1461 research outputs found
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CacyBP/SIP - RPL6 interaction: potential influence on ribosome function
Full text linkPreviously, we have shown that CacyBP/SIP interacts with NPM1, a protein involved in ribosome biogenesis. In this work, we extended our previous studies to look for the potential impact of CacyBP/SIP on ribosome biogenesis and/or function. Using mass spectrometry analysis, we have found that several RPs could be potential CacyBP/SIP targets. Since RPL6 was one of the proteins with the best quality scores identified in this analysis we focused on the possible interaction between CacyBP/SIP and RPL6. By applying various biochemical methods, we confirmed this interaction and showed that it was direct. Moreover, in silico analysis allowed us to establish the domains/fragments of both proteins involved in the binding. To further explore the possible role of CacyBP/SIP in ribosome function we performed several analyses using neuroblastoma NB2a cell line with stably silenced CacyBP/SIP expression. We have found, by applying OPP (O-propargyl-puromycin), which labels nascent polypeptides, that the number of cells with enhanced staining in the perinuclear area, reminiscent of rough ER localization, was significantly lower in the cell line with diminished CacyBP/SIP level. To verify the influence of CacyBP/SIP on the efficiency of protein synthesis we investigated the level of Hsp70, a stress-inducible protein, in NB2a cells subjected to heat shock. The results, showing markedly higher Hsp70 production in control cells, indicate that CacyBP/SIP, most probably through interaction with RPL6 and/or other RPs, may have some influence on ribosome function and, possibly, on protein synthesis in the cell
The Fine Structure of Genome Statistics—The Frequency and Size
Full text linkA determination and mathematical analysis of the statistics of gene numbers in genomes was proposed. It establishes sampling ranges and provides an analytical description of the probability density function, which represents the likelihood of the number of genes in sequenced genomes falling within a specific range of values. The components of the developed statistical multi-Poissonian model revealed the fundamental mechanisms underlying the evolution of life and identified the specific ranges of their dominant influence. The quantitative relations between the statistics of the number of genes and the genome size were shown. A mathematical model of genome size evolution was proposed, identifying subpopulations of intensive and extensive genes associated with protein-coding genes, pseudogenes, and non-coding genes
Differential scanning fluorimetry followed by microscale thermophoresis and/or isothermal titration calorimetry as an efficient tool for ligand screening
Full text linkVarious biophysical and biochemical techniques have been developed to measure the affinity of interacting molecules. This review analyzes the combination of three methods: differential scanning fluorimetry as the initial high-throughput screening technique and microscale thermophoresis and isothermal titration calorimetry as complementary methods to quantify binding affinity. The presented work is the first to detailed compare the strengths and flaws of these three specific methods, as well as their application possibilities and complementarity. The fundamentals of these methods will be covered, including the most often-used models for characterizing observable phenomena and an emphasis on methods for analyzing data.
A comprehensive review of numerous approaches to data analysis found in the literature is additionally provided, with the benefits and drawbacks of each, as well as the pitfalls and related concerns. Finally, examples of different systems will be presented, and methods used and some discrepancies in results will be described and discussed
Genome sequences of polar Carnobacterium maltaromaticum strains 2857 and 2862 with genes for glycerol and 1,2-propanediol pathways
Full text linkWe report genome sequences of two polar Carnobacterium maltaromaticum strains: 2857 (draft, 3.54 Mb, 34.4% GC) and 2862 (complete, 3.61 Mb, 34.6% GC, five plasmids). Sequencing used Illumina (both) and Nanopore (2862). Genome analysis revealed genes for glycerol conversion to 1,2-propanediol, suggesting potential for sustainable bioprocessing in cold environments
Metabolome analysis as a potential source of endometriosis biomarkers with the use of multiomics approach in its diagnosis
Full text linkEndometriosis poses diagnostic challenges. This study aimed to analyze the metabolomic profiles of plasma and peritoneal fluid samples obtained from women with endometriosis compared to controls. Our multicenter study involved sample collection from women undergoing laparoscopic surgery. The metabolomic profiles of plasma samples obtained from 73 women with endometriosis and 35 controls, as well as peritoneal fluid samples from 53 women with endometriosis and 34 controls, were analysed using mass spectrometry techniques. Differences in lipid profiles were observed between the groups. Chemometric analyses identified a set of 20 metabolites present in peritoneal fluid and 26 compounds in plasma, which serve as potential diagnostic tools for endometriosis. Then, we used a simple approach to build a classification model based on the sets of metabolites in combination with autoantibodies selected using protein microarrays from our previous study. The classification performance obtained on the joined metabolomic and proteomic feature sets exceeds that achievable for separate assays (sensitivity/specificity for plasma and peritoneal fluid were respectively 0.98/0.86 and 0.92/0.82). Identified metabolites present promising candidates for biomarkers. Utilizing these metabolites in a diagnostic panel may enhance endometriosis detection. Moreover, we observed the potential benefits of a multi-omics approach based on integrated metabolomic and proteomic analysis to endometriosis research
Food Sensitization Is Associated With Atopic DermatitisSeverity, Gut‐Derived Metabolites and Leaky Gut in Adults
Full text linkBackground: Gut microbiome dysbiosis may cause metabolic dysregulation and intestinal barrier impairment. The latter are hypothesized to provoke food allergy and aggravate cutaneous inflammation. Our objective was to determine the prevalence of food sensitization in adult patients with atopic dermatitis and relate it to the disease severity and the biomarkers of the gut-skin axis.
Methods: 50 adult patients with atopic dermatitis and 25 controls were enrolled in this cross-sectional study. Disease severity was determined by using SCORAD and EASI scores. Liquid chromatography-mass spectrometry, Luminex, and Polycheck immunoassays were performed to detect serum concentrations of total IgE, food-specific IgEs, gut-derived metabolites, and leaky gut-related biomarkers.
Results: Food sensitization was significantly more prevalent in patients with atopic dermatitis than in the controls. The severity of atopic dermatitis (EASI, SCORAD) was higher in patients with food sensitization and correlated with the number of positive food-specific IgEs. Higher concentrations of total IgE and higher numbers of positive food-specific IgEs were associated with lower concentrations of short-chain fatty acids and higher concentrations of indoxyl and leaky gut-related biomarkers (LBP, syndecan-4, IL-10, IL-22).
Conclusion: The results suggest a relationship between food sensitization and the severity of atopic dermatitis. This could be partly associated with gut-derived metabolites and intestinal barrier impairment. Fiber-rich diet and restriction of protein could hold potential for upregulating short-chain fatty acids and downregulating indoxyl, which may translate to decreasing the likelihood of food sensitization in atopic dermatitis. Notably, the cross-sectional nature of this exploratory study limits the ability to draw causal inferences, which should be further examined in future prospective research
Low-complexity regions in fungi display functional groups and are depleted in positively charged amino acids
Full text linkReports on the diversity and occurrence of low-complexity regions (LCR) in Eukaryota are limited. Some studies have provided a more extensive characterization of LCR proteins in prokaryotes. There is a growing body of knowledge about a plethora of biological functions attributable to LCRs. However, it is hard to determine to what extent observed phenomena apply to fungi since most studies of fungal LCRs were limited to model yeasts. To fill this gap, we performed a survey of LCRs in proteins across all fungal tree of life branches. We show that the abundance of LCRs and the abundance of proteins with LCRs are positively correlated with proteome size. We observed that most LCRs are present in proteins with protein domains but do not overlap with the domain regions. LCRs are associated with many duplicated protein domains. The quantity of particular amino acids in LCRs deviates from the background frequency with a clear over-representation of amino acids with functional groups and a negative charge. Moreover, we discovered that each lineage of fungi favors distinct LCRs expansions. Early diverging fungal lineages differ in LCR abundance and composition pointing at a different evolutionary trajectory of each fungal group
Tandem mass tag-based proteomic analysis of granulosa and theca interna cells of the porcine ovarian follicle following in vitro treatment with vitamin D3 and insulin alone or in combination
Full text linkThis study was performed to investigate the proteomic basis underlying the interaction between vitamin D3 (VD) and insulin (I) within ovarian follicle using the pig as a model. Porcine antral follicles were incubated in vitro for 12 h with VD alone and I alone or in combination (VD + I) or with no treatment as the control (C). In total, 7690 and 7467 proteins were identified in the granulosa and theca interna compartments, respectively. Comparative proteomic analysis revealed 97 differentially abundant proteins (DAPs) within the granulosa layer and 11 DAPs within the theca interna layer. In the granulosa compartment, VD affected proteome leading to the promotion of cell proliferation, whereas I influenced mainly proteins related to cellular adhesion. The VD + I treatment induced granulosa cell proliferation probably via the DAPs involved in DNA synthesis and the cell cycle regulation. In the theca interna layer, VD alone or in co-treatment with I affected DAPs associated with cholesterol transport and lipid and steroid metabolic processes that was further confirmed by diminished lipid droplet accumulation
SWI/SNF-type complexes–transcription factor interplay: a key regulatory interaction
No full textATP-dependent switch/sucrose nonfermenting-type chromatin remodeling complexes (SWI/SNF CRCs) are multiprotein machineries altering chromatin structure, thus controlling the accessibility of genomic DNA to various regulatory proteins including transcription factors (TFs). SWI/SNF CRCs are highly evolutionarily conserved among eukaryotes. There are three main subtypes of SWI/SNF CRCs: canonical (cBAF), polybromo (pBAF), and noncanonical (ncBAF) in humans and their functional Arabidopsis counterparts SYD-associated SWI/SNF (SAS), MINU-associated SWI/SNF (MAS), and BRAHMA (BRM)-associated SWI/SNF (BAS). Here, we highlight the importance of interplay between SWI/SNF CRCs and TFs in human and Arabidopsis and summarize recent advances demonstrating their role in controlling important regulatory processes. We discuss possible mechanisms involved in TFs and SWI/SNF CRCs-dependent transcriptional control of gene expression. We indicate that Arabidopsis may serve as a valuable model for the identification of evolutionarily conserved SWI/SNF–TF interactions and postulate that further exploration of the TFs and SWI/SNF CRCs-interplay, especially in the context of the role of particular SWI/SNF CRC subtypes, TF type, as well as cell/tissue and conditions, among others, will help address important questions related to the specificity of SWI/SNF–TF interactions and the sequence of events occurring on their target genes
RNA polymerase III transcription machinery and tRNA processing are regulated by the ubiquitin ligase Rsp5
Full text linkTransfer RNA (tRNA) biogenesis in yeast involves synthesis of the primary transcript by RNA polymerase III (Pol III), followed by processing to remove 5′ and 3′ ends, further maturation, and export to the cytoplasm. In the present study, we found that both tRNA transcription and the initial processing of tRNA precursors are affected by the ubiquitin ligase Rsp5. We observed high levels of unprocessed primary tRNA transcripts in rsp5 mutants at elevated temperature, which were reduced upon the overexpression of RPR1, the catalytic subunit of RNase P. This observation suggests a role for Rsp5 in the maturation of 5′ ends of tRNA precursors. Under the same conditions, in vivo labeling showed that the amount of newly synthesized tRNA decreased. Furthermore, we found that Rsp5 directly interacted with the Tfc3 subunit of the TFIIIC transcription factor, which is modified by ubiquitination. The inactivation of Rsp5 catalytic activity influenced the interaction between the general Pol III factors TFIIIB and TFIIIC and decreased the recruitment of TFIIIC to tRNA genes. These findings suggest that Rsp5 ligase is implicated in the control of Pol III transcription in yeast