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Frontiers in Microbiology 2024DGL1, isolated from the arid sandy areas in Dagler, Qinghai Province, China, promotes the growth of variety "Qing Yan 1".
INTRODUCTION
DGL1, isolated from the arid sandy areas in Dagler, Qinghai Province, China, promotes the growth of variety "Qing Yan 1".
METHODS
To elucidate the transcriptomic changes in the oat root system following interaction with DGL1 and to reveal the molecular mechanism by which DGL1 promotes oat growth, treatment and control groups of oat roots at 2, 4, 8, and 12 h after inoculation with a suspension of strain DGL1 were analyzed using Illumina high-throughput transcriptome sequencing technology. The differentially expressed genes were determined through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, and the metabolic pathways and key genes were analyzed.
RESULTS
The results showed that 7874, 13,392, 13,169, and 19,026 differentially expressed genes were significantly enriched in the glycolysis/gluconeogenesis pathway, amino acid metabolism, nitrogen metabolism, plant hormone signal transduction, and other related metabolic pathways in the oat roots at 2, 4, 8, and 12 h after inoculation with a DGL1 suspension. The GO and KEGG enrichment analyses revealed that the genes encoding plasma membrane ATPase, phosphoglycerate kinase gene , ammonium transporter protein gene , cellulose synthase gene , and growth hormone response family gene were significantly upregulated.
DISCUSSION
It is hypothesized that the pro-growth mechanism of strain DGL1 in oats is the result of the coordination of multiple pathways through the promotion of oat energy metabolism, phytohormone signaling, secondary metabolite synthesis, and amino acid metabolism.
PubMed: 38633698
DOI: 10.3389/fmicb.2024.1321989 -
Communications Biology Aug 2023Understanding the molecular interaction between ligand and receptor is important for providing the basis for the development of regenerative drugs. Although it has been...
Understanding the molecular interaction between ligand and receptor is important for providing the basis for the development of regenerative drugs. Although it has been reported that extracellular phosphoglycerate kinase 1 (Pgk1) can promote the neurite outgrowth of motoneurons, the Pgk1-interacting neural receptor remains unknown. Here we show that neural membranous Enolase-2 exhibits strong affinity with recombinant Pgk1-Flag, which is also evidently demonstrated by immunoelectron microscopy. The 325-417 domain of Pgk1 interacts with the 405-431 domain of Enolase-2, but neither Enolase-1 nor Enolase-3, promoting neurite outgrowth. Combining Pgk1 incubation and Enolase-2 overexpression, we demonstrate a highly significant enhancement of neurite outgrowth of motoneurons through a reduced p-P38-T180/p-Limk1-S323/p-Cofilin signaling. Collectively, extracellular Pgk1 interacts neural membrane receptor Enolase-2 to reduce the P38/Limk1/Cofilin signaling which results in promoting neurite outgrowth. The extracellular Pgk1-specific neural receptor found in this study should provide a material for screening potential small molecule drugs that promote motor nerve regeneration.
Topics: Actin Depolymerizing Factors; Membrane Proteins; Motor Neurons; Neurites; Neuronal Outgrowth; Phosphopyruvate Hydratase; Phosphoglycerate Kinase
PubMed: 37582937
DOI: 10.1038/s42003-023-05223-0 -
Toxics Apr 2024Obesity, a chronic metabolic disorder, is related to cardiovascular diseases, diabetes, cancer, and reproductive disorders. The relationship between obesity and male...
BACKGROUND
Obesity, a chronic metabolic disorder, is related to cardiovascular diseases, diabetes, cancer, and reproductive disorders. The relationship between obesity and male infertility is now well recognized, but the mechanisms involved are unclear. We aimed to observe the effect of obesity on spermatogenesis and to investigate the role of histone ubiquitination and acetylation modifications in obesity-induced spermatogenesis disorders.
METHODS
Thirty male C57BL/6J mice were randomly divided into two groups. The control group was fed with a general maintenance diet (12% fat), while a high-fat diet (HFD) group was fed with 40% fat for 10 weeks; then, they were mated with normal females. The fertility of male mice was calculated, testicular and sperm morphology were observed, and the expression levels of key genes and the levels of histone acetylation and ubiquitination modification during spermatogenesis were detected.
RESULTS
The number of sperm was decreased, as well as the sperm motility, while the number of sperm with malformations was increased. In the testes, the mRNA and protein expression levels of gonadotropin-regulated testicular RNA helicase (GRTH/DDX25), chromosome region maintenance-1 protein (CRM1), high-mobility group B2 (HMGB2), phosphoglycerate kinase 2 (PGK2), and testicular angiotensin-converting enzyme (tACE) were decreased. Furthermore, obesity led to a decrease in ubiquitinated H2A (ubH2A) and reduced levels of histone H3 acetylation K18 (H3AcK18) and histone H4 acetylation K5, K8, K12, and K16 (H4tetraAck), which disrupted protamine 1 (Prm1) deposition in testis tissue.
CONCLUSION
These results suggest that low levels of histone ubiquitination and acetylation are linked with obesity-induced disorders during spermatogenesis, contributing to a better understanding of obesity-induced damage to male reproduction.
PubMed: 38668519
DOI: 10.3390/toxics12040296 -
Biology Direct Jan 2024Phosphoglycerate kinase 1 (PGK1) is a metabolic enzyme that participates in various biological and pathological processes. Dysregulated PGK1 has been observed in...
BACKGROUND
Phosphoglycerate kinase 1 (PGK1) is a metabolic enzyme that participates in various biological and pathological processes. Dysregulated PGK1 has been observed in numerous malignancies. However, whether and how PGK1 affects non-small cell lung cancer (NSCLC) is not yet fully elucidated.
METHODS
Herein, the non-metabolic function of PGK1 in NSCLC was explored by integrating bioinformatics analyses, cellular experiments, and nude mouse xenograft models. The upstream regulators and downstream targets of PGK1 were examined using multiple techniques such as RNA sequencing, a dual-luciferase reporter assay, Co-immunoprecipitation, and Western blotting.
RESULTS
We confirmed that PGK1 was upregulated in NSCLC and this upregulation was associated with poor prognosis. Further in vitro and in vivo experiments demonstrated the promoting effects of PGK1 on NSCLC cell growth and metastasis. Additionally, we discovered that PGK1 interacted with and could be O-GlcNAcylated by OGT. The inhibition of PGK1 O-GlcNAcylation through OGT silencing or mutation at the T255 O-GlcNAcylation site could weaken PGK1-mediated NSCLC cell proliferation, colony formation, migration, and invasion. We also found that a low miR-24-3p level led to an increase in OGT expression. Additionally, PGK1 exerted its oncogenic properties by augmenting ERK phosphorylation and MCM4 expression.
CONCLUSIONS
PGK1 acted as a crucial mediator in controlling NSCLC progression. The miR-24-3p/OGT axis was responsible for PGK1 O-GlcNAcylation, and ERK/MCM4 were the downstream effectors of PGK1. It appears that PGK1 might be an attractive therapeutic target for the treatment of NSCLC.
Topics: Animals; Mice; Humans; Carcinoma, Non-Small-Cell Lung; Lung Neoplasms; MicroRNAs; Cell Proliferation; Up-Regulation; Cell Line, Tumor; Cell Movement; Phosphoglycerate Kinase
PubMed: 38163864
DOI: 10.1186/s13062-023-00448-9 -
Biomolecules Aug 2023A protein fold is defined as a structural arrangement of a secondary structure in a three-dimensional space. It would be interesting to know whether a particular fold...
A protein fold is defined as a structural arrangement of a secondary structure in a three-dimensional space. It would be interesting to know whether a particular fold can be assigned to certain features of the corresponding folding/unfolding transitions. To understand the underlying principles of the manifold folding transitions in more detail, single-molecule FRET is the method of choice. Taking the two-domain protein phosphoglycerate kinase (PGK) as an example, we investigated denaturant-induced unfolded states of PGK using the above method. For this purpose, different intramolecular distances within the two domains were measured. In addition to the known two-state transition, a transition with a compact folding intermediate was also identified in each of the two domains. Based on the structural homology of the domains (characterized by a Rossmann fold) and the striking similarity in the features of the measured distance changes during unfolding, clear evidence emerged that the underlying domain topology plays an important role in determining the observed structural changes.
PubMed: 37759680
DOI: 10.3390/biom13091280 -
Genes Feb 2024L. is an economically valuable plant with tolerance to drought and salinity. Its leaves are utilized in tea production and pharmaceuticals, while the stem bark serves...
L. is an economically valuable plant with tolerance to drought and salinity. Its leaves are utilized in tea production and pharmaceuticals, while the stem bark serves as a high-quality fiber material. To gain insights into the gene expression patterns of using quantitative real-time PCR (qRT-PCR), it is crucial to identify appropriate reference genes. This study selected nine candidate genes, including α-tubulin (), β-tubulin (), actin (), cyclophilin (), elongation factor-1α (), the B family of regulatory subunits of protein phosphatase (, , and ), and phosphoglycerate kinase (), to determine the most appropriate reference genes in the leaf, stem, and root tissues of . A comprehensive ranking by geNorm, NormFinder, BestKeeper, and RefFinder software and Venn diagrams was used to screen more stable reference genes in different tissues. The two most stable reference genes were and in leaves, and in stems, and and in roots, respectively. The relative expression values of the four genes involved in proline metabolism under polyethylene glycol treatment were used to validate the screened reference genes, and they exhibited highly stable expression levels. These findings represent the first set of stable reference genes for future gene expression studies in . They significantly contribute to enhancing the accuracy and reliability of gene expression analyses in this economically important plant species.
Topics: Real-Time Polymerase Chain Reaction; Peptide Elongation Factor 1; Apocynum; Reproducibility of Results; Genes, Plant
PubMed: 38397220
DOI: 10.3390/genes15020231 -
MBio Apr 2024Liquid-liquid phase separation (LLPS) plays a crucial role in various biological processes in eukaryotic organisms, including immune responses in mammals. However, the...
UNLABELLED
Liquid-liquid phase separation (LLPS) plays a crucial role in various biological processes in eukaryotic organisms, including immune responses in mammals. However, the specific function of LLPS in immune responses in remains poorly understood. Cactin, a highly conserved protein in eukaryotes, is involved in a non-canonical signaling pathway associated with Nuclear factor-κB (NF-κB)-related pathways in . In this study, we investigated the role of Cactin in LLPS and its implications for immune response modulation. We discovered that Cactin undergoes LLPS, forming droplet-like particles, primarily mediated by its intrinsically disordered region (IDR). Utilizing immunoprecipitation and mass spectrometry analysis, we identified two phosphorylation sites at serine residues 99 and 104 within the IDR1 domain of Cactin. Co-immunoprecipitation and mass spectrometry further revealed phosphoglycerate kinase (PGK) as a Cactin-interacting protein responsible for regulating its phosphorylation. Phosphorylation of Cactin by PGK induced a transition from stable aggregates to dynamic liquid droplets, enhancing its ability to interact with other components in the cellular environment. Overexpression of PGK inhibited C virus (DCV) replication, while PGK knockdown increased replication. DCV infection also increased Cactin phosphorylation. We also found that phosphorylation enhances the antiviral ability of Cactin by promoting liquid-phase droplet formation. These findings demonstrate the role of Cactin-phase separation in regulating DCV replication and highlight the modulation of its antiviral function through phosphorylation, providing insights into the interplay between LLPS and antiviral defense mechanisms.
IMPORTANCE
Liquid-liquid phase separation (LLPS) plays an integral role in various biological processes in eukaryotic organisms. Although several studies have highlighted its crucial role in modulating immune responses in mammals, its function in immune responses in remains poorly understood. Our study investigated the role of Cactin in LLPS and its implications for immune response modulation. We identified that phosphoglycerate kinase (PGK), an essential enzyme in the glycolytic pathway, phosphorylates Cactin, facilitating its transition from a relatively stable aggregated state to a more dynamic liquid droplet phase during the phase separation process. This transformation allows Cactin to rapidly interact with other cellular components, enhancing its antiviral properties and ultimately inhibiting virus replication. These findings expand our understanding of the role of LLPS in the antiviral defense mechanism, shedding light on the intricate mechanisms underlying immune responses in .
Topics: Animals; Carrier Proteins; Drosophila; Drosophila melanogaster; Drosophila Proteins; Phase Separation; Phosphoglycerate Kinase; Phosphorylation
PubMed: 38446061
DOI: 10.1128/mbio.01378-23 -
Frontiers in Immunology 2023Severe equine asthma (SEA) is a common, chronic respiratory disease of horses characterized by hyperreactivity to hay dust which has many similarities to severe...
INTRODUCTION
Severe equine asthma (SEA) is a common, chronic respiratory disease of horses characterized by hyperreactivity to hay dust which has many similarities to severe neutrophilic asthma in humans. SEA-provoking antigens have not been comprehensively characterized, but molds and mites have been suggested as relevant sources. Here, we identified relevant antigen candidates using immunoproteomics with IgG isotype-binding analyses.
METHODS
Proteins from () were separated by two-dimensional gel electrophoresis followed by immunoblotting (2D immunoblots) resulting in a characteristic pattern of 440 spots. After serum incubation, antibody (Ig)-binding of all Ig (Pan-Ig) and IgG isotypes (type-2-associated IgG3/5, type-1-associated IgG4/7) was quantified per each spot and compared between asthmatic and healthy horses' sera (n=5 per group).
RESULTS
Ig binding differences were detected in 30 spots. Pan-Ig binding was higher with asthmatics compared to healthy horses' sera on four spots, and IgG3/5 binding was higher on 18 spots. Small IgG4/7 binding differences were detected on 10 spots with higher binding with asthmatics' sera on four but higher binding with healthy horses' sera on six spots. Proteins from the spots with group differences including mite and yeast proteins were identified by liquid chromatography mass spectrometry. The latter likely originated from the feeding substrate of the culture. Prioritized antigen candidates amongst the proteins identified were Der p 1, Der p 11, group 15 allergens, myosin heavy chain, and uncharacterized proteins. Additionally, yeast enolases, alcohol dehydrogenase (ADH), phosphoglycerate kinase (PGK), glyceraldehyde-3-phosphate dehydrogenase, and heat shock proteins were prioritized. Eleven antigen candidates were tested for confirmation by ELISAs using the respective proteins separately. Differences in asthmatics vs. healthy horses' serum Ig binding to Der p 1, Der p 18, and three yeast enzymes (enolase, ADH, and PGK) confirmed these as promising antigens of immune responses in SEA.
DISCUSSION
Antigens with relevance in SEA were newly identified by immunoproteomics, and yeast antigens were considered for SEA for the first time. Serum IgG3/5 binding to relevant antigens was increased in SEA and is a novel feature that points to increased type-2 responses in SEA but requires confirmation of the corresponding cellular responses.
Topics: Humans; Animals; Horses; Immunoglobulin G; Saccharomyces cerevisiae; Immunoglobulin E; Antigens, Dermatophagoides; Asthma; Allergens; Fungal Proteins; Pyroglyphidae
PubMed: 38162673
DOI: 10.3389/fimmu.2023.1293684 -
Genes Aug 2023Smoking has been linked to male infertility by affecting the sperm epigenome and genome. In this study, we aimed to determine possible changes in the transcript levels...
Smoking has been linked to male infertility by affecting the sperm epigenome and genome. In this study, we aimed to determine possible changes in the transcript levels of (the phosphoglycerate mutase family member 5), (protein tyrosine phosphatase, N2-type receptor), and (tyrosine protein kinase receptor) in heavy smokers compared to non-smokers, and to investigate their association with the fundamental sperm parameters. In total, 118 sperm samples (63 heavy-smokers (G1) and 55 non-smokers (G2)) were included in this study. A semen analysis was performed according to the WHO guidelines. After a total RNA extraction, RT-PCR was used to quantify the transcript levels of the studied genes. In G1, a significant decrease in the standard semen parameters in comparison to the non-smokers was shown ( < 0.05). Moreover, and were differentially expressed ( ≤ 0.03 and ≤ 0.01, respectively) and downregulated in the spermatozoa of G1 compared to G2. In contrast, no difference was observed for ( ≤ 0.3). In G1, the mRNA expression level of the studied genes was correlated negatively with motility, sperm count, normal form, vitality, and sperm membrane integrity ( < 0.05). Therefore, smoking may affect gene expression and male fertility by altering the DNA methylation patterns in the genes associated with fertility and sperm quality, including , , and .
Topics: Male; Humans; Semen; Infertility, Male; Fertility; Semen Analysis; Smoking; Receptor-Like Protein Tyrosine Phosphatases, Class 8; Phosphoprotein Phosphatases; Mitochondrial Proteins
PubMed: 37628668
DOI: 10.3390/genes14081617 -
Journal of Proteome Research May 2024The delay in making a correct diagnosis of causes concern in the healthcare system setting, and immunoproteomics studies are important to identify immunoreactive...
The delay in making a correct diagnosis of causes concern in the healthcare system setting, and immunoproteomics studies are important to identify immunoreactive proteins for new diagnostic strategies. In this study, immunocompetent murine systemic infections caused by non-aggregative and aggregative phenotypes of and by and were carried out, and the obtained sera were used to study their immunoreactivity against proteins. The results showed higher virulence, in terms of infection signs, weight loss, and histopathological damage, of the non-aggregative isolate. Moreover, was less virulent than but more than . Regarding the immunoproteomics study, 13 spots recognized by sera from mice infected with both phenotypes and analyzed by mass spectrometry corresponded to enolase, phosphoglycerate kinase, glyceraldehyde-3-phosphate dehydrogenase, and phosphoglycerate mutase. These four proteins were also recognized by sera obtained from human patients with disseminated infection but not by sera obtained from mice infected with or . Spot identification data are available via ProteomeXchange with the identifier PXD049077. In conclusion, this study showed that the identified proteins could be potential candidates to be studied as new diagnostic or even therapeutic targets for .
Topics: Animals; Mice; Candida; Humans; Candidiasis; Immunoglobulin G; Antigens, Fungal; Proteomics; Candida albicans; Fungal Proteins; Phosphoglycerate Mutase; Phosphoglycerate Kinase; Glyceraldehyde-3-Phosphate Dehydrogenases; Antibodies, Fungal; Female; Virulence
PubMed: 38572994
DOI: 10.1021/acs.jproteome.3c00752