Clustal W and Clustal X version 2.0

Insights into the Role of GhTAT2 Genes in Tyrosine Metabolism and Drought Stress Tolerance in Cotton

Gossypium hirsutum is a key fiber crop that is sensitive to environmental factors, particularly drought stress, which can reduce boll size, increase flower shedding, and impair photosynthesis. The aminotransferase (AT) gene is essential for abiotic stress tolerance. A total of 3 Gossypium species were analyzed via genome-wide analysis, and the results unveiled 103 genes in G. hirsutum, 47 in G. arboreum, and 53 in G. raimondii. Phylogenetic analysis, gene structure examination, motif analysis, subcellular localization prediction, and promoter analysis revealed that the GhAT genes can be classified into five main categories and play key roles in abiotic stress tolerance. Using RNA-seq expression and KEGG enrichment analysis of GhTAT2, a coexpression network was established, followed by RT-qPCR analysis to identify hub genes. The RT-qPCR results revealed that the genes Gh_A13G1261, Gh_D13G1562, Gh_D10G1155, Gh_A10G1320, and Gh_D06G1003 were significantly upregulated in the leaf and root samples following drought stress treatment, with Gh_A13G1261 identified as the hub gene. The GhTAT2 genes were considerably enriched for tyrosine, cysteine, methionine, and phenylalanine metabolism and isoquinoline alkaloid, tyrosine, tryptophan, tropane, piperidine, and pyridine alkaloid biosynthesis. Under drought stress, KEGG enrichment analysis manifested significant upregulation of amino acids such as L-DOPA, L-alanine, L-serine, L-homoserine, L-methionine, and L-cysteine, whereas metabolites such as maleic acid, p-coumaric acid, quinic acid, vanillin, and hyoscyamine were significantly downregulated. Silencing the GhTAT2 gene significantly affected the shoot and root fresh weights of the plants compared with those of the wild-type plants under drought conditions. RT-qPCR analysis revealed that GhTAT2 expression in VIGS-treated seedlings was lower than that in both wild-type and positive control plants, indicating that silencing GhTAT2 increases sensitivity to drought stress. In summary, this thorough analysis of the gene family lays the groundwork for a detailed study of the GhTAT2 gene members, with a specific focus on their roles and contributions to drought stress tolerance.

Identification and Expression Analysis of Acid Phosphatase Gene (PAP) in Brassica napus: Effects of cis-Acting Elements on Two BnaPAP10 Genes in Response to Phosphorus Stress

Purple acid phosphatases (PAPs) play a key role in phosphorus (P) assimilation and redistribution in plants, catalyzing the hydrolysis of phosphate esters to produce inorganic phosphate (Pi). In this study, a total of 77 PAP genes were identified in B. napus. The candidate genes were divided into three groups and ten subgroups based on the phylogenetic analyses and exon-intron organization. Among these 77 BnaPAP proteins, 35 exhibit typical metal-ligating residues characteristic of known PAPs, whereas certain unaltered amino acid residues were absent or displaced in other BnaPAPs. A computational prediction was conducted, revealing that the majority of PAPs contain signal peptide motifs and display a range of N-glycosylation levels, as well as transmembrane helix motifs. An analysis of previously obtained RNA-seq data revealed that 55.84% (43 of 77) of the BnaPAPs responded to Pi deficiency. Moreover, we conducted a preliminary examination of the expression profiles of BnaPAP genes in response to salt stress, and discovered that 42.86% (33 of 77) of these genes were induced under salt stress, either in the shoots or in the roots. Further qRT-PCR and GUS analyses revealed that BnaC9.PAP10 and BnaA7.PAP10, two paralogs of BnaPAP10s, were induced by Pi deficiency. Notably, BnaC9.PAP10 exhibits robust induction, compared to the relatively mild induction observed in BnaA7.PAP10. Our research shows that BnaA7.PAP10 uniquely responds to Pi stress via the W-box, while BnaA7.PAP10 predominantly responds via the P1BS element, and the differences in cis-regulatory elements (CREs) within their promoter regions specifically contribute to their distinct expression levels under Pi stress. Our findings provide valuable insights and establish a foundation for future functional studies of BnaPAPs.

Multiple combinatorial interactions among natural structural variants of Brassica SOC1 promoters and SVP: conservation of binding affinity despite diversity in bimolecular interactions

BACKGROUND

Analysis of binding patterns of biomolecules underpin new paradigms for trait engineering. One way of designing early flowering crops is to manipulate genes controlling flowering time. SOC1, a central integrator of flowering, is downregulated by SVP. In amphidiploid Brassica juncea, flowering is plausibly mediated by combinatorial interactions involving natural variants of SOC1 promoter and SVP protein homologs. Although fluctuating temperatures influence energetics of molecular interactions and phenotypes, mechanistic insights on these remain unknown. Herein, we report diversity in 50 homologs of SVP proteins from 25 Brassicaceae species.

MATERIALS AND METHODS AND RESULTS

Sequence and phylogenetic analysis of 9 natural variants of B. juncea SVP revealed differences in MIKC domains and sub-genome of origin. Generation and refinement of 15 SVP protein models (natural and hypothetical) using I-TASSER and ALPHAFOLD, and 3 SOC1 promoter fragments using 3D-DART, revealed structural diversity. Notwithstanding, binding affinity of 48 docked complexes analysed using HADDOCK and PreDBA were similar. Analysis of 27 docked complexes for distribution of shared or unique binding patterns and type of molecular contacts (π-π stacking, hydrophobic interactions, Van-der-Waals forces, H-bonds) using PyMOL, CCP4i, DNAproDB, PremPDI and DIMPLOT revealed extensive variation implicating compensatory mutations in preserving binding affinity. Yeast one-hybrid assays validated binding potential predicted in docked complexes. Conserved amino-acid and nucleotide residues involved in non-covalent interactions were identified. Computational alanine substitution established cruciality of amino-acid hotspots conferring stability to docked complexes.

CONCLUSIONS

Our study is important as identification of crucial amino-acid hotspots is essential for rational protein design. Targeted mutagenesis resulting in modified binding spectrum of regulatory proteins suggests a way forward for trait engineering.

Carnitine O-Acetyltransferase as a Central Player in Lipid and Branched-Chain Amino Acid Metabolism, Epigenetics, Cell Plasticity, and Organelle Function

Carnitine O-acetyltransferase (CRAT) is a key mitochondrial enzyme involved in maintaining metabolic homeostasis by mediating the reversible transfer of acetyl groups between acetyl-CoA and carnitine. This enzymatic activity ensures the optimal functioning of mitochondrial carbon flux by preventing acetyl-CoA accumulation, buffering metabolic flexibility, and regulating the balance between fatty acid and glucose oxidation. CRAT's interplay with the mitochondrial carnitine shuttle, involving carnitine palmitoyltransferases (CPT1 and CPT2) and the carnitine carrier (SLC25A20), underscores its critical role in energy metabolism. Emerging evidence highlights the structural and functional diversity of CRAT and structurally related acetyltransferases across cellular compartments, illustrating their coordinated role in lipid metabolism, amino acid catabolism, and mitochondrial bioenergetics. Moreover, the structural insights into CRAT have paved the way for understanding its regulation and identifying potential modulators with therapeutic applications for diseases such as diabetes, mitochondrial disorders, and cancer. This review examines CRAT's structural and functional aspects, its relationships with carnitine shuttle members and other carnitine acyltransferases, and its broader role in metabolic health and disease. The potential for targeting CRAT and its associated pathways offers promising avenues for therapeutic interventions aimed at restoring metabolic equilibrium and addressing metabolic dysfunction in disease states.

Infection status of Baylisascaris transfuga in captive Asiatic black bears (Ursus thibetanus) from three bile farms in South Korea, with molecular analyses

Bears harbor various endoparasites that pose risks to humans and other animals. However, information on parasitic infections in Asiatic black bears in South Korea (Korea) is limited, and potential hazards still exist because of the close contact between bears and humans on bile farms. The present study was conducted to assess the gastrointestinal parasite infection status in captive Asiatic black bears (Ursus thibetanus) at bile farms in Korea. Additionally, we aimed to characterize the molecular aspects of Baylisascaris transfuga (Nematoda: Ascarididae), the sole species investigated throughout the study. Fecal examinations were performed on a total of 84 fecal samples collected from three bear farms in Hwacheon-gun (gun = County) and Donghae-si (si = City), Gangwon-do (do = Province), and Dangjin-si, Chungcheongnam-do. Eggs were identified morphologically, and an adult worm expelled in the feces was analyzed molecularly using the partial cytochrome c oxidase subunit 1 and 2 (cox1 and cox2) gene markers. The prevalence of helminthic eggs was 10.7 %, identified as B. transfuga based on morphological characteristics. The eggs, which were oval and brown with thick shells, had a mean length of 87.3 ± 8.9 μm on the long axis and 70.7 ± 6.1 μm on the short axis (n = 30). An adult female roundworm found in the feces of one individual, measuring 27 cm in length and 0.4 cm in width, was also identified as same species through genetic methods. Herein, we described the prevalence of B. transfuga in captive bears in Korea and its molecular characteristics for the first time. Additionally, we reviewed the sequences of the genus Baylisascaris available in the International Nucleotide Sequence Database Collection, noting that many of these sequences often have ambiguous or potentially incorrect identifications, complicating the understanding of their phylogenetic status. This investigation is part of disease screening efforts aimed at enhancing the welfare of captive bears prior to their imminent relocation to sanctuaries. Health monitoring and endoparasite control in farmed bears should be carried out in both veterinary and public health contexts.

Characterization of pecan PEBP family genes and the potential regulation role of CiPEBP-like1 in fatty acid synthesis

Phosphatidyl ethanolamine-binding protein (PEBP) plays important roles in plant growth and development. However, few studies have investigated the PEBP gene family in pecan (Carya illinoinensis), particularly the function of the PEBP-like subfamily. In this study, we identified 12 PEBP genes from the pecan genome and classified them into four subfamilies: MFT-like, FT-like, TFL1-like and PEBP-like. Multiple sequence alignment, gene structure, and conserved motif analyses indicated that pecan PEBP subfamily genes were highly conserved. Cis-element analysis revealed that many light responsive elements and plant hormone-responsive elements are found in CiPEBPs promoters. Additionally, RNA-seq and RT-qPCR showed that CiPEBP-like1 was highly expressed during kernel filling stage. GO and KEGG enrichment analysis further indicated that CiPEBP-like1 was involved in fatty acid biosynthesis and metabolism progress. Overexpression of CiPEBP-like1 led to earlier flowering and altered fatty acid composition in Arabidopsis seeds. RT-qPCR confirmed that CiPEBP-like1 promoted fatty acid synthesis by regulating the expression of key genes. Overall, this study contributes to a comprehensive understanding of the potential functions of the PEBP family genes and lay a foundation to modifying fatty acid composition in pecan kernel.

Integrative morphological, cytogenetic and molecular characterization of the Andean climbing catfish Astroblepus mindoensis (Regan, 1916) (Siluriformes:Astroblepidae)

Astroblepus species, commonly known as Andean climbing catfish, exhibit a unique challenge in species delimitation, leading to ongoing taxonomic debates. Here we report data on Astroblepus mindoensis, a vulnerable species endemic to Ecuador, obtained by an integrative approach that includes cytogenetic analysis, molecular identification of the specimens, and recording of morphological and morphometric characters useful for species diagnosis. Thus, this study aimed to associate the karyotype data of the specimens analyzed with morphological and molecular characters, improving and expanding the existing taxonomic information, thus contributing to the systematics of the species. Our morphology results, unlike Regan's original description, which is brief and ambiguous, provide a more detailed morphometric and meristic description. Molecular phylogenetic reconstruction and genetic distance based on a fragment of the cytochrome c oxidase subunit I (COI) showed that our samples constitute a well-supported and monophyletic clade within the A. grixalvii species complex. The cytogenetic analysis identified distinct chromosomal markers, including a single cluster of major ribosomal genes (on chromosome pair 3) and of minor ribosomal genes (on chromosome pair 12) with their localization differing from those reported in other Astroblepus species analyzed. Additionally, the presence of a heteromorphic chromosome pair in males suggests the presence of an XX/XY sex-determination system that has not been identified in other congeneric species. Further investigation is necessary to determine if these chromosomes are associated with the accumulation of repeated sequences, as typically occurs with sex chromosomes, and to assess their presence in other species of the genus.

The replication efficacy of NADC34-like porcine reproductive and respiratory syndrome virus 2 is not directly associated with the pathogenicity

NADC34-like porcine reproductive and respiratory syndrome virus 2 (NADC34-like PRRSV-2) is currently a major prevalent strain in Chinese swine industry. Within which, recombination events are frequently detected. Previous studies have shown that the pathogenicity of NADC34-like PRRSV-2 isolates is highly variable. However, the characteristics between NADC34-like PRRSV-2 recombinant and non-recombinant isolates are rarely compared. In this study, two PRRSV-2 strains (BJ1805-2 and SDLY23-1742) were isolated from samples collected at 2018 and 2023 in China. ORF5-based phylogenetic analysis supported that both isolates are clustered with ORF5 RFLP 1-7-4 (NADC34-like) strains. However, genome-based phylogenetic tree showed that BJ1805-2 is still grouped with NADC34-like isolates but SDLY23-1742 is clustered with NADC30-like viruses. Furthermore, fragment comparisons and recombination detections also supported that SDLY23-1742 was recombined from NADC30-like, NADC34-like, and JXA1-like isolates while no recombination event was detected in BJ1805-2. Noticeably, BJ1805-2 had higher replication efficacy than SDLY23-1742 both in PAMs and in piglets. However, SDLY23-1742 caused longer high fever period and more severe histopathological lung lesions than BJ1805-2, indicating that SDLY23-1742 has higher pathogenicity than BJ1805-2. Overall, this study provides the first evidence that the pathogenicity of NADC34-like PRRSV-2 is not directly correlated with viral replication efficacy.

Degradation of anthracene and phenanthrene by strain Streptomyces sp. M-1 and its application in the treatment of PAHs-contaminated water

Polycyclic aromatic hydrocarbons (PAHs) are persistent organic pollutants with mutagenicity, carcinogenicity and teratogenicity, widely distributed in the environment. Effective biodegradation of PAHs is highly required, especially in wastewater. An efficient PAHs degrading strain Streptomyces sp. M-1 was isolated from polluted kerosene. The degradation capacity of anthracene and phenanthrene was evaluated under various PAHs concentrations, pH, and temperatures by M-1. To find the degradation pathways, the key intermediates were detected by mass spectrometry and the enzyme-encoding genes were analyzed by many bioinformatics tools. Furthermore, the potential of the strain for bioremediation in PAH-contaminated water was evaluated. The results showed that the maximal degradation rate of anthracene and phenanthrene reached 93.14% (100 mg L-1, 7 days) and 49.25% (50 mg L-1, 7 days), respectively. Their average degradation rate increased within the concentration of 50-800 mg L-1 and reached 2.72 mg d-1 for anthracene and 1.28 mg d-1 for phenanthrene at 800 mg L-1. M-1 exhibited high and stable anthracene degradation rate under tested pH and temperatures, and high phenanthrene degradation under tested pH and higher temperatures. Based on the analysis of both intermediates and enzyme-encoding genes, it is proposed that anthracene undergoes degradation via the phthalic acid pathway, while phenanthrene follows the salicylic acid pathway. Finally, 98.98% degradation of anthracene and 72.77% degradation of phenanthrene in water was realized over 14 days. We thus propose that Streptomyces sp. M-1 is an effective degrader for bioremediation of PAHs pollution.

Monoclonal antibodies against jellyfish collagen

Collagens are abundant structural proteins found in both mammalian and marine species, and attractive biomaterials used in various fields. Jellyfish collagen-based products have become increasingly popular because of their clinically proven health benefits such as the effects of skin wound healing and immune stimulation. To develop detection tools for jellyfish collagen, we generated four monoclonal antibodies, MCOL1, 2, 3, and 4, by immunizing mice with moon jellyfish collagen. The nucleotide and amino acid sequences of the variable regions of the monoclonal antibodies were determined. The antibody-binding kinetics toward collagens from moon jellyfish were evaluated using a surface plasmon resonance (SPR) biosensor, and the binding specificity was evaluated in comparison with binding to collagens from edible jellyfish, fish scales, and pig and cow skins. MCOL1, 3, and 4 specifically bound to moon jellyfish collagen, whereas MCOL2 bound to both moon and edible jellyfish collagens. Considering the results showing that the SPR responses of MCOL2 binding were greater than those seen with the other antibodies, MCOL2 could recognize the common and repetitive sequences of the two jellyfish collagens. Therefore, this monoclonal antibody will be most applicable for detecting jellyfish collagen.

Antrihabitans spumae sp. nov., a novel bacterium isolated from stable foams formed in wastewater treatment plants and emended description of the genus Antrihabitans

Three strains, designated as J27, J71T and J72, belonging to the genus Antrihabitans, were isolated from stable foams formed in activated sludge wastewater treatment plants (WWTPs) in New South Wales, Australia. Phenotypic and genomic analyses revealed that these strains belong to the Nocardiaceae family and are closely related to Antrihabitans stalagmiti. However, distinct genomic and physiological characteristics, including overall genomic relatedness indices, phylogenomic analysis, genomic metabolic profiles and MALDI-TOF MS (Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry), confirmed their status as a new species.Ecologically, these strains showed a wide metabolic versatility, like enhanced membrane transport systems for amino acids, metals and phosphate, as well as the ability to synthesize mycolic acids, contributing to their hydrophobic nature and involvement in foam stabilization. Their adaptations likely provide a competitive advantage in WWTPs, where they persist in nutrient-rich, metal-laden and foam-stabilizing environments. The species did not present the typical rod-coccus cycle, described previously as a defining characteristic of the Antrihabitans genus. Based on their unique genomic, phenotypic and ecological features, we propose the name Antrihabitans spumae sp. nov., with strain J71T (JCM 34493T, NCIMB 15450T) designated as the type strain. Additional strains include J27 (JCM 33914, NCIMB 15449) and J72 (NCIMB 15448).

The Incidence and Genetic Analysis of Two Betaflexiviruses Capillovirus alphavii and Tepovirus tafpruni in Iran

Viral diseases have emerged as a serious threat to cherry trees production in Iran. To determine which virus(es) are present, three leaves from a sweet cherry tree (Qz5) with diffuse white blotch spots and deformation were subjected to high-throughput sequencing. After de novo assembly, blast analysis revealed that 12 contigs ranging from 360 to 7,433 nucleotides (nts) shared 78-96% nt identities with Capillovirus alphavii (cherry virus A, CVA) and seven contigs, ranging from 350 to 6,844 nts, shared 79-88% nt identities with Tepovirus tafpruni (prunus virus T, PrVT). During a survey, CVA, PrVT, and CVA + PrVT infections were detected in 12.6%, 5.1%, and 7.9% of 724 sour and sweet cherry samples. Phylogenetic analysis revealed that Iranian CVA was grouped into GIIIB, whereas PrVT fell into a distinct branch, which was confirmed by diversity plots. The within-population diversity was lower than the between-population diversity suggesting the contribution of a founder effect on diversification of CVA isolates. Host-specific codon adaptation analysis revealed the highest adaptation of CVA to sour cherry. This could suggest that sour cherry may be one of the closest Prunus species to wild progenitors. It raises the possibility that viruses such as CVA may have exerted evolutionary pressures influencing domestication processes. Additionally, the similarity index indicated that the common plum (Prunus domestica) may have exerted significant evolutionary pressure on CVA and PrVT. The association of CVA and PrVT was reported for the first time in the mid-Eurasian region, specifically in Iran, which represents an issue in phytosanitary certification of cherry plants.

Response of ZmPHO1 family members to low phosphorus stress and association of natural variation in ZmPHO1;2a reveal the role of low phosphorus tolerance

Phosphorus (Pi) is an essential nutrient for plants to sustain normal life processes. In this study, we found that the ZmPHO1 proteins had similar molecular weights and the same conserved domain. Phylogenetic and cis-acting element analysis showed that ZmPHO1s were divided into 4 subgroups, in which ZmPHO1;2a and ZmPHO1;2b were closely phylogenetic with OsPHO1;2b, and the promoter region of ZmPHO1s contained abundant abiotic stress-related elements. Quantitative real-time PCR (RT-qPCR) analyses showed that the expression of ZmPHO1s were induced under low-Pi stress, among ZmPHO1;2a and ZmPHO1;2b were up-regulated in 178 (low-Pi tolerance) roots. Further, pho1;2a mutant exhibited a reduction in Pi uptake, leading to decreased shoot biomass. Additionally, 196 single nucleotide polymorphism (SNPs) and 127 insertion-deletions (InDels) were detected in ZmPHO1;2a DNA region among the 278 inbred lines, and 14 natural variants were identified that were significantly associated with 14 phenotypic traits by using mixed linear model (MLM). Notably, we defined five haplotypes according to the variants that were significantly associated with low-Pi tolerance index and haplotype 2 can enhance biomass by promoting root diameter and volume. Similarly, 7 natural variants were detected in the promoter region of ZmPHO1;2a that were significantly associated with 18 phenotypic traits and included a pleiotropy variant (SNP-1302) whose allele G/G exhibited positive genetic effects on biomass. This study will provide a theoretical reference for further dissecting the molecular mechanism of ZmPHO1s regulating of the low-Pi stress response and contribute to the development of genetic markers.

Unraveling the Bryocladia scopulorum complex from the Southwestern Atlantic Ocean with the description of three new species of Bryocladia (Rhodomelaceae, Rhodophyta)

The filamentous red algal genus Bryocladia was recently deeply revised based on molecular and morphological data. However, data from the Southwestern Atlantic Ocean are scarce. Here, we provide a phylogenetic study of Bryocladia representatives from the Brazilian coast with new additions to the genus. Our samples were collected from the north to southeastern Brazilian coast in marine and estuarine areas. We carried out a morphological and molecular study based on COI-5P and rbcL gene sequences. Our phylogenetic analyses confirmed the presence of seven species on the Brazilian coast, four of which were previously known: B. cuspidata, B. subtilissima, B. thyrsigera, and B. villum. Three new species are described here, B. itaipensis sp. nov., B. oceanica sp. nov., and B. mucuripensis sp. nov., all morphologically included in the B. scopulorum complex. Bryocladia subtilissima was observed only in Brazilian estuarine areas. However, it was split into two subclades, which require further investigation. The three new species expand the known diversity of the B. scopulorum complex from 12 to 15 species. Bryocladia itaipensis is closely related to B. canariensis and B. caespitosa, whereas B. oceanica and B. mucuripensis formed distinct lineages with unsolved relationships. All new species are restricted to their type localities in Brazilian waters, reinforcing the need for further study of tiny species, especially from the tribes Polysiphonieae and Streblocladieae.

First description of the fish-killing raphidophyceae Chattonella marina complex in Argentina: From genetics to ichthyotoxicity unveiled

Species of the harmful algal bloom (HAB)-forming genus Chattonella (Raphidophyceae) are responsible for massive fish kills worldwide. Despite this, the genus remains still unexplored in Argentinean waters in the Southwestern Atlantic. Three Chattonella strains (LPCc045, LPCc046, and LPCc047) were isolated and cultured as part of a harmful phytoplankton monitoring program in the marine coastal waters of Buenos Aires Province to determine: 1) taxonomic and genetic identification, 2) pigment compositions, and 3) ichthyotoxic potency and ROS production. Morphological observations (light and transmission electron microscopy) matched classical descriptions of C. marina. Phylogenetic reconstruction using a partial sequence of the ribosomal gene (LSU D1-D2) confirmed the cluster of the three strains within the C. marina complex clade (99 % bootstrap support). Pigment analyses by HPLC showed that the most abundant was chlorophyll-a, followed by fucoxanthin and other carotenoids. Gill cell damage, used as a proxy of cytotoxicity, was assessed using the rainbow trout RTgill-W1 cell-based assay against cell supernatant and intracellular treatments. Cytotoxic potency was positively correlated with cell abundance, with supernatant treatment causing more gill cell damage than intracellular content, reducing gill cell viability down to 60 % of control at 1.9 × 103 cells mL-1. Superoxide production was comparable with other globally distributed strains (supernatant 7.63 ± 0.67 pmol O2- cell-1 h-1; intracellular 8.1 ± 0.56 pmol O2- cell-1 h-1). This study provides the first morphological, phylogenetic, physiological and toxicological characterization of the fish-killing algae C. marina complex in Argentinean waters.

NbNAC1 enhances plant immunity against TMV by regulating isochorismate synthase 1 expression and the SA pathway

Salicylic acid (SA) plays important roles in plant local and systemic resistance. Isochorismate synthase 1 (ICS1) is a key enzyme in SA synthesis. Pathogens infection triggered the ICS1 expression and induced SA production. However, the molecular regulation mechanism of ICS1 against virus infection remains unclear. Here, we employed molecular genetics and physiobiochemical approaches to confirm a transcription factor NbNAC1 from Nicotiana benthamiana is a positive regulator of resistance against tobacco mosaic virus (TMV). The pathways NbNAC1 and NbICS1 can be triggered by TMV infection. Silencing NbNAC1 accelerated TMV-induced oxidative damage and increased reactive oxygen species (ROS) production. It also weakened both local and systemic resistance against TMV and decreased the expression of NbICS1, SA signaling gene NbNPR1, and SA defense-related genes. The effects of NbNAC1-silencing were restored by overexpression of NbICS1 or foliar SA applications. Overexpressing NbNAC1 prevented oxidative damage and reduced the production of ROS, enhanced plant resistance against viral pathogen, and activated NbICS1 expression, and SA downstream signaling and defense-related genes. NbNAC1 localized in nuclear and emerged the ability of transcriptional regulation. ChIP and EMSA results indicated that NbNAC1 directly binds to a fragment containing GAAATT motif of NbICS1 promoter. Luciferase reporter assays confirmed that NbNAC1 activates NbICS1 expression. Taken together, our results demonstrate that NbNAC1 plays a critical role in plant immunity through activation of SA production.

Benefits of HIV-1 transmission cluster surveillance: a French retrospective observational study of the molecular and epidemiological co-evolution of recent circulating recombinant forms 94 and 132

INTRODUCTION

Molecular surveillance is an important tool for detecting chains of transmission and controlling the HIV epidemic. This can also improve our knowledge of molecular and epidemiological factors for the optimization of prevention. Our objective was to illustrate this by studying the molecular and epidemiological evolution of the cluster including the new circulating recombinant form (CRF) 94_cpx of HIV-1, detected in 2017 and targeted by preventive actions in 2018.

METHODS

In June 2022, 32 HIV-1 sequence databases from French laboratories were screened to identify all individuals who had acquired CRF94_cpx or a similar strain, whatever the date of diagnosis. Phylogenetic analyses were performed with the sequences identified, and biological parameters were collected at the time of diagnosis and after the start of treatment to analyse the evolution of the cluster. Full genomes were sequenced to characterize the new strains.

RESULTS

We analysed 98 HIV-1 isolates: 63 were CRF94, three were unclassifiable, and the other 32 formed a new cluster containing a new recombinant, CRF132_94B, derived from CRF94 and a subtype B strain. At least 95% of the individuals in both the CRF94 and CRF132 clusters were men who have sex with men (MSM), most of whom had acquired HIV less than 12 months before diagnosis. The number of CRF94 diagnoses declined drastically after 2018, but CRF132 strains spread widely between 2020 and 2022, into a different area of Ile-de-France region and within a younger population nevertheless aware of pre-exposure prophylaxis. Higher viraemia, lower CD4 cell counts and delayed treatment efficacy suggested that CRF94 was more virulent than CRF132, possibly due to the F subtype fragment of the vif gene.

CONCLUSIONS

These findings highlight the role of the MSM transmission cluster in spreading HIV and new variants. They show also the benefits of cluster surveillance for improving the targeting of preventive interventions, detecting the emergence of new strains and enriching our knowledge on virulence mechanisms. However, these investigations require support with sufficient resources dedicated to a regional or national programme to be responsive and effective.

The heterogeneous expression, extraction, and purification of recombinant Caldanaerobacter subterraneus subsp. tengcongensis apurine/apyrimidine endonuclease in Escherichia coli

Thermostable apurinic/apyrimidinic (AP) endonuclease (TtAP), cloned from Caldanaerobacter subterraneus subsp. tengcongensis, is an exonuclease III (Exo III) family protein with high-heat resistance, has activities of AP site endonuclease, 3'-5' exonuclease, and 3'-nuclease, and facilitates efficient amplification of lengthy DNA fragments in PCR. However, the research of the combinant TtAP in Escherichia coli with its expression, large-scale extraction and purification of its protein was limited. In this study, we optimized the codons of TtAP gene for expression in E. coli and constructed a fusion gene encoding TtAP with a 6His tag (TtAP-6His). TtAP-6His was put into vector pET-30a(+) to form the expression vector pET-30a(+)-TtAP-6His, and was then introduced into E. coli strain Rosetta (DE3). We established a systematic process for the extraction of TtAP protein using 5 liters of bacterial suspension, including the optimization of IPTG induction time (6 h), followed by protein extraction using enzymolysis buffers, the heat treatment of temperature (70 °C) with 60 min to remove impurity, precipitation with ammonium sulfate (55 %), protein purification with Ni-affinity chromatography, and the enzyme activities finally were determined. The purification yield of TtAP-6His ranged from 73.67 to 115.25 mg/L (47 KU/mg).

Genomic characterization of the NAC transcription factors in carnation and function analysis of DcNAC41 involved in thermotolerance

As pivotal regulators unique to plants, NAC family extensively orchestrate various life processes ranging from seed germination through growth and development to responses to environmental stresses. This study unraveled 71 NAC TFs in the carnation (Dianthus caryophyllus L.) genome, designated as DcNAC1 to DcNAC71, encoding amino acid sequences ranging from 80 to 718 residues. Subcellular localization predictions revealed a predominance of nuclear localization among these DcNACs. Phylogenetic analysis classified DcNACs into 14 distinct subgroups, each exhibiting similar gene structures and motifs. Promoter analysis highlighted the abundance of cis-regulatory elements (CREs) associated with plant growth and development regulation, hormone signaling, light response, and diverse stress responses, with stress-responsive CREs being the most prevalent, with at least one stress-responsive CRE detected in all DcNAC promoters. To assess their functional roles, 12 DcNACs, were randomly selected from different subgroups for expression profiling under heat, ABA, cold, and salt stress conditions, revealing distinct expression patterns for specific stress types. Notably, DcNAC41, which exhibited marked up-regulation under heat stress, was isolated and subsequently transformed into Arabidopsis. In heat-stressed conditions, transgenic Arabidopsis overexpressing DcNAC41 exhibited significant improvements in growth performance, survival rates, enhanced photosynthetic capacity, and strengthened ROS scavenging abilities. This study offers valuable insights into the comprehensive response of carnation DcNACs towards heat stress, particularly underscoring the potential of DcNAC41 as a promising candidate for enhancing thermotolerance in plants.

A pivotal switch in β-domain determines the substrate selectivity of terpene synthases involved in Gardenia jasminoides floral scent synthesis

Plants have evolved a diverse array of secondary metabolites to enhance their adaptability to environmental stresses, with volatile terpenoids being a notable example. Gardenia (Gardenia jasminoides), celebrated for its unique fragrance, is a key natural source of volatile terpenoids. Using our chromosome-level genome and transcriptome data of G. jasminoides, we previously identified six terpene synthases (TPSs) involved in the production of its floral scent. Here, we functionally characterized these six key TPS enzymes, aligning their product profiles with volatile organic compound (VOC) analysis. Notably, we identified two highly similar TPSs, GjTPS1 and GjTPS2, which share high sequence homology but differ in substrate selectivity. Through AI-based predictions and site-directed mutagenesis, we pinpointed a single amino acid in the β-domain that acts as a "switch," modulating substrate selectivity-an unusual finding, as this residue is outside the active site region. Comparative genomic analyses with Coffea canephora and other eudicots revealed that G. jasminoides TPS genes primarily expanded through dispersed duplications (DSD) and tandem duplications (TD). Our study is the first to reveal a "switch" in a previously deemed "non-functional" region, regulating substrate selectivity in TPS proteins. These insights could facilitate breeding elite Gardenia varieties and support the rational engineering of terpene synthases.

Antibacterial and antibiofilm properties of two cyclic dipeptides produced by a new desert Streptomyces sp. HG-17 strain against multidrug-resistant pathogenic bacteria

INTRODUCTION

The emergence of multidrug-resistant bacteria and biofilms requires discovering new antimicrobial agents from unexplored environments.

OBJECTIVES

This study aims to isolate and characterize a new actinobacterial strain from the Hoggar Mountains in southern Algeria and evaluate its ability to produce bioactive molecules with potential antibacterial and antibiofilm activities.

METHODS

A novel halotolerant actinobacterial strain, designated HG-17, was isolated from the Hoggar Mountains, and identified based on phenotypic characterizations, 16S rDNA sequence analysis, and phylogenetic analysis. The antibacterial and antibiofilm activities of the strain were assessed, and the presence of biosynthetic genes (PKS-I and NRPS) was confirmed. Two active compounds, HG-7 and HG-9, were extracted butanol solvent, purified by HPLC, and their chemical structures were elucidated using ESI mass spectrometry and NMR spectroscopy.

RESULTS

The strain HG-17 was identified as Streptomyces purpureus NBRC with 98.8% similarity. It exhibited strong activity against multidrug-resistant and biofilm-forming bacteria. The two purified active compounds, HG-7 and HG-9, were identified as cyclo-(d-cis-hydroxyproline-l-phenylalanine) and cyclo-(l-prolone-l-tyrosine), respectively. The minimum inhibitory concentrations (MICs) of HG-7 and HG-9 ranged from 3 to 15 μg/mL, comparable to the MICs of tetracycline (8 to 15 μg/mL). Their minimum biofilm inhibitory concentration (MBIC 50%) showed good inhibition from 48.0 to 52.0% at concentrations of 1 to 7 μg/mL against the tested bacteria.

CONCLUSION

This is the first report of cyclo-(d-cis-hydroxyproline-l-phenylalanine) and cyclo-(l-prolone-l-tyrosine) antibiotics from S. purpureus and their anti-multi-drug-resistant and biofilm-forming bacteria. These results indicate that both antibiotics could be used as effective therapeutics to control infections associated with multidrug-resistant bacteria.

Identification and expression analysis of three gonadotropin-releasing hormone genes in the lined seahorse (Hippocampus erectus)

Gonadotropin-releasing hormone (GnRH) plays a crucial role in regulating reproductive behavior in vertebrates through the hypothalamus-pituitary-gonad (HPG) axis. Seahorses exhibit unique male pregnancy behavior, making them an interesting subject for investigating the regulatory mechanisms behind this behavior. In this study, we focused on the lined seahorse (Hippocampus erectus) and obtained the full-length cDNA sequences of three GnRH genes: GnRH1, GnRH2, and GnRH3. Notably, we newly identified GnRH1, filling a gap in previous research that had overlooked this subtype. Through a homologous analysis, we found that the core peptide of GnRH1 in lined seahorses is not common in teleosts, while the core peptides of GnRH2 and GnRH3 are conserved. Real-time PCR was performed to determine the tissue expression patterns of these GnRH genes. Our results showed that all three genes were predominantly expressed in the brain, albeit in different regions. Specifically, GnRH1 was mainly expressed in the hypothalamus, GnRH2 in the optic tectum, and GnRH3 in the telencephalon. Expression dynamics indicated a progressive decrease in GnRH2 and a significant surge in GnRH3 during gonadal development, hinting at an alternating regulatory function. Moreover, GnRH1 and GnRH3 expression levels were considerably higher during pregnancy compared to those in pre-pregnancy and post-pregnancy stages, underscoring their critical role in modulating male pregnancy behavior in lined seahorses. Our findings provide insights into the complex interplay of GnRH subtypes in regulating reproductive processes, particularly in the context of male pregnancy behavior in seahorses.

Diversity and Vertical Distribution of Planctomycetota in the Water Column of the Remote North Pacific

The extensive microbial diversity found in the oceans is becoming to be uncovered despite limited knowledge and cultured representatives for many taxonomic groups. This study analysed the distribution and diversity of Planctomycetota at four water column profiles of the Eastern North Pacific subtropical front (ENPSF) using 16S rRNA gene sequencing. A dual approach, utilising PacBio long-reads and Illumina short-reads, was employed to enhance the accuracy of taxonomic assignment and compare sequencing methods. The diversity of Planctomycetota increased below the deep chlorophyll maximum level (175-200 m) and in the mesopelagic layer (500 m), with beta-diversity clustering distinctly separating samples according to different depths, resulting in pronounced vertical stratification. This community structure mirrors nutrient availability, as Planctomycetota favour depths between 175 and 200 m, where high nitrate levels are present. More Planctomycetota amplicon sequence variants (ASVs) were identified with PacBio than with Illumina, improving detection of these bacteria. Phylogenetic analyses performed after manual curation of ASVs led to the discovery of several unknown genera of Planctomycetota, indicating that substantial diversity within this group remains to be discovered and studied in remote oligotrophic oceans.

Phylogenetic and Functional Diversity of Soluble Di-Iron Monooxygenases

Monooxygenase (MO) enzymes are responsible for the oxidation of hydrocarbons and other compounds in the carbon and nitrogen cycles, are important for the biodegradation of pollutants and can act as biocatalysts for chemical manufacture. The soluble di-iron monooxygenases (SDIMOs) are of interest due to their broad substrate range, high enantioselectivity and ability to oxidise inert substrates such as methane. Here, we re-examine the phylogeny and functions of these enzymes, using recent advances in the field and expansions in sequence diversity in databases to highlight relationships between SDIMOs and revisit their classification. We discuss the impact of horizontal gene transfer on SDIMO phylogeny, the potential of SDIMOs for the biodegradation of pollutants and the importance of heterologous expression as a tool for understanding SDIMO functions and enabling their use as biocatalysts. Our analysis highlights current knowledge gaps, most notably, the unknown substrate ranges and physiological roles of enzymes that have so far only been detected via genome or metagenome sequencing. Enhanced understanding of the diversity and functions of the SDIMO enzymes will enable better prediction and management of biogeochemical processes and also enable new applications of these enzymes for biocatalysis and bioremediation.

Increasing thermostability of the key photorespiratory enzyme glycerate 3-kinase by structure-based recombination

As global temperatures rise, improving crop yields will require enhancing the thermotolerance of crops. One approach for improving thermotolerance is using bioengineering to increase the thermostability of enzymes catalysing essential biological processes. Photorespiration is an essential recycling process in plants that is integral to photosynthesis and crop growth. The enzymes of photorespiration are targets for enhancing plant thermotolerance as this pathway limits carbon fixation at elevated temperatures. We explored the effects of temperature on the activity of the photorespiratory enzyme glycerate kinase (GLYK) from various organisms and the homologue from the thermophilic alga Cyanidioschyzon merolae was more thermotolerant than those from mesophilic plants, including Arabidopsis thaliana. To understand enzyme features underlying the thermotolerance of C. merolae GLYK (CmGLYK), we performed molecular dynamics simulations using AlphaFold-predicted structures, which revealed greater movement of loop regions of mesophilic plant GLYKs at higher temperatures compared to CmGLYK. Based on these simulations, hybrid proteins were produced and analysed. These hybrid enzymes contained loop regions from CmGLYK replacing the most mobile corresponding loops of AtGLYK. Two of these hybrid enzymes had enhanced thermostability, with melting temperatures increased by 6 °C. One hybrid with three grafted loops maintained higher activity at elevated temperatures. Whilst this hybrid enzyme exhibited enhanced thermostability and a similar Km for ATP compared to AtGLYK, its Km for glycerate increased threefold. This study demonstrates that molecular dynamics simulation-guided structure-based recombination offers a promising strategy for enhancing the thermostability of other plant enzymes with possible application to increasing the thermotolerance of plants under warming climates.

Wheat E3 ligase TaPRP19 is involved in drought stress tolerance in transgenic Arabidopsis

TaPRP19, a wheat U-box E3 ligase gene, was isolated and characterized for its role in drought stress tolerance. The gene encodes a 531 amino acid protein with a U-box domain at the N-terminal and a WD40 domain at the C-terminal. Subcellular localization studies using TaPRP19-GFP fusion in Nicotiana benthamiana confirmed predominant nucleus localization. In vitro ubiquitination assays demonstrated that TaPRP19 possesses E3 ligase activity. RT-qPCR analysis revealed higher expression of TaPRP19 in wheat leaves, which increased under PEG, mannitol, and ABA treatments. Transgenic Arabidopsis lines overexpressing TaPRP19 exhibited improved seed germination rates and root elongation under mannitol and ABA stress, as well as enhanced survival rates under drought conditions compared to wild-type (WT) plants. Additionally, these transgenic lines showed upregulated expression of antioxidant-related and drought-marker genes, reduced ROS accumulation, and increased activities of antioxidant enzymes, suggesting enhanced oxidative stress mitigation. These findings highlight TaPRP19 as a potential target for developing drought-tolerant crops, providing insights into its functional mechanisms and paving the way for future genetic engineering applications in wheat and other crops.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-025-01557-7.

Disorder within order: Identification of the disordered loop of STAS domain as the inhibitory domain in SLC26A9 chloride channel

The chloride transporter-channel SLC26A9 is mediated by a reciprocal regulatory mechanism through the interaction between its cytoplasmic sulfate transporter and anti-sigma (STAS) domain and the R domain of cystic fibrosis (CF) transmembrane regulator. In vertebrate Slc26a9s, the STAS domain structures are interrupted by a disordered loop which is conserved in mammals but is variable in nonmammals. Despite the numerous studies involving the STAS domains in SLC26 proteins, the role of the disordered loop region has not been identified. Deletion of the entire Slc26a9-STAS domain results in loss of Cl- channel function. Surprisingly, we found that partial or full deletion of the STAS-disordered loop substantially increases the SLC26A9 chloride transport-channel activity. Bioinformatics analysis reveals that the disordered loops there are three subregions: a K/R-rich region, a "middle" region, and an ordered S/T-rich motif. In this study, the role of this STAS-disordered loop is investigated by using serial deletions and the ordered S/T-rich motif is examined by serial alanine substitution. Substitutions of alanine for serine or threonine in the 620 to 628 S/T-rich motif decrease SLC26A9 chloride channel activity. These experiments parse the functional roles of SLC26A9-STAS-disordered loop and its subdivisions modifying overall SLC26A9 activities. Recently, SLC26A9 has emerged as one of the potential substitutes for abnormal CF transmembrane regulator in CF. Our findings suggest that deletion of variable loop of human SLC26A9 may provide a new gene therapy strategy in the treatment of CF disease.

Comparative analyses of odorant binding protein orthologues in three sympatric Tomicus bark beetles provide insights into functional differentiation of OBPs to ecologically relevant odorants and insecticides

Three Tomicus bark beetles (T. yunnanensis, T. brevipilosus and T. minor) coexist in the trunks of Pinus yunnanensis but possess relatively independent spatio-temporal ecological niches. This makes them become a good case for addressing functional differentiation of chemosensory-related proteins among closely related species in odorant recognition and insecticide sequestering. In this study, we used odorant binding protein (OBP) orthologues highly expressed in antennae to illustrate this question. We first identified 33, 35 and 34 OBPs from T. yunnanensis, T. brevipilosus and T. minor, respectively, with 33 groups of OBP orthologues. Sequence and phylogenetic analyses revealed the conservation and differences of OBP orthologues across three Tomicus beetles. Expression profiles revealed that the majority of Tomicus OBPs were abundantly expressed in antennae where 11 groups of OBP orthologues shared a significantly antenna-enriched distribution. Four groups of antennal OBP orthologues (OBP2, OBP9, OBP10 and OBP16 totaling 12 genes) presented diverse ligand-binding properties, responding differently to five classes of ecologically relevant odorants as well as various insecticides. In particular, OBP orthologues were tuned differentially to host and non-host odorants, and chlorpyrifos was identified as the best ligand for 12 Tomicus OBPs. Our study thus sheds light on functional conservation and divergence of OBP orthologues among three sympatric Tomicus bark beetles, possibly as an implication for the early or late of host colonization, ecological niche differences and the strong habitat adaptation.

Genomic insights into fibrinogen-related proteins and expression analysis in the Pacific white shrimp, Litopenaeusvannamei

Fibrinogen-related domain (FReD) containing proteins are an evolutionarily conserved immune gene family characterized by the C-terminal fibrinogen (FBG) and diverse N-terminal domains. To understand the complexity of this family in crustaceans, we performed genome screening and identified 43 full-length FReDs encoding genes in Litopenaeus vannamei. Structural classification analysis revealed these putative FReDs could be divided into six types, including two reported types (LvFReDI and II) and four new types (LvFReDIII-VI). Sequence and phylogenetic analysis showed that FBG domains were highly conserved throughout and phylogeny clusters correlated strongly with gene type. We analyzed the temporal and spatial expression patterns of LvFReD genes based on the transcriptomes of developmental stages, adult tissues or pathogen infected tissues of L. vannamei. Most LvFReDs were expressed from larval in membrane stage, and exhibited tissue-specific expression patterns and immune-responsive transcription after challenge with bacteria or virus. Further time-course expression analysis suggested that LvFReDII genes with additional coiled-coil region were more sensitive to pathogens than LvFReDI genes. Our findings provided comprehensive gene sequence resources and expression profiles of FReD genes in shrimp, which give insights into clarifying the diversity and function of these genes in crustaceans.

Genome-wide identification of yellow gene family in Hermetia illucens and functional analysis of yellow-y by CRISPR/Cas9

The yellow gene family plays a crucial role in insect pigmentation. It has potential for use as a visible marker gene in genetic manipulation and transgenic engineering in several model and non-model insects. Sadly, yellow genes have rarely been identified in Stratiomyidae species and the functions of yellow genes are relatively unknown. In the present study, we first manually annotated and curated 10 yellow genes in the black soldier fly (BSF), Hermetia illucens (Stratiomyidae). Then, the conserved amino acids in the major royal jelly proteins (MRJPs) domain, structural architecture and phylogenetic relationship of yellow genes in BSF were analyzed. We found that the BSF yellow-y, yellow-c and yellow-f genes are expressed at all developmental stages, especially in the prepupal stage. Using the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, we successfully disrupted yellow-y, yellow-c and yellow-f in the BSF. Consequently, the mutation of yellow-y clearly resulted in a pale-yellow body color in prepupae, pupae and adults, instead of the typical black body color of the wild type. However, the mutation of yellow-c or yellow-f genes did not result in any change in color of the insects, when compared with the wild type. Our study indicates that the BSF yellow-y gene plays a role in body pigmentation, providing an optimal marker gene for the genetic manipulation of BSF.

Regulation mechanism of the long-chain n-alkane monooxygenase gene almA in Acinetobacter venetianus RAG-1

As toxic pollutants, n-alkanes are pervasively distributed in most environmental matrices. Although the alkane monooxygenase AlmA plays a critical role in the metabolic pathway of solid long-chain n-alkanes (≥C20) that are extremely difficult to degrade, the mechanism regulating this process remains unclear. Here, we characterized the function of AlmA in Acinetobacter venetianus RAG-1, which was mainly involved in the degradation of long-chain n-alkanes (C26-C38), among which, n-C32 induced the almA promoter activity most. APR1 (AlmA Positive Regulator) that it is an AraC/XylS-type transcription regulator, a potential transcriptional regulator of almA, was screened by DNA-pull down, which was determined by conserved domain analysis. The deletion of apR1 severely reduced the capacity of strain RAG-1 to utilize long-chain n-alkanes (C22-C38), indicating the involvement of APR1 in n-alkanes degradation. The results of the APR1-dependent reporter system, electrophoretic mobility shift assay, and microscale thermophoresis further proved that APR1 was able to directly bind to the almA promoter region, thus activating the almA transcription. Furthermore, APR1 could inhibit self-expression through autoregulation in the absence of long-chain n-alkanes. n-C32 acted as a ligand of APR1, and the amino acid residues Val10, Gln50, Ala99, and Ile106 at the N-terminus of APR1 were necessary for binding n-C32. In addition, the key amino acid residues of APR1 within the C-terminal helix-turn-helix motif that bound to the downstream promoter region were confirmed by multiple sequence alignment and site-directed mutagenesis. The homologs of AlmA and APR1 shared a similar evolutionary course in the Proteobacteria; thus, this mode of regulation might be relatively conserved.

IMPORTANCE

The extreme hydrophobicity of long-chain n-alkanes ({greater than or equal to}C20) presents a significant challenge to their degradation in natural environments. It is, therefore, imperative to elucidate the regulatory mechanisms of the metabolic pathways of long-chain n-alkanes, which will be of great significance for the future application of hydrocarbon-degrading bacteria to treat oil spills. However, the majority of current studies have focused on the regulatory mechanisms of short- and medium-chain n-alkanes, with long-chain n-alkanes receiving comparatively little attention. In this study, we identified APR1, a transcriptional regulator of the alkane monooxygenase AlmA in Acinetobacter venetianus RAG-1, and characterized its function and regulatory mechanism. In the presence of ligand n-C32, APR1 could directly activate the transcription of almA, which was involved in the n-C32 metabolism. The amino acid residue unique to the C-terminal DNA-binding domain of AraC/XylS type n-alkanes transcription regulators was also identified. These findings further improved our understanding of the long-chain n-alkanes degradation mechanism, which is important for the management of petroleum pollution.

The continued evolution of the L2 cephalosporinase in Stenotrophomonas maltophilia: a key driver of beta-lactam resistance

The Stenotrophomonas maltophilia L2 cephalosporinase is one of two beta-lactamases that afford S. maltophilia beta-lactam resistance. With the overuse of beta-lactams, selective pressures have contributed to the evolution of these proteins, generating proteins with an extended spectrum of activity. Variant L2 cephalosporinases have been detected, as has their distribution into two main clades (clades 1 and 2). Comprehensive analysis of six L2 variants, cloned into pET41a(+) and expressed in Escherichia coli BL21(DE3) cells, revealed that clade 1 variants exhibited higher ceftazidime resistance compared to clade 2. Notably, the Sm5341 L2 variant, carrying a Phe72Ile variation, displayed a significantly reduced resistance profile across all substrates tested, suggesting a key role of Phe72 in enzymatic activity. An Ile72Phe substitution in the pET41a(+) based Sm5341_L2 variant resulted in a gain-of-function for this protein, confirming the role of Phe72 in the activity of L2. Furthermore, residue interaction network analysis elucidated a pi-cation interaction between Tyr272 and Arg244, which may potentially be stabilizing the enzyme and its binding site. The presence of Tyr272 in clade 1 variants correlates with higher ceftazidime affinity, contrasting Asp272 in clade 2 variants. Displaying lower Km values and higher kcat/Km ratios, clade 1 L2 enzymes demonstrated a higher binding efficiency and greater catalytic efficiency for most of the substrates assessed. These results indicate that L2 enzymes are continuing to evolve and adapt to a selective environment fuelled by the overuse of beta-lactams. This adaptation may signal the beginning of an evolutionary process yielding variant L2 cephalosporinases with extended substrate profiles.

Genome-wide identification of short-chain dehydrogenases/reductases genes and functional characterization of ApSDR53C2 in melanin biosynthesis in Arthrinium phaeospermum

Introduction

Arthrinium phaeospermum can cause large areas wilted and death of Bambusa pervariabilis × Dendrocalamopsis grandis, resulting in serious ecological and economic losses. Previous studies found that the appressorium of A. phaeospermum must form to invade the host cells and cause disease. A short-chain dehydrogenase/reductase gene has been shown to maintain the osmotic pressure of the appressorium by synthesizing fungal melanin to penetrate the plant epidermis and cause disease. The SDR gene family of A. phaeospermum was found to be highly expressed during the penetration in the transcriptome sequencing results. Still, the relationship with melanin biosynthesis of A. phaeospermum is not clear.

Methods

We aimed to predict the biological function of the SDR gene family in A. phaeospermum, identify key ApSDR genes with pathogenic roles, and explore the pathogenic mechanism. We have characterized the SDR family of A. pheospermum bioinformatically. Candidate ApSDRs screened by transcriptome sequencing were compared by qPCR experiments to obtain key ApSDRs that may play an important role in infestation and adversity resistance. Knockout mutants, the co-knockout mutant, and backfill mutants of key ApSDRs were obtained for phenotypic and stress conditions analysis. We explored and validated the pathogenic mechanisms through cellulose membrane penetration experiments and analysis of melanin-related gene synthesis levels.

Results and discussion

180 ApSDRs were identified bioinformatically. After screening six candidate ApSDRs with noticeably elevated expression using transcriptome sequencing, qPCR experiments revealed that ApSDR53C2 and ApSDR548U2 had the highest expression. The results of phenotypic and stress conditions analysis indicate that ApSDRs are critical for the growth, development, stress response, and fungicide resistance of A. phaeospermum. The pathogenicity analysis revealed that ApSDR53C2 and ApSDR548U2 play important roles in virulence, with ApSDR53C2 having a stronger effect. A comparison of melanin synthesis levels between wild-type and ΔApSDR53C2 strains showed that ApSDR53C2 positively regulates melanin biosynthesis to promote penetration. The findings demonstrate that ApSDRs are essential for A. phaeospermum to withstand stress and facilitate melanin biosynthesis, which in turn contributes to its virulence.

Cloning and functional characterization of sesquiterpene synthase genes from Inonotus obliquus using a Saccharomyces cerevisiae expression system

Inonotus obliquus (Chaga mushroom) is a large medicinal and edible fungus that contains a wealth of bioactive terpenoids. However, the detection of certain low-abundance sesquiterpenoids remains a challenge due to limitations in extraction and analytical techniques. Furthermore, the synthase genes responsible for the biosynthesis of the identified terpenoids have not yet been clearly elucidated. To address this, our study combined transcriptome mining with yeast heterologous expression to investigate the synthase genes involved in sesquiterpenoid production in I. obliquus. We successfully identified eight sesquiterpene synthase genes and one farnesyltransferase. Among these, only cis-β-farnesene, synthesized by IoTPS2, had been previously detected before in the sclerotium of I. obliquus, while the other nine sesquiterpenoids-including neoisolongifolene-8-ol, β-longipinene, vetiselinenol, isolongifolene, 7,8-dehydro-8a-hydroxy-, 4a,8b,10b,11a-tetramethylbicyclo[6.3.0]undec-1-en-5-one, 6,11-oxido-acor-4-ene, β-maaliene, neointermedeol, and longifolenaldehyde-were discovered for the first time. This research provides a critical scientific foundation for expanding the known repertoire of sesquiterpenoids and their corresponding synthase genes in I. obliquus.

Genome-wide analysis of the MADS-box gene family in mango and ectopic expression of MiMADS77 in Arabidopsis results in early flowering

Mango (Mangifera indica L.) is an important tropical fruit, and timely flowering and fruit setting are very important for mango production. The MADS-box gene family is involved in the regulation of flower induction, floral organ specification, and fruit development in plants. The identification and analysis of the MADS-box gene family can lay a foundation for the study of the molecular mechanism of flowering and fruit development in mango. In this study, 119 MiMADS-box genes were identified on the basis of genome and transcriptome data. Phylogenetic analysis revealed that these genes can be divided into two classes. Forty-one type I proteins were further divided into three subfamilies, and seventy-eight type II proteins were further classified into eleven subfamilies. Several pairs of alternative splicing genes were found, especially in the SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) subfamily. The MiMADS-box genes were distributed on 18 out of the 20 mango chromosomes. Cis-element analysis revealed many light-, stress-, and hormone-responsive elements in the promoter regions of the mango MiMADS-box genes. Expression pattern analysis revealed that these genes were differentially expressed in multiple tissues in mango. The highly expressed MiMADS77 was subsequently transformed into Arabidopsis, resulting in significant early flowering and abnormal floral organs. Yeast two-hybrid (Y2H) assays revealed that MiMADS77 interacts with several MiMADS-box proteins. In addition, we constructed a preliminary flowering regulatory network of MADS-box genes in mango on the basis of related studies. These results suggest that MiMADS77 genes may be involved in flowering regulation of mango.

Quinone extraction drives atmospheric carbon monoxide oxidation in bacteria

Diverse bacteria and archaea use atmospheric CO as an energy source for long-term survival. Bacteria use [MoCu]-CO dehydrogenases (Mo-CODH) to convert atmospheric CO to carbon dioxide, transferring the obtained electrons to the aerobic respiratory chain. However, it is unknown how these enzymes oxidize CO at low concentrations and interact with the respiratory chain. Here, we use cryo-electron microscopy and structural modeling to show how Mo-CODHMs (CoxSML) from Mycobacterium smegmatis interacts with its partner, the membrane-bound menaquinone-binding protein CoxG. We provide electrochemical, biochemical and genetic evidence that Mo-CODH transfers CO-derived electrons to the aerobic respiratory chain through CoxG. Lastly, we show that Mo-CODH and CoxG genetically and structurally associate in diverse bacteria and archaea. These findings reveal the basis of the biogeochemically and ecologically important process of atmospheric CO oxidation, while demonstrating that long-range quinone transport is a general mechanism of energy conservation, which convergently evolved on multiple occasions.

Structural basis of Epstein-Barr virus gp350 receptor recognition and neutralization

Epstein-Barr virus (EBV) is an oncogenic virus associated with multiple lymphoid malignancies and autoimmune diseases. During infection in B cells, EBV uses its major glycoprotein gp350 to recognize the host receptor CR2, initiating viral attachment, a process that has lacked direct structural evidence for decades. In this study, we resolved the structure of the gp350-CR2 complex, elucidated their key interactions, and determined the site-specific N-glycosylation map of gp350. Our findings reveal that CR2 primarily binds to gp350 through an electrostatically complementary and glycan-free interface and that the diversity of key residues in CR2 across different species influences EBV host selectivity mediated by gp350. With the confirmed binding, we constructed a CR2-Fc antibody analog that targets the vulnerable site of gp350, demonstrating a potent neutralization effect against EBV infection in B cells. Our work provides essential structural insights into the mechanism of EBV infection and host tropism, suggesting a potential antiviral agent.

Cross-species comparative single-cell transcriptomics highlights the molecular evolution and genetic basis of male infertility

In male animals, spermatogonia in testes differentiate into sperm, one of the most diverse cell types across species. Despite the evolutionary retention of key genes essential for spermatogenesis, the extent of their conservation remains unclear. To explore the genetic basis of spermatogenesis under strong selective pressure, we compare single-cell RNA sequencing (scRNA-seq) datasets from the testes of humans, mice, and fruit flies. Our analysis identifies conserved genes involved in key molecular programs, such as post-transcriptional regulation, meiosis, and energy metabolism. We perform gene knockout experiments of 20 candidate genes, three of which, when mutated in fruit flies, result in reduced male fertility, emphasizing the conservation of sperm centriole and steroid lipid processes across mammals and Drosophila. Additionally, deep-learning analysis uncovers potential transcriptional mechanisms driving gene-expression evolution. These findings establish a core genetic foundation for spermatogenesis, offering insights into sperm-phenotype evolution and the underlying mechanisms of male infertility.

Morphological identification and phylogenetic analysis of Eimeria coypi and Eimeria fluviatilis (Apicomplexa: Eimeriidae) isolated from nutrias (Myocastor coypus [Rodentia]) in Japan

The nutria (Myocastor coypus) is a semiaquatic rodent that originally inhabited South America. However, the animals have spread to different continents as alien species, and their numbers are quickly increasing, especially in North America, Europe, and Eastern Asia including Japan. Although nutrias have been suggested to serve as reservoirs for pathogens, including parasites, there have been few reports on this subject. In the present study, we surveyed the gastrointestinal parasites in nutrias living in Japan to better understand their prevalence in nutrias. We collected 72 samples of intestinal contents or feces from nutrias in Osaka and Okayama Prefectures. We found that 49 (68.1 %) samples were positive for Eimeria parasites, and two types of oocysts were identified: ellipsoidal (Type A) and subspherical (Type B) oocysts. In addition, Strongyloides myopotami was detected in 44 samples, and Capillaria spp. and Fasciola spp. were detected in one and three samples, respectively. Based on the morphologies of the detected Eimeria oocysts, Types A and B were identified to be E. coypi and E. fluviatilis, respectively. Phylogenetic analyses after PCR and sequencing targeting the cytochrome c oxidase subunit I gene placed the sequences of E. fluviatilis (Type B) as a cluster between the sequences of Eimeria derived from rodents. The sequences of the three subgenotypes of E. coypi (Type A) were included in the cluster containing the sequences of Eimeria spp. from rodents of multiple species, which is referred to as the Apionodes supercluster, and is separate from other clades. It has been suggested that Eimeria spp. from rodents in this cluster can quickly adapt to infect different hosts. Although further analyses are needed to construct more detailed phylogenetic trees, our results revealed the genetical positions of Eimeria spp. in nutrias. In addition, our results may be helpful when considering host specificity as well as host switching by the pathogen.

Human adenovirus species B knob proteins as immunogens for inducing cross-neutralizing antibody responses

The re-emerging human adenovirus (HAdV) types 3, 7, 14, and 55 of species B have caused severe or even fatal acute respiratory disease. Therefore, the development of multivalent vaccines against HAdV types 3, 7, 14, and 55 remains an important goal. In our previous study, we identified a cross-neutralizing epitope that induced broadly reactive monoclonal neutralizing antibodies against the knob proteins of HAdV types 7, 11, 14, and 55. To study the immunogenicity of HAdV species B knob proteins, we evaluated humoral immune responses to the knob proteins in vivo and in vitro. We found that the knob proteins elicited robust binding and neutralizing antibody responses after three immunizations of mice. In addition, mouse antisera raised against the knob proteins exhibited cross-neutralizing activity against original species B members. Furthermore, immunization with a mix of HAdV-3, 7, and 55 knob proteins protected Chinese tree shrews against an experimental HAdV challenge. Our results provide insight into the immunogenicity of HAdV species B knob proteins.IMPORTANCEHuman adenovirus (HAdV) species B are common pathogens causing severe pneumonia in children, and there is currently no vaccine available. Because there are many HAdV species B types, developing broad-spectrum vaccines against HAdV species B is an important research goal. Our study revealed that immunization with recombinant HAdV species B knob proteins effectively elicited cross-neutralizing antibody responses against original species B members with protective immunity. This study provides a novel insight into the immunogenicity of HAdV species B knob proteins.

Convergent evolution of oxidized sugar metabolism in commensal and pathogenic microbes in the inflamed gut

Inflammation-associated perturbations of the gut microbiome are well characterized, but poorly understood. Here, we demonstrate that disparate taxa recapitulate the metabolism of the oxidized sugars glucarate and galactarate, utilizing enzymatically divergent, yet functionally equivalent, gud/gar pathways. The divergent pathway in commensals includes a putative 5-KDG aldolase (GudL) and an uncharacterized ABC transporter (GarABC) that recapitulate the function of their non-homologous counterparts in pathogens. A systematic bioinformatic search for the gud/gar pathway in gut microbes identified 887 species putatively capable of metabolizing oxidized sugars. Previous studies showed that inflammation-derived nitrate, formed by nitric oxide reacting with superoxide, promotes pathogen growth. Our findings reveal a parallel phenomenon: oxidized sugars, also produced from reactions with nitric oxide, serve as alternative carbon sources for commensal microbes. Previously considered a pathogen virulence factor, oxidized sugar metabolism is also present in specific commensals and may contribute to their increased relative abundance in gastrointestinal inflammation.

Biochemical evidence for the diversity of LHCI proteins in PSI-LHCI from the red alga Galdieria sulphuraria NIES-3638

Red algae are photosynthetic eukaryotes whose light-harvesting complexes (LHCs) associate with photosystem I (PSI). In this study, we examined characteristics of PSI-LHCI, PSI, and LHCI isolated from the red alga Galdieria sulphuraria NIES-3638. The PSI-LHCI supercomplexes were purified using anion-exchange chromatography followed by hydrophobic-interaction chromatography, and finally by trehalose density gradient centrifugation. PSI and LHCI were similarly prepared following the dissociation of PSI-LHCI with Anzergent 3-16. Polypeptide analysis of PSI-LHCI revealed the presence of PSI and LHC proteins, along with red-lineage chlorophyll a/b-binding-like protein (RedCAP), which is distinct from LHC proteins within the LHC protein superfamily. RedCAP, rather than LHC proteins, exhibited tight binding to PSI. Carotenoid analysis of LHCI identified zeaxanthin, β-cryptoxanthin, and β-carotene, with zeaxanthin particularly enriched, which is consistent with other red algal LHCIs. A Qy peak of chlorophyll a in the LHCI absorption spectrum was blue-shifted compared with those of PSI-LHCI and PSI, and a fluorescence emission peak was similarly shifted to shorter wavelengths. Based on these results, we discuss the diversity of LHC proteins and RedCAP in red algal PSI-LHCI supercomplexes.

Clinical, pathological, and genotypic analysis of infectious bronchitis virus in broiler chickens in the Abu Dhabi Emirate, United Arab Emirates

Background

Infectious Bronchitis (IB), caused by the infectious bronchitis virus (IBV), is a significant contagious respiratory disease in the poultry industry. The emergence of new variants represents a global challenge for the diagnosis and control of the disease. Despite vaccination efforts in poultry farms in the Abu Dhabi Emirate, United Arab Emirates (UAE), outbreaks continue to occur, raising concerns about the efficacy of vaccination protocols and the potential emergence of new viral strains. This study aims to provide information on clinical, pathological, and genotypes of IBV detected within the Abu Dhabi Emirate, during 2022-2023.

Methods

Epidemiological data were collected from twelve suspected IB outbreaks across seven broiler farms located in the Abu Dhabi Emirate. The cases were investigated through clinical and pathological examinations and Forty-six samples, including lung, spleen, kidney tissues, and oro-cloacal swabs, were collected for further analysis. The virus was detected by RT-qPCR assay, genotyping was determined by phylogenetic analysis of the Spike (S)-1 gene, and differentiation between field and vaccine strains was determined by comparing their sequences.

Results

The age of the affected flocks varies from 2 to 5 weeks. The highest morbidity, mortality and case fatality rates were 36, 33, and 95%, respectively. Necropsy examination revealed characteristic respiratory and renal pathological lesions. Phylogenetic analysis revealed a co-circulation of three lineages of IBV genotype GI-13 or 4/91 serotype (81.8%), GI-1 or Massachusetts serotype (9.1%) and GI-23 or Middle East serotype (9.1%). Approximately 90.9% of the strains classified within GI-1 and G1-13 lineages are 99 to 100% identical to 4/91 and Mass serotypes, respectively, and are considered as vaccine strains. Two strains (9.1%) classified within GI-23 lineage have a < 99% identity to the 4/91 and Mass serotypes vaccine strains and are considered as filed strains.

Conclusion

Co-circulation of three IBV lineages (GI-13, GI-1, and GI-23) in the Abu Dhabi broiler flocks showing IB symptoms were detected. This complex scenario of different IBV lineages circulation may account for the persistent outbreaks despite vaccination efforts. The results of the study are crucial for optimum IB vaccination and monitoring strategies or designing new vaccines based on local IBV field strains.

ECE-CYC1 Transcription Factor CmCYC1a May Interact with CmCYC2 in Regulating Flower Symmetry and Stamen Development in Chrysanthemum morifolium

BACKGROUND

The attractive inflorescence of Chrysanthemum morifolium, its capitulum, is always composed of ray (female, zygomorphy) and disc (bisexual, actinomorphy) florets, but the formation mechanism remains elusive. The gene diversification pattern of the ECE (CYC/TB1) clade has been speculated to correlate with the capitulum. Within the three subclades of ECE, the involvement of CYC2 in defining floret identity and regulating flower symmetry has been demonstrated in many species of Asteraceae, including C. morifolium. Differential expression of the other two subclade genes, CYC1 and CYC3, in different florets has been reported in other Asteraceae groups, yet their functions in flower development have not been investigated.

METHODS

Here, a CYC1 gene, CmCYC1a, was isolated and its expression pattern was studied in C. morifolium. The function of CmCYC1a was identified with gene transformation in Arabidopsis thaliana and yeast two-hybrid (Y2H) assays were performed to explore the interaction between CmCYC1 and CmCYC2.

RESULTS

CmCYC1a was expressed at higher levels in disc florets than in ray florets and the expression of CmCYC1a was increased in both florets during the flowering process. Overexpression of CmCYC1a in A. thaliana changed flower symmetry from actinomorphic to zygomorphic, with fewer stamens. Furthermore, CmCYC1a could interact with CmCYC2b, CmCYC2d, and CmCYC2f in Y2H assays.

CONCLUSIONS

The results provide evidence for the involvement of CmCYC1a in regulating flower symmetry and stamen development in C. morifolium and deepen our comprehension of the contributions of ECE genes in capitulum formation.

Unravelling genomic drivers of speciation in Musa through genome assemblies of wild banana ancestors

Hybridization between wild Musa species and subspecies from Southeast Asia is at the origin of cultivated bananas. The genomes of these cultivars are complex mosaics involving nine genetic groups, including two previously unknown contributors. This study provides continuous genome assemblies for six wild genetic groups, one of which represents one of the unknown ancestor, identified as M.acuminata ssp. halabanensis. The second unknown ancestor partially present in a seventh assembly appears related to M. a. ssp. zebrina. These assemblies provide key resources for banana genetics and for improving cultivar assemblies, including that of the emblematic triploid Cavendish. Comparative and phylogenetic analyses reveal an ongoing speciation process within Musa, characterised by large chromosome rearrangements and centromere differentiation through the integration of different types of repeated sequences, including rDNA tandem repeats. This speciation process may have been favoured by reproductive isolation related to the particular context of climate and land connectivity fluctuations in the Southeast Asian region.

Unelongated Stems are an Active Nitrogen-Fixing Site in Rice Stems Supported by Both Sugar and Methane Under Low Nitrogen Conditions

Enhancing nitrogen (N) fixation in rice plants can reduce N fertilizer application and contribute to sustainable rice production, particularly under low-N conditions. However, detailed microbial and metabolic characterization of N fixation in rice stems, unlike in the well-studied roots, has not been investigated. Therefore, the aim of this study was to determine the active N-fixing sites, their diazotroph communities, and the usability of possible carbon sources in stems compared with roots. The N-fixing activity and copy number of the nitrogenase gene in the rice stem were high in the outer part of the unelongated stem (basal node), especially in the epidermis. N fixation, estimated using the acetylene reduction assay, was also higher in the leaf sheath and root than in the inner part of the unelongated stem and culm. Amplicon sequence variants (ASVs) close to sugar-utilizing heterotrophic diazotrophs belonging to Betaproteobacteria and type II methanotrophic diazotrophs belonging to Alphaproteobacteria were abundant in the outer part of the unelongated stems. Media containing crushed unelongated stems exhibited N-fixing activity when sucrose, glucose, and methane were added as the sole carbon sources. This suggested that N fixation in the unelongated stems was at least partly supported by sugars (sucrose and glucose) and methane as carbon sources. ASVs close to sugar-utilizing heterotrophs belonging to Actinobacteria were also highly abundant in the unelongated stem; however, their functions need to be further elucidated. The present finding that diazotrophs in rice stems can use sugars such as sucrose and glucose synthesized by rice plants provides new insights into enhancing N fixation in rice stems.

Genome-Wide Identification and Characterization of Histone Acetyltransferases and Deacetylases in Cucumber, and Their Implication in Developmental Processes

BACKGROUND/OBJECTIVES

Cucumber (Cucumis sativus) provides a model for exploring the molecular basis of sex determination, particularly the regulation of floral organ differentiation through gene expression. This complex process is modulated by epigenetic factors, such as histone acetyltransferases (HATs) and histone deacetylases (HDACs), which respectively activate and repress gene transcription by adding or removing acetyl groups from histone proteins. Despite their known functions, the roles of HATs and HDACs throughout cucumber's floral developmental stages remain unclear.

METHODS

In this study, we conducted a genome-wide analysis of HAT and HDAC gene families in cucumber, examining their phylogenetic relationships, gene structures, protein domains, and expression profiles across various stages of floral development.

RESULTS

We identified 36 CsHAT and 12 CsHDAC genes, grouping them into families with evolutionary counterparts in other plant species. RNA sequencing revealed stage-specific expression patterns, suggesting dynamic roles for these gene families in floral organ development.

CONCLUSIONS

These findings contribute valuable insights into the epigenetic regulation of gene expression in cucumber flower formation, presenting avenues for further research on the genetic control of plant reproductive development.

First record of Morimotobathynella Serban, 2000 (Bathynellacea, Bathynellidae) from subterranean waters of South Korea, with the description of a new species

This study describes Morimotobathynellakoreana sp. nov., the first new species of Bathynellidae family reported in East Asia since 2000, and it presents the first molecular analysis using CO1 and 18S gene sequences. Morphological analysis reveals that the new species and previously known Morimotobathynella species uniquely share key characteristics in the male and female thoracopods VIII. However, the presence or absence of the median seta on the antenna exopod, along with the length differences between the four spines in the furca, distinguish the new species from M.miurai, 2000. A molecular phylogenetic analysis indicates that the new species has a relatively close relationship to species from the genus Altainella in Mongolia and Russia.

Whole-genome sequencing reveals transmission pattern and drug resistance of Mycobacterium tuberculosis intra- or inter-hosts

Background

Tuberculosis (TB) remains a serious global public health problem. The Mycobacterium tuberculosis (MTB) is responsible for approximately 10 million new TB cases globally each year. This study aimed to investigate transmission pattern and drug resistance of MTB in Shenzhen, China.

Methods

A retrospective study on 286 samples from 184 TB patients collected between 2015 and 2018 in Shenzhen Third People's Hospital was conducted using whole-genome sequencing. Drug susceptibility testing (DST) was performed using both phenotypic DST (pDST) and molecular DST (mDST). Sample diversity was evaluated by SNPs and transmission clusters were identified based on SNP differences of 12 or fewer in genetic clusters.

Results

Except four samples identified as non-tuberculous mycobacteria, 282 MTB samples (181 patients) underwent mDST, with 244 samples (162 patients) undergoing pDST. The overall multidrug-resistant rate in patients was 22.31% in pDST (12.00% for new patients and 40.82% for retreatment patients) and 34.48% in mDST (20.41% for new patients and 58.21% for retreatment patients). Totally 92 transmission clusters were identified, encompassing 70.21% samples (57.46% patients), with 5 clusters containing samples (15, 5.32%) from different patients (9, 4.97%), indicating recent transmission. The drug-resistant mutations in 36 of 45 transmission clusters (80.00%) were identical in all samples, suggesting the transmission of drug resistance. Patients with multiple samples were categorized into simultaneous sampling (SS) and continuous sampling (CS) groups, revealing significant differences in treatment types, treatment outcomes, residential addresses, and drug resistance types. mDST showed greater accuracy than pDST in SS and CS groups. A novel method based on heterozygous SNPs and two-sample Kolmogorov-Smirnov test were developed and identified 12 (4.26%) samples as mixed infection samples. Six of 12 patients had mixed and pure samples together, and major strains of mixed samples were closer to corresponding pure strains than minor strains.

Conclusions

This retrospective study, conducted at the only municipal hospital specializing in infectious diseases in Shenzhen, provides the opportunity to understand drug resistance of TB patients, which mainly are refractory patients. The study revealed transmission patterns of MTB, analyzed mixed infections, and tracked changes in MTB strains during short/long-term treatment.

Fungal evasion of Drosophila immunity involves blocking the cathepsin-mediated cleavage maturation of the danger-sensing protease

Entomopathogenic fungi play a critical role in regulating insect populations, and representative species from the Metarhizium and Beauveria genera have been developed as eco-friendly biocontrol agents for managing agricultural insect pests. Relative to the advances in understanding antifungal immune responses in Drosophila, knowledge of how fungi evade insect immune defenses remains limited. In this study, we report the identification and characterization of a virulence-required effector Fkp1 in Metarhizium robertsii. Library screening and protein pull-down analysis unveiled that Fkp1 targets the cathepsin protease CtsK1 to inhibit its cleavage maturation of the danger-sensing serine protease Persephone (Psh), thereby facilitating fungal evasion of the Drosophila immune defenses. The Fkp1-like gene is also required in Beauveria bassiana for insect infection. Transgenic expression of Fkp1 in Drosophila suppressed hemolymph cysteine protease activity and down-regulated the expression of antifungal genes. Fkp1 can also mask the Psh cleavage site without interfering with its ability to bait fungal subtilisin proteases. Given the evident compensatory relationship, our data indicate that the protease cascade is more crucial than the molecular pattern pathway in defending flies against fungal infections. This work reveals that Metarhizium fungi have evolved distinct effectors to block the dual recognition pathways of flies for immune evasion and sheds lights on the effector mechanisms mediating microbe-animal interactions.