Clustal W and Clustal X version 2.0

Role of fibronectin type III domain in enhancing the substrate accessibility of modular GH9 endocellulase by reducing non-specific binding to lignin

Utilizing lignocellulosic biomass effectively can lessen reliance on fossil fuels and facilitate the production of second-generation biorefinery feedstocks. The nonspecific binding of lignin to cellulases is one of the main factors affecting their enzymatic performance and hampering their efficiency in degrading lignocellulose. Processive endocellulase from Acidothermus cellulolyticus 11B has a modular structure consisting of several carbohydrate-binding modules, a glycoside hydrolase family 9 catalytic domain, and a fibronectin type III (FN3) domain. This study investigated the role of the FN3 in the degradation of lignocellulose by constructing multiple mutants. The results showed that the FN3 could improve the thermal stability of the enzyme and resist the nonspecific binding of lignin to cellulase. This characteristic can significantly increase the lignocellulose's enzymatic efficiency and offer a novel approach to the artificial design of multi-modular cellulases.

The SlWRKY42-SlMYC2 module synergistically enhances tomato saline-alkali tolerance by activating the jasmonic acid signaling and spermidine biosynthesis pathway

Tomato (Solanum lycopersicum) is an important crop but frequently experiences saline-alkali stress. Our previous studies have shown that exogenous spermidine (Spd) could significantly enhance the saline-alkali resistance of tomato seedlings, in which a high concentration of Spd and jasmonic acid (JA) exerted important roles. However, the mechanism of Spd and JA accumulation remains unclear. Herein, SlWRKY42, a Group II WRKY transcription factor, was identified in response to saline-alkali stress. Overexpression of SlWRKY42 improved tomato saline-alkali tolerance. Meanwhile, SlWRKY42 knockout mutants, exhibited an opposite phenotype. RNA-sequencing data also indicated that SlWRKY42 regulated the expression of genes involved in JA signaling and Spd synthesis under saline-alkali stress. SlWRKY42 is directly bound to the promoters of SlSPDS2 and SlNHX4 to promote Spd accumulation and ionic balance, respectively. SlWRKY42 interacted with SlMYC2. Importantly, SlMYC2 is also bound to the promoter of SlSPDS2 to promote Spd accumulation and positively regulated saline-alkali tolerance. Furthermore, the interaction of SlMYC2 with SlWRKY42 boosted SlWRKY42's transcriptional activity on SlSPDS2, ultimately enhancing the tomato's saline-alkali tolerance. Overall, our findings indicated that SlWRKY42 and SlMYC2 promoted saline-alkali tolerance by the Spd biosynthesis pathway. Thus, this provides new insight into the mechanisms of plant saline-alkali tolerance responses triggered by polyamines (PAs).

A leigh syndrome mutation perturbs long-range energy coupling in respiratory complex I

Respiratory complex I is a central enzyme of cellular energy metabolism that couples electron transfer with proton translocation across a biological membrane. In doing so, it powers oxidative phosphorylation that drives energy consuming processes. Mutations in complex I lead to severe neurodegenerative diseases in humans. However, the biochemical consequences of these mutations remain largely unknown. Here, we use the Escherichia coli complex I as a model to biochemically characterize the F124LMT-ND5 mutation found in patients suffering from Leigh syndrome. We show that the mutation drastically perturbs proton translocation and electron transfer activities to the same extent, despite the remarkable 140 Å distance between the mutated position and the electron transfer domain. Our molecular dynamics simulations suggest that the disease-causing mutation induces conformational changes that hamper the propagation of an electric wave through an ion-paired network essential for proton translocation. Our findings imply that malfunction of the proton translocation domain is entirely transmitted to the electron transfer domain underlining the action-at-a-distance coupling in the proton-coupled electron transfer of respiratory complex I.

PuUBL5-mediated ZINC FINGER PROTEIN 1 stability is critical for root development under drought stress in Populus ussuriensis

C2H2-type zinc finger protein (ZFP) transcription factors influence root growth and development. However, their potential roles in inhibiting adventitious root (AR) and lateral root (LR) formation in trees remain unclear. Here, we report that the ABA-responsive C2H2-type zinc finger protein transcription factor (PuZFP1) regulates Populus ussuriensis root development to enhance drought tolerance. PuZFP1 negatively regulates LR development by binding to the PuWRKY46 promoter and inhibiting its expression. At the same time, PuZFP1 promotes AR elongation by repressing Clade E Growth-Regulating (EGR) Type 2C protein phosphatases (PuEGR1). In PuZFP1-overexpressing lines, a higher ABA/IAA ratio in the differentiated zone (DZ) drives PuWRKY46-mediated LR inhibition. Conversely, a lower ABA/IAA ratio is associated with AR elongation and the expression of the downstream target gene PuEGR1 in the elongation zone (EZ). Notably, PuZFP1 physically interacts with Ubiquitin-like protein 5 (PuUBL5) and undergoes 26S proteasome-mediated degradation. Taken together, our findings shed light on the role of the PuUBL5-PuZFP1 module in mediating the crosstalk between LR emergence and AR elongation via ABA/auxin signaling in drought-stressed P. ussuriensis, and provide insights into the regulatory network underlying PuZFP1-mediated root growth in poplar.

Comprehensive analysis of the INDETERMINATE DOMAIN (IDD) gene family in Marchantia polymorpha brings new insight into evolutionary developmental biology

BACKGROUND

SHORTROOT (SHR) and SCARECROW (SCR) are key regulators of plant cell fate. An increasing number of studies have illustrated that the SHR-SCR pathway depends on some INDETERMINATE DOMAIN (IDD) family transcription factors in regulating genes involved in tissue and organ morphogenesis, nutrients transport and metabolism, photoperiodic flowering and stress response. Recent genome sequencing and analysis revealed that only seven IDDs exist in the liverwort Marchantia polymorpha, one of the early diverging extant land plant lineages. However, little is known concerning how the IDDs and the SHR/SCR-IDD pathway work in the ancestral land plants.

RESULTS

In this study, IDD gene family members of this liverwort and other classic model plants were classified into seven branches on the basis of phylogenetic analysis. Gene structure and protein motif analyses suggested that most of the MpIDDs are comparatively evolutionary conserved. Protein structure prediction showed that MpIDDs display similar core domain organization with the IDD proteins from the same branches. Cis-regulatory element prediction demonstrated that MpIDDs might be hormone and stress responsive. The expression levels of most MpIDDs display tissue specificities and could be changed by hormone treatment. All the MpIDDs are located in the nucleus, and most of them have autoactivation activity. Yeast two-hybrid assays confirmed the interactions between MpGRAS8/MpSHR and MpIDD3, MpIDD4 or MpIDD5, as well as MpGRAS3/MpSCR and MpIDD1 or MpIDD2. Taken together, our results provide comprehensive information on IDD gene family in M. polymorpha for further exploring their function in depth, and highlight the importance of the SHR/SCR-IDD pathway in plant development and evolution.

CONCLUSIONS

Through bioinformatics analysis and experimental determination of expression patterns, subcellular localization, autoactivation, and protein interaction, this study provided crucial information for a deeper understanding of the functions of MpIDDs in evolutionary developmental studies.

Identification and Functional Exploration of the ALKBH Gene Family in Oriental Melon Fruit Ripening

N6-methyladenosine (m6A) methylation functions as a vital post-transcriptional and epigenetic modification in higher plants regulated by α-ketoglutarate-dependent dioxygenases (ALKBH). However, the role of ALKBH genes in oriental melon (Cucumis melo L.) fruit ripening has not been explored. Therefore, we treated oriental melon with an exogenous m6A demethylase inhibitor (mechlorfenamic acid) then analyzed endogenous ethylene production and ripening-related indicators to explore the effects of m6A methylation on ripening. Bioinformatics and real-time quantitative PCR analyses were used to determine the impact of ALKBH genes on key ethylene synthesis gene expression. Treatment effectively inhibited endogenous ethylene production, firmness changes, and soluble solid contents, thereby extending fruit ripening. Eight ALKBH gene family members belonging to five major groups were identified in the melon genome. All members were expressed in ripening fruits, with different expression patterns during ripening. CmALKBH6, CmALKBH7, and CmALKBH8 expression was inhibited by an ethylene inhibitor (1-methylcyclopropene). The transient overexpression (OE) of CmALKBH8 in oriental melon led to the increased expression of the ethylene synthesis genes CmACS1, CmACS2, and CmACO1. In summary, the ethylene-regulated gene CmALKBH8 may participate in oriental melon fruit ripening regulation by modulating the methylation levels of ethylene synthesis-related genes. These findings help us better understand how m6A methylation regulates melon ripening.

Genetic diversity and population structure of parasite infrapopulations within and across hosts for two trophically transmitted trematode parasites

Complex parasite life cycles frequently require trophic transfer of parasites from an intermediate host prey to a definitive host predator. This results in aggregated distributions of parasites in predator host populations, which are subsequently expected to host more genetically diverse parasite infrapopulations than lower trophic level hosts. Host dispersal and seasonal population dynamics, particularly in the case of first-intermediate hosts, are also expected to drive population genetic patterns within and across populations. To examine how parasite life history and host ecology influence parasite genetic patterns, we characterized the genetic diversity of within-host infrapopulations, as well as overall population genetic structure, of sympatric tongueworm (Halipegus occidualis) and lungworm (Haematoloechus complexus) freshwater trematode parasite populations. Parasites were collected across three host stages (snail, odonate insect, and frog) and sequenced at the cytochrome oxidase I (COI) mitochondrial region (519 bp for lungworms; 526 bp for tongueworms) to characterize genetic variation within and across hosts. Infection abundance per host and genetic diversity of within-host parasite infrapopulations generally increased with host trophic level, as expected. Additionally, tongueworm assemblages in odonate hosts were essentially equally as genetically diverse (depending on the index used) as those in definitive host frogs; tongueworms have an additional trophic transfer in their life cycle before the odonate stage, which highlights how trophic transmission and multi-host life cycle structure can benefit parasites by increasing genetic diversity of sexually reproducing adult assemblages. We also found that tongueworm populations, which infect a long-lived snail as a first-intermediate host, had higher population genetic diversity than lungworms, which infect a much shorter-lived snail with highly unstable population dynamics. Thus, we expect that first-intermediate host dynamics and dispersal ability played a large role in predicting population-level parasite genetic diversity and genetic structure in this system. This study investigates the effects of small- and large-scale processes on parasite genetic population structure and diversity and provides critical genetic data for future studies on these genera.

Genome data cross-contamination versus interdomain recombination: Equus caballus and Mus musculus genetic loci in the insertion sequence-rich genomes of two clonally related methicillin-resistant Staphylococcus aureus strains from China

BACKGROUND

Methicillin-resistant Staphylococcus aureus (MRSA) represents a significant global health threat, responsible for infections in both humans and animals. Determining genetic patterns associated with the genome plasticity of MRSA is critical for predicting the evolutionary trajectories of its emerging pathogenic clones.

RESULTS

The specific genetic loci of the MRSA strains WH3018 and WH9628 from Wuhan, China, ranging in size from 399 to 3,622 base pairs, were determined to be highly homologous (DNA identity: 90.95-100%) to corresponding chromosomal regions from Equus caballus and Mus musculus in the GenBank database. These eukaryotic-associated loci included the microsatellite DNAs or Y chromosome-specific regions from E. caballus, or 45 S-28 S ribosomal RNA/H19 loci from M. musculus, all exhibiting recurrent patterns across the genomes of both MRSA strains. The SplitsTree and RDP4 analyses did not reveal significant recombination signals for the eukaryotic-associated loci that had mimicked interdomain recombination events in the MRSA strains WH3018 and WH9628. The G + C content of these loci (47.6-65.0%) was notably higher than that of the S. aureus reference genome (32.5%). Furthermore, the MRSA genomes showed a significantly larger number and greater diversity of insertion sequences (ISs) (38 ISs per genome) compared to the S. aureus reference genome (16 ISs). Additionally, these genomes also exhibited an extensive decay of prophages and the accumulation of pseudo-transposases.

CONCLUSIONS

The recurring patterns of the eukaryotic-associated loci strongly suggested genome data contamination across the genomes of the MRSA strains WH3018 and WH9628. These MRSA genomes likely underwent extensive prophage decay and an increased proliferation of pseudo-transposases.

Bacillus haimaensis sp. nov.: a novel cold seep-adapted bacterium with unique biosynthetic potential

Deep-sea cold seeps harbor unique microbial communities that play crucial roles in biogeochemical cycles and possess potential biotechnological applications. Herein, we report the isolation, characterization, and genomic analysis of a novel Bacillus species, Bacillus haimaensis sp. nov. (type strain CSS-39T, CCTCC M20241382), obtained from sediments collected at a depth of 1,350 m in the Haima cold seep, South China Sea. Phylogenomic analysis, revealing an average nucleotide identity of 87.78% and a digital DNA-DNA hybridization value of 34.0% with its closest relative B. tianshenii DSM 25879T, confirms the taxonomic novelty of the genus Bacillus. The complete 4.54 Mb genome of B. haimaensis reveals adaptations to the cold seep environment, including enhanced nutrient acquisition capabilities and stress response mechanisms. Comparative genomic analysis identifies 27 unique gene clusters related to spore germination and sulfate assimilation, suggesting specialized metabolic strategies for this extreme habitat. Furthermore, six biosynthetic gene clusters, including a novel lassopeptide cluster, indicate a potential for secondary metabolite production. Phenotypic characterization demonstrates the strain's ability to utilize diverse carbon sources and tolerate a wide range of environmental conditions. Our findings provide insights into microbial adaptations to deep-sea cold seeps and highlight the potential of B. haimaensis for biotechnological applications in bioremediation and natural product discovery. This study expands our understanding of microbial diversity in extreme marine environments and offers a new model bacterium for investigating bacterial adaptations to deep-sea ecosystems.IMPORTANCEThe discovery of Bacillus haimaensis sp. nov. in the Haima cold seep of the South China Sea represents a significant advancement in our understanding of microbial adaptations to extreme marine environments. This novel species exhibits remarkable metabolic versatility and unique genomic features, providing insights into bacterial survival strategies in nutrient-variable, high-pressure deep-sea ecosystems. Comprehensive genomic analysis reveals distinctive biosynthetic gene clusters, suggesting untapped potential for discovering novel natural product. Furthermore, B. haimaensis exhibits promising capabilities for aromatic compound degradation, indicating potential applications in marine bioremediation. This work not only expands our knowledge of microbial diversity in understudied deep-sea habitats but also highlights the biotechnological promise of extremophiles. The adaptive mechanisms elucidated in B. haimaensis, particularly those related to sporulation and sulfate assimilation, contribute to our broader understanding of microbial ecology in cold seeps and may inform future research on climate change impacts on deep-sea ecosystems.

Microphysiological gut-on-chip enables extended in vitro development of Cryptosporidium hominis

Introduction

Cryptosporidium hominis is the dominant Cryptosporidium species infecting humans, but most advances in developing robust in vitro culturing platforms for Cryptosporidium have utilised C. parvum. Consequently, there is relatively little available information specific to the biology and life cycle of C. hominis. The present study utilised a pumpless and tubeless gut-on-chip to generate a physiologically relevant in vitro environment by applying a constant fluid shear stress of 0.02 dyn cm-2 to HCT-8 cells.

Methods

Gut-on-chips were fabricated using standard soft lithography. C. hominis oocysts isolated from human pathology samples were used to infect the human ileocecal colorectal adenocarcinoma (HCT-8) cell line under a constant fluid shear stress of 0.02 dyn cm-2. Parasite growth was assessed using a C. hominis-specific quantitative PCR, a Cryptosporidium genus-specific immunofluorescence assay, and scanning electron microscopy. Differences in the HCT-8 transcriptome with and without fluid shear stress, and the host-parasite interaction, were both assessed using bulk transcriptomics.

Results

Transcriptomic analysis of the HCT-8 cell line cultured within the gut-on-chip demonstrated a metabolic shift towards oxidative phosphorylation when compared to the same cell line cultured under static conditions. Extended C. hominis (subtype IdA15G1) cultures were sustained for up to 10 days within the gut-on-chip as shown by a C. hominis-specific qPCR and a Cryptosporidium genus-specific immunofluorescence assay, which demonstrated ~30-fold amplification in the gut-on-chip over the duration of the experiment. Scanning electron microscopy of infected monolayers identified trophozoites, meronts, merozoites, macrogamonts, microgamonts, and possible gamont-like stages at 48 h post-infection. The potential role of gamonts in the Cryptosporidium life cycle remains unclear and warrants further investigation. Transcriptomes of HCT-8 cells infected with C hominis revealed upregulation of biological processes associated with cell cycle regulation and cell signalling in C. hominis-infected cells under fluid shear stress compared to static culture.

Conclusions

These data demonstrate that bioengineered gut-on-chip models support extended C. hominis growth and can be used to interrogate responses of host cells to infection. Owing to its relative simplicity, the pumpless and tubeless gut-on-chip can be accessible to most laboratories with established HCT-8 infection models for Cryptosporidium culture.

Virome analysis of field-collected chilli samples reveals diverse viruses

BACKGROUND

Chilli (Capsicum annuum L.), an important spice crop, is susceptible to diverse viral infections. Traditional detection methods including PCR and its variants had difficulty in identifying the complete spectrum of viruses, especially in mixed infections. High-throughput sequencing (HTS) has emerged as a successful tool for comprehensive virome analyses, enabling the identification of the known and novel viruses in the infected samples. Using HTS, we investigated virome analyses to identify known and novel viruses in chilli.

METHODS

In 2021-22, 19 leaf samples were collected from chili plants in farmer fields in Karnataka, India, showing symptoms such as leaf curling, vein banding, mosaic, mottling, filiform, leathery, dull-colored, and bunchy leaves. Total RNA was extracted, pooled at equimolar concentrations, and subjected to virome profiling. rRNA-depleted RNA was used to prepare mRNA and sRNA libraries, which were sequenced on the Illumina NovaSeq 6000 platform. Bioinformatics tools were used to analyze the sequencing data and identify plant viruses.

RESULTS

Viral disease incidences varied from 26.6 to 47.5% in the farmer fields surveyed. Virome analyses revealed complete/ near-complete genomes of six different viruses: chilli leaf curl virus (ChiLCV), cucumber mosaic virus (CMV), groundnut bud necrosis orthotospovirus (GBNV), pepper cryptic virus-2 (PCV-2), pepper vein yellows virus (PeVYV) and bell pepper alphaendornavirus (BPEV). The viral copy number of ChiLCV was found to be the highest (45.36%) and had the least mutational frequency (SNPs) and was also associated with five satellites. Recombination breakpoints were observed in ChiLCV (coat protein and AC4 regions), CMV RNA2 (2a protein) and PeVYV (P0, P3 and P5 proteins), indicating their origins from intra- and interspecific recombination events. Identified viruses in the pooled RNA sample were confirmed by PCR. Further, novel loop-mediated isothermal amplification (LAMP) diagnostic assays were developed for diagnosing the identified viruses for future use. Among the six viruses identified in chilli, PeVYV and BPEV are the first reports from India.

CONCLUSIONS

This study presents the first virome profiling of chili using HTS and identified known and previously unreported viruses in farmer fields of Karnataka, India. Understanding viral diversity provides insights for developing diagnostic tools and effective management strategies.

SGBP-B-like bimodular cellulose-binding protein CHU_1279 is essential for cellulose utilization by Cytophaga hutchinsonii

The widespread cellulolytic specialist Cytophaga hutchinsonii belonging to the phylum Bacteroidetes adopted a unique cellulose utilization strategy that did not conform to the known cellulose-degrading paradigms involving free cellulases or cellulosomes. The strategy used by C. hutchinsonii still remains largely unclear. In this study, we showed that chu_1279 within the chu_1276-chu_1280 gene cluster, which has been previously shown to be important for cellulose utilization by C. hutchinsonii, encodes an outer membrane protein, and its elimination prohibited bacterial growth on cellulose. Structural prediction revealed that CHU_1279 is a surface glycan-binding protein B (SGBP-B)-like protein comprising two putative carbohydrate-binding module (CBM)-like domains. Further analyses verified that recombinant CHU_1279 displayed significant cellulose-binding protein, and its C-terminal domain is predominantly responsible for cellulose binding. Expression of the C-terminal domain but not the N-terminal domain restored cellulose utilization of ∆chu_1279. Moreover, site-directed mutagenesis analyses identified three aromatic residues important for cellulose binding of the recombinant CHU_1279 protein. The defective cellulose utilization of ∆chu_1279 cells otherwise could be recovered by CHU_1279 variants with significantly damaged cellulose-binding capability. Sequence analyses revealed that orthologs of CHU_1279 as well as the atypical polysaccharide utilization loci (PUL) constituted by the gene cluster chu_1276-chu_1280 are also present in two other cellulolytic Bacteroidetes bacteria, Cytophaga aurantiaca and Sporocytophaga myxococcoides, which are closely related to C. hutchinsonii. Our results contribute to unveiling the unique mechanism underlying the efficient cellulose utilization by C. hutchinsonii and similar cellulolytic bacteria.IMPORTANCEMost members of the phylum Bacteroidetes are highly competitive and efficient degraders of complex polysaccharides largely ascribed to their employment of a SusC-like system encoded by a polysaccharide utilization locus (PUL). However, characterization of PULs is limited to those responsible for utilization of (semi)soluble glycans. PULs involved in the utilization of cellulose, the most abundant renewable polymer, have not been identified and functionally characterized yet. We demonstrated that chu_1279 in the cellulolytic specialist C. hutchinsonii encodes an SGBP-B-like protein that is required for cellulose utilization, supporting that the gene cluster chu_1276-chu_1280 in C. hutchinsonii encodes an atypical PUL system dedicated to cellulose assimilation. Further analyses showed that this atypical PUL system is also present in two other cellulolytic Bacteroidetes bacteria. This study not only contributes to unveiling the unusual cellulose utilization strategy adopted by C. hutchinsonii and similar cellulolytic bacteria but also helps expand our understanding of atypical PULs for nutrient acquisition by cellulolytic bacteria.

Comprehensive Characterization and Functional Analysis of the Lateral Organ Boundaries Domain Gene Family in Rice: Evolution, Expression, and Stress Response

In this study, the LBD (Lateral Organ Boundaries Domain) gene family, a group of plant-specific transcription factors critical for plant growth and development as well as metabolic regulation, was comprehensively characterized in rice. We identified 36 LBD genes using multi-source genomic data and systematically classified them into Class I (31 genes) and Class II (5 genes). Analysis of their physicochemical properties revealed significant variations in amino acid length, molecular weight, isoelectric points, and hydropathicity. Motif analysis identified conserved LOB domains and other motifs potentially linked to functional diversity. Cis-acting element analysis indicated the involvement of these genes in various biological processes, including light response, hormone signaling, and stress response. Expression profiling demonstrated tissue-specific expression patterns, with several genes, such as XM_015770711.2, XM_015776632.2, and XM_015792766.2, showing relatively high expression in rice roots, implying their important role in root development. Transcriptome data further supported the involvement of specific genes in responses to phytohormones such as jasmonic acid (JA) and abscisic acid (ABA), as well as environmental stresses like cold and drought. Notably, XM_015770711.2, XM_015776632.2, and XM_015772758.2 may contribute to the regulation of rice environmental adaptability by mediating ABA and JA signaling pathways, respectively. In conclusion, this study identified members of the LBD gene family through the screening of two rice gene databases, and performed a comprehensive analysis of their physicochemical properties, evolutionary relationships, and expression profiles under various conditions. These findings provided valuable insights for further functional studies of LBD genes. Moreover, this study provides a foundation for targeting LBD genes to enhance stress resilience (e.g., drought/cold tolerance) and root architecture optimization. The LBD gene family possesses dual values in both stress resistance regulation and developmental optimization. The construction of its multidimensional functional map lays the theoretical and resource foundation for the precise design of high-yield and stress-resistant varieties.

Modification of intracellular metabolism by expression of a C-terminal variant of phosphoribulokinase from Synechocystis sp. PCC 6803

Phosphoribulokinase (PRK) is a key enzyme in the Calvin cycle of cyanobacteria required for CO2 fixation and enhancing intracellular PRK activity will contribute to altering the metabolic state. In Synechocystis sp. PCC 6803, PRK activity is inhibited by the small protein CP12 and intramolecular disulfide bonds in its C-terminal loop. This study aimed to increase PRK activity by expressing a mutant PRK where inhibitory Cys residues (positions 229 and 235) in the C-terminal loop were replaced with Ser. The engineered strain showed increased PRK activity under photomixotrophic conditions. Metabolomic analysis revealed that this strain accumulates organic acids downstream of glycolysis and the tricarboxylic acid cycle, highlighting its potential for producing chemicals using these metabolites as precursors. These findings suggest that preventing disulfide bond formation in the PRK C-terminal loop enhances its activity, providing a promising approach for metabolic engineering in cyanobacteria.

Genome-Wide Characterization, Comparative Analysis, and Expression Profiling of SWEET Genes Family in Four Cymbidium Species (Orchidaceae)

The SWEET (Sugar Will Eventually be Exported Transporters) protein family plays a key role in plant growth, adaptation, and stress responses by facilitating soluble sugar transport. However, their functions in Cymbidium remain poorly understood. This study identified 59 SWEET genes across four Cymbidium species, encoding conserved MtN3/saliva domains. Despite variations in exon-intron structures, gene motifs and domains were highly conserved. Phylogenetic analysis grouped 95 SWEET proteins from six species into four clades, with gene expansion driven by whole-genome, segmental, and tandem duplications. Cis-element analysis and expression profiling across 72 samples revealed diverse regulatory patterns. Notably, SWEET genes showed peak expression in floral development, leaf morph variations, and diurnal rhythms. qRT-PCR and transcription factor binding analysis further highlighted their regulatory roles in floral patterning, leaf variation, and metabolic rhythms. These findings provide a foundation for future studies on SWEET gene function and their potential molecular breeding value in orchids.

Proposal of Paenibacillus kandeliae sp. nov, Isolataed from Leaf of Kandelia candel

A novel bacterial strain, designated JQZ6Y-1T, was isolated from the leaf of Kandelia candel at Maowei sea Mangrove Nature Reserve, Guangxi Zhuang Autonomous Region, China. The 16S rRNA gene sequence phylogenetic and phylogenomic analysis revealed that strain JQZ6Y-1T formed a stable clade with Paenibacillus wenxiniae DSM 100576T and Paenibacillus hunanensis CGMCC 1.8907T within the genus Paenibacillus. The 16S rRNA gene sequence similarities of strain JQZ6Y-1T with the related species P. wenxiniae DSM 100576T and P. hunanensis CGMCC 1.8907T were 98.3% and 98.2%, respectively. The average nucleotide identity values of strain JQZ6Y-1T with the related species P. wenxiniae DSM 100576T and P. hunanensis CGMCC 1.8907T were 77.5% and 80.4%, respectively. The digital DNA-DNA hybridization values of strain JQZ6Y-1T with the related species P. wenxiniae DSM 100576T and P. hunanensis CGMCC 1.8907T were 22.9% and 23.0%, respectively. These values clearly indicated that strain JQZ6Y-1T represented a novel species. The diagnostic diamino acid in the cell-wall peptidoglycan of strain JQZ6Y-1T was meso-diaminopimelic acid, and MK-7 was the predominant menaquinone. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified phospholipids, and one unidentified lipid. The major fatty acids were anteiso-C15:0 and C16:0. Cells of strain JQZ6Y-1T were Gram positive and rod shaped. Optimum growth occurred at pH 7.0, 30 ℃, and with 1-2% (w/v) NaCl. Based on phylogenomic and phylogenetic analyses coupled with phenotypic and chemotaxonomic characterizations, strain JQZ6Y-1T could be classified as a novel species of the genus Paenibacillus, for which the name Paenibacillus kandeliae sp. nov. is proposed. The type strain is JQZ6Y-1T (=CGMCC 1.18974T = JCM 34547T).

Velamins: green-light-emitting calcium-regulated photoproteins isolated from the ctenophore Velamen parallelum

Ca2+-regulated photoproteins (CaPhs) consist of single-chain globular proteins to which coelenterazine, a widely distributed marine luminogenic substrate (the luciferin), binds along with molecular oxygen, producing a stable peroxide. Upon Ca2+ addition, CaPhs undergo conformational changes leading to the cyclization of the peroxide and the formation of a high-energy intermediate. Subsequently, its decomposition yields coelenteramide in an excited state and results in the emission of a flash of light. To date, most known CaPh systems emit blue light (λmax 465-495 nm), except for two bolinopsin isospecies that emit green light (λmax 500 nm). Here, we report the cloning and functional characterization of wild-type CaPhs capable of emitting green light: velamins, isolated from the bioluminescent ctenophore Velamen parallelum. Ten unique photoprotein-like sequences were recovered and grouped in three main clusters. Representative sequences were cloned, expressed, purified, and regenerated into the active His-tagged α-, β-, and γ-velamins. Upon injection of a calcium-containing buffer into the velamin, a flash of green light (λmax 500-508 nm) was observed across pH values ranging from 7 to 9. Whilst α-velamin isoforms exhibited the highest light emission activity, β- and γ-velamins were found to be more thermostable at higher temperatures. Velamins are the wild-type CaPhs with the longest-wavelength light emission yet reported, making them an excellent model for investigating spectral modulation mechanisms in photoproteins.

A Hypovirulence-Associated Partitivirus and Re-Examination of Horizontal Gene Transfer Between Partitiviruses and Cellular Organisms

Previous research has unearthed the integration of the coat protein (CP) gene from alphapartitivirus into plant genomes. Nevertheless, the prevalence of this horizontal gene transfer (HGT) between partitiviruses and cellular organisms remains an enigma. In our investigation, we discovered a novel partitivirus, designated Sclerotinia sclerotiorum alphapartitivirus 1 (SsAPV1), from a hypovirulent strain of Sclerotinia sclerotiorum. Intriguingly, we traced homologs of the SsAPV1 CP to plant genomes, including Helianthus annuus. To delve deeper, we employed the CP and RNA-dependent RNA polymerase (RdRP) sequences of partitiviruses as "bait" to search the NCBI database for similar sequences. Our search unveiled a widespread occurrence of HGT between viruses from all five genera within the family Partitiviridae and other cellular organisms. Notably, numerous CP-like and RdRP-like genes were identified in the genomes of plants, protozoa, animals, fungi, and even, for the first time, in an archaeon. The majority of CP and RdRP genes were integrated into plant and insect genomes, respectively. Furthermore, we detected DNA fragments originating from the SsAPV1 RNA genome in some subcultures of virus-infected strains. It suggested that SsAPV1 RdRP may possesses reverse transcriptase activity, facilitating the integration of viral genes into cellular organism genomes, and this function requires further confirmation. Our study not only offers a hypovirulence-associated partitivirus with implications for fungal disease control but also sheds light on the extensive integration events between partitiviruses and cellular organisms and enhances our comprehension of the origins, evolution, and ecology of partitiviruses, as well as the genome evolution of cellular organisms.

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

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

Phylogeographic Patterns and Genetic Diversity of Anopheles stephensi: Implications for Global Malaria Transmission

Background: Anopheles stephensi, a primary malaria vector in South Asia, is expanding its geographic range, raising concerns about increased malaria transmission. However, critical aspects of its genetic diversity, population structure, and evolutionary dynamics remain poorly understood in Khyber Pakhtunkhwa (KP), Pakistan, an endemic malaria region where An. stephensi is adapting to urban settings, posing challenges for the development of targeted vector control strategies. This study addresses this gap by analyzing COI, COII (cytochrome oxidase subunit I and II), and ITS2 (internal transcribed spacer 2) sequences from An. stephensi populations in KP and comparing them with global isolates. Additionally, egg morphology analysis was conducted to identify the biological form. Methods: Mosquitoes were collected from malaria-endemic districts (Nowshera, Charsadda, and Peshawar) using ovitraps. Eggs were characterized morphologically, and DNA was extracted for PCR amplification of COI, COII, and ITS2 markers. Sequences from 17 Pakistani isolates, along with global sequences, were analyzed. Phylogenetic relationships, haplotype networks, genetic diversity, and neutrality tests (Tajima's D and Fu's Fs) were assessed. Results: Egg morphology confirmed the mysorensis form (13-15 ridges per egg) in KP. COI sequences clustered into two subclades (Punjab and KP), with >99% similarity to global isolates. COII and ITS2 sequences showed high similarity (99.46-100%) with populations from China, Iran, India, and Brazil, reflecting strong genetic connectivity rather than distinct regional clustering. Haplotype analysis identified six COI, ten COII, and ten ITS2 haplotypes, with Hap_2 (50.7%) and Hap_1 (43.3%) being the most prevalent in COI, Hap_7 (29.4%) in COII, and Hap_3 (80.8%) in ITS2. Population genetic analysis revealed higher COI diversity in Pakistan and India, with moderate diversity in COII. Neutrality tests suggested balancing selection in COI for both countries, while COII and ITS2 indicated population contraction in Iran. Conclusions: The findings reveal strong genetic connectivity within regions (e.g., Pakistan) and differentiation across global populations of An. stephensi, highlighting its potential for further expansion and adaptation. These insights are critical for informing global malaria control strategies, particularly in regions vulnerable to vector invasion.

Detection of Histoplasma capsulatum in Bats from the Brazilian Western Amazon

Histoplasma capsulatum is a saprophytic dimorphic fungus that causes histoplasmosis, a systemic infectious disease of relevance to public health. Bats can be important agents in the epidemiological cycle of the disease since they act as reservoirs of microorganisms. The aim of this study was to detect Histoplasma capsulatum in the lung tissue of bats captured in urban forest fragments in the municipality of Rio Branco, Acre, in the Western Amazon. Twenty-two bat species were captured from five urban forest fragments. The samples taken were subjected to histopathological, mycological, and molecular analysis. Among the 96 animals analyzed, the fungus was detected in 32.29% (31/96). This was the first study to detect the pathogen in bats in the Western Amazon. It is also the first record of the fungus being detected in six bat species. The state of Acre is located in a region with a rich diversity of bats. Furthermore, this area is constantly suffering from climatic and environmental changes that can favor the emergence and re-emergence of diseases. Thus, active epidemiological research and surveillance of neglected fungal infections are essential, especially considering the concept of One Health.

A pangenome reference of wild and cultivated rice

Oryza rufipogon, the wild progenitor of Asian cultivated rice Oryza sativa, is an important resource for rice breeding1. Here we present a wild-cultivated rice pangenome based on 145 chromosome-level assemblies, comprising 129 genetically diverse O. rufipogon accessions and 16 diverse varieties of O. sativa. This pangenome contains 3.87 Gb of sequences that are absent from the O. sativa ssp. japonica cv. Nipponbare reference genome. We captured alternate assemblies that include heterozygous information missing in the primary assemblies, and identified a total of 69,531 pan-genes, with 28,907 core genes and 13,728 wild-rice-specific genes. We observed a higher abundance and a significantly greater diversity of resistance-gene analogues in wild rice than in cultivars. Our analysis indicates that two cultivated subpopulations, intro-indica and basmati, were generated through gene flows among cultivars in South Asia. We also provide strong evidence to support the theory that the initial domestication of all Asian cultivated rice occurred only once. Furthermore, we captured 855,122 differentiated single-nucleotide polymorphisms and 13,853 differentiated presence-absence variations between indica and japonica, which could be traced to the divergence of their respective ancestors and the existence of a larger genetic bottleneck in japonica. This study provides reference resources for enhancing rice breeding, and enriches our understanding of the origins and domestication process of rice.

Identification and characterization of Spätzle in Myzus persicae and its role during microbial infection

As a Toll receptor ligand, Spätzle (Spz) plays a crucial role in activating the Toll pathway and participating in the innate immune response of insects. However, the immune function of Spz in Myzus persicae remains poorly understood. In this study, we identified and cloned 7 Spz genes from M. persicae, all containing a Spz domain (cystine-knot domain). Phylogenetic analysis revealed that the 7 different MpSpzs were divided into 6 groups within a single cluster with each Spz of Drosophila melanogaster and Acyrthosiphon pisum. These genes were mainly expressed in 1st-instar nymphs, hemolymph, and embryos and showed varying levels of positive response to infection with Escherichia coli, Staphylococcus aureus, and Beauveria bassiana. After gene-silencing of MpSpzs by RNA interference with injection of target gene-specific double-stranded RNA, microbial infection significantly increased the mortality of M. persicae compared to control groups. Further studies revealed that the suppression of MpSpz resulted in a significant reduction in lysozyme expression. The present study offers novel insights into the role of Spätzle in the innate immune response against microbial infection in M. persicae.

Genome-Wide Identification and Expression Analysis of m6A Methyltransferase Family in Przewalskia tangutica Maxim

N6-methyladenosine (m6A) RNA modification plays important regulatory roles in plant development and adaptation to the environment. However, there has been no research regarding m6A RNA methyltransferases (MT-A70) in Przewalskia tangutica Maxim. Here, we performed a comprehensive analysis of the MT-A70 family in Przewalskia tangutica (PtMTs), including gene structures, phylogenetic relationships, conserved motifs, gene location, promoter analysis, GO enrichment analysis, and expression profiles. We identified seven PtMT genes. Phylogeny analysis indicated that the seven PtMT genes could be divided into three groups; two MTA genes, three MTB genes, and two MTC genes, and domains and motifs exhibited similar patterns within the same group. These PtMT genes were found to contain a large number of cis-acting elements associated with plant hormones, light response, and stress response, suggesting their widespread regulatory function. Furthermore, the expression profiling of different tissues was investigated using RNA-seq data, and the expression of seven genes was further validated by qPCR analysis. These results provided valuable information to further elucidate the function of m6A regulatory genes and their epigenetic regulatory mechanisms in Przewalskia tangutica.

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

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

Identification and characterization of Eco-miR 169-EcNF-YA13 gene regulatory network reveal their role in conferring tolerance to dehydration and salinity stress in finger millet

The finger millet (Eleusine coracana (L.) Gaertn) genome, comprised 166 conserved microRNAs (miRNAs) belonging to 39 families and three novel miRNAs. The miR169 is one of the most conserved miRNA families, while Eco_N1 is a species-specific miRNA prevalent in finger millet. Its members regulate the expression of genes encoding the Nuclear Factor-Y subunit A (NF-YA) via transcript cleavage. However, the role of miRNA genes in regulating the expression of NF-YA transcription factors in finger millet needs to be deciphered. The present study characterized 166 conserved and novel miRNAs (Eco_N1, Eco_N2 and Eco_N3). Further, secondary structures were predicted, and the potential miR genes targeting the NF-YA transcription factors regulating abiotic stress tolerance were analysed. Twenty-three Eco-miR169 members and one Eco_N1 miRNA targeting EcNF-YA13 were identified in the finger millet genome. The presence of relevant cis-elements such as ABRE (abscisic acid-responsive elements), DRE (dehydration-responsive element), and MYB (myeloblastosis) indicates that the target of Eco-miR169 might be involved in abiotic stress responses. The tissue-specific RNA-seq transcriptomic expression pattern of Eco-miR169 showed variable fold of expression in seedlings compared to the control. At the same time, the expression of EcNF-YA13 (target genes of Eco-miR169 members and Eco_N1) presented a downregulated trend under salinity and dehydration conditions compared to the control. Tissue-specific RNA-seq followed by expression analysis confirmed the antagonistic effect of Eco-miR genes on EcNF-YA13. In a nutshell, the results of this study could be utilized as a platform for further exploration and characterization of finger millet Eco-miR169-EcNF-YA13gene regulatory network.

Cathepsin X is a conserved cell death protein involved in algal response to environmental stress

Phytoplankton are responsible for half of the global photosynthesis and form vast blooms in aquatic ecosystems. Bloom demise fuels marine microbial life and is suggested to be mediated by programmed cell death (PCD) induced by diverse environmental stressors. Despite its importance, the molecular basis for algal PCD remains elusive. Here, we reveal novel PCD genes conserved across distant algal lineages using cell-to-cell heterogeneity in the response of the diatom Phaeodactylum tricornutum to oxidative stress. Comparative transcriptomics of sorted sensitive and resilient subpopulations following oxidative stress revealed genes directly linked to their contrasting fates of cell death and survival. Comparing these genes with those found in a large-scale mutant screen in the green alga Chlamydomonas reinhardtii identified functionally relevant conserved PCD gene candidates, including the cysteine protease cathepsin X/Z (CPX). CPX mutants in P. tricornutum CPX1 and C. reinhardtii CYSTEINE ENDOPEPTIDASE 12 (CEP12) exhibited resilience to oxidative stress and infochemicals that induce PCD, supporting a conserved function of these genes in algal PCD. Phylogenetic and predictive structural analyses show that CPX is highly conserved in eukaryotes, and algae exhibit strong structural similarity to human Cathepsin X/Z (CTSZ), a protein linked to various diseases. CPX is expressed by diverse algae across the oceans and correlates with upcoming demise events during toxic Pseudo-nitzschia blooms, providing support for its ecological significance. Elucidating PCD components in algae sheds light on the evolutionary origin of PCD in unicellular organisms and on the cellular strategies employed by the population to cope with stressful conditions.

Protein-RNA Docking Benchmark v3.0 Integrated With Binding Affinity

We introduce an updated non-redundant protein-RNA docking benchmark version 3.0 (PRDBv3.0) containing 197 test cases curated from 288 unique protein-RNA complexes available in the Protein Data Bank until July 2024. Among these, 27 are unbound-unbound (UU) type where both the binding partners are available in their unbound states, 160 are unbound-bound (UB) type where only the protein is available in unbound state and remaining 10 are bound-unbound (BU) type where only the RNA is available in unbound state. The benchmark is categorized into three classes based on the conformational flexibility of the protein interface: 117 rigid-body (R) complexes with minimal structural changes, 41 semi-flexible (S) complexes showing moderate conformational changes and 29 full-flexible (F) complexes with significant conformational changes. The current benchmark represents a 62% increase in the number of test cases compared to its previous version. Binding affinity (Kd) values for a subset of 105 protein-RNA complexes from PRDBv3.0 are catalogued along with additional experimental details to develop a comprehensive protein-RNA affinity benchmark. Moreover, a total of 255 unique RNA-binding domains, present in RNA-binding proteins, are also catalogued in this updated benchmark. PRDBv3.0 will facilitate the evaluation of both rigid-body and flexible docking methods as well as the methods that aim to predict binding affinity. The updated benchmark is freely available at http://www.csb.iitkgp.ac.in/applications/PRDBv3/PRDBv3.php.

Sedimentitalea sediminis sp. nov., a novel bacterium isolated from marine sediment

Strain HM32M-2 T, an aerobic, catalase-positive, oxidase-positive, and Gram-stain-negative bacterium, was isolated from a sandy sediment sample collected from Qinzhou Gulf in Guangxi Zhuang Autonomous Region, China. Strain HM32M-2 T grew at 15-37 °C (optimum, 30 °C), at pH 5.5-9.5 (optimum, pH 8.5), and with 1.0-12.0% (w/v) NaCl (optimum, 3.0%). Strain HM32M-2 T exhibited the highest 16S rRNA gene sequence similarity with Sedimentitalea nanhaiensis NH52FT (98.4%). Phylogenetic analyses based on 16S rRNA gene sequences and whole-genome sequences showed that strain HM32M-2 T formed a distinct lineage with Sedimentitalea nanhaiensis NH52FT. The draft genome of strain HM32M-2 T was 3.40 Mbp in size and its DNA G + C content was 63.6%. Comparative genome analysis revealed that average nucleotide identity and digital DNA-DNA hybridization among strain HM32M-2 T and other Sedimentitalea species were below cut-off levels of 95-96% and 70%, respectively. Chemotaxonomic analyses indicated that strain HM32M-2 T contained Q-10 as the respiratory quinone, C18:1ω7c as the major cellular fatty acid, and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified aminolipid, and one unidentified lipid as the major polar lipids. Strain HM32M-2 T had a typical chemical composition of fatty acids, polar lipids, and quinones for Sedimentitalea species, but could be distinguished from known species of the genus Sedimentitalea. On the basis of the polyphasic evidence, strain HM32M-2 T should be classified as a novel species of the genus Sedimentitalea, for which the name Sedimentitalea sediminis sp. nov. is proposed. The type strain is HM32M-2 T (= MCCC 1K08873T = KCTC 8272 T).

ConSeqUMI, an error-free nanopore sequencing pipeline to identify and extract individual nucleic acid molecules from heterogeneous samples

Nanopore sequencing has revolutionized genetic analysis by offering linkage information across megabase-scale genomes. However, the high intrinsic error rate of nanopore sequencing impedes the analysis of complex heterogeneous samples, such as viruses, bacteria, complex libraries, and edited cell lines. Achieving high accuracy in single-molecule sequence identification would significantly advance the study of diverse genomic populations, where clonal isolation is traditionally employed for complete genomic frequency analysis. Here, we introduce ConSeqUMI, an innovative experimental and analytical pipeline designed to address long-read sequencing error rates using unique molecular indices for precise consensus sequence determination. ConSeqUMI processes nanopore sequencing data without the need for reference sequences, enabling accurate assembly of individual molecular sequences from complex mixtures. We establish robust benchmarking criteria for this platform's performance and demonstrate its utility across diverse experimental contexts, including mixed plasmid pools, recombinant adeno-associated virus genome integrity, and CRISPR/Cas9-induced genomic alterations. Furthermore, ConSeqUMI enables detailed profiling of human pathogenic infections, as shown by our analysis of SARS-CoV-2 spike protein variants, revealing substantial intra-patient genetic heterogeneity. Lastly, we demonstrate how individual clonal isolates can be extracted directly from sequencing libraries at low cost, allowing for post-sequencing identification and validation of observed variants. Our findings highlight the robustness of ConSeqUMI in processing sequencing data from UMI-labeled molecules, offering a critical tool for advancing genomic research.

GRAPHICAL ABSTRACT

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

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

Reconstructing the phylogeny and evolutionary history of freshwater fishes (Nemacheilidae) across Eurasia since early Eocene

Eurasia has undergone substantial tectonic, geological, and climatic changes throughout the Cenozoic, primarily associated with tectonic plate collisions and a global cooling trend. The evolution of present-day biodiversity unfolded in this dynamic environment, characterised by intricate interactions of abiotic factors. However, comprehensive, large-scale reconstructions illustrating the extent of these influences are lacking. We reconstructed the evolutionary history of the freshwater fish family Nemacheilidae across Eurasia and spanning most of the Cenozoic on the base of 471 specimens representing 279 species and 37 genera plus outgroup samples. Molecular phylogeny using six genes uncovered six major clades within the family, along with numerous unresolved taxonomic issues. Dating of cladogenetic events and ancestral range estimation traced the origin of Nemacheilidae to Indochina around 48 mya. Subsequently, one branch of Nemacheilidae colonised eastern, central, and northern Asia, as well as Europe, while another branch expanded into the Burmese region, the Indian subcontinent, the Near East, and northeast Africa. These expansions were facilitated by tectonic connections, favourable climatic conditions, and orogenic processes. Conversely, aridification emerged as the primary cause of extinction events. Our study marks the first comprehensive reconstruction of the evolution of Eurasian freshwater biodiversity on a continental scale and across deep geological time.

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.

Somnuekiaflaviflora (Malvaceae, Brownlowioideae), a new genus and species from Thailand

Somnuekia is described as a new genus of Malvaceae, currently known only from a few locations in the upper part of Tenasserim in northern and peninsular Thailand. Morphological and molecular phylogenetic analyses, based on plastid DNA sequence regions, support the recognition of this new genus within the Brownlowioideae (Malvaceae). Its distinct phylogenetic position, along with a distinct set of morphological and palynological characteristics, strongly support the recognition of Somnuekia as a new genus. A formal description of Somnuekiaflaviflora is provided along with illustrations, photographs, a distribution map and conservation notes. Furthermore, this new genus is compared to other Asian genera within the subfamily.

Morphology and phylogeny of Prorocentrum venetum Tolomio & Cavolo (Dinophyceae)

Prorocentrum venetum was one of the first species of the genus Prorocentrum described by scanning electron microscopy by Tolomio and Cavolo in 1985. Since the first observation of the species in the Venice Lagoon (Italy) in summer 1981, it has not been reported again in published phytoplankton records of Mediterranean waters or elsewhere. Two strains were isolated from a French Mediterranean lagoon, which were morphologically identified as P. venetum by microscopy. Based on rDNA sequences (spanning the 18S to the D3 region of 28S rDNA), the phylogenetic analysis demonstrated that P. venetum belongs to the same clade as Prorocentrum triestinum and Prorocentrum redfieldii. The analysis of scanning electron micrographs provided an in-depth morphological description of the theca, particularly on the pore pattern of thecal plates and new structural details of the platelets in the periflagellar area. These morphological characteristics were compared with the closely related species within the P. triestinum clade, which showed synapomorphic characters in the periflagellar area (small accessory pore, platelet pattern, shape of the apical wing). Further comparison of characteristics varying between species in this clade and in the sister clade encompassing species related to Prorocentrum micans suggests some features of morphological evolution within this part of the genus.

ZNHIT3 Regulates Translation to Ensure Cell Lineage Differentiation in Mouse Preimplantation Development

Upon fertilization, the mouse zygotic genome is activated and maternal RNAs as well as proteins are degraded. Early developmental programs are built on proteins encoded by zygotic mouse genes that are needed to guide early cell fate commitment. The box C/D snoRNA ribonucleoprotein (snoRNP) complex is required for rRNA biogenesis, ribosome assembly and pre-mRNA splicing essential for protein translation. Zinc finger, HIT type 3 (encoded by Znhit3) is previously identified as a component in the assembly of the box C/D snoRNP complex. Using gene-edited mice, it identifies Znhit3 as an early embryonic gene whose ablation reduces protein translation and prevents mouse embryos development beyond the morula stage. The absence of ZNHIT3 leads to decreased snoRNA and rRNA abundance which causes defects of ribosomes and mRNA splicing. Microinjection of Znhit3 cRNA partially rescues the phenotype and confirms that ZNHIT3 is required for mRNA translation during preimplantation development.

Streptomyces citrinus sp. nov., with yellow diffusible pigment

An actinomycete, designated strain Q6T, was isolated from tea plant rhizosphere soil sample in Hefei, China. Strain Q6T produced straight chains of smooth-surfaced spores and grew well on International Streptomyces Project 1-7 media. Phenotypic and genotypic analyses indicated that strain Q6T represented a member of the genus Streptomyces. The 16S rRNA gene sequence data of strain Q6T indicated that strain Q6T had the highest sequence similarity to Streptomyces xanthii CRXT-Y-14T (98.9%), Streptomyces davaonensis JCM 4913T (98.9%) and Streptomyces atriruber NRRL B-24165T (98.9%), followed by Streptomyces adustus WH-9T (98.8%), Streptomyces avermitilis MA-4680T (98.6%) and Streptomyces kunmingensis NBRC 14463T (98.6%). The phylogenomic tree, using the genome blast distance phylogeny method, showed that strain Q6T represents a new branch among the Streptomyces and has the closest genetic relationship with S. kunmingensis 80-3024T. The diagnostic diamino acid was ll-diaminopimelic acid. The major menaquinones were MK-9 (H6), MK-9 (H8) and MK-8 (H6). The dominant fatty acids were C16 : 0 (18.6%), iso-C16 : 0 (18.3%), anteiso-C15 : 0 (15.4%) and summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c; 13.8%). The main polar lipids were diphosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine (PE) and phosphatidylinositol mannoside. The DNA G+C content of strain Q6T was 71.3 mol%. Average nucleotide identity and digital DNA-DNA hybridization values between the genome sequence of strain Q6T and its closely related type strains were 77.0-87.5% and 22.4-29.7%, respectively. On the basis of these data, strain Q6T represents a novel species within the genus Streptomyces, for which the name Streptomyces citrinus sp. nov. is proposed. The type strain is strain Q6T (=CGMCC 4.7886T=NBRC 116061T).

Genome-Wide Identification and Characterization of the Growth-Regulating Factor Gene Family Responsive to Abiotic Stresses and Phytohormone Treatments in Populus ussuriensis

As a unique class of plant-specific transcription factors, the GROWTH-REGULATING FACTORs (GRFs) play pivotal roles in regulating plant growth, development, and stress responses. In this study, the woody plant Populus ussuriensis was taken as the research object. Nineteen PuGRFs were identified and classified into six clades, and their potential evolutionary relationships were analyzed. The possible biological functions of PuGRFs were speculated through bioinformatics analysis. Combining real-time fluorescence quantitative PCR, PuGRFs were determined to be actively expressed in young tissues, and there are distinct tissue-specific expressions in the mature tissues of woody plants. We also conducted RT-qPCR of PuGRFs under different abiotic stresses and phytohormone treatments, most of the family members were induced under the treatments of methyl jasmonate (MEJA) and salicylic acid (SA), and we also found that 4 of 19 PuGRFs might participate in abscisic acid (ABA)-mediated osmotic stress in roots. Protein-protein interaction prediction analysis showed that six PuGRFs can interact with two types of growth-regulating interaction factors (GIFs). Further prediction and verification revealed that PuGRF1/2c and PuGRF1/2d, which belong to the same clade and have highly similar sequences, exhibited divergent interaction capabilities with GIFs, indicating evolutionary fine-tuning and functional redundancy within the GRF family. These findings lay a foundation for studying the molecular mechanisms of PuGRFs in P. ussuriensis, suggest that PuGRFs play important roles in responding to hormones and environmental changes, and the potential interaction relationships are worthy of exploration.

PhyloForge: Unifying Micro- and Macroevolution With Comprehensive Genomic Signals

The dimensions of phylogenetic research have expanded to encompass the study of large-scale populations at the microevolutionary level and comparisons between different species or taxonomic units at the macroevolutionary level. Traditional phylogenetic tools often struggle to handle the diverse and complex data required for these different evolutionary scales. In response to this challenge, we introduce PhyloForge, a robust tool designed to seamlessly integrate the demands of both micro- and macroevolution, comprehensively utilising diverse phylogenomic signals, such as genes, SNPs, and structural variations, as well as mitochondrial and chloroplast genomes. PhyloForge's innovation lies in its capability to seamlessly integrate multiple phylogenomic signals, enabling the unified analysis of multidimensional genomic data. This unique feature empowers researchers to gain a more comprehensive understanding of diverse aspects of biological evolution. PhyloForge not only provides highly customisable analysis tools for experienced researchers but also features an intuitively designed interface, facilitating effortless phylogenetic analysis for beginners. Extensive testing across various domains, including animals, plants and fungi, attests to its broad applicability in the field of phylogenetics. In summary, PhyloForge has significant potential in the era of large-scale genomics, offering a new perspective and toolset for a deeper understanding of the evolution of life. PhyloForge codes could be found in GitHub (https://github.com/wangyayaya/PhyloForge/), and the program could be installed in Conda (https://anaconda.org/wangxiaobei/phyloforge).

First Report of 'Soft Flesh' Induced by the Parasite Kudoa thyrsites (Myxosporea) in Commercial Codfish From Norway

Kudoa thyrsites is a myxosporean parasite that infects the skeletal muscle of various teleost fish species globally. Severe infections lead to 'soft flesh' in fish fillets, resulting in food spoilage and subsequent discard. While K. thyrsites has previously been identified in migratory Atlantic mackerel in the northern Northeast Atlantic Ocean, it has not been observed in resident or farmed fish species in Norwegian waters until now. This study presents the first evidence of K. thyrsites infection and the associated 'soft flesh' condition in resident commercially important gadoid species from Norwegian waters, including Norwegian coastal cod (NCC), Northeast Arctic cod (NEA) and tusk. Molecular analyses confirmed the parasitic infection in 'soft flesh'-affected fish sampled from multiple coastal locations in Norway. The life cycle of Kudoa remains unknown but likely involves an alternating annelid host as in other myxosporeans. These findings in resident hosts suggest that the parasite completes its life cycle also at higher latitudes, in northern Norway. Consequently, there is a risk for the Norwegian fishing industry, as the effect of the parasite on fish fillet texture can occasionally occur and impact both consumer acceptance and industry revenues.

Complete Mitochondrial Genome Analysis Reveals Genetic Diversity in the Narrow-Ridged Finless Porpoise (Neophocaena asiaeorientalis) Across East Asian Waters

The narrow-ridged finless porpoise (Neophocaena asiaeorientalis Pilleri & Gihr 1972) is one of the most endangered cetacean species inhabiting East Asian waters. Complete mitogenome analysis offers accurate phylogenetic insights; however, complete mitogenome sequences for the narrow-ridged finless porpoise have so far been restricted to specific regions, mainly in China, and no sequences are available from Korean or Japanese populations. To address this gap, in this study, we developed a multiplex PCR primer panel to sequence the complete mitochondrial genome of the porpoise and sequenced 23 individuals of N. a. sunameri, a subspecies of N. asiaeorientalis, from Korean waters using next-generation sequencing. Phylogenetic analyses based on maximum likelihood and Bayesian inference revealed three major, well-supported monophyletic clades within the species. Two sequences of the Yangtze finless porpoise (N. a. asiaeorientalis), another subspecies, displayed significantly higher genetic divergence compared to N. a. sunameri sequences. The 23 mitochondrial genome sequences exhibited a nucleotide diversity of 0.142% and a haplotype diversity of 99.6%, with 22 unique haplotypes identified. These findings contribute to our understanding of the evolutionary history and genetic diversity of the species, providing valuable insights for future conservation efforts and further genetic research.

Complete genome sequences of two different broad bean stain virus isolates

Here, the complete genome sequences of two broad bean stain virus (BBSV; genus Comovirus) strains - Tunisia (RNA1, 5,965 nt; RNA2, 3,467 nt) and Syria (RNA1, 5,976 nt; RNA2, 3,449 nt) - were determined using next-generation sequencing (NGS) and rapid amplification of cDNA ends (RACE). These strains showed 79.2% and 71.6% nucleotide sequence identity to each other in RNA1 and RNA2, respectively. The predicted amino acid sequence identity was 95.2% in the proteinase-polymerase and 93.9% in the coat protein, indicating that these strains belong to the same species in the genus Comovirus. Phylogenetic analysis showed that both strains are closely related to red clover mottle virus (genus Comovirus). This is the first report of the complete genome sequences of two BBSV strains.

Otodectes cynotis (Acari: Psoroptidae) infestations in Southern pudus (Pudu puda): In situ and ex situ data of an unexpected host-parasite record

Otodectes cynotis (Acari: Psoroptidae) constitutes an obligate, non-burrowing ectoparasite and causes otodectic mange primarily in domestic and wild carnivores. Only few studies have described this parasite in herbivore hosts so far. In the current study, we report O. cynotis infestations in Southern pudus (Pudu puda), categorized in the IUCN red list as near threatened. Otodectes cynotis was detected in free-ranging animals in Chile (in situ), as well as in zoo-housed pudus at the Zoo Wuppertal, Germany (ex situ). During clinical work, two free-ranging pudus temporarily rehabilitated at the Centro de Rehabilitación de Fauna Silvestre (CEREFAS), Valdivia, Chile, were observed with low to moderate yellowish-brown secretions and encrustations inside the pinna and external auditory canal accompanied by an inflammatory Otitis externa. Analysis via light microscopy exhibited the presence of mange mites, which were identified as O. cynotis via morphological characteristics and molecular analysis. At the Zoo Wuppertal, ear mites were detected in 15 pudus between 2015 and 2024, however, a definite species identification (O. cynotis) was carried out in 4 animals within the current study between 2023 and 2024. Some affected pudus showed bald spots around the ears and the head and exhibited headshaking behavior, whilst others were asymptomatic. In some cases, mites were found as a secondary finding when clinical examination under general anesthesia was performed for other reasons. To the best of our knowledge, this signifies the first report of O. cynotis infestations in pudus by combining morphological and molecular identification. We here present clinical in situ and ex situ data and show that zoological gardens and widlife rehabilitation centers play an important role in research and monitoring of neglected wildlife diseases.

A portable, nanopore-based genotyping platform for near real-time detection of Puccinia graminis f. sp. tritici lineages and fungicide sensitivity

BACKGROUND

Fungal plant disease outbreaks are increasing in both scale and frequency, posing severe threats to agroecosystem stability, native biodiversity and food security. Among these, the notorious wheat stem rust fungus, Puccinia graminis f.sp. tritici (Pgt), has threatened wheat production since the earliest days of agriculture. New Pgt strains continue to emerge and quickly spread over vast distances through the airborne dispersal of asexual urediniospores, triggering extensive disease outbreaks as these exotic Pgt strains often overcome resistance in dominant crop varieties of newly affected regions. This highlights the urgent need for a point-of-care, real-time Pgt genotyping platform to facilitate early detection of emerging Pgt strains.

RESULTS

In this study, we developed a simple amplicon-based re-sequencing platform for rapid genotyping of Pgt isolates. This system is built around a core set of 276 Pgt genes that we found are highly polymorphic between Pgt isolates and showed that the sequence of these genes alone could be used to accurately type Pgt strains to particular lineages. We also developed a simplistic DNA preparation method and an automated bioinformatic pipeline, to enable these Pgt gene markers to be sequenced and analysed rapidly using the MinION nanopore sequencing device. This approach successfully enabled the typing of Pgt strains within approximately 48 h of collecting Pgt-infected wheat samples, even in resource-limited locations in Kenya and Ethiopia. In addition, we incorporated monitoring capabilities for sequence variations in Pgt genes that encode targets of the azole and succinate dehydrogenase inhibitor fungicides, enabling real-time tracking of potential shifts in fungicide sensitivity.

CONCLUSION

The newly developed Pgt Mobile And Real-time, PLant disEase (MARPLE) diagnostics platform we established, now allows precise typing of individual Pgt strains while simultaneously tracking changes in fungicide sensitivity, providing an early warning system for potential indicators of changes in the Pgt population and emerging fungicide resistance. Further integration of this Pgt MARPLE diagnostics platform into national surveillance programmes will support more informed management decisions and timely responses to Pgt disease outbreaks, helping reduce the devastating crop losses currently caused by this 'cereal killer'.

The genomic landscape of gene-level structural variations in Japanese and global soybean Glycine max cultivars

Japanese soybeans are traditionally bred to produce soy foods such as tofu, miso and boiled soybeans. Here, to investigate their distinctive genomic features, including genomic structural variations (SVs), we constructed 11 nanopore-based genome references for Japanese and other soybean lines. Our assembly-based comparative method, designated 'Asm2sv', identified gene-level SVs comprehensively, enabling pangenome analysis of 462 worldwide cultivars and varieties. Based on these, we identified selective sweeps between Japanese and US soybeans, one of which was the pod-shattering resistance gene PDH1. Genome-wide association studies further identified several quantitative trait loci that accounted for large-seed phenotypes of Japanese soybean lines, some of which were also close to regions of the selective sweeps, including PDH1. Notably, specific combinations of alleles, including SVs, were found to increase the seed size of some Japanese landraces. In addition to the differences in cultivation environments, distinct food processing usages might result in changes in Japanese soybean genomes.

Efficacy of different disinfecting methods for contact lenses against Acanthamoeba castellanii

PURPOSE

To analyze the efficacy of different disinfecting methods for contact lenses (CL) against Acanthamoeba castellanii (AC) using quantitative PCR (qPCR) based on RNA detection.

METHODS

Three CL materials: rigid gas permeable (RGP), hydrogel (Hy), and silicone hydrogel (SiHy), were contaminated with 1x105 amoebae/ml and incubated for 24 h at 30 °C. After contamination, pre-cleaning steps were performed before using four maintenance solutions based on hydrogen peroxide (HP), sodium hypochlorite (SH), povidone-iodine (PI), and a multipurpose solution (MS). The pre-cleaning steps involved using a cleaner (20 % isopropyl alcohol) and rinsing the CL. Disinfection systems 1 and 2 involved no cleaner and rinsed the CL with tap water or saline solution, respectively. Systems 3 and 4 included a cleaner and rinsed with tap water or saline, respectively. After cleaning, A. castellanii was extracted and stored for qPCR analysis, using Hsp70 and TPBF genes to detect RNA A. castellanii. Results were presented as the percentage of positives or negatives (presence or absence of amoebae), with a p-value < 0.05 considered statistically significant.

RESULTS

Disinfection system 1 with MS resulted in 56 % positives for RGP lenses and 100 % positives for both hydrogel materials. When MS was combined with a cleaner, 12.5 % positives were found for SiHy and 100 % negatives for Hy and RGP lenses (p < 0.05). PI solution alone yielded 38 % and 12 % positives for hydrogel and silicone hydrogel lenses, respectively, but was 100 % effective when combined with a cleaner. HP and SH, whether combined with a cleaner or not, were effective against AC for all CL materials, except HP without a cleaner for Hy lenses.

CONCLUSION

All disinfection methods showed some efficacy against Acanthamoeba on any CL material. The most effective solutions were those based on hydrogen peroxide and sodium hypochlorite. Using a cleaner enhanced the final disinfecting efficacy, especially with the multipurpose solution.

A venom serpin from the assassin bug Sycanus croceovittatus exhibiting inhibitory effects on melanization, development, and insecticidal activity towards its prey

Serine protease inhibitors (SPIs) have been identified as main common components in the venom of the predatory bugs, while their functional roles remain unexplored. In this study, we identified 35 SPI genes belonging to three subfamilies of serpin, canonical SPI, and A2M in genome of the assassin bug, Sycanus croceovittatus. The amino acid sequences of these SPI genes reveal conserved functional regions, albeit with mutations or deletions at certain active site residues. Transcriptomic and qPCR analyses of gene expression patterns in various tissues across developmental stages indicate that most SPI genes exhibit high expression levels in venom apparatus, suggesting their role as venom proteins. Notably, the ScSPI5 gene from the serpin class was found to be most abundantly expressed in all three distinct venom glands, indicating its significant role as a venomous protein. Functional characterization demonstrated that this venom serpin effectively inhibits trypsin activity in vitro and suppresses phenoloxidase activity, thereby blocking hemolymph melanization in preys, including Spodoptera frugiperda, Achelura yunnanensis, and Tenebrio molitor. When ingested, it reduces the larval and pupal weight of the fall armyworm by impeding trypsin activity in the midgut. Upon injection, ScSPI5 exhibits a dose-dependent insecticidal effect against T. molitor, with an LD50 of 5.6 ± 1.1 μg/g. These findings elucidate the specific functions of SPIs in the venom of predatory bugs, enhancing our understanding of their predation efficiency, and highlighting the potential application of venomous SPIs as protease inhibitors in pest management strategies.

Characterization, whole-genome sequence analysis, and protease production of a new thermophilic Bacillus licheniformis strain isolated from Debagh hot spring, Algeria

A new thermophilic strain, designated as Bacillus sp. LMB3902, was isolated from Hammam Debagh, the hottest spring in Algeria (up to 98 °C). This isolate showed high protease production in skim milk media at 55 °C and exhibited significant specific protease activity by using azocasein as a substrate (157.50 U/mg). Through conventional methods, chemotaxonomic characteristics, 16S rRNA gene sequencing, and comparative genomic analysis with the closely related strain Bacillus licheniformis DSM 13 (ATCC 14580 T), the isolate Bacillus sp. LMB3902 was identified as a potentially new strain of Bacillus licheniformis. In addition, the gene functions of Bacillus sp. LMB3902 strain were predicted using the Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Clusters of Orthologous Groups, Non-Redundant Protein Sequence Database, Swiss-Prot, and Pfam databases. The results showed that the genome size of Bacillus sp. LMB3902 was 4.279.557 bp, with an average GC content of 46%. The genome contained 4.760 predicted genes, including 8 rRNAs, 78 tRNAs, and 24 sRNAs. A total of 235 protease genes were annotated including 50 proteases with transmembrane helix structures and eight secreted proteases with signal peptides. Additionally, the majority of secondary metabolites found by antiSMASH platform showed low similarity to identified natural products, such as fengicin (53%), lichenysin (57%), and surfactin (34%), suggesting that this strain may encode for novel uncharacterized natural products which can be useful for biotechnological applications. This study is the first report that describes the complete genome sequence, taxono-genomics, and gene annotation as well as protease production of the Bacillus genus in this hydrothermal vent.

Pink-Pigmented Variant of Clavibacter michiganensis Expands Phenotypic Range of Tomato Bacterial Canker Pathogen

Bacterial canker of tomato caused by the gram-positive corynebacterial species Clavibacter michiganensis is one of the most destructive seedborne diseases in both open-air and greenhouse tomatoes. The pathogen is a regulated agent in all tomato-producing countries, as translocation of infected tomato materials transports the bacterium into new areas. C. michiganensis is generally known to have yellow-pigmented colonies on culture media, which is a key differentiative phenotypic feature in standard diagnostic guidelines. During 2020 and 2021, pink-pigmented corynebacterial strains were isolated from tomato seeds (cultivar Sun 6189F1) and plants showing severe canker symptoms in Southern Iran. The six pink-pigmented strains were pathogenic on tomato and pepper seedlings under greenhouse conditions and yielded positive results with C. michiganensis-specific primers pairs described in the literature. Phylogenomics and DNA similarity calculations showed that the pink-pigmented strains were highly similar to the authentic yellow-pigmented members of the pathogen. Thus, they were identified as a new phenotypic variant of tomato bacterial canker pathogen. Whole-genome screenings accomplished with PCR-based assays showed that the pink strains contain all pathogenicity-determinant genes described in C. michiganensis. Further, orthologous gene clusters in the pink-pigmented strains were more similar to the pathogenic members of C. michiganensis than to those of nonpathogenic tomato-associated Clavibacter species. The results obtained in this study demonstrate the emergence of a new pink-pigmented variant of C. michiganensis and highlight the importance of colony pigmentation/morphology in culture-based detection of the bacterium. The need for updating diagnostic guidelines on the colony variants of the pathogen is further discussed.

Deleted in malignant brain tumors 1 (DMBT1) gene relate to immune priming and phagocytosis modulation in the small abalone Haliotis diversicolor

The small abalone (Haliotis diversicolor) is an economic shellfish cultured in the south coast of China. In recent years, the frequent occurrence of the disease has led to significant mortality in abalone farms. Deleted in malignant brain tumors 1 (DMBT1), a member of the scavenger receptor cysteine-rich (SRCR) protein family, plays an important role in host defense. However, its function in H. diversicolor remains unknown. In order to evaluate the immune priming effect after secondary infection and elucidate possible regulatory mechanism, a novel DMBT1 from the small abalone H. diversicolor (designated as HdDMBT1) was cloned and characterized in this study. The open reading frame of HdDMBT1 was 2331 bp encoding 776 amino acids with a molecular weight of 84.73 kDa. HdDMBT1 contained conserved active sites with DMBT1 from other species, detected in all tested tissues and had higher expression levels in hepatopancreas. The temporal expression profiles of HdDMBT1 after two challenges of Vibrio harveyi were examined to evaluate priming response in the small abalone. The expression level of HdDMBT1 mRNA in hepatopancreas increased significantly after V. harveyi challenge. Meanwhile, the expression level of HdDMBT1 after the second challenge was significantly higher than that after the first challenge (4.23-fold). RNA interference (RNAi) experiments were conducted to examine the role of HdDMBT1 in response to V. harveyi infection. Knocking down HdDMBT1 decreased the hemocytes phagocytosis (0.48-fold). In addition, the bacterial density in hemolymph and the mortality of abalone raised, when infected with V. harveyi after dsHdDMBT1 injection. These results indicated that HdDMBT1 might play an important role in tolerance to bacterial infection.