Search Results (1,072)

Agricultural intensification in greenhouse systems leads to a substantial accumulation of pesticides, yet its role in reshaping soil microbial interactions and their network stability remains poorly understood. This study reveals a critical ecological paradox: contrary to classical theory, greenhouse soils under chronic pesticide contamination exhibit significantly enhanced network stability (quantified as the robustness of network global efficiency under targeted node removal simulations) despite a concurrent sharp decline in bacterial diversity. We investigated this counter-intuitive phenomenon by integrating 16S rRNA sequencing, motif-based network analysis, and resilience modeling. Our findings suggest that this enhanced stability is not explained by species richness but, rather, coincides with a fundamental restructuring of the network’s local interaction architecture. Pesticide residues, acting as a strong deterministic selection pressure, shaped the microbial community into a “low-aggregation, high-redundancy” network topology. This was characterized by a decrease in highly clustered, “brittle” interaction motifs (e.g., M3-2) and an increase in sparse triangular anti-motifs (e.g., M3-1). This new architecture mitigates the risk of cascading failures, thereby elevating the network’s collapse threshold. Triazole fungicides (e.g., Tricyclazole and Hexaconazole) were significantly associated with this structural shift. Our study establishes a novel mechanistic link from pesticide stress to motif-level restructuring and enhanced system stability, offering new insights for assessing the health of highly stressed agricultural ecosystems. Full article

Soybean seed composition, particularly the oil and protein content of the seed, has been a longstanding focus of research due to the economic and nutritional importance of these components for both feed and industrial applications. Through forward genetic screening of a mutagenized population derived from the soybean cultivar Williams-82, a mutant line designated PID 17238 was identified for high seed oil content. This phenotype is associated with a decrease in levels of protein with respect to Williams-82. The phenotype was mapped to chromosome 2 to a region near Satt459. Fine mapping and whole-genome resequencing were used to identify the causative mutation. Analysis of the resequencing data within the candidate region uncovered 55 sequence variants. Glyma.02G270800 contained a single nucleotide polymorphism (SNP) within the coding sequence. Glyma.02G270800 encodes a lysin motif (LysM) receptor-like kinase previously reported in the literature as GmNFR1α. Importantly, this locus is allelic to the well-characterized rj1 locus, a recessive mutation known to cause a non-nodulating phenotype in soybean. Nodulation in soybeans, which enables nitrogen fixation, is crucial for protein synthesis in seeds, and the lack of nodulation may explain the lower protein content in PID 17238. Full article

Microorganism employs sophisticated strategies to adapt to acidic environments, with transcription factors occupying pivotal nodes within their hierarchical regulatory networks. In this study, we performed functional characterization of the AraR transcription factor LP_RS14895 via integrated multiomics approaches. RNA sequencing revealed 40 acid-responsive targets that were enriched in pathways related to pentose/glucuronate interconversions and amino sugar and nucleotide sugar metabolism. A genome-wide binding analysis via DAP-seq identified 1279 interaction sites and the most significantly enriched motif is “ARCCMATMAHC”. The results revealed that AraR plays a crucial role in regulating acid tolerance and metabolizable sugar (including arabinose, glucose, fructose, ribose, mannose, and trehalose). Overall, these findings offer mechanistic insights into microbial stress responses and provide a valuable method for addressing inhibitory processes of carbohydrate metabolizability under high-acid conditions. Full article

Background: Intratumour heterogeneity (ITH) is one of the key characteristics of cancer and is closely associated with patient prognosis, treatment resistance, and tumor metastasis. Nevertheless, the study of ITH in hepatocellular carcinoma (HCC) remains limited. Methods: The present study elucidated the influence of ITH on the tumor microenvironment (TME) in HCC. We applied Non-negative Matrix Factorization (NMF) analysis to a cohort of 78 single-cell RNA sequencing (scRNA-seq) HCC samples to systematically characterize ITH. Furthermore, by integrating spatial transcriptomics (ST) data from five HCC patients, we comprehensively analyzed the spatial organization and functional properties of distinct niches within HCC. We conducted a detailed analysis of the cell-type co-localization relationships within the TME and constructed a comprehensive atlas of HCC spatial organization. Results: We observed a co-localization relationship between hypoxia tumor cells, plasmalemma vesicle-associated protein (PLVAP⁺) endothelial cells (EC), and vascular endothelial growth factor A (VEGFA⁺) cancer-associated fibroblasts (CAF), suggesting a key role for hypoxia tumor cells in VEGFA⁺ CAF transformation and tumor angiogenesis. We identified a unique boundary region enriched with dendritic cells1 (DC1), interferon-expressing tumor cells, lymphatic EC, C–X–C Motif Chemokine Ligand 10 (CXCL10⁺) macrophages (Mac), and secreted phosphoprotein 1 (SPP1⁺) Mac located between the tumor-infiltrating immune cells and tumor regions. Furthermore, we found that CXCL10⁺ Mac and SPP1⁺ Mac, despite co-localizing in the boundary region, exhibit distinct functions, which may be attributed to their unique spatial locations, with the former being closer to the immune-infiltrated region and the latter more proximal to the tumor area. Conclusions: Our study highlights the critical role of spatial interactions between tumor cells and the microenvironment in HCC. The findings offer new insights into ITH and underscore the importance of spatial organization in understanding cancer biology and designing future precision therapies. Full article

The WUSCHEL-related homeobox (WOX) transcription factors (TF) regulate critical developmental processes in plants, including organ formation and stem cell maintenance. Although characterized in model species, the WOX family remains unexplored in passion fruit (Passiflora edulis). In this study, 10 WOX genes were identified in passion fruit, which are distributed across six chromosomes. We analyzed the phylogenetic relationships, gene structure, conserved motifs, and syntenic relationships of the PeWOX genes. Multiple sequence alignment analysis revealed strong conservation of the homeodomain region among WOX TF family members. Phylogenetic reconstruction further demonstrated that the 10 identified PeWOX genes in passion fruit could be classified into three distinct evolutionary clades: the WUS clade, the Intermediate clade, and the Ancient clade. The conserved motif and gene structure of WOX TF family members in the same evolutionary clade were highly consistent. Expression analysis based on RNA-seq and RT-qPCR showed that most PeWOX genes were expressed during ovule development. The expression level of PeWOX genes varies with different stress conditions. Subcellular localization analysis of tobacco leaf epidermal cells showed that PeWOX3/7/10 proteins were localized in the nucleus and cell membrane. Collectively, this study lays a foundation for future functional studies of passion fruit WOX genes. Full article

The red flower aphid (Uroleucon gobonis) is a significant agricultural pest causing damage via direct feeding and virus transmission. Chemical sensory proteins (CSPs) are critical for insecticide resistance, mediating the detection of semiochemicals or the sequestration of neuroactive insecticides. This study provides the first comprehensive identification and functional characterization of chemosensory gene families in Uroleucon gobonis to elucidate their roles in chemoperception and resistance. We conducted de novo transcriptome sequencing and assembly to identify chemosensory genes. Their phylogenetic relationships and structural motifs were analyzed. Developmental expression patterns were assessed via RNA-seq, and tissue-specific expression was validated using quantitative real-time PCR (qRT-PCR). We identified 40 chemosensory genes: 12 odorant-binding proteins (OBPs), 8 CSPs, 14 odorant receptors (ORs), and 6 gustatory receptors (GRs). Phylogenetic analysis revealed species-specific adaptations, including the absence of GR clades 2/4 and minimal representation in CSP Subgroup III. Structural motifs were highly conserved in ORs/OBPs but divergent in CSPs/GRs. RNA-seq identified 1896 differentially expressed genes (DEGs) between instars, including stage-specific regulation of UgobCSP4, UgobCSP6, UgobOBP3, and UgobOBP10. qRT-PCR confirmed extreme spatial expression, such as leg-specific UgobCSP6 and antennae-specific UgobOBP10. These findings elucidate key molecular adaptations in chemosensory gene families governing perception and potential insecticide resistance in Uroleucon gobonis. The identified stage- and tissue-specific genes provide targets for developing species-specific pest control strategies. Full article

To broaden the scope of research on the characteristics and evolutionary relationships within the heat shock protein 70 (Hsp70) family, encompassing its non-canonical members, amino acid sequences of Hsp70-12, Hsp70-13, and Hsp70-14, alongside those of traditional Hsp70, were collected and analyzed. The findings indicate that, during the evolution of metazoans, the various Hsp70 groups diverged from one another. Specifically, Hsp70-12 emerges as the least conserved member, as evidenced by structural alignment data and the Ka/Ks ratio. It not only represents the most distantly related group to traditional Hsp70 but also stands out as the sole alkaline group within the family. In contrast, Hsp70-13 exhibits a close evolutionary relationship with traditional Hsp70, albeit with the notable loss of its C-terminal domain. Hsp70-14 occupies an intermediate position between Hsp70-12 and Hsp70-13. Phylogenetic analysis suggests that these groups diverged prior to the advent of invertebrates. Furthermore, five conserved motifs within the ATP-binding domain of Hsp70, which serve as distinguishing features for Hsp70 groups, were identified. The diverse characters of the non-canonical Hsp70s are probably related to their special cellular location and tissue specificity. Together, the results of this research will help identify and categorize Hsp70s. Further research that aims at identifying additional non-canonical Hsp70 members and elucidating the distinct characteristics and functions of these molecular chaperones will enhance our comprehension of the origin and evolutionary trajectory of the Hsp70 family. Full article

SH3 domains are widespread protein modules that mostly bind to proline-rich short linear motifs (SLiMs). Most known SH3 domain-motif interactions and canonical or non-canonical recognition specificities are described for individual SH3 domains. Although cooperation and coordinated motif binding between tandem SH3 domains has already been described for members of the p47^phox-related protein family, individual cases have never been collected and analyzed collectively, which precluded the definition of the binding preferences and targeted discovery of further instances. Here, we apply an integrative approach that includes data collection, curation, bioinformatics analyses and state-of-the-art structure prediction methods to fill these gaps. A search of the human proteome with the sequence signatures of SH3 tandemization and follow-up structure analyses suggest that SH3 tandemization could be specific for this family. We define the optimal binding preference of tandemly arranged SH3 domains as [PAVIL]PPR[PR][^DE][^DE] and propose potential new instances of this SLiM among the family members and their binding partners. Structure predictions suggest the possibility of a novel, reverse binding mode for certain motif instances. In all, our comprehensive analysis of this unique SH3 binding mode enabled the identification of novel, interesting tandem SH3-binding motif candidates with potential therapeutic relevance. Full article

Background: Antimicrobial resistance is a growing global health threat, with beta-lactamases playing a central role in resistance to beta-lactam antibiotics. Building on our previous survey of 2340 putative beta-lactamases, we conducted an in-depth analysis of 129 prioritized candidates (70–98.5% amino acid identity to characterized enzymes) detected in 102 bacterial genera across 13 phylogenetic classes from environmental, animal, and human sources worldwide. Methods: We applied a motif-centric assessment of class-defining catalytic residues, evaluated the genomic context using a heuristic Index of Proximal Mobility (IPM) derived from the two immediately adjacent open reading frames, and examined the phylogenetic placement. AI-based substrate predictions were generated at a restricted scope as exploratory evidence. Results: Candidates spanned all Ambler classes (A–D); preservation of catalytic motifs was common and consistent with potential catalytic activity. Twelve of 129 (9.3%) loci had nearby mobile-element types (e.g., insertion sequences, integrases, transposases) and scored High IPM, indicating genomic contexts compatible with horizontal gene transfer. We also observed near-identical class A enzymes across multiple genera and continents, frequently adjacent to mobilization proteins. Conclusions: We propose a reproducible, bias-aware, early warning framework that prioritizes candidates based on motif integrity and mobility context. The framework complements existing surveillance (GLASS/EARS-Net) and aligns with a One Health approach integrating human, animal, and environmental reservoirs. Identity thresholds and IPM are used for inclusion and contextual prioritization, rather than as proof of function or mobility; AI-based predictions serve as hypothesis-generating tools. Experimental studies will be essential to confirm enzymatic activity, mobility, and clinical relevance. Full article

Xanthium strumarium L. is a plant species native to North America; however, it has become a serious invasive threat in northern China due to its great environmental adaptability in the colonized regions. Therefore, elucidating its genetic traits is crucial to understanding its adaptive success. Simple sequence repeats (SSRs) comprise 1–6 nucleotides within plant genomes, which are available for evaluating the level of plant genetic diversity. However, the comprehensive analysis of high-coverage SSR markers in Xanthium is limited. This study identified 450,847 SSR loci in the X. strumarium genome. The number of SSR loci decreased with increasing SSR length within the range of 10–100 bp. Dinucleotide repeats constituted the majority (49.81%), totaling 221,154, with AT/TA motifs being the most frequent (66.62%). We developed 169 gSSR markers covering all X. strumarium chromosomes, with 5–15 markers per chromosome. Moreover, the number of different alleles (Na), number of effective alleles (Ne), Shannon’s information index (I), observed heterozygosity (Ho), expected heterozygosity (He), and polymorphism information content (PIC) were varied from 1.2 to 3.3, 1.077 to 2.385, 0.087 to 0.903, 0 to 1, 0.056 to 0.558, and 0.161 to 0.853, respectively. This marks the first systematic development of high-coverage SSR markers in the genus Xanthium, which increases the number of available SSR markers and reveals the molecular foundation of adaptation to invasion. Full article

Methyl jasmonic acid (MeJA) is a vital phytohormone that plays a key role in plant growth and adaptation to various environmental stresses. In the present study, on the basis of the longan genome, we identified a total of seven versatile putative abscisic acid-insensitive genes, which are the key players in plant growth and stress response. On the basis of bioinformatics analysis, transcriptome data, exogenous treatment experiments, and RT-qPCR findings, a comprehensive evolutionary pattern of ABI genes in different plant species and the effect of different MeJA treatments during early somatic embryogenesis in D. longan was carried out. The phylogeny results revealed that the seven DlABI genes evolved independently in monocots and dicots, having high protein sequence similarity, especially with Arabidopsis ABI genes. The comparative findings of gene structure, motif prediction, and synteny analysis suggest that DlABI genes disperse mainly through duplication events rather than localized tandem repeats. Furthermore, the correlations among the expressions of DlABI genes propose that the organization of the cis-regulatory elements in the promoter regions may regulate the temporal and spatial transcription activation of these genes. The qRT-PCR results revealed that the 50 µM MeJA treatment significantly upregulated the expression of DlABI3, followed by DlABI1, DlABI2, DlABI5, DlABI4, and DlABI8, respectively. The ROS findings clearly revealed that MeJA distinctly elevated the SOD, POD, and H₂O₂ activities while reducing catalase and MDA contents. The subcellular localization of DlABI3 further confirmed its presence in the nucleus, suggesting its predicated transcriptional regulatory role in MeJA-mediated early SE in longan. Our findings reveal that the ABI genes are integral to the mechanism of MeJA-induced early somatic embryogenesis in longan by maintaining the ROS activity. Full article

Translation of mRNAs is a tightly regulated process in gene expression. In mRNA, the 5′ untranslated region (5′ UTR) controls ribosome recruitment and frequently contains structured elements that modulate translation efficacy. This study investigates stable structural motifs within the 5′ UTR of DDX23 mRNA, encoding a protein relevant for anticancer therapy, as potential regulators and targets for antisense oligonucleotides (ASOs). Despite bioinformatic predictions and transcriptomic validations suggesting RNA G-quadruplex (rG4) formation, comprehensive structural analysis using a light-up assay and CD, UV, and NMR spectroscopy revealed that most putative rG4-forming sequences do not fold into stable rG4 structures, although one of them exists in an equilibrium between rG4 and an alternative, likely hairpin, conformation. Reporter assays using a robust G4 stabilizer also argue against the significant regulatory role of rG4s in DDX23 mRNA translation. Instead, we identified and characterized a stable hairpin structure with potential regulatory function. Based on these findings, we designed fully locked nucleic acid (LNA)-modified ASOs to target this hairpin and regions flanking the upstream open reading frame (uORF) and start codon of the coding sequence. A reporter assay demonstrated that cap-proximal targeting achieved robust translation inhibition up to 80%. In contrast, targeting the efficiently translated uORF was ineffective, presumably due to steric hindrances from the ribosomal complex. The study yields crucial design principles for translation-regulating ASOs: avoid targeting regions shielded by efficient uORF translation and carefully tune ASO-RNA duplex stability to surpass endogenous structures without disrupting regulatory mechanisms. These findings provide insights into the regulation of DDX23 expression and establish a framework for developing ASO-based therapeutics with broad implications for mRNA targeting in anticancer applications. Full article

Background: The cytochrome P450 family 21 subfamily A member 2 gene (CYP21A2) encodes 21-hydroxylase, a key enzyme in adrenal steroid biosynthesis. Despite its physiological importance, the diversity of CYP21A2 transcript variants and their tissue-specific expression in domestic animals, including cattle, remains largely unexplored. This study aimed to characterize CYP21A2 transcription in adrenal glands and ovaries and assess the potential transcriptional activity of its pseudogene, CYP21A1P. Methods: CYP21A2 transcription was investigated in adrenal and ovarian tissues of 12 healthy cows using semi-quantitative PCR and Sanger sequencing. Real-time PCR was performed to confirm expression levels. Melting curve analysis and electrophoresis were used to validate distinct amplicons corresponding to different transcript variants. Extended amplicons were sequenced to identify transcripts corresponding to reference sequences and potential pseudogene products. Results: A single transcript variant (NM_001013596.1) was consistently detected in adrenal glands, whereas ovaries expressed two variants: NM_001013596.1 and XM_024983378.2. Semi-quantitative analysis showed significantly higher CYP21A2 expression in adrenal glands compared to ovaries (p < 0.01). In ovarian samples, the NM_001013596.1 variant was more abundant than the XM_024983378.2 (p < 0.01). Sanger sequencing revealed two products matching CYP21A2 reference transcripts and an additional, longer product containing sequence motifs specific to the pseudogene CYP21A1P, indicating its transcriptional activity. Conclusions: These results provide the first evidence of tissue-specific expression and differential abundance of CYP21A2 transcript variants in cattle and suggest the transcription of the CYP21A1P pseudogene. The findings reveal the complexity of CYP21A2 expression in steroidogenic tissues and suggest potential regulatory roles for transcript and pseudogene variants in bovine physiology. Full article

FAM20C, previously known as Golgi casein kinase (GCK), is a serine/threonine kinase localized to the Golgi apparatus and classified within the acidophilic kinase family. Its phosphorylation motif is characterized by a glutamic acid residue at the +2 position relative to the target site. Before its molecular identity was established, analysis of a limited number of phosphosites in secreted proteins showed that around 70% matched the GCK consensus sequence, suggesting that GCK is the principal kinase for secreted proteins. Following the identification of GCK as FAM20C, the generation of FAM20C knockout cell lines and phosphoproteomic data confirmed its role: approximately 80% of serine/threonine phosphosites in the secretome of two different human cell lines were shown to depend on FAM20C. In this study, comparative analysis of in vitro phosphorylation datasets from a broad panel of recombinant Ser/Thr kinases confirmed that the FAM20C consensus sequence is distinct from those of other acidophilic kinases. Examination of experimentally identified human phosphosites within the secretory pathway revealed strong conservation of the FAM20C consensus, firmly establishing this enzyme as the master Ser kinase of the entire pathway. From this dataset, we defined the putative FAM20C substratome, comprising 443 phosphosites across 256 proteins, ~77% of which had not been previously linked to FAM20C. This represents the most extensive FAM20C substratome to date and a valuable resource for functional studies. Notably, enrichment analysis highlights strong links between FAM20C and major extracellular pathways, including collagen fibril organization, complement activation, and blood coagulation, underscoring an underappreciated role for this kinase in regulating hemostasis and innate immunity. Full article

Multiplier onion (Allium cepa L. var. aggregatum) is an important bulbous vegetable widely utilized for culinary, condimental, and medicinal purposes. However, limited research on its genetic diversity and phenotypic variation has hindered the development and utilization of superior cultivars. In this study, we conducted full-length transcriptome profiling to obtain unique transcripts and develop large-scale simple sequence repeat (SSR) markers. Subsequently, we employed integrative analysis to characterize the genetic and phenotypic variation of 263 multiplier onion accessions in China. Full-length transcriptome sequencing utilizing PacBio technology generated 61,108 high-quality non-redundant transcripts with an average length of 1816 bp, from which we developed 4124 SSR markers encompassing 100 motif types. Population structure, principal component analysis, and neighbor-joining phylogenetic analysis classified the 263 multiplier onion accessions into two distinct subpopulations: Pop1, consisting of 236 accessions primarily from Heilongjiang Province, and Pop2, comprising 27 accessions mostly from Shaanxi Province. Phenotypic evaluation demonstrated significant variation in bulb traits, with single bulb weight (SBW) exhibiting the highest variability (0.75–29.94 g; CV = 70.10%), followed by total bulb weight per plant (BW) (5.00–168.83 g; CV = 58.34%), indicating considerable potential for breeding high-yield varieties. Correlation analysis indicated that the SBW and BW had significantly positive correlations with multiple traits, including bulb height, bulb transverse diameter, diameter of basal plate of bulb, diameter of bulb neck, and number of cloves per bulb. Our findings provide a valuable genetic and phenotypic resource for the conservation and utilization of multiplier onion germplasms. Full article