Homologous Proteins Research Articles

Major advances in protein function assignment by remote homolog detection with protein language models - A review.

There is an ever-increasing need for accurate and efficient methods to identify protein homologs. Traditionally, sequence similarity-based methods have dominated protein homolog identification for function identification, but these struggle when the sequence identity between the pairs is low. Recently, transformer architecture-based deep learning methods have achieved breakthrough performances in many fields. One type of model that uses transformer architecture is the protein language model (pLM). Here, we describe methods that use pLMs for protein homolog identification intended for function identification and describe their strengths and weaknesses. Several important ideas emerge, such as filtering the substitution matrix generated from embeddings, selecting specific pLM layers for specific purposes, compressing the embeddings, and dividing proteins into domains before searching for homologs that improve remote homolog detection accuracy considerably. All of these approaches produce huge numbers of new homologs that can reliably extend the reach of protein relationships for a deeper understanding of evolution and many other problems.

Protein binding and folding through an evolutionary lens.

Protein-protein associations are often mediated by an intrinsically disordered protein region interacting with a folded domain in a coupled binding and folding reaction. Classic physical organic chemistry approaches together with structural biology have shed light on mechanistic aspects of such reactions. Further insight into general principles may be obtained by interpreting the results through an evolutionary lens. This review attempts to provide an overview on how the analysis of binding and folding reactions can benefit from an evolutionary approach, and is aimed at protein scientists without a background in evolution. Evolution constantly reshapes existing proteins by sampling more or less fit variants. Most new variants are weeded out as generations and new species come and go over hundreds to hundreds of millions of years. The huge ongoing genome sequencing efforts have provided us with a snapshot of existing adapted fit-for-purpose protein homologs in thousands of different organisms. Comparison of present-day orthologs and paralogs highlights general principles of the evolution of coupled binding and folding reactions and demonstrate a great potential for evolution to operate on disordered regions and modulate affinity and specificity of the interactions.

Radiogenomics and machine learning predict oncogenic signaling pathways in glioblastoma

BackgroundGlioblastoma (GBM) is a highly aggressive brain tumor associated with a poor patient prognosis. The survival rate remains low despite standard therapies, highlighting the urgent need for novel treatment strategies. Advanced imaging techniques, particularly magnetic resonance imaging (MRI), are crucial in assessing GBM. Disruptions in various oncogenic signaling pathways, such as Receptor Tyrosine Kinase (RTK)-Ras-Extracellular signal-regulated kinase (ERK) signaling, Phosphoinositide 3- Kinases (PI3Ks), tumor protein p53 (TP53), and Neurogenic locus notch homolog protein (NOTCH), contribute to the development of different tumor types, each exhibiting distinct morphological and phenotypic features that can be observed at a microscopic level. However, identifying genetic abnormalities for targeted therapy often requires invasive procedures, prompting exploration into non-invasive approaches like radiogenomics. This study explores the utility of radiogenomics and machine learning (ML) in predicting these oncogenic signaling pathways in GBM patients.MethodsWe collected post-operative MRI scans (T1w, T1c, FLAIR, T2w) from the BRATS-19 dataset, including scans from patients with both GBM and LGG, linked to genetic and clinical data via TCGA and CPTAC. Signaling pathway data was manually extracted from cBioPortal. Radiomic features were extracted from four MRI modalities using PyRadiomics. Dimensionality reduction and feature selection were applied and Data imbalance was addressed with SMOTE. Five ML models were trained to predict signaling pathways, with Grid Search optimizing hyperparameters and 5-fold cross-validation ensuring unbiased performance. Each model’s performance was evaluated using various metrics on test data.ResultsOur results showed a positive association between most signaling pathways and the radiomic features derived from MRI scans. The best models achieved high AUC scores, namely 0.7 for RTK-RAS, 0.8 for PI3K, 0.75 for TP53, and 0.4 for NOTCH, and therefore, demonstrated the potential of ML models in accurately predicting oncogenic signaling pathways from radiomic features, thereby informing personalized therapeutic approaches and improving patient outcomes.ConclusionWe present a novel approach for the non-invasive prediction of deregulation in oncogenic signaling pathways in glioblastoma (GBM) by integrating radiogenomic data with machine learning models. This research contributes to advancing precision medicine in GBM management, highlighting the importance of integrating radiomics with genomic data to understand tumor behavior and treatment response better.

Genetic diversity of Plasmodium falciparum reticulocyte binding protein homologue-5, which is a potential malaria vaccine candidate: baseline data from areas of varying malaria endemicity in Mainland Tanzania

BackgroundThe limited efficacy of the two recently approved malaria vaccines, RTS,S/AS01 and R21/Matrix- M™, highlights the need for alternative vaccine candidate genes. Plasmodium falciparum Reticulocyte Binding Protein Homologue 5 (Pfrh5) is a promising malaria vaccine candidate, given its limited polymorphism, its essential role in parasite survival, a lack of immune selection pressure and higher efficacy against multiple parasites strains. This study evaluated the genetic diversity of Pfrh5 gene among parasites from regions with varying malaria transmission intensities in Mainland Tanzania, to generate baseline data for this potential malaria vaccine candidate.MethodsThis study utilized secondary data of 697 whole-genome sequences which were generated by the MalariaGEN Community Network. The samples which were sequenced to generated the data were collected between 2010 and 2015 from five districts within five regions of Mainland Tanzania, with varying endemicities (Morogoro-urban district in Morogoro region, Muheza in Tanga, Kigoma-Ujiji in Kigoma, Muleba in Kagera, and Nachingwea district in Lindi region). Wright's fixation index (FST), Wright’s inbreeding coefficient (Fws), Principal component analysis (PCA), nucleotide diversity (π), haplotype network, haplotype diversity (Hd), Tajima's D, and Linkage disequilibrium (LD) were used to assess the diversity of the gene.ResultsOf the sequences used in this study, 84.5% (n = 589/697) passed quality control and 313 (53.1%) were monoclonal (contained infections from a single strain of P. falciparum) and were used for haplotype diversity and haplotype network analysis. High within-host diversity (Fws < 0.95) was reported in Kigoma-Ujiji (60.7%), Morogoro-urban (53.1%), and Nachingwea (50.8%), while Muleba (53.9%) and Muheza (61.6%) had low within-host diversity (Fws ≥ 0.95). PCA did not show any population structure and the mean FST value was 0.015. Low nucleotide diversity values were observed across the study sites (mean π = 0.00056). A total of 27 haplotypes were observed among the 313 monoclonal samples and under-fives exhibited higher haplotype counts. The Pf3D7 was detected as Hap_1, which occurred in 16/313 (5.1%) monoclonal sequences. Negative Tajima's D values were observed among the parasite populations in all the study sites.ConclusionLow levels of polymorphism in the pfrh5 gene were observed based on low nucleotide and haplotype diversity, a lack of population structure and negative Tajima’s D values. This study provides essential data on the diversity of the Pfrh5 gene indicating that it can be considered in the development of the next generation malaria vaccines. Robust and intensive studies of this and other candidate genes are crucial to support the prioritization of the Pfrh5 gene for potential inclusion in a broadly cross-protective malaria vaccine.

Sagittaria sagittifolia polysaccharide extract regulates Nrf2 to improve endoplasmic reticulum stress-mediated apoptosis in rat cataracts and HLEB3 cells.

Age-related cataract (ARC) remains the leading cause of blindness worldwide. Sagittaria sagittifolia polysaccharide (SSP) extract, a key component of Sagittaria sagittifolia L., exhibits anti-oxidant and anti-apoptotic effects with potential applications in ARC. This study aimed to explore the therapeutic potential of SSP in ARC and the underlying mechanisms. In sodium selenite-induced cataracts in rats and hydrogen peroxide (H2O2)-induced human lens epithelial B3 (HLEB3) cells, SSP significantly improved lens opacity and pathological changes and alleviated apoptosis and endoplasmic reticulum stress (ERS)-related injury indicators (by inhibiting the intracellular Ca2+ and protein expression of Bcl-2-associated X, cleaved caspase-3, binding immunoglobulin heavy chain protein, protein kinase RNA-like kinase), inositol-requiring enzyme 1α, activating transcription factor 6, C/EBP homology protein, c-Jun N terminal kinase, caspase-12, and calpain-2). In addition, SSP increased the expression of nuclear factor erythroid 2-related factor 2 (Nrf2), heme oxygenase-1, sarco/endoplasmic reticulum-type calcium transport ATPase 2, and B-cell lymphoma-2. After applying Nrf2 knockdown technology by transferring short interfering RNA in HLEB3 cells, SSP demonstrated its protective role by activating Nrf2 and inhibiting ERS-mediated apoptosis. These findings indicate that SSP may protect against ARC by regulating Nrf2/ERS-mediated apoptosis, providing potential evidence for its use in preventing or delaying ARC.

P0210 ORMDL proteins regulate intestinal epithelial cell homeostasis by modulating ER architecture, autophagy, and DNA damage response

Abstract Background ORM1-like protein 3 (ORMDL3) is a risk gene for asthma and inflammatory bowel disease (IBD), identified in genome-wide association studies (GWAS).1,2 It encodes an endoplasmic reticulum (ER)-resident transmembrane protein implicated in calcium homeostasis, sphingolipid biosynthesis, and regulation of the unfolded protein response (UPR) upon ER stress.3,4 However, the role of ORMDL3 and its homologous protein family members ORMDL1 and ORMDL2, which exhibit partly redundant functions, remains unclear in the context of intestinal inflammation. Methods Constitutive and conditional intestinal epithelial cell-specific knockout (KO) mice for Ormdl1, Ormdl2, and Ormdl3 were generated. Histological analysis of small intestinal (SI) Paneth cells (lysozyme immunohistochemistry), goblet cells (periodic acid-Schiff staining) and ER morphology in Paneth cells (transmission electron microscopy [TEM]) was conducted. Interactions between ORMDL proteins and autophagy-related proteins were examined by co-immunoprecipitation and immunoblot assays in irradiated mouse embryonic fibroblasts (iMEFs). Organoids derived from Ormdl1/2/3ΔIEC mice were used for bulk RNA sequencing. Results The Ormdl1/2/3 triple KO was embryonically lethal, while Ormdl3-KO and Ormdl1/3 double KO mice exhibited reduced body size, weight, and embryonic viability, along with fewer Paneth and goblet cells. To eliminate any compensatory effects of the multiple ORMDL proteins, the Ormdl1/2/3ΔIEC mice were analyzed. These mice showed no macroscopic phenotype but displayed microscopic inflammation, reduced Paneth and goblet cells, and increased SI tuft cells. Both constitutive and conditional Ormdl knockout mice showed massive dilation of the ER. While autophagy is a known compensatory mechanism resolving ER stress, we demonstrated that ORMDL3 co-localized and co-precipitated with the autophagy-related protein LC3 (microtubule-associated protein 1A/1B-light chain 3). Consistent with this, loss of ORMDL proteins compromised autophagic flux. Bulk RNA sequencing of SI organoids from Ormdl1/2/3ΔIEC mice revealed reduced expression of genes involved in lipid biosynthesis, tuft cell differentiation via BMP-signalling, and innate immunity, including antimicrobial peptides, likely due to loss of Paneth cells. In contrast, DNA damage response genes were upregulated, as reflected by an increase in γ-H2AX-positive epithelial cells. Conclusion The data suggest a critical regulatory role for ORMDL proteins in the ER-autophagy axis within epithelial cells, shaping mucosal homeostasis and expression of antimicrobial peptides, thereby conferring protection against IBD. Further studies are required to elucidate the molecular basis of the function of ORMDL proteins in intestinal inflammation.

Lycopene mitigates paclitaxel-induced cognitive impairment in mice; Insights into Nrf2/HO-1, NF-κB/NLRP3, and GRP-78/ATF-6 axes.

Chemotherapy-induced cognitive impairment, referred to as "chemobrain", is widely acknowledged as a significant adverse effect of cancer therapy. Paclitaxel, a chemotherapeutic drug, has been reported to cause cognitive impairment clinically and in animal models. However, the precise mechanisms are not fully understood. The current study explored the potential neuroprotective effect of lycopene in paclitaxel-induced cognitive impairment in mice and its potential underlying mechanisms. Mice were randomly allocated into six groups: control, paclitaxel-treated (10 mg/kg), lycopene-treated (5, 10, and 20 mg/kg) + paclitaxel, and lycopene alone-treated (20 mg/kg) groups. The effect of lycopene treatment on behavioral function and histological examination was assessed. Lycopene (20 mg/kg) was selected for additional investigation into the underlying mechanisms. Lycopene treatment counteracted paclitaxel-induced oxidative stress by reducing lipid peroxidation and enhancing catalase levels. Additionally, lycopene-treated mice demonstrated a significant elevation in nuclear factor erythroid 2-related factor 2 with no significant effect on hemeoxygenase-1. Moreover, paclitaxel administration elevated endoplasmic reticulum stress markers; glucose-regulated protein78, activating Transcription Factor 6, C/EBP homologous protein, and apoptosis marker annexin V which were significantly reduced by lycopene treatment. Furthermore, lycopene mitigated paclitaxel-induced neuroinflammation through the reduction of the levels of the NLR Family Pyrin Domain Containing 3 (NLRP3) inflammasome axis markers; nuclear factor-κB, NLRP3, caspase-1, interleukin-1β, and interleukin-18. Our study findings may provide new evidence that lycopene mitigates paclitaxel-induced cognitive impairment in mice by reversing oxidative stress, endoplasmic reticulum stress, and inflammatory mechanisms.

JrMYB44 is required for the accumulation of polyphenols and contributes to drought tolerance in Juglans regia

Juglans regia, an important economic tree species, is planted all over the world, and drought is one of the crucial factors limiting its growth and development. The various polyphenol content in walnut plants constitutes one of the material bases for the differences in stress resistance among various germplasms. However, the molecular mechanism underlying stress response mediated by polyphenol -dependent pathways remains unclear. v-Myb avian myeloblastosis viral oncogene homolog (MYB) protein of transcription factors play important regulatory roles in the process of plant stress responses. Previously, we identified JrMYB44 could be involved in osmotic stress response in walnut. In this study, we confirmed that the drought resistance of four walnut cultivars (‘Chandler’, ‘Xiangling’, ‘Xilin2’ and ‘Xifu1’) is positively correlated with the accumulation of polyphenols. The content and component changes of polyphenols in JrMYB44 overexpression (OE) and suppression (SE) lines in both walnut and Arabidopsis thaliana demonstrated that JrMYB44 positively regulated polyphenols accumulation. The variation of JrMYB44 expression and polyphenol levels under drought treatment indicated significant correlation between JrMYB44-induced drought tolerance and polyphenol accumulation, which was involved in reactive oxidative species (ROS) balance. The differentially expressed genes (DEGs) between OE and WT implied that JrMYB44 could positively activate downstream genes to participate in the drought stress response. Yeast one-hybrid (Y1H), transient GUS expression assay and dual-luciferase reporter assay (DLR) confirmed that JrMYB44 could recognize downstream JrWRKY7 and JrDREB2A, two transcription factors previously reported to be involved in drought response. Meanwhile, it was confirmed by Y2H, GST-pull down and luciferase complementation imaging assay (LCI) that JrMYB44 could interact with JrMYC2 and JrDof1, another two previously reported potential drought response regulators. Collectively, these results indicated that JrMYB44 could activate JrWRKY7, JrDREB2A and interact with JrMYC2 and JrDof1 to promote walnut polyphenol accumulation and improve drought resistance in a ROS dependent manner.

Plant BCL-DOMAIN HOMOLOG proteins play a conserved role in SWI/SNF complex stability

The SWItch/Sucrose Non-Fermenting (SWI/SNF) complexes are evolutionarily conserved, ATP-dependent chromatin remodelers crucial for multiple nuclear functions in eukaryotes. Recently, plant BCL-DOMAIN HOMOLOG (BDH) proteins were identified as shared subunits of all plant SWI/SNF complexes, significantly impacting chromatin accessibility and various developmental processes in Arabidopsis. In this study, we performed a comprehensive characterization of bdh mutants, revealing the role of BDH in hypocotyl cell elongation. Through detailed analysis of BDH domains, we identified a plant-specific N-terminal domain that facilitates the interaction between BDH and the rest of the complex. Additionally, we uncovered the critical role of the BDH β-hairpin domain, which is phylogenetically related to mammalian BCL7 SWI/SNF subunits. While phylogenetic analyses did not identify BDH/BCL7 orthologs in fungi, structure prediction modeling demonstrated strong similarities between the SWI/SNF catalytic modules of plants, animals, and fungi and revealed the yeast Rtt102 protein as a structural homolog of BDH and BCL7. This finding is supported by the ability of Rtt102 to interact with the Arabidopsis catalytic module subunit ARP7 and partially rescue the bdh mutant phenotypes. Further experiments revealed that BDH promotes the stability of the ARP4-ARP7 heterodimer, leading to the partial destabilization of ARP4 in the SWI/SNF complexes. In summary, our study unveils the molecular function of BDH proteins in plant SWI/SNF complexes and suggests that β-hairpin-containing proteins are evolutionarily conserved subunits crucial for ARP heterodimer stability and SWI/SNF activity across eukaryotes.

Characterization of Human Senescent Cell Biomarkers for Clinical Trials.

There is an increasing need for biomarkers of senescent cell burden to facilitate the selection of participants for clinical trials. p16Ink4a is encoded by the CDKN2A locus, which produces five variant transcripts in humans, two of which encode homologous p16 proteins: p16Inka4a, encoded by p16_variant 1, and p16ɣ, encoded by p16_variant 5. While distinct quantitative polymerase chain reaction primers can be designed for p16_variant 5, primers for p16_variant 1 also measure p16_variant 5 (p16_variant 1 + 5). In a recent clinical trial evaluating the effects of the senolytic combination, dasatinib + quercetin (D + Q), on bone metabolism in postmenopausal women, we found that women in the highest tertile for T-cell expression of p16_variant 5 had the most robust skeletal responses to D + Q. Importantly, the assessment of p16_variant 5 was more predictive of these responses than p16_variant 1 + 5. Here, we demonstrate that invitro, p16_variant 1 + 5 increased rapidly (Week 1) following the induction of DNA damage, whereas p16_variant 5 increased later (Week 4), suggesting that p16_variant 5 becomes detectable only when the abundance of senescent cells reaches some threshold. Further analysis identified a SASP panel in plasma that performed as well in identifying postmenopausal women with a positive skeletal response to D + Q. Collectively, our findings provide further support for the T-cell p16_variant 5 assay as a biomarker for selecting participants in clinical trials of senolytic interventions. In addition, our data indicate that correlated plasma SASP markers could be used in lieu of the more technically challenging T-cell p16 assay. Trial Registration: ClinicalTrials.gov identifier: NCT04313634.

Discovery of Small Molecules that Bind to Son of Sevenless 2 (SOS2).

The Son of Sevenless (SOS) protein family includes two highly homologous proteins, SOS1 and SOS2, that act as guanine nucleotide exchange factors (GEFs) for RAS proteins. They catalyze the GDP-to-GTP exchange, resulting in an increase of the active GTP-bound form of RAS. Despite highly similar structures and expression patterns, SOS1 is generally accepted as the dominant RAS GEF for downstream signaling in pathological states. Nonetheless, SOS2 has been reported to critically impact the RAS-PI3K/AKT signaling axis, especially in KRAS-driven cancer cell lines and in the absence of SOS1. Hence, therapeutic targeting of SOS2 may be an attractive strategy to target RAS-driven malignancies. Herein, we report the discovery and initial optimization of a selective quinazoline-based compound series that binds with micromolar affinity to the catalytic site of SOS2. We also disclose an additional, previously unreported binding site on SOS2 occupied by a different small molecule class.

Selective Synthesis of Cyclopeptides with a 2-Oxindole or 3a-Hydroxy-hexahydropyrrolo-[2,3-b]indole Structure by Cytochrome P450 Enzymes.

The structural groups of 2-oxindole and tricyclic 3a-hydroxy-hexahydropyrrolo-[2,3-b]indole (HO-HPI) are important pharmacophores. Chemical synthesis of complex alkaloids containing a 2-oxindole or HO-HPI moiety, especially the latter one, has been a long-standing challenge. Herein, we characterized the P450 enzyme AfnD, and its homologue proteins, HmtT, ClpD, KtzM, and LtzR, as cyclopeptide 2-oxindole and HO-HPI monooxygenases (cpOPMOs) that could introduce a 2-oxindole or HO-HPI moiety into the tryptophan-containing cyclopeptides in a pH-dependent manner. A universal catalytic mechanism was proposed for the five cpOPMOs, in which two conserved residues, Asp and Ser (Thr for LtzR), were proposed to divergently open the epoxide intermediates, thereby forming a 2-oxindole or HO-HPI moiety. Based on this, we constructed ten Asp or Ser/Thr mutants of cpOPMOs, which could synthesize cyclopeptides with an HO-HPI or 2-oxindole structure, selectively, under appropriate reaction conditions. All of the ten cpOPMO mutants exhibited high substrate promiscuities and usually performed well with cyclopeptides that are structurally similar to their native substrates. Overall, our work discovers a group of intriguing P450 enzymes, the cpOPMOs, and provides a powerful enzymatic toolkit for the selective synthesis of HO-HPI- or 2-oxindole-containing cyclopeptides.

Dual regulation of the levels and function of Start transcriptional repressors drives G1 arrest in response to cell wall stress

BackgroundMany different stress signaling pathways converge in a common response: slowdown or arrest cell cycle in the G1 phase. The G1/S transition (called Start in budding yeast) is a key checkpoint controlled by positive and negative regulators. Among them, Whi7 and Whi5 are transcriptional repressors of the G1/S transcriptional program, yeast functional homologs of the Retinoblastoma family proteins in mammalian cells. Under standard conditions, Whi7 plays a lesser role than Whi5 in Start inhibition. However, under cell wall stress, Whi7 is induced and plays a more important role in G1/S control. In this work, we investigated the functional hallmarks of Whi7 and Whi5, which determine their strength as Start inhibitors under cell wall stress.MethodsThe response of Saccharomyces cerevisiae to Calcofluor White was investigated to characterize the regulation and function of Whi7 and Whi5 under cell wall stress. To control their protein levels, we used dose-dependent β-estradiol-induced expression and auxin-induced degron protein fusions. We also performed Chromatin Immunoprecipitation assays to investigate Whi7 and Whi5 association with Start promoters and scored cell cycle arrest and re-entry using cell microscopy assays.ResultsWe found that cell wall stress promoted the specific upregulation of the Whi7 Start repressor. First, although cell wall stress increases Whi7 protein levels, this is not the only determinant behind the Whi7 function in promoting G1 arrest. Indeed, artificial induction of Whi5 at the same protein level resulted in a lower G1 block. Second, under cell wall stress, Whi7 was specifically recruited to SBF-target promoters, independent of the increase in its protein levels or cell cycle stage. Finally, we found that Whi7 protein instability further increased during cell wall stress and that Whi7 degradation triggered advanced cell cycle re-entry.ConclusionsHere, we show that cell wall stress signaling specifically enhances Whi7 function as a Start transcriptional repressor. Importantly, we identified new Whi7-specific regulatory mechanisms that do not operate in the Whi5 repressor. Our results indicate that cells may benefit from stress-specific repressors to ensure the stress-induced G1 arrest and that Whi7 rapid degradation may be particularly important to resume cell cycle upon adaptation.

Early Evaluation of the Interaction and Gender Differences in Combination of Apatinib and Metoprolol Using Humanized CYP2D6 Model.

Apatinib, a commonly used tyrosine kinase inhibitor in cancer treatment, can cause adverse reactions such as hypertension. Hypertension, in turn, can increase the risk of certain cancers. The coexistence of these diseases makes the use of combination drugs more common in clinical practice, but the potential interactions and regulatory mechanisms in these drug combinations are poorly understood. We used the humanized CYP2D6 mouse model to predict the effect of apatinib on the pharmacokinetics and pharmacodynamics of metoprolol and investigated the interactional mechanism. The inhibitory effects and mechanisms of apatinib on metoprolol were investigated in vitro by using wild-type mouse liver microsomes (WT MLMs), humanized CYP2D6 mouse liver microsomes (hCYP2D6 MLMs), and human liver microsomes (HLMs). Molecular docking was utilized to explore the structural basis of the observed inhibitory mode. And in vivo interaction between apatinib and metoprolol was assessed by pharmacokinetics study using the humanized CYP2D6 mice. In vitro studies and molecular docking experiments indicated that apatinib competitively inhibited the metabolism of metoprolol. In vivo findings revealed that the administration of apatinib combined with metoprolol resulted in a significant increase in the AUC(0-t), AUC(0-∞) and Cmax of metoprolol; additionally, there was a reduction in the CLz/F and heart rate, indicating that apatinib strongly inhibited metoprolol metabolism. And the homologous CYP2D6 protein in WT mice was more sensitive to apatinib compared to the hCYP2D6 mice. Gender analysis revealed that metoprolol accumulation was more pronounced in male mice when combined with apatinib, indicating a higher susceptibility to cardiotoxicity in males.

Hantaan virus glycoprotein Gc induces NEDD4-dependent PTEN ubiquitination and degradation to escape the restriction of autophagosomes and facilitate viral propagation.

Hantaan virus (HTNV) infection causes severe hemorrhagic fever with renal syndrome (HFRS) in humans and the infectious process can be regulated by autophagy. The phosphatase and tensin homolog (PTEN) protein has antiviral effects and plays a critical role in the autophagy pathway. However, the relationship between PTEN and HTNV infection is not clear and whether PTEN-regulated autophagy involves in HTNV replication is unknown. Here, we identified that HTNV infection inhibits PTEN expression invitro and invivo. The HTNV glycoprotein Gc promotes PTEN ubiquitination and degradation through 26S-proteasome pathway via the E3 ubiquitin ligase NEDD4. In addition, knockdown of PTEN prevents autophagy and increases HTNV production, while overexpression of PTEN induces autophagosome formation which can wrap HTNV particles, thus leading to restrain the production of progeny viruses. Altogether, our findings reveal the role of PTEN in HTNV infection by autophagy, highlighting the potential importance of PTEN and autophagy in the treatment of HFRS diseases.

SUGT1 is a prognostic biomarker and is associated with immune infiltrates in ovarian cancer

BackgroundOvarian cancer (OC) is a prevalent gynecological malignancy with a relatively dismal prognosis. The SGT1 homolog (SUGT1) protein, which interacts with heat shock protein 90 and is essential for the G1/S and G2/M transitions, was formerly thought to be a cancer promoter, but its precise role in OC remains unknown.MethodsWe conducted a comprehensive bioinformatics analysis of SUGT1 expression in patients with OC compared with their normal controls, including the data from the cancer genome atlas (TCGA), genotype–tissue expression (GTEx) databases, gene ontology (GO) analysis, Kyoto Encylopedia of Genes and Genomes (KEGG) analysis, gene set enrichment analysis (GSEA), single sample gene set enrichment analysis (ssGSEA). In addition, Kaplan–Meier (KM) analysis, univariate and multivariate Cox analyses were applied to investigate the prognostic role of SUGT1 in ovarian cancer. Furthermore, we validated the expression of SUGT1 in OC and normal tissues through immunohistochemistry.ResultsSUGT1 was significantly overexpressed in OC than in normal tissues. In addition, the GO, KEGG and GSEA analysis revealed that SUGT1 was associated with the functions related to immunoglobulin complex, antigen binding, immunoglobulin receptor binding, among others. Besides, ssGSEA demonstrated a positive correlation between SUGT1 expression and the abundance of T central memory cells, natural killer cells, and T gamma delta cells, although it showed a negative association with activated dendritic cells, cytotoxic cells, T cells, and T helper 1 cells. Subsequently, KM survival analysis revealed that high SUGT1 expression indicated a shorter overall survival, disease specific survival and progression free interval in OC patients. Univariate and multivariate Cox regression revealed that SUGT1 could serve as an independent risk factor for prognosis of patients with OC.ConclusionsAll these results of this study show that SUGT1 is an important molecular component in immune infiltration in OC and may have a new significant prognostic role in OC.

Discovery of novel tepovirus genomes with a nucleic acid-binding protein homolog by systematic analysis of plant transcriptome data

Discovery of novel tepovirus genomes with a nucleic acid-binding protein homolog by systematic analysis of plant transcriptome data

Molecular Evolution of Paralogous Cold Shock Proteins in E. coli: A Study of Asymmetric Divergence and Protein Functional Networks.

Nine homologous Cold Shock Proteins (Csps) have been recognized in the E.coli Cold Shock Domain gene family. These Csps function as RNA chaperones. This study aims to establish the evolutionary relationships among these genes by identifying and classifying their paralogous counterparts. It focuses on the physicochemical, structural, and functional analysis of the genes to explore the phylogeny of the Csp gene family. Computational tools were employed for protein molecular modeling, conformational analysis, functional studies, and duplication-divergence assessments. The research also examined amino acid conservation, protein mutations, domain-motif patterns, and evolutionary residue communities to better understand residual interactions, evolutionary coupling, and co-evolution. H33, M5, W11 and F53 residues were highly conserved within the protein family. It was further seen that residues M5, G17, G58, G61, P62, A64, V67 were intolerant to any kind of mutation whereas G3, D40, G41, Y42, S44, T54, T68, S69 were most tolerable towards substitutions. The study of residue communities displayed that the strongest residue coupling was observed in N13, F18, S27, F31, and W11. It was observed that all the gene pairs except CspF/CspH had new motifs generated over time. It was ascertained that all the gene pairs underwent asymmetric expression divergence after duplication. The Ka/ Ks ratio also revealed that all residues undertook neutral and purifying selection pressure. New functions were seen to develop in gene pairs evident from generation of new motifs. The discovery of new motifs and functions in Csps highlights their adaptive versatility, crucial for E. coli's resilience to environmental stressors and valuable for understanding bacterial stress response mechanisms. These findings will pave the way for future investigations into Csp evolution, with potential applications in microbial ecology and antimicrobial strategy development.

The Functional Identification of the CYP2E1 Gene in the Kidney of Lepus yarkandensis.

This study aims to identify the function of the cytochrome P450 2E1 (CYP2E1) gene in the kidneys of Lepus yarkandensis. CYP2E1 is a significant metabolic enzyme involved in the metabolism of various endogenous and exogenous compounds and is associated with the occurrence and progression of multiple diseases. Given L. yarkandensis's ability to survive in the extremely arid L. yarkandensis, we hypothesize that CYP2E1 in its kidneys plays a crucial role in adaptability. Through molecular cloning and sequence analysis, we discovered that the CYP2E1 gene of Lepus yarkandensis encodes a protein of 493 amino acids. The 493-amino acid protein encoded by the Lepus yarkandensis CYP2E1 gene shows 13 amino acid variation sites compared to the homologous protein in Oryctolagus cuniculus. The protein is primarily localized to the endoplasmic reticulum membrane and lacks transmembrane structures. In the yeast expression system, the heterologous expression of the CYP2E1 gene enhanced the yeast's tolerance to drought, salinity, and high temperatures, achieved by increasing antioxidant enzyme activity and reducing levels of oxidative stress markers. Additionally, this study identified a "Yeast Oxidative Stress Lethal Threshold (Yeast OSLT)" under specific stress conditions. Once this threshold is exceeded, the cell's antioxidant defense system can no longer maintain cellular homeostasis, leading to massive cell death. Although CYP2E1 did not change this threshold, it contributed to cell survival to some extent. These findings not only reveal the function of L. yarkandensis CYP2E1 in stress adaptation but also provide valuable molecular insights into its survival strategy in extreme environments.

Curcumin-Loaded Maltodextrin-Based Proniosomes Potentially Effective against Gemcitabine-Resistant Cholangiocarcinoma.

Cholangiocarcinoma (CCA) or bile-duct cancer is most prevalent in Southeast Asian counties including Thailand. Patients present at an advanced stage when the cancer is often drug resistant, leading to chemotherapy failure. Curcumin has therapeutic potential with various anticancer properties. However, its effectiveness is limited by its low bioavailability, poor solubility, and instability. This study aimed to synthesize, characterize and evaluate the efficacy of curcumin-loaded maltodextrin-based proniosomes (CMPNs) to overcome the limitations of curcumin for treating gemcitabine-resistant CCA cells (KKU-213BGemR) in vitro and in vivo. Various proniosome formulations were developed and tested for their efficacy against KKU-213BGemR cells using cytotoxicity, clonogenic, migration, and invasion assays. The potential mechanism involving in cell cycle arrest, apoptosis, expression of C/EBP homologous protein (CHOP), a pro-apoptotic transcription factor, and other apoptotic markers were investigated. The results showed that nanoscale CMPNs exhibited a good curcumin loading capacity and an entrapment efficiency of over 97%, as well as good stability and permeability through porcine esophageal mucosa. CMPNs inhibited proliferation, colony formation, migration/invasion and induced apoptosis in KKU-213BGemR cells. Western blot analysis revealed CMPNs significantly increased CHOP, the cleavage products of poly(ADP-ribose) polymerase-1 (PARP-1), apoptosis-inducing factor, and caspase-3 expression in KKU-213BGemR cells. A xenograft model revealed that 62.5 mg/kg BW CMPNs significantly suppressed proliferating cell nuclear antigen and increased CHOP-mediated apoptosis, leading to significantly reduced tumor volume. In conclusion, CMPNs effectively overcome limitations of curcumin and offer an effective strategy against gemcitabine-resistant CCA via CHOP-mediated pathways. These proniosomes are promising as an alternative treatment approach for CCA.