Signal Recognition Particle Research Articles

Force and the α-C-terminal domains bias RNA polymerase recycling

After an RNA polymerase reaches a terminator, instead of dissociating from the template, it may diffuse along the DNA and recommence RNA synthesis from the previous or a different promoter. Magnetic tweezers were used to monitor such secondary transcription and determine the effects of low forces assisting or opposing translocation, protein roadblocks, and transcription factors. Remarkably, up to 50% of Escherichia coli (E. coli) RNA polymerases diffused along the DNA after termination. Force biased the direction of diffusion (sliding) and the velocity increased rapidly with force up to 0.7 pN and much more slowly thereafter. Sigma factor 70 (σ70) likely remained associated with the DNA promoting sliding and enabling re-initiation from promoters in either orientation. However, deletions of the α-C-terminal domains severely limited the ability of RNAP to turn around between successive rounds of transcription. The addition of elongation factor NusG, which competes with σ70 for binding to RNAP, limited additional rounds of transcription. Surprisingly, sliding RNA polymerases blocked by a DNA-bound lac repressor could slowly re-initiate transcription and were not affected by NusG, suggesting a σ-independent pathway. Low forces effectively biased promoter selection suggesting a prominent role for topological entanglements that affect RNA polymerase translocation.

Natural restoration of arsenic-contaminated environment with Quercus robur L. and Tilia cordata Mill.: 5-Year longitudinal study of dendroremediation dynamics

Investigating natural processes in arsenic (As) polluted areas and plants that have naturally chosen to grow there pose practical restoration recommendations. This study aimed to assess long-term changes in natural As dendroremediation dynamics for Quercus robur L. and Tilia cordata Mill., tree species capable of growing in areas polluted by mining activities. We examined total As and its forms, as well as B, Ca, K, Mg, Na and P, in soil and trees over 5 years. We also characterized pH and EC of soil, examined proline content in tree organs, and calculated Bioconcentration Factor (BCF) and Translocation Factor (TF) for As.Initial As concentrations in soil were 37.0 mg kg⁻1 under Q. robur and 34.7 mg kg⁻1 under T. cordata, significantly decreasing after 5 years to 10.5 mg kg⁻1 and 9.51 mg kg⁻1, respectively. This corresponds to pollution reduction of up to 71.8%. A notable decrease in As(III) and dimethylarsinic acid, along with increase in other organic As forms in soil, was observed. Additionally, concentrations of essential elements in soil, as well as its pH and EC, decreased over time.Both tree species accumulated substantial amounts of As in their organs, but the dynamics of this process were species-specific. During first 4 years, T. cordata accumulated more As and exhibited higher BCF, but in the 5th year, it was clearly surpassed by Q. robur. The highest TF was calculated for Q. robur in year 3, and for T. cordata in years 2 and 3. Generally, limited aboveground movement of As was indicated: BCF >1 were calculated for years 2 and 3, while TF were consistently <1. Proline content increased significantly in all organs, correlating with As, especially in Q. robur. In contrast, Q. robur leaves mapping revealed stable macroelement distributions, but clear variations were observed for T. cordata., which may suggest specific reaction to stress.These findings suggest that both species can effectively restore As-polluted areas, though with different dynamics. The selection of species for dendrorestoration should be based on whether the goal is faster remediation with lesser overall reduction (e.g. T. cordata) or slower remediation with ultimately greater pollution reduction (e.g. Q. robur).

In-silico Identification of citrus phytochemicals for chemical interaction of CotH of Mucor and human GRP78 receptor and its experimental verification through FTIR spectroscopy

After suffering from serious critical disease such as recent COVID-19 pandemic, secondary fungal infection (Specially Mucormycosis) has become a serious concern throughout the world. Glucose regulated protein 78 (GRP78) is a multifunctional protein which acts as a receptor in human body for spore Coat homolog (CotH) cell surface protein of Mucorales. The development of immunity with easily available plant products is vital and essential due to having less effect on other biological activities. Here, In-silico method has been employed to screen antifungal citrus phyto-chemicals through molecular docking with CotH and its ADMET study due its rapid and cost effective quality compared to the trial and error methods using experimental studies. Limonin and naringin have been selected as potential ligands due to having its low binding affinity and no risk factor as per Lipinski's rule of five and medicinal chemistry. Molecular interaction of naringin and limonin with CotH obtained by molecular docking shows better binding affinity of −8.7 and – 8.9 kcal/mol respectively. The binding of CotH-GRP78 complex (developed through protein-protein molecular docking) with limonin resists more in the spreading of Mucormycosis in comparison to naringin. The FTIR spectra of limonin-CotH and Naringin-CotH sample exhibits the evidences of hydrogen bond for the formation of both strong limonin-CotH and naringin-CotH complex assuring the development of immunity with citrus fruit containing limonin and naringin.

The Potential of Talisay-Dagat (Terminalia catappa L.) for Phytoremediation in Langihan Lagoon, Butuan City, Agusan del Norte, Philippines

The study aims to determine the potential of Talisay-dagat (Terminalia catappa L.) for phytoremediation and to examine its influence on reducing concentrations of heavy metals in the soil of Langihan Lagoon, Butuan City. Soil, roots, and leaves were collected and brought to the Regional Soils Laboratory using microwave-assisted aqua-regia digestion and determination through Inductively Coupled Plasma Optical Emission Spectrometer. The study made use of mathematical computations such as translocation factor (TF), bioconcentration factor (BCF), and enrichment factor (EF) to determine whether the tree is a hyperaccumulator, excluder, or indicator. In the TF results, T. catappa was a hyperaccumulator for Ni and Cu, considering that the concentration exceeds one (1) while demonstrating as a possible excluder for Cr. There was also an emphasis on limited absorption of heavy metals, as evidenced by the BCF and EF value of less than 1. The results show that based on TF, BCF, and EF values, only TF shows the effectivity of restricting the root-shoot ratio translocation of Ni and Cu (TF &gt; 1). Regression analysis found that the absorption of T. catappa was not influenced by the amount of heavy metal in the soil within the studied condition. This insight was crucial in understanding the plant’s absorption and could guide further research or practical applications in environmental management and phytoremediation. Keywords: bioconcentration factor, hyperaccumulator, phytoremediation, Terminalia catappa, translocation factor

Kinetics of uptake, translocation, and metabolism of organophosphate esters in japonica rice (Oryza sativa L.): Hydroponic experiment combined with model

Hydroponics combined with fugacity model was employed to investigate the kinetics of uptake, accumulation, and metabolism of organophosphate esters (OPEs) by japonica rice. The time-dependent process for uptake and accumulation of 5 OPEs and their diester-metabolites in both rice root and shoot fitted well with the pseudo-first-order kinetic model. The peak OPE accumulations in rice root and shoot were significantly positively or negatively correlated with their octanol-water partition coefficient (logKow) respectively, but not for their apparent accumulation rates. Root concentration factors (RCFs) and root-to-shoot translocation factors (TFs) of OPEs were found to be positively and negatively correlated with their logKow, respectively. Triphenyl phosphate with benzene ring substituents showed the highest RCF, but the lowest TF, because of its high potential for root adsorption due to the π electron-rich structures. Sterilized root exudates can hinder the root adsorption and absorption of OPEs from solution probably through competitive adsorption of OPEs with root surface. The first-hand transport and metabolism rates were also obtained by generating these rates to fit the dynamic fugacity model with the measurement values. The simulation indicated that the kinetics of OPE accumulation in rice plants may be controlled by multiple processes and physicochemical properties besides Kow.

Alleviation of cadmium uptake in rice (Oryza sativa L.) by iron plaque on the root surface generated by Providencia manganoxydans via Fe(II) oxidation.

Iron plaque is believed to be effective in reducing the accumulation of heavy metals in rice. In this work, a known soil-derived Mn(II)-oxidizing bacterium, LLDRA6, which represents the type strain of Providencia manganoxydans, was employed to investigate the feasibility of decreasing cadmium (Cd) accumulation in rice by promoting the formation of iron plaque on the root surface. Firstly, the Fe(II) oxidation ability of LLDRA6 was evaluated using various techniques including Fourier Transform infrared spectroscopy, X-ray diffraction, X-ray photoelectron spectroscopy, phenanthroline photometry, and FeS gel-stabilized gradient assays. Subsequently, the formation of iron plaque on the root surface by LLDRA6 was investigated under hydroponic and pot conditions. Finally, Cd concentrations were examined in rice with and without iron plaque through pot and paddy-field tests. The results showed that LLDRA6 played an efficient role in the formation of iron plaque on seedling roots under hydroponic conditions, generating 44.87 and 36.72g kg- 1 of iron plaque on the roots of Huazhan and TP309, respectively. In pot experiments, LLDRA6 produced iron plaque exclusively in the presence of Fe(II). Otherwise, it solely generated biofilm on the root surface. Together with Fe(II), LLDRA6 effectively reduced the concentrations of Cd in Huazhan roots, straws and grains by 25%, 46% and 44%, respectively. This combination also demonstrated a significant decrease in the Cd concentrations of TP309 roots, straws and grains by 20%, 52% and 44%, respectively. The data from the Cd translocation factor indicate that obstruction of Cd translocation by iron plaque predominantly occurred during the root-to-straw stage. In paddy-field tests, the Cd concentrations of grains harvested from the combination treatment of LLDRA6 and Fe(II) exhibited a decline ranging from 40 to 53%, which fell below the maximum acceptable value for Cd in rice grains (0.2mg kg- 1) as per the China national standard for food security (GB2762-2017). Meanwhile, the relevant phenotypic traits regarding the yield were not adversely affected. These findings have demonstrated that LLDRA6 can impede the uptake of Cd by rice in Cd-contaminated soils through the formation of iron plaque on roots, thus providing a promising safe Cd-barrier for rice production.

Investigating the Effects of Chelidonic Acid on Oxidative Stress-Induced Premature Cellular Senescence in Human Skin Fibroblast Cells.

This study investigated the effects of chelidonic acid (CA) on hydrogen peroxide (H2O2) induced cellular senescence in human skin fibroblast cells (BJ). Cellular senescence is a critical mechanism that is linked to age-related diseases and chronic conditions. CA, a γ-pyrone compound known for its broad pharmacological activity, was assessed for its potential to mitigate oxidative stress and alter senescence markers. A stress-induced premature senescence (SIPS) model was designed in BJ fibroblast cells using the oxidative stress agent H2O2. After this treatment, cells were treated with CA, and the potential effect of CA on senescence was evaluated using senescence-related β-galactosidase, 4',6-diamino-2-phenylindole (DAPI), acridine-orange staining (AO), comet assay, molecular docking assays, gene expression, and protein analysis. These results demonstrate that CA effectively reduces senescence markers, including senescence-associated β-galactosidase activity, DNA damage, lysosomal activity, and oxidative stress indicators such as malondialdehyde. Molecular docking revealed CA's potential interactions with critical proteins involved in senescence signalling pathways, suggesting mechanisms by which CA may exert its effects. Gene expression and protein analyses corroborated the observed anti-senescent effects, with CA modulating p16, p21, and pRB1 expressions and reducing oxidative stress markers. In conclusion, CA appeared to have senolytic and senomorphic potential in vitro, which could mitigate and reverse SIPS markers in BJ fibroblasts.

NHEJ is promoted by the phosphorylation and phosphatase activity of PTEN via regulation of DNA-PKcs

DNA double-strand breaks (DSBs) are considered one of the most harmful forms of DNA damage. These DSBs are repaired through non-homologous end joining (NHEJ) and homologous recombination (HR) pathways and defects in these processes can lead to genomic instability and promote tumorigenesis. Phosphatase and Tensin homolog (PTEN) are crucial in HR repair. However, its involvement in the NHEJ repair pathway has remained elusive. In this study, we investigate the function of epigenetic regulation of PTEN in the NHEJ repair pathway. Our findings indicate that both the phosphorylation and phosphatase activity of PTEN are required for efficient NHEJ-mediated DSB repair. During the DNA damage response, we observed a reduced expression and chromatin attachment of the key NHEJ proteins, including Ku70/80, DNA-PKcs, XRCC4, and XLF, in PTEN-null cells. This reduction was attributed to the instability of these NHEJ proteins, as confirmed by our protein half-life assay. We have demonstrated that the DNA-PKcs inhibitor, NU7026, suppresses the DNA damage-induced phosphorylation of the C-terminal of PTEN. Thus, our study indicates that PTEN could be a target of DNA-PKcs. Protein-protein docking analysis also shows that PTEN interacts with the C-terminal region of DNA-PKcs. PTEN null cells exhibit compromised DNA-PKcs foci after DNA damage as it is in a hyper-phosphorylated state. Phospho-PTEN assists in recruiting DNA-PKcs on the DNA damage site by maintaining its hypo-phosphorylated state which also depends on its phosphatase activity. Therefore, after DNA damage, crosstalk between PTEN and DNA-PKcs modulates the NHEJ pathway. Thus, during DNA damage, PTEN gets phosphorylated directly or indirectly by DNA-PKcs and attaches to chromatin, resulting in the dephosphorylation of DNA-PKcs and subsequently recruitment of other NHEJ factors on chromatin occurs for efficient execution of the NHEJ pathway. Thus, our research provides a molecular understanding of the epigenetic regulation of PTEN and its significant role in controlling the NHEJ pathway.

Synchrotron induced X-ray fluorescence spectroscopy reveals heavy metal translocation in sludge amended soil-plant systems: assessment of ecological and health risks.

The use of composted sludge from sewage treatment plants as a soil amendment is a common practice of recycling nutrients like organic carbon, nitrogen, and phosphorus. The sewage generated in larger cities of developing countries is often contaminated with various heavy metals (HMs) that ultimately end up in composted sludge. Thus, using such composted sludge is likely to pose ecological and human health risks. Hence, the knowledge of HM translocation in sludge-soil-plant systems is of vital importance. The present study was aimed at investigating the HM translocation in sludge-soil-plant system. The HM translocation was measured using synchrotron radiation-induced x-ray fluorescence spectrometry and atomic absorption spectroscopic techniques. The results indicated high HM mobility (up to 2628.5mgkg-1) from sludge to spinach plant. The metal accumulation (mgkg-1) ranged in the order-Fe (950.55-2628.5) > Zn (20.11-172.13) > Cu (13.86-136.17) > Mn (2.13-34.67) > Cd (0.11-31.17) > Pb (1.50-30.16) > Co (0.18-9.85) As (0.02-7.80) > Cr (0.01-5.69). This observed accumulation depended on the volume of sewage being treated in the sewage treatment plant (STP) and varied in the order control < (8 MLD Bhagwanpur, STP 1) < (80 MLD Dinapur, STP2) < (140 MLD Dinapur, STP3) hence the HM load coming into STPs. The metal transfer factor, bioconcentration factor, and translocation factor values also correlated with the abundance of Fe, Cu, Pb, Cd, and Zn in spinach root and shoot compartments. The carcinogenic risk for heavy metal carcinogens like As, Cd, Cr, and Pb revealed children being more prone to cancer upon spinach consumption. Hence, it is necessary to assess the heavy metals present in the sludge prior to its application in agricultural fields.

Metals Transfer in Mushroom Tricholoma matsutake from Regional High Geochemical Background Areas: Environmental Influences and Human Health Risk.

Wild-grown edible mushrooms are important in world diets and are also efficient metal accumulators. Yunnan, Southwest China, is the main producing region, with typically high levels of geochemical metals. The environmental factors, bioaccumulation, distribution and human health risks of metals were examined in paired soil and Tricholoma matsutake (n = 54). T. matsutake grows on acidified soils (pH = 3.95-6.56), and metals show a strong heterogeneity, with Fe, Mn, Zn and Cu in the ranges of 16-201, 0.046-8.58 g kg-1, and 22.6-215, 3.7-155 mg kg-1. High soil Fe content led to great accumulation in T. matsutake (0.24-18.8 g kg-1). However, though the soil Mn content was higher than that of Zn and Cu, their concentrations in T. matsutake were comparable (21.1-487 vs. 38.7-329 and 24.9-217 mg kg-1). This suggested that T. matsutake prefers to accumulate Zn and Cu compared to Mn, and this is supported by the bioaccumulation factors (BAFs = 0.32-17.1 vs. 0.006-1.69). Fe was mainly stored in stipes, while Mn, Zn and Cu were stored in caps, and the translocation factors (TFs) were 0.58 vs. 1.28-1.94. Therefore, stipe Fe showed the highest health risk index (HRI) at 1.28-26.9, followed by cap Cu (1.01-2.33), while 98-100% of the Mn and Zn were risk-free. The higher concentration and greater risk of Fe was attributed to the significant effect of soil Fe content (R = 0.34) and soil pH (R = -0.57). This study suggested that Fe, as an essential mineral, may exert toxic effects via the consumption of T. matsutake from high geochemical background areas.

Casein kinase 1α mediates estradiol secretion via CYP19A1 expression in mouse ovarian granulosa cells

BackgroundCasein kinase 1α (CK1α), expressed in both ovarian germ and somatic cells, is involved in the initial meiosis and primordial follicle formation of mouse oocytes. Using in vitro and in vivo experiments in this study, we explored the function and mechanism of CK1α in estrogen synthesis in mice ovarian granulosa cells.MethodsA CK1α knockout (cKO) mouse model, targeted specifically to ovarian granulosa cells (GCs), was employed to establish the influence of CK1α on in vivo estrogen synthesis. The influence of CK1α deficiency on GCs was determined in vivo and in vitro by immunofluorescence analysis and Western blot assay. Transcriptome profiling, differentially expressed genes and gene functional enrichment analyses, and computation protein–protein docking, were further employed to assess the CK1α pathway. Furthermore, wild-type female mice were treated with the CK1α antagonist D4476 to elucidate the CK1α's role in estrogen regulation.ResultsOvarian GCs CK1α deficiency impaired fertility and superovulation of female mice; also, the average litter size and the estradiol (E2) level in the serum of cKO female mice were decreased by 57.3% and 87.4% vs. control mice, respectively.This deficiency disrupted the estrous cycle and enhanced the apoptosis in the GCs. We observed that CK1α mediated the secretion of estradiol in mouse ovarian GCs via the cytochrome P450 subfamily 19 member 1 (CYP19A1).ConclusionsThese findings improve the existing understanding of the regulation mechanism of female reproduction and estrogen synthesis.Trial registrationNot applicable.

Ellagic acid improves osteoarthritis by inhibiting PGE2 production in M1 macrophages via targeting PTGS2.

Osteoarthritis (OA) is a degenerative joint disease characterised by inflammation and cartilage degeneration. Ellagic acid (EA) might have therapeutic potential in OA, but its molecular mechanisms of action remain unclear. In this study, we aimed to identify the docking protein of EA in M1 macrophage-related pro-inflammation in OA. Bioinformatics analysis was performed to identify ellagic acid's potential targets among OA-related dysregulated genes. THP-1 cells were induced into M0 and polarised into M1 macrophages for in vitro studies. Mice knee models of OA were generated for in vivo studies. Results showed that PTGS2 (also known as COX-2) is a potential target of ellagic acid among OA-related dysregulated genes. EA has multiple low-energy binding sites on PTGS2, including sites containing amino acid residues critical for the enzyme's catalytic activity. Surface plasmon resonance (SPR) assays confirmed the physical interaction between ellagic acid and recombinant PTGS2 protein, with a dissociation constant (KD) of 5.03 ± 0.84 μM. EA treatment suppressed PTGS2 expression and prostaglandin E2 (PGE2) production in M1 macrophages. Besides, ellagic acid can directly inhibit PTGS2 enzyme activity, with an IC50 around 50 μM. Importantly, in a mouse model of OA, ellagic acid administration alleviated disease severity, reduced collagen II degradation and MMP13 generation, and decreased serum PGE2 levels. Collectively, these results suggest that PTGS2 is a key target of ellagic acid's anti-inflammatory and chondroprotective effects in OA.

Alleviation of cadmium toxicity in soybean (Glycine max L.): Up-regulating antioxidant capacity and enzyme gene expressions and down-regulating cadmium uptake by organic or inorganic selenium

Although much interest has been focused on the role of selenium (Se) in plant nutrition over the last 20 years, the influences of organic selenium (selenomethionine; Se-Met) and inorganic selenium (potassium selenite; Se-K) on the growth and physiological characters of cadmium (Cd)-stressed Glycine max L.) seedlings have not yet been studied. In this study, the impacts of Se-Met or Se-K on the growth, water physiological parameters (gaseous exchange and leaf water content), photosynthetic and antioxidant capacities, and hormonal balance of G. max seedlings grown under 1.0 mM Cd stress were studied. The results showed that 30 μM Se-K up-regulates water physiological parameters, photosynthetic indices, antioxidant systems, enzymatic gene expression, total antioxidant activity (TAA), and hormonal balance. In addition, it down-regulates levels of reactive oxygen species (ROS; superoxide free radicals and hydrogen peroxide), oxidative damage (malondialdehyde content as an indicator of lipid peroxidation and electrolyte leakage), Cd translocation factor, and Cd content of Cd-stressed G. max seedlings. These positive findings were in favor of seedling growth and development under Cd stress. However, 50 μM Se-Met was more efficient than 30 μM Se-K in promoting the above-mentioned parameters of Cd-stressed G. max seedlings. From the current results, we conclude Se-Met could represent a promising strategy to contribute to the development and sustainability of crop production on soils contaminated with Cd at a concentration of up to 1.0 mM. However, further work is warranted to better understand the precise mechanisms of Se-Met action under Cd stress conditions.

Assessment of growth, metal uptake efficiency and yield traits of castor bean genotypes for phytoremediation of lead contaminated soils of Chakera-Faisalabad having history of long term irrigation with waste water

The agricultural soil of Chakera village, Faisalabad, Pakistan is under significant threat due to irrigation with wastewater containing Pb. Castor bean (Ricinus communis L.), a non-edible oil seed crop showed considerable capacity for phytoremediation of heavy metals. Restoration of Pb contaminated soil of Chakera using castor bean until physiological maturity could be an effective approach for mitigating hazardous impacts of Pb contamination in the soil. Hence, the present study aimed to evaluate the growth, biochemical traits, phytoremediation potential, and yield attributes of two castor bean genotypes (NIAB-2020 and DS-30) under the conditions of two different soil-filled pots; uncontaminated soil of NIAB (0 mg Pb kg−1) and contaminated soil of Chakera (250 mg Pb kg−1). Results have shown that plant agronomic, biochemical and seed compositional analysis have revealed a faint drop on Chakera soil. Metal accumulation response resulted in highest shoot Pb uptake in DS-30 compared to NIAB-2020. Conversely, maximum Pb uptake in roots of NIAB-2020 (4470 µg plant−1) was recorded when compared with DS-30 (3576 µg plant−1). Highest translocation factor (TF) was calculated for DS-30, whereas, for the metal tolerance index (MTI), both genotypes exhibited non-significant difference. Interestingly, concentration of Pb in seeds remained undetected for both genotypes. The study indicates that NIAB-2020 exhibited slightly higher tolerance than DS-30, potentially leading to economic gains through widespread use of castor oil across industries, positioning castor bean as a promising candidate for rehabilitation of contaminated soils. Nevertheless, additional in-situ investigations are necessary to validate the findings of current pot study.

Insights into the mechanism of crotamine and potential targets involved in obesity-related metabolic pathways

Crotamine (Ctm) is a peptide isolated from Crotalus durissus terrificus venom. This molecule has been demonstrated to diminish body weight gain and enhance browning in adipose tissue, glucose tolerance, and insulin sensitivity; hence, it has been postulated as an anti-obesogenic peptide. However, the mechanism to elicit the anti-obesogenic effects has yet to be elucidated. Thus, we investigated the possible interaction of Ctm with receptors involved in obesity-related metabolic pathways through protein-protein docking and molecular dynamics refinement. To test the anti-obesogenic mechanism of Ctm, we selected and retrieved 18 targets involved in obesity-related drug discovery from Protein Data Bank. Then, we performed protein-protein dockings. The best three Ctm-target models were selected and refined by molecular dynamics simulations. Molecular docking demonstrated that Ctm was able to interact with 13 of the 18 targets tested. Having a better docking score with glucagon-like peptide-1 receptor (GLP-1R) (−1430.2 kcal/mol), DPP-IV (dipeptidyl peptidase-IV) (−1781.7 kcal/mol) and α-glucosidase (−1232.3 kcal/mol). These three models were refined by molecular dynamics. Ctm demonstrated a higher affinity for GLP-1R (ΔG: −41.886 ± 2.289 kcal/mol). However, Ctm interaction was more stable with DPP-IV (RMSD: 0.360 ± 0.015 nm, Radius of gyration: 2.781 ± 0.009 nm). Moreover, the number of interactions and the molecular mechanics energies of Ctm residues suggest that the interaction of Ctm with these receptors is mainly mediated by basic-hydrophobic dyads Y1-K2, W31-R32, and W33-R34. Together, all these results allow elucidating a possible molecular mechanism behind the previously described anti-obesogenic effects.

Comprehensive analysis of Novel mutations in CCM1/KRIT1 and CCM2/MGC4607 and their clinical implications in Cerebral Cavernous malformations

BackgroundCerebral Cavernous Malformations (CCM) is a genetic disease characterized by vascular abnormalities in the brain and spinal cord, affecting 0.4-0.5 % of the population. We identified two novel pathogenic mutations, CCM1/KRIT1 c.811delT (p.Trp271GlyfsTer5) and CCM2/MGC4607 c.613_614insGG p.Glu205GlyfsTer31), which disrupt crucial protein domains and potentially alter disease progression. ObjectiveThe study aims to comprehensively analyze a Brazilian cohort of CCM patients, integrating genetic, clinical, and structural aspects. Specifically, we sought to identify novel mutations within the CCM complex, and explore their potential impact on disease progression. MethodsWe conducted a detailed examination of neuroradiological and clinical features in both symptomatic and asymptomatic CCM patients, performing genetic analyses through sequencing of the CCM1/KRIT1, CCM2/MGC4607, and CCM3/PDCD10 genes In silico structural predictions were carried out using PolyPhen-2, SIFT, and Human Genomics Community tools. Protein-protein interactions and docking analyses were explored using the STRING database. ResultsGenetic analysis identifies 6 pathogenic mutations, 4 likely pathogenic, 1 variants of uncertain significance, and 7 unclassified mutations, including the novel mutations in CCM1 c.811delT and CCM2 c.613_614insGG. In silico structural analysis revealed significant alterations in protein structure, supporting their pathogenicity. Protein-protein interaction analysis indicated nuanced impacts on cellular processes. Clinically, we observed a broad spectrum of symptoms, including seizures and focal neurological deficits. However, no statistically significant differences were found in lesion burden, age of first symptom onset, or sex between the identified CCM1/KRIT1 and CCM2/MGC4607 mutations among all patients studied. ConclusionThis study enhances the understanding of CCM by linking clinical variability, genetic mutations, and structural effects. The identification of these novel mutations opens new avenues for research and potential therapeutic strategies.

Quantitative Characterization of the Impact of Protein-Protein Interactions on Ligand-Protein Binding: A Multi-Chain Dynamics Perturbation Analysis Method.

Many protein-protein interactions (PPIs) affect the ways in which small molecules bind to their constituent proteins, which can impact drug efficacy and regulatory mechanisms. While recent advances have improved our ability to independently predict both PPIs and ligand-protein interactions (LPIs), a comprehensive understanding of how PPIs affect LPIs is still lacking. Here, we examined 63 pairs of ligand-protein complexes in a benchmark dataset for protein-protein docking studies and quantified six typical effects of PPIs on LPIs. A multi-chain dynamics perturbation analysis method, called mcDPA, was developed to model these effects and used to predict small-molecule binding regions in protein-protein complexes. Our results illustrated that the mcDPA can capture the impact of PPI on LPI to varying degrees, with six similar changes in its predicted ligand-binding region. The calculations showed that 52% of the examined complexes had prediction accuracy at or above 50%, and 55% of the predictions had a recall of not less than 50%. When applied to 33 FDA-approved protein-protein-complex-targeting drugs, these numbers improved to 60% and 57% for the same accuracy and recall rates, respectively. The method developed in this study may help to design drug-target interactions in complex environments, such as in the case of protein-protein interactions.

Signal recognition particle RNA is critical for genetic competence and virulence of Streptococcus pneumoniae.

Streptococcus pneumoniae (pneumococcus) causes multiple important infectious diseases in humans. The signal recognition particle (SRP) complex, which comprised 4.5S small cytoplasmic RNA (ScRNA), and the Ffh and FtsY proteins, mediates membrane targeting and translocation of secreted proteins in all organisms. However, the role of SRP and ScRNA has not been characterized during the induction of the competence system for genetic transformation and virulence in pneumococcus. By using a combination of genetic, biochemical, proteomic, and imaging approaches, we demonstrated that the SRP complex plays a significant role in membrane targeting of competence system-regulated effectors important for genetic transformation, virulence during bacteremia and pneumonia infections, and nutritional acquisition.

Co-exposure to Organophosphate esters (OPEs) and Cadmium alleviated their accumulation in rice (Oryza sativa L.) by inhibiting transports' transcription

Combined contamination of Organophosphate esters (OPEs) and heavy metal has been concerning on their potential threaten to human health through food chain. In order to estimate effects of OPEs and heavy metal's combined contamination on crop, the growth of rice seedlings, pollutant accumulations and their involved in transcript regulation pathway under OPEs and Cd contamination were investigated. In results, only single OPEs pollution improved the biomass of rice, while single Cd pollution inhibited the growth of plants. Although the combined contaminations of OPEs and Cd also showed negative effect for plant growth, OPEs could alleviate the negative effect of Cd on rice. The Octanol-water partition coefficients (log Kow) of OPEs were positively correlated with root concentration factor (RCF) values in the trend line and negatively correlated with shoot concentration factor (SCRF) and translocation factor (TF). OPEs and Cd inferred with each other's accumulations in plants through reducing RCF, SCRF and TF. After addition of Cd, the expressions of OsTIL, OsLTP4, OsLTPL1, and OsMLP423 genes involved in OPEs accumulation were downregulated. Moreover, the presence of Cd also affected the binding sites and binding energy of the four proteins with OPEs. Meanwhile, the expression of OsNramp1, OsNramp5, OsHMA2, OsGS1, and OsPCS1 genes involved in Cd accumulation and toleration were also downregulated after addition of OPEs. These results suggested that OPEs and Cd directly repressed each other gene transcript involved in accumulation and toleration process.

SRP54 of black carp negatively regulates MDA5-mediated antiviral innate immunity

Signal Recognition Particle 54 kDa (SRP54) is a subunit of the signal recognition particle (SRP), a cytoplasmic ribonucleoprotein complex guiding the transportation of newly synthesized proteins from polyribosomes to endoplasmic reticulum. In mammals, it has been reported to regulate the RLR signaling pathway negatively by impairing the association between MAVS and MDA5/RIG-I. However, the role of SRP54 in teleost antiviral innate immune response remains obscure. In this study, the SRP54 homolog of black carp (bcSRP54) has been cloned, and its function in antiviral innate immunity has been elucidated. The CDS of bcSRP54 gene consists of 1515 nucleotides and encodes 504 amino acids. Immunofluorescence (IF) showed that bcSRP54 was mainly distributed in the cytoplasm. Overexpressed bcSRP54 significantly reduced bcMDA5-mediated transcription of interferon (IFN) promoter in reporter assay. Co-expression of bcSRP54 and bcMDA5 significantly suppressed bcMDA5-mediated IFN signaling and antiviral activity, while bcSRP54 knockdown increased the antiviral ability of host cells. In addition, the results of the immunofluorescence staining demonstrated the subcellular overlapping between bcSRP54 and bcMDA5, and the co-immunoprecipitation (co-IP) experiment identified their association. Furthermore, the over-expression of bcSRP54 did not influence the protein expression and ubiquitination modification level of bcMDA5, however, hindered the binding of bcMDA5 to bcMAVS. In summary, our results conclude that bcSRP54 targets bcMDA5 and inhibits the interaction between bcMDA5 and bcMAVS, thereby negatively regulating antiviral innate immunity, which provides insight into how teleost SRP54 regulates IFN signaling.