Biochemical Society transactions最新文献_第10页

Transcriptional control of neural stem cell activity. 神经干细胞活动的转录控制

IF 3.8 3区生物学

Biochemical Society transactions Pub Date : 2024-04-24 DOI: 10.1042/BST20230439

Takashi Kaise, Ryoichiro Kageyama

引用次数: 0

The application of single-molecule optical tweezers to study disease-related structural dynamics in RNA. 应用单分子光镊研究 RNA 中与疾病相关的结构动态。

IF 3.8 3区生物学

Biochemical Society transactions Pub Date : 2024-04-24 DOI: 10.1042/BST20231232

Tycho Marinus, Toshana L Foster, Katarzyna M Tych

{"title":"The application of single-molecule optical tweezers to study disease-related structural dynamics in RNA.","authors":"Tycho Marinus, Toshana L Foster, Katarzyna M Tych","doi":"10.1042/BST20231232","DOIUrl":"10.1042/BST20231232","url":null,"abstract":"RNA, a dynamic and flexible molecule with intricate three-dimensional structures, has myriad functions in disease development. Traditional methods, such as X-ray crystallography and nuclear magnetic resonance, face limitations in capturing real-time, single-molecule dynamics crucial for understanding RNA function. This review explores the transformative potential of single-molecule force spectroscopy using optical tweezers, showcasing its capability to directly probe time-dependent structural rearrangements of individual RNA molecules. Optical tweezers offer versatility in exploring diverse conditions, with the potential to provide insights into how environmental changes, ligands and RNA-binding proteins impact RNA behaviour. By enabling real-time observations of large-scale structural dynamics, optical tweezers emerge as an invaluable tool for advancing our comprehension of RNA structure and function. Here, we showcase their application in elucidating the dynamics of RNA elements in virology, such as the pseudoknot governing ribosomal frameshifting in SARS-CoV-2.","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11088911/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140292631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The molecular mechanisms underpinning maternal mRNA dormancy. 母体 mRNA 休眠的分子机制。

IF 3.9 3区生物学

Biochemical Society transactions Pub Date : 2024-04-24 DOI: 10.1042/BST20231122

Laura Lorenzo-Orts, Andrea Pauli

{"title":"The molecular mechanisms underpinning maternal mRNA dormancy.","authors":"Laura Lorenzo-Orts, Andrea Pauli","doi":"10.1042/BST20231122","DOIUrl":"10.1042/BST20231122","url":null,"abstract":"A large number of mRNAs of maternal origin are produced during oogenesis and deposited in the oocyte. Since transcription stops at the onset of meiosis during oogenesis and does not resume until later in embryogenesis, maternal mRNAs are the only templates for protein synthesis during this period. To ensure that a protein is made in the right place at the right time, the translation of maternal mRNAs must be activated at a specific stage of development. Here we summarize our current understanding of the sophisticated mechanisms that contribute to the temporal repression of maternal mRNAs, termed maternal mRNA dormancy. We discuss mechanisms at the level of the RNA itself, such as the regulation of polyadenine tail length and RNA modifications, as well as at the level of RNA-binding proteins, which often block the assembly of translation initiation complexes at the 5' end of an mRNA or recruit mRNAs to specific subcellular compartments. We also review microRNAs and other mechanisms that contribute to repressing translation, such as ribosome dormancy. Importantly, the mechanisms responsible for mRNA dormancy during the oocyte-to-embryo transition are also relevant to cellular quiescence in other biological contexts.","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11088918/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140108995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Beyond protein synthesis: non-translational functions of threonyl-tRNA synthetases. 蛋白质合成之外：苏氨酸-tRNA 合成酶的非翻译功能。

IF 3.9 3区生物学

Biochemical Society transactions Pub Date : 2024-04-24 DOI: 10.1042/BST20230506

Pallob Barai, Jie Chen

引用次数: 0

New insights into Gasdermin D pore formation. 关于 Gasdermin D 孔隙形成的新见解。

IF 3.9 3区生物学

Biochemical Society transactions Pub Date : 2024-04-24 DOI: 10.1042/BST20230549

Shirin Kappelhoff, Eleonora G Margheritis, Katia Cosentino

{"title":"New insights into Gasdermin D pore formation.","authors":"Shirin Kappelhoff, Eleonora G Margheritis, Katia Cosentino","doi":"10.1042/BST20230549","DOIUrl":"10.1042/BST20230549","url":null,"abstract":"Gasdermin D (GSDMD) is a pore-forming protein that perforates the plasma membrane (PM) during pyroptosis, a pro-inflammatory form of cell death, to induce the unconventional secretion of inflammatory cytokines and, ultimately, cell lysis. GSDMD is activated by protease-mediated cleavage of its active N-terminal domain from the autoinhibitory C-terminal domain. Inflammatory caspase-1, -4/5 are the main activators of GSDMD via either the canonical or non-canonical pathways of inflammasome activation, but under certain stimuli, caspase-8 and other proteases can also activate GSDMD. Activated GSDMD can oligomerize and assemble into various nanostructures of different sizes and shapes that perforate cellular membranes, suggesting plasticity in pore formation. Although the exact mechanism of pore formation has not yet been deciphered, cysteine residues are emerging as crucial modulators of the oligomerization process. GSDMD pores and thus the outcome of pyroptosis can be modulated by various regulatory mechanisms. These include availability of activated GSDMD at the PM, control of the number of GSDMD pores by PM repair mechanisms, modulation of the lipid environment and post-translational modifications. Here, we review the latest findings on the mechanisms that induce GSDMD to form membrane pores and how they can be tightly regulated for cell content release and cell fate modulation.","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140142710","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Raman micro-spectroscopy as a tool to study immunometabolism. 拉曼显微光谱学是研究免疫代谢的一种工具。

IF 3.9 3区生物学

Biochemical Society transactions Pub Date : 2024-04-24 DOI: 10.1042/BST20230794

Jiabao Xu, Karl J Morten

{"title":"Raman micro-spectroscopy as a tool to study immunometabolism.","authors":"Jiabao Xu, Karl J Morten","doi":"10.1042/BST20230794","DOIUrl":"10.1042/BST20230794","url":null,"abstract":"In the past two decades, immunometabolism has emerged as a crucial field, unraveling the intricate molecular connections between cellular metabolism and immune function across various cell types, tissues, and diseases. This review explores the insights gained from studies using the emerging technology, Raman micro-spectroscopy, to investigate immunometabolism. Raman micro-spectroscopy provides an exciting opportunity to directly study metabolism at the single cell level where it can be combined with other Raman-based technologies and platforms such as single cell RNA sequencing. The review showcases applications of Raman micro-spectroscopy to study the immune system including cell identification, activation, and autoimmune disease diagnosis, offering a rapid, label-free, and minimally invasive analytical approach. The review spotlights three promising Raman technologies, Raman-activated cell sorting, Raman stable isotope probing, and Raman imaging. The synergy of Raman technologies with machine learning is poised to enhance the understanding of complex Raman phenotypes, enabling biomarker discovery and comprehensive investigations in immunometabolism. The review encourages further exploration of these evolving technologies in the rapidly advancing field of immunometabolism.","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11088913/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140108994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Emerging mechanisms in the redox regulation of mitochondrial cytochrome c oxidase assembly and function. 线粒体细胞色素 c 氧化酶组装和功能的氧化还原调控新机制。

IF 3.9 3区生物学

Biochemical Society transactions Pub Date : 2024-04-24 DOI: 10.1042/BST20231183

Suleva Povea-Cabello, Michele Brischigliaro, Erika Fernández-Vizarra

{"title":"Emerging mechanisms in the redox regulation of mitochondrial cytochrome c oxidase assembly and function.","authors":"Suleva Povea-Cabello, Michele Brischigliaro, Erika Fernández-Vizarra","doi":"10.1042/BST20231183","DOIUrl":"10.1042/BST20231183","url":null,"abstract":"In eukaryotic cells, mitochondria perform cellular respiration through a series of redox reactions ultimately reducing molecular oxygen to water. The system responsible for this process is the respiratory chain or electron transport system (ETS) composed of complexes I-IV. Due to its function, the ETS is the main source of reactive oxygen species (ROS), generating them on both sides of the mitochondrial inner membrane, i.e. the intermembrane space (IMS) and the matrix. A correct balance between ROS generation and scavenging is important for keeping the cellular redox homeostasis and other important aspects of cellular physiology. However, ROS generated in the mitochondria are important signaling molecules regulating mitochondrial biogenesis and function. The IMS contains a large number of redox sensing proteins, containing specific Cys-rich domains, that are involved in ETS complex biogenesis. The large majority of these proteins function as cytochrome c oxidase (COX) assembly factors, mainly for the handling of copper ions necessary for the formation of the redox reactive catalytic centers. A particular case of ROS-regulated COX assembly factor is COA8, whose intramitochondrial levels are increased by oxidative stress, promoting COX assembly and/or protecting the enzyme from oxidative damage. In this review, we will discuss the current knowledge concerning the role played by ROS in regulating mitochondrial activity and biogenesis, focusing on the COX enzyme and with a special emphasis on the functional role exerted by the redox sensitive Cys residues contained in the COX assembly factors.","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140206314","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome organization across scales: mechanistic insights from in vitro reconstitution studies. 跨尺度的基因组组织：体外重组研究的机理启示。

IF 3.9 3区生物学

Biochemical Society transactions Pub Date : 2024-04-24 DOI: 10.1042/BST20230883

Elisa Oberbeckmann, A Marieke Oudelaar

{"title":"Genome organization across scales: mechanistic insights from in vitro reconstitution studies.","authors":"Elisa Oberbeckmann, A Marieke Oudelaar","doi":"10.1042/BST20230883","DOIUrl":"10.1042/BST20230883","url":null,"abstract":"Eukaryotic genomes are compacted and organized into distinct three-dimensional (3D) structures, which range from small-scale nucleosome arrays to large-scale chromatin domains. These chromatin structures play an important role in the regulation of transcription and other nuclear processes. The molecular mechanisms that drive the formation of chromatin structures across scales and the relationship between chromatin structure and function remain incompletely understood. Because the processes involved are complex and interconnected, it is often challenging to dissect the underlying principles in the nuclear environment. Therefore, in vitro reconstitution systems provide a valuable approach to gain insight into the molecular mechanisms by which chromatin structures are formed and to determine the cause-consequence relationships between the processes involved. In this review, we give an overview of in vitro approaches that have been used to study chromatin structures across scales and how they have increased our understanding of the formation and function of these structures. We start by discussing in vitro studies that have given insight into the mechanisms of nucleosome positioning. Next, we discuss recent efforts to reconstitute larger-scale chromatin domains and loops and the resulting insights into the principles of genome organization. We conclude with an outlook on potential future applications of chromatin reconstitution systems and how they may contribute to answering open questions concerning chromatin architecture.","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11088924/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140048603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Type III intermediate filaments in redox interplay: key role of the conserved cysteine residue. 氧化还原相互作用中的 III 型中间丝：保守半胱氨酸残基的关键作用。

IF 3.9 3区生物学

Biochemical Society transactions Pub Date : 2024-04-24 DOI: 10.1042/BST20231059

María A Pajares, Dolores Pérez-Sala

{"title":"Type III intermediate filaments in redox interplay: key role of the conserved cysteine residue.","authors":"María A Pajares, Dolores Pérez-Sala","doi":"10.1042/BST20231059","DOIUrl":"10.1042/BST20231059","url":null,"abstract":"Intermediate filaments (IFs) are cytoskeletal elements involved in mechanotransduction and in the integration of cellular responses. They are versatile structures and their assembly and organization are finely tuned by posttranslational modifications. Among them, type III IFs, mainly vimentin, have been identified as targets of multiple oxidative and electrophilic modifications. A characteristic of most type III IF proteins is the presence in their sequence of a single, conserved cysteine residue (C328 in vimentin), that is a hot spot for these modifications and appears to play a key role in the ability of the filament network to respond to oxidative stress. Current structural models and experimental evidence indicate that this cysteine residue may occupy a strategic position in the filaments in such a way that perturbations at this site, due to chemical modification or mutation, impact filament assembly or organization in a structure-dependent manner. Cysteine-dependent regulation of vimentin can be modulated by interaction with divalent cations, such as zinc, and by pH. Importantly, vimentin remodeling induced by C328 modification may affect its interaction with cellular organelles, as well as the cross-talk between cytoskeletal networks, as seems to be the case for the reorganization of actin filaments in response to oxidants and electrophiles. In summary, the evidence herein reviewed delineates a complex interplay in which type III IFs emerge both as targets and modulators of redox signaling.","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11088922/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140048604","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A dynamic role for transcription factors in restoring transcription through mitosis. 转录因子在有丝分裂过程中恢复转录的动态作用

IF 3.9 3区生物学

Biochemical Society transactions Pub Date : 2024-04-24 DOI: 10.1042/BST20231022

Marek A Budzyński, Alexander K L Wong, Armin Faghihi, Sheila S Teves

{"title":"A dynamic role for transcription factors in restoring transcription through mitosis.","authors":"Marek A Budzyński, Alexander K L Wong, Armin Faghihi, Sheila S Teves","doi":"10.1042/BST20231022","DOIUrl":"10.1042/BST20231022","url":null,"abstract":"Mitosis involves intricate steps, such as DNA condensation, nuclear membrane disassembly, and phosphorylation cascades that temporarily halt gene transcription. Despite this disruption, daughter cells remarkably retain the parent cell's gene expression pattern, allowing for efficient transcriptional memory after division. Early studies in mammalian cells suggested that transcription factors (TFs) mark genes for swift reactivation, a phenomenon termed 'mitotic bookmarking', but conflicting data emerged regarding TF presence on mitotic chromosomes. Recent advancements in live-cell imaging and fixation-free genomics challenge the conventional belief in universal formaldehyde fixation, revealing dynamic TF interactions during mitosis. Here, we review recent studies that provide examples of at least four modes of TF-DNA interaction during mitosis and the molecular mechanisms that govern these interactions. Additionally, we explore the impact of these interactions on transcription initiation post-mitosis. Taken together, these recent studies call for a paradigm shift toward a dynamic model of TF behavior during mitosis, underscoring the need for incorporating dynamics in mechanistic models for re-establishing transcription post-mitosis.","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11088908/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140206298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0