Metabolomics and transcriptomics reveal the toxic mechanism of Cd and nano TiO2 coexposure on rice (Oryza sativa L.)

Journal of Hazardous Materials, Journal Year: 2023, Volume and Issue: 453, P. 131411 - 131411

Published: April 13, 2023

Language: Английский

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The Last Universal Common Ancestor of Ribosome-Encoding Organisms: Portrait of LUCA

Journal of Molecular Evolution, Journal Year: 2024, Volume and Issue: 92(5), P. 550 - 583

Published: Aug. 19, 2024

Language: Английский

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Ribosomal Biogenesis and Heterogeneity in Development, Disease, and Aging

Epigenomes, Journal Year: 2023, Volume and Issue: 7(3), P. 17 - 17

Published: Aug. 11, 2023

Although reported in the literature, ribosome heterogeneity is a phenomenon whose extent and implications cell organismal biology not fully appreciated. This has been case due to lack of appropriate techniques approaches. Heterogeneity can arise from alternative use differential content protein RNA constituents, as well post-transcriptional post-translational modifications. In few examples we have, it apparent that ribosomal offers an additional level potential for gene expression regulation might be way towards tuning metabolism, stress, growth programs external internal stimuli needs. Here, introduce biogenesis discuss various occasions. We conclude systematic approach multiple organisms will needed delineate this biological its contributions growth, aging, disease. Finally, mutations their roles

Language: Английский

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The Expanding Universe of Extensions and Tails: Ribosomal Proteins and Histones in RNA and DNA Complex Signaling and Dynamics

Genes, Journal Year: 2025, Volume and Issue: 16(1), P. 45 - 45

Published: Jan. 1, 2025

This short review bridges two biological fields: ribosomes and nucleosomes—two nucleoprotein assemblies that, along with many viruses, share proteins featuring long filamentous segments at their N- or C-termini. A central hypothesis is that these extensions tails perform analogous functions in both systems. The evolution of structures appears closely tied to the emergence regulatory networks signaling pathways, facilitating increasingly complex roles for nucleosome alike. begins by summarizing nucleosomes, followed a detailed comparison highlighting similarities differences, particularly light recent findings on ribosomal ribosome dynamics. analysis seeks uncover whether systems operate based shared principles mechanisms. nucleosome–ribosome analogy may offer valuable insights into unresolved questions fields. For instance, new structural from might shed potential motifs formed histone tails. From an evolutionary perspective, this study revisits origins regulation ancient assemblies, suggesting represent remnants earliest network governing dynamic control.

Language: Английский

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Specialized ribosomes: integrating new insights and current challenges

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2025, Volume and Issue: 380(1921)

Published: March 6, 2025

Variation in the composition of different ribosomes, termed ribosome heterogeneity, is a now well established phenomenon. However, functional implications this heterogeneity on regulation protein synthesis are only beginning to be revealed. While there numerous examples heterogeneous comparatively few bona fide specialized ribosomes described. Specialization requires that compositionally distinct through their subtly altered structure, have consequence translational output. Even for those specialization been characterized, precise mechanistic details how changes and rRNA enable regulate translation still missing. Here, we suggest looking at evolution across tree life may help reveal central principles regulation. We consider structural studies provided insight into potential mechanisms which could affect translation, including mRNA open reading frame selectivity, elongation dynamics post-translational folding. Further, highlight some challenges must addressed show review contribution various models. Several discussed, recent starting shed light molecular specialization. Finally, discuss future studies, where advances technology will likely next wave research questions. Recent work has helped provide more comprehensive understanding affects control.This article part discussion meeting issue 'Ribosome diversity its impact synthesis, development disease'.

Language: Английский

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Biomarkers Related to Interferon-γ Pathway in Myocardial Ischemia–Reperfusion Injury and the Potential Molecular Mechanisms

Cardiovascular Toxicology, Journal Year: 2025, Volume and Issue: unknown

Published: May 9, 2025

Although reperfusion therapy can reduce the mortality of myocardial infarction, it results in ischemia-reperfusion injury (MIRI). The molecular mechanism by which interferon-γ pathway affects MIRI is unclear, so we addressed this problem mining transcriptome and single-cell sequencing data. GSE160516 GSE83472 datasets, single cell RNA (scRNA-seq) data GSE227088 dataset 182 related genes (IRGs) were retrieved incorporated into study. differentially expressed (DEGs) between control samples searched, candidate obtained intersecting DEGs with IRGs. protein-protein interaction (PPI) analysis was utilized for selecting key from genes. Moreover, significant expression consistent trend datasets selected as biomarkers. biological functions regulatory biomarkers investigated enrichment predicting upstream molecules targeting them. Ulteriorly, clusters identified via unsupervised cluster merged different types annotation. Cell observably crucial types. Finally, communication pseudo-time implemented based on Totally 34 searched overlapping 1,930 Nine singled out genes, Myd88 Trp53 significantly upregulated they Besides, participated pathways such ribosome, spliceosome cycle. might be simultaneously regulated mmu-miR-361-3p mmu-miR-421-3p, could Abl1 Tead2. 25 six types, three (cardiomyocyte, fibroblast, macrophage) interact each other through receptor-ligand. Pseudo-time revealed states 1, 2, 5 macrophages associated MIRI. Two (Myd88 Trp53) to IRGs mined, providing a reference elucidating

Language: Английский

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GTPase Era at the heart of ribosome assembly

Frontiers in Molecular Biosciences, Journal Year: 2023, Volume and Issue: 10

Published: Oct. 4, 2023

Ribosome biogenesis is a key process in all organisms. It relies on coordinated work of multiple proteins and RNAs, including an array assembly factors. Among them, the GTPase Era stands out as especially deeply conserved protein, critically required for bacterial-type ribosomes from Escherichia coli to humans. In this review, we bring together analyze wealth phylogenetic, biochemical, structural, genetic physiological data about extensively studied but still insufficiently understood factor. We do so using comparative and, wherever possible, synthetic approach, by confronting observations diverse groups bacteria eukaryotic organelles (mitochondria chloroplasts). The emerging consensus posits that intervenes relatively early small subunit essential proper shaping platform which, its turn, prerequisite efficient translation. timing action ribosome defined interactions with guanosine nucleotides [GTP, GDP, (p)ppGpp], ribosomal RNA, likely other factors trigger or delay activity. As critical nexus biogenesis, subject sophisticated regulatory mechanisms at transcriptional, post-transcriptional, post-translational levels. Failure these deficiency function entail dramatic generalized consequences protein synthesis far-reaching, pleiotropic effects organism physiology, such Perrault syndrome

Language: Английский

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Study on the inhibitory activity and mechanism of Mentha haplocalyx essential oil nanoemulsion against Fusarium oxysporum growth

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: July 11, 2024

Abstract Mentha haplocalyx essential oil (MEO) has demonstrated inhibitory effects on Fusarium oxysporum . Despite its environmentally friendly properties as a natural product, the limited water solubility of MEO restricts practical application in field. The use nanoemulsion can improve bioavailability and provide an eco-friendly approach to prevent control Panax notoginseng root rot. In this study, Tween 80 anhydrous ethanol (at mass ratio 3) were selected carriers, ultrasonic method was utilized produce (MNEO) with average particle size 26.07 nm. Compared MTEO (MEO dissolved aqueous solution 2% DMSO 0.1% 80), MNEO exhibited superior inhibition against F. terms spore germination hyphal growth. Transcriptomics metabolomics results revealed that after treatment, expression levels certain genes related glycolysis/gluconeogenesis, starch sucrose metabolism significantly suppressed along accumulation metabolites, leading energy disorder growth stagnation contrast, effect from treatment less pronounced. Furthermore, also meiosis, ribosome function, biogenesis process. These findings suggest possesses enhanced stability antifungal activity, which effectively hinders through inducing disorder, meiotic stagnation, well dysfunction, thus indicating potential for development green pesticide prevention P. rot caused by F.oxyosporum

Language: Английский

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Assembly of the bacterial ribosome with circularly permuted rRNA

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 52(18), P. 11254 - 11265

Published: July 22, 2024

Abstract Co-transcriptional assembly is an integral feature of the formation RNA–protein complexes that mediate translation. For ribosome synthesis, prior studies have indicated strict order transcription rRNA domains may not be obligatory during bacterial biogenesis, since a series circularly permuted rRNAs are viable. In this work, we report structural insights into large subunit (LSU) based on cryo-EM density maps intermediates accumulate in vitro synthesis using set (CiPer) rRNAs. The observed ensemble 23 resolved reveals conserved routes with underlying hierarchy among cooperative blocks. There intricate interdependencies for key helices revealed from circular permutation rRNA. While domain obligatory, association does appear to proceed particular order, likely due strong evolutionary pressure efficient synthesis. This work reinforces robustness known ribosomal and offers coherent view how CiPer can understood context.

Language: Английский

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Decoding ribosome complexity: role of ribosomal proteins in cancer and disease

NAR Cancer, Journal Year: 2024, Volume and Issue: 6(3)

Published: July 9, 2024

Abstract The ribosome is a remarkably complex machinery, at the interface with diverse cellular functions and processes. Evolutionarily conserved, yet intricately regulated, ribosomes play pivotal roles in decoding genetic information into synthesis of proteins generation biomass critical for physiological functions. Recent insights have revealed existence heterogeneity multiple levels. Such extends to cancer, where aberrant biogenesis function contribute oncogenesis. This led emergence concept ‘onco-ribosomes’, specific ribosomal variants altered structural dynamics, contributing cancer initiation progression. Ribosomal (RPs) are involved many these alterations, acting as factors translational reprogramming cells. In this review article, we highlight RPs biogenesis, how mutations their paralogues reshape landscape, driving clonal evolution therapeutic resistance. Furthermore, present recent evidence providing new post-translational modifications RPs, such ubiquitylation, UFMylation phosphorylation, they regulate recycling, fidelity stress responses. Understanding intricate interplay between complexity, RP-mediated regulatory mechanisms pathology offers profound biology unveils novel avenues targeting machinery cancer.

Language: Английский

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