Search Results (79)

Nucleotide-binding site-leucine-rich repeat (NLR) proteins are key intracellular immune receptors in plants. Integrated domains (IDs) can occasionally be fused with NLRs, contributing to their functional diversity. However, the diversity and evolutionary patterns of NLR-IDs across angiosperms remain poorly understood. In this study, we analyzed 305 angiosperm genomes and found that the proportion of NLR genes containing IDs (NLR-ID genes) ranges from 0% to 38.3%, with an average of 10.6%. A total of 1226 unique IDs were identified, some of which are widely distributed, while others are specific to particular taxa. Notably, 415 of these IDs are homologous to plant proteins targeted by pathogen effectors, suggesting their role as candidate decoys. Comparative analysis of NLR-IDs in two subfamilies—TIR-NLR (TNL) and CC-NLR (CNL)—revealed that TNL genes have a significantly higher frequency of IDs, with the C-JID and DUF3542 domains being most prevalent. N-terminal fusion of the DUF3542 domain in CNL genes correlates with the loss of the MADA motif. Our findings expand the understanding of NLR-ID diversity and provide insights into the dynamic evolution of NLR protein architecture in angiosperms. Full article

The spotted-leaf mutant, characterized by spontaneous lesion formation resembling pathogen-induced hypersensitive cell death, serves as an ideal model for studying the molecular mechanisms behind rice (Oryza sativa) disease resistance and programmed cell death, as these plants display hypersensitive responses that mimic those triggered by pathogen infection. In this study, we generated a knockout line using CRISPR/Cas9 technology in homologous mutant HM113-induced calli. LOC_Os07g30510 encodes a cysteine-rich receptor kinase with a DUF26 domain, consisting of 688 amino acids. HM113 was localized to the cytosol and expressed in most rice tissues at various growth stages. A single nucleotide substitution from A to T was observed at the 847th base of LOC_Os07g30510, causing an amino acid change from serine to cysteine. Our results demonstrated that the A847T mutation was responsible for the spotted-leaf phenotype in the HM113 mutant through gene editing technology, as new frameshift mutations were introduced upstream of the A847T site in the HM113 gene. The mutation phenotype of HM113 was eliminated and resistance to bacterial blight was also lost, indicating that it is a gain-of-function gene. Full article

Haploid breeding technology offers a promising means of significantly shortening the breeding cycle by rapidly generating homozygous inbred lines. Previous studies have shown that DMP8 is involved in haploid induction across various plant species. In this study, we performed whole-genome identification and bioinformatics analyses to investigate the evolutionary relationships, gene structures, conserved domains, and expression patterns of DMP gene family members in tomato (Solanum lycopersicum), pepper (Capsicum annuum) and eggplant (S. melongena). A total of seven, six, and eight DMP genes were identified in the genomes of tomato, pepper, and eggplant, respectively. All encoded proteins contained the DUF679 domain, and the DMP family members were clustered into three distinct groups. Collinearity analysis revealed species-specific expansions of DMP genes in the Solanaceae family. Phylogenetic analysis indicated that CaDMP8 and SmDMP8 are homologous to SlDMP8, with conserved gene and protein structures, suggesting that CaDMP8 and SmDMP8 are potential targets for developing haploid induction lines. Expression pattern analysis demonstrated that SlDMP4 and SlDMP8 are highly expressed in tomato flower tissues, suggesting their potential functional synergy. This study provides the first comprehensive insight into the evolutionary characteristics and functional diversification of the DMP gene family in Solanaceous vegetables. The findings offer a theoretical foundation for the targeted editing of DMP8 homologs to create haploid induction lines, which is critical for accelerating the genetic improvement of Solanaceous crops. Full article

Polyproline residues are well known to induce ribosomal stalling during translation. Our previous work demonstrated that inserting a short translation-enhancing peptide, Ser-Lys-Ile-Lys (SKIK), immediately upstream of such difficult-to-translate sequences can significantly alleviate ribosomal stalling in Escherichia coli. In this study, we provide a quantitative evaluation of its translational effect by kinetically analyzing the influence of the SKIK peptide on polyproline motifs using a reconstituted E. coli in vitro translation system. Translation rates estimated under reasonable assumptions fitted well to a Hill equation within a Michaelis–Menten-like kinetic framework. We further revealed that repetition of the SKIK tag did not provide any positive effect on translation. Moreover, introduction of the SKIK tag increased the production of polyproline-containing proteins, including human interleukin 11, human G protein signaling modulator 3, and DUF58 domain–containing protein from Streptomyces sp. in E. coli cell-free protein synthesis. These findings not only provide new insight into the fundamental regulation of translation by nascent peptides but also demonstrate the potential of the SKIK peptide as a practical tool for synthetic biology, offering a strategy to improve the production of difficult-to-express proteins. Full article

Fractional-order models provide a powerful framework for capturing memory-dependent and viscoelastic dynamics in mechanical systems, which are often inadequately represented by classical integer-order characterizations. This study addresses the identification of dynamic parameters in both single-degree-of-freedom (1-DOF) and three-degree-of-freedom (3-DOF) Duffing oscillators with fractional damping, modeled using the Grünwald–Letnikov characterization. The 1-DOF system includes a cubic nonlinear restoring force and is excited by a harmonic input to induce steady-state oscillations. For both systems, time domain simulations are conducted to capture long-term responses, followed by Fourier decomposition to extract steady-state displacement, velocity, and acceleration signals. These components are combined with a GL-based fractional derivative approximation to construct structured regressor matrices. System parameters—including mass, stiffness, damping, and fractional-order effects—are then estimated using pseudoinverse techniques. The identified models are validated through a comparison of reconstructed and original trajectories in the phase space, demonstrating high accuracy in capturing the underlying dynamics. The proposed framework provides a consistent and interpretable approach for frequency domain system identification in fractional-order nonlinear systems, with relevance to applications such as mechanical vibration analysis, structural health monitoring, and smart material modeling. Full article

Soybean mosaic virus (SMV) is a major viral pathogen that causes significant yield losses and a reduction in seed quality in susceptible soybean cultivars. Resistance breeding is the most effective, economical, and eco-friendly strategy for prevention of SMV-induced damage. Accurate and convenient assessment of SMV resistance is an essential prerequisite for resistance breeding. In this study, we constructed a green fluorescent protein (GFP)-tagged SMV recombinant virus (SMV-GFP) by yeast homologous recombination technology. It was proved that the recombinant virus can not only be used to track the viral infection process in Nicotiana benthamiana and soybean, but also to quantify the viral load based on relative fluorescence area (RFA) value. Using this recombinant virus, the resistance of 286 soybean germplasms from Northeast China to SMV was evaluated. A genome-wide association study (GWAS) was conducted using the RFA values of the 286 soybean accessions to find possible SMV-resistance genes. The results revealed 72 single nucleotide polymorphism (SNP) loci on chromosome 13 closely associated with SMV resistance, and a total of 40 genes were discovered within the candidate regions. By integrating the results of gene functional annotation and haplotype analysis, Glyma.13g176600 encoding a membrane attack complex/perforin (MACPF) domain-containing protein and Glyma.13g177000 encoding a DUF761-containing protein were identified as the most probable candidate genes associated with SMV resistance. Overall, the GFP-based rapid evaluation system developed in this study will facilitate breeding for resistance to SMV in soybean. Full article

Background/Objectives: The aetiology of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS), a chronic and severe debilitating disease with a complex phenotype, remains elusive. Associations with infectious diseases and autoimmune and neuropsychiatric disorders have been observed, without the identification of mechanisms. Previous studies suggest that genetic predisposition plays a role, but results are difficult to replicate, with Genome-Wide Association Studies of ME/CFS being challenging due to the relative rareness and heterogeneity of the disorder. Methods: We studied a well-defined Australian patient cohort diagnosed via the International Consensus Criteria, recruited by a specialist ME/CFS clinic. The whole-exome sequences of 77 patients were contrasted against genome variation in the 1000 Genome Project’s genome-matched population. Results: Significant associations with ME/CFS were harboured in genes that belong to the Neuroblastoma Breakpoint Family encoding Olduvai (DUF1220) domains, namely NBPF1 (rs3897177, p-value = 3.15 × 10⁻⁸), NBPF10 (rs1553120233, p-value = 9.262 × 10⁻¹³), and NBPF16 (rs200632836, p-value = 1.04 × 10⁻⁶). Other significantly associated variants were detected in the ATR, RSPH10B, ADGRE5-CD97, and NTRK2 genes, among others. Replication of these results was attempted via a GWAS on raw data from a US cohort, which confirmed shared significant associations with variation identified in the PTPRD, CSMD3, RAPGEF5, DCC, ALDH18A1, GALNT16, UNC79, and NCOA3 genes. Conclusions: These genes are involved in cortical neurogenesis, brain evolution, and neuroblastoma, and have been implicated by several studies in schizophrenia and autism. The sharing of these associations by the two cohorts supports their validity and grants the necessity of future studies to evaluate the implications for ME/CFS aetiology. Full article

The PADRE (Pathogen and abiotic stress response, cadmium tolerance, disordered region-containing) family of genes, which contains the structural DUF4228 domain of unknown function (DUF), has been reported to be associated with plant responses to abiotic stresses. However, the specific functions of this family in the salt stress response remain unknown. AtPADRE13 is induced by salt stress and ABA (abscisic acid). After the overexpression of AtPADRE13 in Arabidopsis, seeds were found to be insensitive to ABA treatment. After salt treatment, the overexpression lines presented a significantly lower survival rate, increased MDA (Malondialdehyde) content, and reduced antioxidant enzyme activities compared with the wild-type, and were more sensitive to salt stress. Transcriptome data analysis further revealed that AtPADRE13 overexpression resulted in different degrees of down-regulation for a series of positive regulators related to ABA catabolism, transport, and their mediated plant responses to salt stress. In addition, the expression of genes related to ROS (reactive oxygen species) scavenging was down-regulated. In conclusion, AtPADRE13 plays a negative regulatory role in the response to salt stress in Arabidopsis. Full article

‘Candidatus Phytoplasma mali’ is associated with apple proliferation, a devastating disease in fruit production. Using genome analysis, a gene encoding a hemolysin-like protein was identified. It was postulated that this protein could be an effector. However, the function of this protein is unknown. It is shown that the hemolysin-like protein binds to a GTP binding protein, Toc33, of Arabidopsis thaliana in yeast two-hybrid analysis and that the Toc33-binding domain is located in the C-terminus of the domain of unknown function (DUF21) of the protein. The biochemical studies reveal that the protein can hydrolyze phosphate of purine and pyrimidine nucleotides. Transgenic Nicotiana benthamiana plants expressing the protein show no discernible change in phenotype. Phytoplasma have a much-reduced genome, lacking important genes for catabolic pathways or nucleotide production; therefore, the hemolysin-like protein plays a role in the uptake of plant nucleotides from their host and hydrolyzes these nucleotides for energy and their own biosynthesis. Full article

In this study, we propose a new nonlinear polarization model that modifies the polarization equation to account for the material’s nonlinear response. Specifically, the nonlinear restoring force in our model is reformulated as an electric field-dependent function, derived from the nonlinear Lorentz model. Additionally, we perform a comparative analysis of the Kerr model, the Duffing model, the nonlinear Lorentz model, and our modified nonlinear Lorentz model (MNL) by solving Maxwell’s equations using the finite-difference time-domain (FDTD) method. This research focuses on the third-order nonlinearity of these models under varying light intensities and different ratios of resonant frequency to carrier frequency. First, in the example we studied, our results show that the MNL model produces results closer to the Kerr model when the light intensity is significantly high. Second, the comparison under different resonant frequencies reveals that all models converge to the Kerr model when the carrier frequency is much lower than the resonant frequency. However, when the carrier frequency significantly exceeds the resonant frequency, the differences between the Kerr model and the other models become more noticeable. The third-order nonlinearity of our MNL model aligns more closely with the Kerr model than the nonlinear Lorentz and Duffing models do when the ratio of resonant frequency to carrier frequency is between 1 and 2. Full article

Background/Objectives: The MAST kinases are ancient AGC kinases associated with many human diseases, such as cancer, diabetes, and neurodevelopmental disorders. We set out to describe the origins and diversification of MAST kinases from a structural and bioinformatic perspective to inform future research directions. Methods: We investigated MAST-lineage kinases using database and sequence analysis. We also estimate the functional consequences of disease point mutations on protein stability by integrating predictive algorithms and AlphaFold. Results: Higher-order organisms often have multiple MASTs and a single MASTL kinase. MAST proteins conserve an AGC kinase domain, a domain of unknown function 1908 (DUF), and a PDZ binding domain. D. discoideum contains MAST kinase-like proteins that exhibit a characteristic insertion within the T-loop but do not conserve DUF or PDZ domains. While the DUF domain is conserved in plants, the PDZ domain is not. The four mammalian MASTs demonstrate tissue expression heterogeneity by mRNA and protein. MAST1-4 are likely regulated by 14-3-3 proteins based on interactome data and in silico predictions. Comparative ΔΔG estimation identified that MAST1-L232P and G522E mutations are likely destabilizing. Conclusions: We conclude that MAST and MASTL kinases diverged from the primordial MAST, which likely operated in both biological niches. The number of MAST paralogs then expanded to the heterogeneous subfamily seen in mammals that are all likely regulated by 14-3-3 protein interaction. The reported pathogenic mutations in MASTs primarily represent alterations to post-translational modification topology in the DUF and kinase domains. Our report outlines a computational basis for future work in MAST kinase regulation and drug discovery. Full article

Proteins of the PF10950 family feature the DUF2775 domain of unknown function. The most studied are specific tissue (ST) proteins with tandem repeats, which are putative precursors of cyclopeptide alkaloids. Here, we study uncharacterised short ST (SST) proteins with the DUFF2775 domain by analysing 194 sequences from 120 species of 39 taxonomic families in silico. SST proteins have a signal peptide and their size and several other characteristics depend on their individual taxonomic family. Sequence analyses revealed that SST proteins contain two well-conserved regions, one resembling the ST repeat, which could constitute the core of cyclopeptide alkaloids. We studied the unique SST1 gene of Arabidopsis thaliana, which is adjacent to and co-expressed with a gene encoding a protein with a BURP domain, associated with cyclopeptide production. The empirical analysis indicated that the SST1 promoter is mainly activated in the roots, where most of the transcripts accumulate, and that the SST1 protein accumulates in the root vascular cambium. At the cellular level, SST fused to GFP appears in vesicles that co-localise with the endoplasmic reticulum and the vacuole. Thus, SSTs are a new type of PF10950 protein found in core eudicots with two conserved regions that could be involved in root biology. Full article

Background/Objectives: The Suppressor of Female Function (SOFF) and Shy Girl (SyGI) gene families play vital roles in sex determination in dioecious plants. However, their evolutionary dynamics and functional characteristics remain largely unexplored. Methods: Through this study, a systematic bioinformatics analysis of SOFF and SyGI families was performed in plants to explore their evolutionary relationships, gene structures, motif synteny and functional predictions. Results: Phylogenetic analysis showed that the SOFF family expanded over time and was divided into two subfamilies and seven groups, while SyGI was a smaller family made of compact molecules with three groups. Synteny analysis revealed that 125 duplicated gene pairs were identified in Kiwifruit where WGD/segmental duplication played a major role in duplicating these events. Structural analysis predicted that SOFF genes have a DUF 247 domain with a transmembrane region, while SyGI sequences have an REC-like conserved domain, with a “barrel-shaped” structure consisting of five α-helices and five β-strands. Promoter region analysis highlighted their probable regulatory roles in plant development, hormone signaling and stress responses. Protein interaction analysis exhibited only four SOFF genes with a close interaction with other genes, while SyGI genes had extensive interactions, particularly with cytokinin signal transduction pathways. Conclusions: The current study offers a crucial understanding of the molecular evolution and functional characteristics of SOFF and SyGI gene families, providing a foundation for future functional validation and genetic studies on developmental regulation and sex determination in dioecious plants. Also, this research enhances our insight into plant reproductive biology and offers possible targets for breeding and genetic engineering approaches. Full article

As a subfamily of the PD-(D/E)XK nuclease superfamily, DUF506 family shows great potential in abiotic stress responding of higher plant, yet its clues of structure, evolution and functions remain largely unexplored due to their distant phylogenetic relationship with other nuclease families, especially in Triticum aestivum. In this study, 26 T. aestivum DUF506 genes (TaDUF506) were identified from genome-wide level through bioinformatic techniques. Phylogenetic and structural analyses revealed that TaDUF506 genes exhibit conserved motif and gene structure patterns intra-phylogenetic clusters but display significant divergence inter-clusters. Gene duplication identification showed that whole-genome duplication event (WGD) was the primary driver of TaDUF506 family expansion, while Ka/Ks analysis indicated that whole TaDUF506 family experienced purifying selection generally. Gene ontology analysis and protein-protein interaction prediction suggested that DUF506 plays a potential role in transcription regulation and nucleotide-excision generally. Promoter analyses highlighted an enrichment of hormone-responsive elements linked to salt stress in TaDUF1.3-3D TaDUF5.1-3A, with expression analysis demonstrated their significant upregulation under salt stress, suggesting the potential roles in stress responses. Altogether, our study advances the understanding of DUF506 gene family in higher plant from structural, evolutional and functional aspects, and thereby provides a foundation for the development of salt-tolerant wheat varieties. Full article

Stamens are vital reproductive organs in angiosperms, essential for plant growth, reproduction, and development. The genetic regulation and molecular mechanisms underlying stamen development are, however, complex and varied among different plant species. MSL-lncRNAs, a gene specific to the Y chromosome of Populus deltoides, is predominantly expressed in male flower buds. Heterologous expression of MSL-lncRNAs in Arabidopsis thaliana resulted in an increase in both stamen and anther count, without affecting pistil development or seed set. To reveal the molecular regulatory network influenced by MSL-lncRNAs on stamen development, we conducted transcriptome sequencing of flowers from both wild-type and MSL-lncRNAs-overexpressing Arabidopsis. A total of 678 differentially expressed genes were identified between wild-type and transgenic Arabidopsis. Among these, 20 were classified as transcription factors, suggesting a role for these regulatory proteins in stamen development. GO enrichment analysis revealed that the differentially expressed genes were significantly associated with processes such as pollen formation, polysaccharide catabolic processes, and secondary metabolism. KEGG pathway analysis indicated that MSL-lncRNAs might promote stamen development by upregulating genes involved in the phenylpropanoid biosynthesis pathway. The top three upregulated genes, all featuring the DUF295 domain, were found to harbor an F-box motif at their N-termini, which is implicated in stamen development. Additionally, in transgenic Arabidopsis flowers, genes implicated in tapetum formation and anther development were also observed to be upregulated, implying a potential role for MSL-lncRNAs in modulating pollen development through the positive regulation of these genes. The findings from this study establish a theoretical framework for elucidating the genetic control exerted by MSL-lncRNAs over stamen and pollen development. Full article