsorption efficiency, and one-step growth curve of phage vB_KpnP_IME1309 were determined by the double-layer agar plate culture method. The morphology of the phage was observed by transmission electron microscopy. Phage nucleic acids were extracted for whole-genome sequencing, and the phage-encoded depolymerase gene ORF37 was amplified by polymerase chain reaction. Next, a recombinant plasmid was constructed to induce depolymerase expression, which was verified using sodium dodecyl sulfate-polyacrylamide gel electrophoresis. In vitro bactericidal activity was determined using a combined serum assay, and the anti-K. pneumoniae biofilm effect of depolymerase was determined by crystal violet staining. Finally, a Galleria mellonella larvae infection model was established to investigate the therapeutic effect of depolymerase on larvae in vivo. Here, we isolated and characterized a phage vB_KpnP_IME1309 targeting ST11 K64 CRKP, which featured a latent period of 20 min and a burst size of approximately 290 plaque-forming units/cell. It contained 41 predicted open reading frames, of which ORF37 encoded depolymerase. The expressed and purified depolymerase Dep37 cleaved only ST11 K64 CRKP and formed a translucent halo on the agar plate. Dep37 increased the susceptibility of K. pneumoniae B1 to serum killing, inhibited CRKP biofilm formation, and degraded mature biofilms. The combination of Dep37 and kanamycin was significantly more effective in treating CRKP biofilms compared to either Dep37 or kanamycin alone. An injection of Dep37 at 5 min and 2 h after the CRKP infection of Galleria mellonella larvae increased their survival rates by up to 73% and 53%, respectively. Depolymerase Dep37 may be used as a potential method for capsule typing of K. pneumoniae, showing great promise for the development of novel alternative therapeutic strategies against ST11 K64 CRKP.

IMPORTANCE

A novel phage vB_KpnP_IME1309 targeting ST11 K64 carbapenem-resistant Klebsiella pneumoniae (CRKP) was isolated and characterized. The ORF37 encoding depolymerase gene of phage vB_KpnP_IME1309 was successfully expressed and purified. Depolymerase increases the susceptibility of CRKP to serum killing, inhibits CRKP biofilm formation, and degrades mature biofilms. The combination of depolymerase and kanamycin is significantly more effective than either depolymerase or kanamycin alone in the treatment of CRKP biofilm. Depolymerase injection at 5 min and 2 h after CRKP infection of Galleria mellonella larvae increased the survival rate of larvae by up to 73% and 53%, respectively. Depolymerase Dep37 may be used as a method for the development of novel alternative therapeutic strategies against ST11 K64 CRKP.

Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide

Reference genome assemblies are the basis for comprehensive genomic analyses and comparisons. Due to declining sequencing costs and growing computational power, genome projects are now feasible in smaller labs. De novo genome sequencing for non-model or emerging model organisms requires knowledge about genome size and techniques for extracting high molecular weight DNA. Next to quality, the amount of DNA obtained from single individuals is crucial, especially, when dealing with small organisms. While long-read sequencing technologies are the methods of choice for creating high quality genome assemblies, pure short-read assemblies might bear most of the coding parts of a genome but are usually much more fragmented and do not well resolve repeat elements or structural variants. Several genome initiatives produce more and more non-model organism genomes and provide rules for standards in genome sequencing and assembly. However, sometimes the organism of choice is not part of such an initiative or does not meet its standards. Therefore, if the scientific question can be answered with a genome of low contiguity in intergenic parts, missing the high standards of chromosome scale assembly should not prevent publication. This review describes how to set up an animal genome sequencing project in the lab, how to estimate costs and resources, and how to deal with suboptimal conditions. Thus, we aim to suggest optimal strategies for genome sequencing that fulfil the needs according to specific research questions, e.g. "How are species related to each other based on whole genomes?" (phylogenomics), "How do genomes of populations within a species differ?" (population genomics), "Are differences between populations relevant for conservation?" (conservation genomics), "Which selection pressure is acting on certain genes?" (identification of genes under selection), "Did repeats expand or contract recently?" (repeat dynamics).

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

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

Using AlphaFold-Multimer to study novel protein-protein interactions of predation essential hypothetical proteins in Bdellovibrio

Bdellovibrio bacteriovorus is the most studied member of a group of small motile Gram-negative bacteria called Bdellovibrio and Like Organisms (BALOs). B. bacteriovorus can prey on Gram-negative bacteria, including multi-drug resistant pathogens, and has been proposed as an alternative to antibiotics. Although the life cycle of B. bacteriovorus is well characterized, some molecular aspects of B. bacteriovorus-prey interaction are poorly understood. Hypothetical proteins with unestablished functions have been implicated in B. bacteriovorus predation by many studies. Our approach to characterize these proteins employing Alphafold has revealed novel interactions among attack phase-hypothetical proteins, which may be involved in less understood mechanisms of the Bdellovibrio attack phase. Here, we overlapped attack phase genes from B. bacteriovorus transcriptomic data sets and from transposon sequencing data sets to generate a set of proteins that are both expressed at the attack phase and are necessary for predation, which we termed Attack Phase Predation-Essential Proteins (AP-PEP). By applying Markov Cluster Algorithm and AlphaFold-Multimer to analyze the protein network and interaction partners of the AP-PEPs, we predicted high-confidence protein-protein interactions and two structurally similar but unique novel protein complexes formed among proteins of the Bd2209-Bd2212 and Bd2723-Bd2726 operons. Furthermore, we confirmed the interaction between hypothetical proteins Bd0075 and Bd0474 using the Bacteria Adenylate Cyclase Two-Hybrid system. In addition, we confirmed that the C-terminal domain of Bd0075, which contains Tetratricopeptide repeat motifs, participates principally in its interaction with Bd0474. This study revealed previously unknown cooperation among predation essential hypothetical proteins in the attack phase B. bacteriovorus and has paved the way for further work to understand molecular mechanisms of BALO predation processes.

Phage Endolysins as Promising and Effective Candidates for Use Against Uropathogenic Escherichia coli

The presented in silico and phylogenetic analysis of putative endolysins potentially produced by phages infecting uropathogenic Escherichia coli (UPEC) demonstrates their remarkable diversity. These proteins exhibit significant variations in sequence length, molecular weight, isoelectric point, and stability, as well as diverse functional domains determining their enzymatic activity, including lysin, lysozyme, hydrolase, amidase, and peptidase functions. Due to their predicted lytic properties, endolysins hold great promise in combating UPEC bacteria, including those within biofilms, which are often highly resistant to conventional treatments. Despite their potential, several challenges hinder the full utilization of endolysins. These include the relatively small number of identified proteins, challenges in the annotation process, and the scarcity of studies evaluating their efficacy in vitro and in vivo against Gram-negative bacteria. In this work, we emphasize these challenges while also underlining the potential of endolysins as an effective tool against UPEC infections. Their effectiveness could be significantly enhanced when combined with agents that disrupt the outer membrane of these bacteria, making them a promising alternative or complement to existing antimicrobial strategies. Further research is necessary to fully explore their therapeutic potential.

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

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

The chromosome-scale genomes of two cultivated safflowers (Carthamus tinctorius) provide insights into the genetic diversity resulting from domestication

KEY MESSAGE

Two cultivated safflowers from distinct areas elucidate the genetic diversity present in the linoleic acid biosynthesis, flowering time and flavonoid biosynthesis. The process of domestication facilitates the adaptation of crops to agricultural environments. In this study, we selected two representative safflower cultivars that has been domesticated in two distinct areas in China as samples to investigate their genetic diversity due to local environmental adaption. Yunhong-7 is a locally bred safflower (Carthamus tinctorius) cultivar, that has been currently widely cultivated in Yunnan Province, Southwest China, and Anhui-1 is a safflower cultivar that was locally bred in Anhui Province, East China. We firstly generated the chromosome-scale genome assembly for yunhong-7 cultivar by combining PacBio and Hi-C technologies. Through comparative genomic analysis, we identified structural variations (SVs) between yunhong-7 and anhui-1, which revealed their genetic differences in the pathways of fatty acid biosynthesis, circadian rhythm and flavonoid biosynthesis. Subsequently, a total of 40 non-redundant fatty acid desaturase 2 (FAD2) genes (39 for yunhong-7 and 20 for anhui-1) were identified, revealing the presence of copy-number variation and major genes change between yunhong-7 and anhui-1. The presented results suggested that changes in SVs may induce alterations in the expression of flowering-related genes, which could explain the observed early flowering phenotype in yunhong-7 compared to anhui-1. We identified a total of 197 non-redundant UDP-glucuronosyltransferases (UGT) genes. Based on prokaryotic expression system, we investigated the catalytic functions of two unique UGT genes (CtUGT.18 and CtUGT.191). The current study increases our knowledge of genetic diversity among crop cultivars resulting from distinct domestication processes and thus could contribute to the advancement of traits research and the safflower breeding.

Unraveling the functional dynamics of Caenorhabditis elegans stress-responsive omega class GST-44

Glutathione transferases from the omega class are notable for their roles in redox regulation and cellular stress response. In this study, we conducted a comprehensive functional characterization of GST-44, an omega-class glutathione S-transferase (GSTO), in Caenorhabditis elegans, focusing on its role in cellular defense mechanisms against stress. Biochemical analysis revealed GSTO-specific enzymatic activities of recombinant GST-44, including dehydroascorbate reductase, thioltransferase, and arsenate reductase activities. Using transgenic GFP reporter strains, we identified predominant expression of GST-44 in the intestine and excretory H-cell, with significant upregulation observed under diverse stress conditions. Induction of GST-44 was particularly pronounced in the intestine in response to pathogen-, oxidative-, and endoplasmic reticulum stress. Notably, under arsenic stress, the expression of gst-44 was significantly upregulated in the excretory system of the worm, underscoring its critical role in mediating arsenic detoxification. Moreover, we demonstrated the induction of GST-44 using dimethyl fumarate, a highly specific mammalian Nrf-2 activator. The upregulation of GST-44 during arsenic stress was dependent not only on the oxidative stress response transcription factor SKN-1/Nrf2 but also on PHA-4. The deletion mutant strain gst-44(tm6133) exhibited reduced stress resistance and a shortened lifespan, with a highly diminished survival rate under arsenic stress compared to other CRISPR-generated C. elegans GSTO deletion mutants. Our findings highlight the essential role of GST-44 in mediating arsenic detoxification, as well as in stress adaptation and defense mechanisms in C. elegans.

Chromosome-scale genome assembly and annotation of Xenocypris argentea

Xenocypris argentea is a small to medium-sized freshwater cyprinid fish. It distributes widely in the rivers and lakes of China, and is often used as a tool fish for water quality improvement and optimizing aquaculture structures. In recent years, natural populations of X. argentea have decreased rapidly due to human activities, yet little is known about the genetics and genomics of this fish. In the present work, we reported a chromosome-level reference genome of X. argentea based on PacBio HiFi, Hi-C and Illumina paired-end sequencing technologies. The assembled genome was 984.96 Mb in length, with a contig N50 of 36.02 Mb. Using Hi-C interaction information, 99.47% of the contigs were anchored onto 24 chromosomes, and 18 of the chromosomes were gap-free. Further analysis identified 560.27 Mb of repeat sequences and 28,533 protein-coding genes in the genome, of which, 95.62% (27,284) genes were functionally annotated. This high-quality genome offers an invaluable resource for population genetics and phylogeny, comparative genomics, adaptive evolution and functional exploration of X. argentea.

GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data

Rice is a vital staple crop, sustaining over half of the global population, and is a key model for genetic research. To support the growing need for comprehensive and accessible rice genomic data, GrameneOryza (https://oryza.gramene.org) was developed as an online resource adhering to FAIR (Findable, Accessible, Interoperable, and Reusable) principles of data management. It distinguishes itself through its comprehensive multispecies focus, encompassing a wide variety of Oryza genomes and related species, and its integration with FAIR principles to ensure data accessibility and usability. It offers a community curated selection of high-quality Oryza genomes, genetic variation, gene function, and trait data. The latest release, version 8, includes 28 Oryza genomes, covering wild rice and domesticated cultivars. These genomes, along with Leersia perrieri and seven additional outgroup species, form the basis for 38 K protein-coding gene family trees, essential for identifying orthologs, paralogs, and developing pan-gene sets. GrameneOryza's genetic variation data features 66 million single-nucleotide variants (SNVs) anchored to the Os-Nipponbare-Reference-IRGSP-1.0 genome, derived from various studies, including the Rice Genome 3 K (RG3K) project. The RG3K sequence reads were also mapped to seven additional platinum-quality Asian rice genomes, resulting in 19 million SNVs for each genome, significantly expanding the coverage of genetic variation beyond the Nipponbare reference. Of the 66 million SNVs on IRGSP-1.0, 27 million acquired standardized reference SNP cluster identifiers (rsIDs) from the European Variation Archive release v5. Additionally, 1200 distinct phenotypes provide a comprehensive overview of quantitative trait loci (QTL) features. The newly introduced Oryza CLIMtools portal offers insights into environmental impacts on genome adaptation. The platform's integrated search interface, along with a BLAST server and curation tools, facilitates user access to genomic, phylogenetic, gene function, and QTL data, supporting broad research applications. Database URL: https://oryza.gramene.org.

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

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

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

Motivation

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

Results

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

The discovery of the Sph-gated plasma membrane Ca2+ channel in trypanosomatids. A difficult path for a surprising kind of L-Type VGCC

Ca2⁺ plays a crucial role in signaling pathways in all eukaryotic cells, including trypanosomatids. These represent a large family of parasites including the causative agents of several human infectious diseases, such as Chagas' disease and leishmaniasis. Accordingly, the intracellular free Ca2+ concentration ([Ca2⁺]i) is subject to rigorous regulation. In these parasites, the cytosolic concentration is maintained at approximately 100 nM by various intracellular organelles, including the single mitochondrion, the endoplasmic reticulum, and acidocalcisomes, which as compartments, are limited to capacity confines. It is therefore the responsibility of plasma membrane mechanisms to ensure the long-term regulation of [Ca2+]i, whereas a plasma membrane Ca2+ channel is responsible for Ca2+ entry and a Ca2+-ATPase regulates extrusion. However, the identification of this channel has remained a challenge until the ligand that induces its opening was identified: the sphingolipid sphingosine. Miltefosine, the only oral medication currently approved for the treatment of leishmaniasis, has been shown to mimic sphingosine. This review outlines the history of the trypanosomatid Ca2⁺ channel, beginning with its initial discovery and concluding with its incorporation into giant liposomes. This enabled the channel to be characterized by electrophysiological studies using "patch clamp" techniques. These studies revealed similarities and significant differences when compared with the human orthologue, which could be exploited for therapeutic purposes. Given that previous research has indicated the potential existence of an L-type VGCC in various trypanosomatids, we conducted a comparative analysis of putative genomic sequences, which demonstrated that, despite the low level of primary identity, this Ca2⁺ channel exhibits functional and structural homology with the mammalian counterpart.

Jan and mini-Jan, a model system for potato functional genomics

Potato (Solanum tuberosum) is the third-most important food crop in the world. Although the potato genome has been fully sequenced, functional genomics research of potato lags behind that of other major food crops, largely due to the lack of a model experimental potato line. Here, we present a diploid potato line, 'Jan,' which possesses all essential characteristics for facile functional genomics studies. Jan exhibits a high level of homozygosity after seven generations of self-pollination. Jan is vigorous, highly fertile and produces tubers with outstanding traits. Additionally, it demonstrates high regeneration rates and excellent transformation efficiencies. We generated a chromosome-scale genome assembly for Jan, annotated its genes and identified syntelogs relative to the potato reference genome assembly DMv6.1 to facilitate functional genomics. To miniaturize plant architecture, we developed two 'mini-Jan' lines with compact and dwarf plant stature through CRISPR/Cas9-mediated mutagenesis targeting the Dwarf and Erecta genes involved in growth. One mini-Jan mutant, mini-JanE, is fully fertile and will permit higher-throughput studies in limited growth chamber and greenhouse space. Thus, Jan and mini-Jan offer a robust model system that can be leveraged for gene editing and functional genomics research in potato.

Crystal structure of the S-adenosylmethionine-dependent mycolic acid synthase UmaA from Mycobacterium tuberculosis

Mycobacterium tuberculosis is a Gram-positive bacillus that causes tuberculosis and is a leading cause of mortality worldwide. This disease is a growing health threat due to the occurrence of multidrug resistance. Mycolic acids are essential for generating cell walls and their modification is important to the virulence and persistence of M. tuberculosis. A family of S-adenosylmethionine-dependent mycolic acid synthases modify mycolic acids and represent promising drug targets. UmaA is currently the least-understood member of this family. This paper describes the crystal structure of UmaA. UmaA is a monomer composed of two domains: a structurally conserved SAM-binding domain and a variable substrate-binding auxiliary domain. Fortuitously, our structure contains a nitrate in the active site, a structural mimic of carbonate, which is a known general base in cyclopropane-adding synthases. Further investigation indicated that the structure of the N-terminus is highly flexible. Finally, we have identified S-adenosyl-N-decyl-aminoethyl as a promising potential inhibitor.

The virome of the panglobal, wide host-range plant pathogen Phytophthora cinnamomi: phylogeography and evolutionary insights

Phytophthora cinnamomi stands out as one of the most devastating plant pathogens worldwide, rapidly expanding its range and impacting a wide range of host species. In this study, we investigated the virome of P. cinnamomi across 222 isolates from Africa, Asia, Europe, Oceania, and the Americas using stranded total RNA sequencing, reverse transcription polymerase chain reaction screening, and Sanger sequencing of selected isolates. Our analysis revealed that virus infections were prevalent across all sampled populations, including RNA viruses associated with the orders Ghabrivirales, Martellivirales, and Tolivirales, and the classes Amabiliviricetes, Bunyaviricetes, and the recently proposed Orpoviricetes. Viruses were mainly found in East and Southeast Asian populations, within the geographic origin of P. cinnamomi but have also spread to new regions where the pathogen has emerged as a clonal destructive pathogen. Among the identified viruses, eight species, including two bunya-like viruses, one narna-like virus, and five ormycoviruses, exhibit a global distribution with some genetic divergence between continents. The interaction between P. cinnamomi and its virome indicates a dynamic coevolution across diverse geographic regions. Indonesia is indicated to be the viral epicentre of P. cinnamomi, with the highest intra- and interspecies diversity of viruses. Viral diversity is significantly enhanced in regions where sexual recombination of P. cinnamomi occurs, while regions with predominantly asexual reproduction harbour fewer viral species. Interestingly, only the partially self-fertile mating type (MAT) A2, associated with the global pandemic, facilitates the spread of viruses across different biogeographic regions, whereas viruses are absent in the self-sterile MAT A1 in its areas of introduction like Australia and South Africa. Intriguingly, the presence of a plant tombusvirus suggests a potential cross-kingdom infection among Chilean isolates and a plant host. This study sheds further light on the geographical origin of P. cinnamomi from a novel virome perspective.

Unveiling the functional nature of retrogenes in dinoflagellates

Retroposition is a gene duplication mechanism that uses RNA molecules as intermediaries to generate new gene copies. Dinoflagellates are proposed as an ideal model for exploring this process due to the tagging of retrogenes with DNA-encoded remnants of the dinoflagellate-specific splice-leader motif at their 5' end. We conducted a comprehensive search for retrogenes in dinoflagellate transcriptomes to uncover their functional nature and the processes underlying their redundancy. We obtained a high-confidence set of hypothetical functional retrogenes widespread through the dinoflagellate lineage. Through annotations and gene ontology enrichment analysis, we found that the functional diversity of retrogenes reflects the most prevalent and active processes during stress periods, particularly those involving post-translational modifications and cell signalling pathways. Additionally, the significant presence of retrogenes linked to specific biological processes involved in symbiosis and toxin production underscores the role of retrogenes in adaptation. The expression profile and codon composition similar to protein-coding genes confirm the operational status of retrogenes and strengthen the idea that retrogenes recapitulate parental gene expression and function. This study provides new evidence supporting widespread gene retroposition across dinoflagellates and highlights the functional link of retrogenes with the core activity of the cell.

From Genes to Molecules: The Fusarium PKS16 Gene Cluster Facilitates the Biosynthesis of Proliferapyrones

Ascomycete fungi of the genus Fusarium are found in manifold ecological niches and thus pursue several lifestyles. On average, individual Fusarium species have the genetic capability to produce 50 natural products (NPs), which are in general thought to improve the fungus's fitness in defined environments. This also includes NPs with toxic potential (mycotoxins) contaminating food and feed sources. Recent research has shown that the production of NPs is tightly regulated on the transcriptional level and depends on the delicate balance between the deposition and removal of histone marks. Within this study, we show that the expression of the prior cryptic Fusarium PKS16 biosynthetic gene cluster (BGC) greatly depends on modifications at histone H3 lysine 27 (H3K27). By combining molecular-, chemical-, and bioinformatic analyses we show that the PKS16 BGC from F. fujikuroi B14 (FfB14) consists of nine genes, including a positively acting pathway-specific transcription factor, which although absent in some fusaria, functions in activating other PKS16 cluster genes. Moreover, we linked the PKS16 BGC to the biosynthesis of proliferapyrone (PRO) E, an isomer of the recently isolated PRO A.

A powdery mildew core effector protein targets the host endosome tethering complexes HOPS and CORVET in barley

Powdery mildew fungi are serious pathogens affecting many plant species. Their genomes encode extensive repertoires of secreted effector proteins that suppress host immunity. Here, we revised and analyzed the candidate secreted effector protein (CSEP) effectome of the powdery mildew fungus, Blumeria hordei (Bh). We identified seven putative effectors that are broadly conserved in powdery mildew species, suggesting that they are core effectors of these phytopathogens. We showed that one of these effectors, CSEP0214, interacts with the barley (Hordeum vulgare) vacuolar protein-sorting 18 (VPS18) protein, a shared component of the class C core vacuole/endosome tethering (CORVET) and homotypic fusion and protein-sorting (HOPS) endosomal tethering complexes that mediate fusion of early endosomes and multivesicular bodies, respectively, with the central vacuole. Overexpression of CSEP0214 and knockdown of either VPS18, HOPS-specific VPS41, or CORVET-specific VPS8 blocked the vacuolar pathway and the accumulation of the fluorescent vacuolar marker protein (SP)-RFP-AFVY in the endoplasmic reticulum. Moreover, CSEP0214 inhibited the interaction between VPS18 and VPS16, which are both shared components of CORVET as well as HOPS. Additionally, introducing CSEP0214 into barley leaf cells blocked the hypersensitive cell death response associated with resistance gene-mediated immunity, indicating that endomembrane trafficking is required for this process. CSEP0214 expression also prevented callose deposition in cell wall appositions at attack sites and encasements of fungal infection structures. Our results indicate that the powdery mildew core effector CSEP0214 is an essential suppressor of plant immunity.

Independent origins and non-parallel selection signatures of triclabendazole resistance in Fasciola hepatica

Triclabendazole (TCBZ) is the primary treatment for fascioliasis, a global foodborne zoonosis caused by Fasciola hepatica. Widespread resistance to TCBZ (TCBZ-R) in livestock and a rapid rise in resistant human infections are significant concerns. To understand the genetic basis of TCBZ-R, we sequenced the genomes of 99 TCBZ-sensitive (TCBZ-S) and 210 TCBZ-R adult flukes from 146 bovine livers in Cusco, Peru. We identify genomic regions of high differentiation (FST outliers above the 99.9th percentile) that encod genes involved in the EGFR-PI3K-mTOR-S6K pathway and microtubule function. Transcript expression differences are observed in microtubule-related genes between TCBZ-S and -R flukes, both without drug treatment and in response to treatment. Using only 30 SNPs, it is possible to differentiate between TCBZ-S and -R parasites with ≥75% accuracy. Our outlier loci are distinct from the previously reported TCBZ-R-associated QTLs in the UK, suggesting an independent evolution of resistance alleles. Effective genetics-based TCBZ-R surveillance must consider the heterogeneity of loci under selection across diverse geographical populations.

Molecular dynamic simulations to assess the structural variability of ClpV from Enterobacter cloacae

The Enterobacter cloacae complex (ECC) consists of six Enterobacter species (E. cloacae, hormaechei, kobei, ludwigii, nimipressuralis and asburiae) that have emerged as nosocomial pathogens of interest, with E. cloacae and Enterobacter hormachei being the most frequently isolated ECC species in human clinical specimens and intensive care unit (ICU) patients. Many nosocomial outbreaks of E. cloacae have been related to transmission through contaminated surgical equipment and operative cleaning solutions. As this pathogen evades the action of antibiotics, it is important to find alternative targets to limit the devastating effects of these pathogens. ClpV is a Clp ATPase which dissociates and recycles the contracted sheath of the bacterial type VI secretion system (T6SS), thereby regulating bacterial populations and facilitating environmental colonization. Seventy-one Enterobacter strains were mined for Clp ATPase proteins. All the investigated strains contained ClpA, ClpB, ClpX and ClpV while only 20% contained ClpK. All the investigated strains contained more than one ClpV protein, and the ClpV proteins showed significant variations. Three ClpV proteins from E. cloacae strain E3442 were then investigated to determine the structural difference between each protein. Homology modelling showed the proteins to be structurally similar to each other, however the physicochemical characteristics of the proteins vary. Additionally, physicochemical analysis and molecular dynamic simulations showed that the proteins were highly dynamic and not significantly different from each other. Further investigation of the proteins in silico and in vitro in the presence and absence of various ligands and proteins could be performed to determine whether the proteins all interact with their surroundings in the same manner. This would allow one to determine why multiple homologs of the same protein are expressed by pathogens.

Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius

Crucian carp (Carassius carassius), a member of the carp family (Cyprinidae), is known for its remarkable anoxia tolerance. The physiological responses and adaptations to anoxia are well documented, but there is a need for better understanding of the molecular regulation and evolutionary mechanisms behind these adaptations. Here we present a high-quality, functionally annotated, chromosome-level genome assembly that can facilitate such further studies. Genomic DNA was obtained from a wild-caught crucian carp specimen and used for PacBio long-read, Illumina short-read and Hi-C sequencing. Short-read mRNA data were used for structural annotation using the BRAKER3 pipeline, while PacBio long-read RNA sequencing data were used for annotation of untranslated regions and refinement of gene-isoform relationships, using the PASA pipeline. The full assembly had a contig-level N50 of 15Mbp in 290 scaffolds and 98.6% of the total length (1.65Gbp) placed in 50 chromosomes. Structural annotation resulted in 82,557 protein-coding transcripts (in 45,667 genes), with a BUSCO completeness of 99.6% and of which 77,370 matched a protein in the UniProtKB/Swiss-Prot database.

Comprehensive biochemical, molecular and structural characterization of subtilisin with fibrinolytic potential in bioprocessing

Enzyme deployment is proliferating extensively in industries owing to their environmentally friendly and easily degradable attributes. This article undertakes an exhaustive examination of wild subtilisin enzyme, covering purification, biochemical delineation, analytical techniques, and practical implementations. The purification methodology involved partial refinement, anionic exchange, and gel filtration chromatography, culminating in a purification factor of 3.406, corroborated by SDS-PAGE showcasing a molecular weight of ~ 42 kDa. Biochemical scrutiny unveiled the enzyme's response, with an optimal pH at 9 and temperature peak at 60 ℃. Various surfactants, metal ions, organic solvents and inhibitors exhibited notable efficacy. Substrate specificity and kinetics showcased the utmost specificity with N-Suc-F-A-A-F-pNA, registering Km and Vmax values of 0.731 ± 0.5 mM and 0.87 ± 9 × 103 U/mg, respectively. Different bioanalytical techniquesproffered insights into structural and biophysical facets. Practical applications encompassed goat skin depilation, feather disintegration, blood clot dissolution, exemplifying the enzyme's multifaceted utility. To embark upon the elucidation of structure-function relationships, a three-dimensional model was devised through homology modelling, leveraging existing subtilisin structures (PDB: 3WHI). Molecular docking score of - 8.8 kcal/mol and dynamic simulations augmented the comprehension of molecular interactions with N-Suc-F-A-A-F-pNA. This research significantly contributes to unravelling the biochemical intricacies of wild subtilisin and underscores potential industrial and biomedical prowess. Subtilisin can be explored for its thrombolytic potential in several cardiovascular diseases. It may aid in the management of thrombosis by dissolving blood clots in conditions like deep pulmonary embolism, myocardial infarction, ischemic strokes, and in atherosclerosis by breaking down fibrin in arterial plaques, thus preventing heart attacks and strokes.