Search Results (2,035)

Pathogenesis-related protein-1 (PR1) encodes a water-soluble protein produced in plants after pathogen infection or abiotic stimulation. It plays a crucial role in plant-induced resistance by attacking pathogens, degrading cell wall macromolecules and pathogen toxins, and inhibiting the binding of viral coat proteins to plant receptor molecules. Compared to model plants, the mechanism of action of PR1 in wheat remains underexplored. In this study, the recently published wheat genome database (IWGSC RefSeq V2.1) was used to identify 83 genes in the TaPR1 gene family. Compared to previous work, the duplicate genes were removed and we corrected misannotated genes. Fourteen TaPR1 genes involved in the wheat–Pst interaction were identified based on RNA sequencing from Xinchun 32. The expression patterns of eight genes were validated using qRT-PCR, and the results showed that PR1 was highly expressed following Puccinia striiformis f. sp. tritici (Pst) infection. This study enhances previous research on wheat PR1, contributing to a more comprehensive understanding of the TaPR1 gene family and providing a reference for the screening of more broad-spectrum and high-resistance wheat populations. Full article

Valine-glutamine (VQ) motif-containing proteins play important roles in diverse plant developmental processes and signal transduction in response to biotic and abiotic stresses. However, no systematic investigation has been conducted on VQ genes in watermelon. In this study, we identified 31 watermelon VQ genes, which were classified into six subfamilies (I–VI). All of the deduced proteins contained a conserved FxxxVQxL/F/VTG motif. Eleven ClVQs were involved in segment duplication, which was the main factor in the expansion of the VQ family in watermelon. Numerous stress- and hormone-responsive cis-elements were detected in the putative promoter region of the ClVQ genes. Green fluorescent protein fusion proteins for ten selected ClVQs were localized in the nucleus, but three ClVQs also showed signals in cell membranes and the cell wall, thus confirming their predicted divergent functionality. Quantitative real-time PCR (qRT-PCR) analysis indicated that the majority of ClVQ genes were specifically or preferentially expressed in certain tissues or organs, especially in the male flower. Analyses of RNA-sequencing data under osmotic, cold, and drought stresses and Cucumber green mottle mosaic virus (CGMMV) infection revealed that the majority of ClVQ genes, especially those from subfamily IV, were responsive to these stresses. The results provide useful information for the functional characterization of watermelon ClVQ genes to unravel their biological roles. Full article

As the mobile cassette carrier of the methicillin resistance gene mecA that is transported across staphylococci species, the evolution and origin of Staphylococcal Cassette Chromosome mec (SCCmec)—and in particular, the composition of mecA and SCCmec—have been extensively discussed in the scientific literature; however, information regarding its dissemination across geographical limits and evolution over decades remains limited. In addition, whole-genome sequencing-based macro-analysis was unable to provide sufficiently detailed evolutionary information on SCCmec. Herein, the cassette chromosome recombinase genes ccrAB/C, as essential components of SCCmec, were employed to explore the evolution of SCCmec. This work established the basic taxonomy of 33 staphylococci species. The CUB of mecA, ccrAB/C of 12 SCCmec types and core genome of 33 staphylococci species were subsequently compared; the phylogenetic relationship of ccrAB/C was observed via SCCmec typing on a temporal and geographical scale; and the duplicate appearance of ccrAB/C was illustrated by comparing SCCmec compositions. The results highlighted a deviation in the CUB of mecA and ccrAB/C, which evidenced their exogenous characteristics to staphylococci, and provided theological support for the phylogenetic analysis of ccrAB/C as representative of SCCmec. Importantly, the phylogenetic relationship of ccrAB/C did not exhibit centralization over time; instead, similarly to mecA, ccrAB/C with similar identities had close clades across decades and geographical limits and different SCCmec types, which enabled us to discriminate SCCmec based on the sequence identity of ccrAB/C. In addition, the duplicate appearance of ccrAB/C and fixed composition of the ccrAB/C complex among different strains were indicative of more complicated transmission mechanisms than targeting direct repeats of SCCmec. Full article

Background/Objectives: Strabismus is the most common ocular disorder of childhood. Three rare, recurrent genetic duplications have been associated with both esotropia and exotropia, but the mechanisms by which they contribute to strabismus are unknown. This work aims to investigate the mechanisms of the smallest of the three, a 23 kb duplication on chromosome 4 (hg38|4:25,554,985-25,578,843). Methods: Using CRISPR and bridging oligos, we introduced the duplication into the Kolf2.1J iPSC line. We differentiated the parent line and the line with the duplication into cortical neurons using a three-dimensional differentiation protocol, and performed bulk RNASeq on neural progenitors (day 14) and differentiated neurons (day 63). Results: We successfully introduced the duplication into Kolf2.1J iPSCs by nucleofecting a bridging oligo for the newly formed junction along with cas9 ribonucleoparticles. We confirmed that the cells had a tandem duplication without inversion or deletion. The parent line and the line with the duplication both differentiated into neurons reliably. There were a total of 37 differentially expressed genes (DEGs) at day 63, 25 downregulated and 12 upregulated. There were 55 DEGs at day 14, 18 of which were also DEGs at day 63. The DEGs included a number of protocadherins, several genes involved in neuronal development, including SLITRK2, CSMD1, and VGF, and several genes of unknown function. Conclusions: A copy number variant (CNV) that confers risk for strabismus affects gene expression of several genes involved in neural development, highlighting that strabismus most likely results from abnormal neural development, and identifying several new genes and pathways for further research into the pathophysiology of strabismus. Full article

Prunus mume, a traditional ornamental species native to China, is highly valued for both its captivating weeping variety and economic value. The glycosylation of metabolites, which is mediated by UDP-glycosyltransferases (UGTs), is essential for the regulation of secondary metabolic pathways in plants. Here, we systematically identified and analyzed the UGTs in P. mume. A total of 182 PmUGTs were identified using genomic data and categorized into 16 distinct subfamilies (A–P). All PmUGTs were distributed unevenly across the eight chromosomes, with clear evidence of tandem duplication. Additionally, synteny analysis revealed a close evolutionary relationship between P. mume and Prunus persica. A promoter cis-acting element analysis indicated that PmUGTs may respond to light, hormones, and external stresses. A heatmap analysis revealed that PmUGTs had specific expression patterns across different tissues, under various hormone treatments, and in different developmental stages of stem lignification. Notably, qRT-PCR verification showed significant differences in PmUGT163 expression between straight and weeping stems, underscoring its role in regulating plant architecture formation. Taken together, our study elucidates the evolutionary trajectory of PmUGTs and lays the groundwork for the further validation of the candidate genes involved in plant architectural formation. Full article

Deletion and duplication in the human 16p11.2 chromosomal region are closely linked to neurodevelopmental disorders, specifically autism spectrum disorder. Data from neuroimaging studies suggest white matter microstructure aberrations across these conditions. In 16p11.2 deletion and duplication carriers, potential gene dosage effects may impact white matter organisation, contributing to phenotypes including impaired cognition. However, the biological mechanisms underlying this white matter pathology remain unclear. To bridge this knowledge gap, we utilised mouse models of 16p11.2 deletion and duplication to explore changes in corpus callosum oligodendrocytes, myelination, axon caliber, and astrocytes. Immunofluorescence staining was employed to measure lineage and mature oligodendrocyte numbers, as well as myelin basic protein and glial fibrillary acidic protein fluorescence intensity. Transmission electron microscopy was utilised to evaluate axonal structural alterations related to myelin, such as myelinated axon percentage, diameter, myelin thickness, and g-ratio. Our findings reveal changes in the number of mature oligodendrocytes, myelination levels, axon diameter, and astrocytes in the corpus callosum of mice with 16p11.2 deletion and duplication. Deletion mice displayed a tendency toward reduced counts of mature oligodendrocytes and myelination levels, while duplication mice exhibited a notable increase. Axon diameter variations included a significant increase in axon diameter and myelin thickness in both deletion and duplication mice, but with irregular structure in duplication mice. Variances in astrocytes between genotypes showed significant early increases in development for both deletion and duplication mice compared to wild-type mice, with this rise sustained in duplication mice but significantly diminished in deletion mice at a later stage. Our research reveals changes in the biological mechanisms impacting white matter. Comparison of reciprocal trends in 16p11.2 deletion and duplication mice with wild-type mice suggests the possibility of gene dosage effects. Identification of these mechanisms offers an initial step in unveiling therapeutic targets for associated neurodevelopmental disorder phenotypes. Full article

This study characterizes the evolution of the tumor necrosis factor superfamily (TNFSF) across vertebrate lineages, both cyclostomes and gnathostomes, by combining sequence similarity and synteny data for the genes from 23 model species. The available evidence supports a simple model in which most of the diversity found in living species can be attributed to the expansion of four genes found in an ancestor of all vertebrates before the first of the genome duplications that occurred in the vertebrate lineages. It is inferred that the ancestor of all cyclostomes possessed only six TNFSF genes. A cyclostome-specific genome triplication had little effect on the total number of these genes. The ancestor of all gnathostomes, due to the effect of a second genome duplication plus additional single-gene duplications, already had 21 TNFSF genes. In several gnathostome lineages, particularly in some tetrapods, the TNF superfamily has significantly contracted due to numerous gene losses. This evolutionary model provides a framework for exploring functional data, showing that the descendants of different ancestral genes have acquired distinct roles, most prominently in the innate and adaptive immune systems, which led to a species-specific refinement of which TNFSF genes were conserved or lost. Several data hitherto difficult to interpret (the interactions of very different TNFSF ligands with the same receptors; the ability of the same ligands to bind alternative receptors, with or without death domains; and the cooperation of different ligands in specific functions) can be explained as consequences of the evolutionary history of the TNF superfamily. Full article

Phytochrome-interacting factors (PIFs) play a crucial role in regulating plant growth and development. However, studies on soybean PIFs are limited. Here, we identified 22 GmPIF genes from the soybean genome and classified the GmPIF proteins into 13 subfamilies based on amino acid sequence homology, secondary and tertiary structures, protein structure, and conserved motifs. Genome-wide collinearity analysis revealed that fragment duplication events play a dominant role in expanding the GmPIF gene family. Cis-acting element analysis revealed that the GmPIF gene family is involved in light response, hormone response, biotic–abiotic stress response elements, and plant growth and development. Gene expression analysis in different temperature environments showed that the GmPIF family was found to be induced by phytohormone treatments, with a significant increase in the expression level of GmPIF3g. GmPIF3g plays a key role in the regulation of the entire network, and in addition, 30 proteins interacting with the GmPIF3g promoter were identified through the use of a novel biofilm interference technique. This technique showed that the transcription factor Dof (DNA binding with one finger) binds to the GmPIF3g promoter, and Y1H assays indicated that Dof regulates its expression by binding to the PIF promoter. These results provide a theoretical basis for further studies on the regulatory network of GmPIF genes to improve the structure of soybean plants under shade environments, as well as a new method for analyzing regulatory elements that interact with gene promoters. Full article

Late embryogenesis abundant (LEA) proteins are a class of proteins associated with osmotic regulation and plant tolerance to abiotic stress. However, studies on the LEA gene family in the alpine cold-tolerant herb are still limited, and the phylogenetic evolution and biological functions of its family members remain unclear. In this study, we conducted genome-wide identification, phylogenetic evolution, and abiotic stress response analyses of LEA family genes in Notopterygium species, alpine cold-tolerant medicinal herbs in the Qinghai–Tibet Plateau and adjacent regions. The gene family identification analysis showed that 23, 20, and 20 LEA genes were identified in three Notopterygium species, N. franchetii, N. incisum, and N. forrestii, respectively. All of these genes can be classified into six LEA subfamilies: LEA_1, LEA_2, LEA_5, LEA_6, DHN (Dehydrin), and SMP (seed maturation protein). The LEA proteins in the three Notopterygium species exhibited significant variations in the number of amino acids, physical and chemical properties, subcellular localization, and secondary structure characteristics, primarily demonstrating high hydrophilicity, different stability, and specific subcellular distribution patterns. Meanwhile, we found that the members of the same LEA subfamily shared similar exon–intron structures and conserved motifs. Interestingly, the chromosome distributions of LEA genes in Notopterygium species were scattered. The results of the collinearity analysis indicate that the expansion of the LEA gene family is primarily driven by gene duplication. A Ka/Ks analysis showed that paralogous gene pairs were under negative selection in Notopterygium species. A promoter cis-acting element analysis showed that most LEA genes possessed multiple cis-elements connected to plant growth and development, stress response, and plant hormone signal transduction. An expression pattern analysis demonstrated the species-specific and tissue-specific expression of NinLEAs. Experiments on abiotic stress responses indicated that the NinLEAs play a crucial role in the response to high-temperature and drought stresses in N. franchetii leaves and roots. These results provide novel insights for further understanding the functions of the LEA gene family in the alpine cold-tolerant Notopterygium species and also offer a scientific basis for in-depth research on the abiotic stress response mechanisms and stress-resistant breeding. Full article

The APETALA2/ethylene-responsive factor (AP2/ERF) is a well-researched superfamily of plant transcription factors. The APETALA2 (AP2) subfamily is essential for plant growth and development. However, a systematic analysis of the AP2 subfamily in poplar has yet to be conducted. This study identified 29 AP2 genes in the poplar genome, classifying them into three clades—euAP2, euANT, and basalANT based on evolutionary relationships. These genes are distributed across 12 chromosomes and one scaffold. Results from the syntenic analysis suggest that whole-genome duplication events are the primary factors driving the expansion of the AP2 subfamily in poplar. Cis-element analysis reveals that numerous PtAP2 genes possess hormone-related cis-elements. These genes also contain cis-elements linked to plant development and stress responses. PtAP2s from different clades exhibit significantly tissue-specific expression patterns in poplar. Gene expression levels in the euAP2 clade are significantly higher than in the euANT and basalANT clades across various tissues, with basalANT showing the lowest expression. Through RT-qPCR and recombinant Saccharomyces cerevisiae assays under salt stress, it was discovered that the majority of AP2 genes showed a negative response in salt stress regulation in poplar trees. In conclusion, this study offers valuable insights into salt tolerance in poplar trees and the role of AP2 genes under salt stress conditions. Full article

Chalcone synthase (CHS), the first key structural enzyme in the flavonoid biosynthesis pathway, plays a crucial role in regulating plant responses to abiotic stresses and hormone signaling. However, its molecular functions remain largely unknown in Phyllostachys edulis, which is one of the most economically and ecologically important bamboo species and the most widely distributed one in China. This study identified 17 CHS genes in Phyllostachys edulis and classified them into seven subgroups, showing a closer evolutionary relationship to CHS genes from rice. Further analysis of PeCHS genes across nine scaffolds revealed that most expansion occurred through tandem duplications. Collinearity analysis indicated strong evolutionary conservation among CHS genes. Motif and gene structure analyses confirmed high structural similarity, suggesting shared functional characteristics. Additionally, cis-acting element analysis demonstrated that PeCHS genes are involved in hormonal regulation and abiotic stress responses. RNA-Seq expression profiles in different bamboo shoot tissues and heights, under various hormone treatments (gibberellin (GA), naphthaleneacetic acid (NAA), abscisic acid (ABA), and salicylic acid (SA)), as well as salinity and drought stress, revealed diverse response patterns among PeCHS genes, with significant differential expression, particularly under hormone treatments. Notably, PeCHS14 consistently maintained high expression levels, suggesting its key role in stress response mechanisms. qRT-PCR analysis further validated the expression differences in five PeCHS genes under GA and ABA treatments. Subcellular localization analysis demonstrated that PeCHS14 and PeCHS15 proteins are localized in the nucleus. This study provides a foundation for investigating the potential functions of PeCHS genes and identifies candidate genes for future research on the responses of Phyllostachys edulis to abiotic stresses and hormone signaling. Full article

The Na⁺/H⁺ antiporter (NHX) gene family plays a pivotal role in plant salt tolerance in regulating intracellular Na⁺ and H⁺ homeostasis. In this study, seven candidate OsNHX genes (OsNHX1 to OsNHX7) were identified in the rice genome and classified into three phylogenetic clusters (Vac, Endo, and PM) based on their predicted subcellular localization. Five OsNHX gene pairs (OsNHX1/OsNHX2, OsNHX1/OsNHX3, OsNHX1/OsNHX4, OsNHX2/OsNHX6, and OsNHX5/OsNHX6) were found to have arisen from dispersed duplication events and exhibited purifying selection, indicating functional conservation. Analysis of cis-regulatory elements (CREs) revealed a diverse range of elements associated with tissue-specific expression, hormone signaling, and stress responses, particularly to dehydration and salinity. Notably, CREs associated with tissue/organelle-specific expression and stress responses were the most abundant, suggesting a potential role for OsNHX genes in regulating growth, development, and stress tolerance in rice. Importantly, expression profiling revealed that OsNHX1, OsNHX2, OsNHX3, and OsNHX5 were upregulated under salt stress, with significantly higher expression levels in the salt-tolerant rice cultivar Pokkali compared to the salt-sensitive cultivar IR64. Our findings provide a comprehensive analysis of the evolutionary, structural, and functional features of the OsNHX gene family and highlights their critical role in rice salt tolerance, offering insights into potential applications for crop improvement. Full article

SKP1 constitutes the Skp1-Cullin-F-box ubiquitin E3 ligase (SCF), which plays a role in plant growth and development and biotic and abiotic stress in ubiquitination. However, the response of the SKP1-like gene family to abiotic and biotic stresses in cotton has not been well characterized. In this study, a total of 72 SKP1-like genes with the conserved domain of SKP1 were identified in four Gossypium species. Synteny and collinearity analyses revealed that segmental duplication played a major role in the expansion of the cotton SKP1-like gene family. All SKP1-like proteins were classified into three different subfamilies via phylogenetic analysis. Furthermore, we focused on a comprehensive analysis of SKP1-like genes in G. hirsutum. The cis-acting elements in the promoter site of the GhSKP1-like genes predict their involvement in multiple hormonal and defense stress responses. The expression patterns results indicated that 16 GhSKP1-like genes were expressed in response to biotic or abiotic stresses. To further validate the role of the GhSKP1-like genes in salt stress, four GhSKP1-like genes were randomly selected for gene silencing via VIGS. The results showed that the silencing of GhSKP1-like_7A resulted in the inhibition of plant growth under salt stress, suggesting that GhSKP1-like_7A was involved in the response to salt stress. In addition, yeast two-hybrid results revealed that GhSKP1-like proteins have different abilities to interact with F-box proteins. These results provide valuable information for elucidating the evolutionary relationships of the SKP1-like gene family and aiding further studies on the function of SKP1-like genes in cotton. Full article

The Really Interesting New Gene (RING) E3 ubiquitin ligases represent the largest class of E3 ubiquitin ligases involved in protein degradation and play a pivotal role in plant growth, development, and environmental responses. Despite extensive studies in numerous plant species, the functions of RING E3 ligases in cotton remain largely unknown. In this study, we performed systematic identification, characterization, and expression analysis of RING genes in cotton. A total of 514, 509, and 914 RING genes were identified in Gossypium arboretum, G. raimondii, and G. hirsutum, respectively. Duplication analysis indicates that segmental duplication may be the primary mechanism responsible for the expansion of the cotton RING gene family. Moreover, the Ka/Ks analysis suggests that these duplicated genes have undergone purifying selection throughout the evolutionary history of cotton. Notably, 393 G. hirsutum RING genes exhibited differential expression in response to salt stress. The overexpression of the specific C3H2C3 RING gene, GhZFRG1, in Arabidopsis resulted in enhanced tolerance to salt stress. This study contributes to our understanding of the evolution of cotton RING ligases and paves the way for further functional analysis of the RING E3 ligase genes in cotton. Full article

Background/Objectives: Atherosclerosis is a chronic inflammatory disease developing and progressing in the presence of risk factors including hyperlipidemia, hypercholesterolemia, and chronic inflammation, among others. Atherosclerosis commonly precipitates as ischemic events, transient ischemic attacks, and myocardial infarction. Saturated fatty acids are risk factors; however, their association with epigenetics in the pathophysiology of atherosclerosis is not clearly understood. The preclinical and clinical trials associating atherosclerosis with epigenetics are scarcely documented, and most of the studies reported the use of drugs inhibiting methylation and histone modification to improve atherosclerosis. This narrative review aims to discuss various aspects and the association between a high-fat diet, epigenetic reprogramming, and atherosclerosis. Methods: A literature search with the keywords high-fat diet, epigenetics, and atherosclerosis, alone or in combination, was conducted to search for articles in the English language. Duplicate articles were removed, and articles related to the subject of this review article were included in this review. Results: A review of the literature suggests that a high-fat diet with saturated fatty acids is a risk factor for atherosclerosis, but this association is multifactorial, and epigenetics play a critical role. However, the connecting link and the underlying molecular and cellular mechanisms are not clearly understood yet and warrant more research. Conclusions: A high-fat diet rich in saturated fatty acids is a risk factor for atherosclerosis involving epigenetic reprogramming and altered gene expression. The existing preclinical and clinical trials support the role of epigenetics and reversing it using drugs to attenuate atherosclerosis, but definitive evidence warrants larger clinical trials. Further, a high-fat diet in pregnant mothers can manifest as cardiovascular disease in offspring; caution must be taken in pregnant mothers for their diet and nutrients. Full article