Biochemical Society transactions最新文献_第7页

A closer look at the role of deubiquitinating enzymes in the Hypoxia Inducible Factor pathway. 仔细研究去泛素化酶在缺氧诱导因子途径中的作用。

IF 3.8 3区生物学

Biochemical Society transactions Pub Date : 2024-12-19 DOI: 10.1042/BST20230861

Tekle Pauzaite, James A Nathan

{"title":"A closer look at the role of deubiquitinating enzymes in the Hypoxia Inducible Factor pathway.","authors":"Tekle Pauzaite, James A Nathan","doi":"10.1042/BST20230861","DOIUrl":"10.1042/BST20230861","url":null,"abstract":"Hypoxia Inducible transcription Factors (HIFs) are central to the metazoan oxygen-sensing response. Under low oxygen conditions (hypoxia), HIFs are stabilised and govern an adaptive transcriptional programme to cope with prolonged oxygen starvation. However, when oxygen is present, HIFs are continuously degraded by the proteasome in a process involving prolyl hydroxylation and subsequent ubiquitination by the Von Hippel Lindau (VHL) E3 ligase. The essential nature of VHL in the HIF response is well established but the role of other enzymes involved in ubiquitination is less clear. Deubiquitinating enzymes (DUBs) counteract ubiquitination and provide an important regulatory aspect to many signalling pathways involving ubiquitination. In this review, we look at the complex network of ubiquitination and deubiquitination in controlling HIF signalling in normal and low oxygen tensions. We discuss the relative importance of DUBs in opposing VHL, and explore roles of DUBs more broadly in hypoxia, in both VHL and HIF independent contexts. We also consider the catalytic and non-catalytic roles of DUBs, and elaborate on the potential benefits and challenges of inhibiting these enzymes for therapeutic use.","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":" ","pages":"2253-2265"},"PeriodicalIF":3.8,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11668284/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142709182","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 expectations: the development and biological activity of cytokinin oxidase/dehydrogenase inhibitors. 超越期望：细胞分裂素氧化酶/脱氢酶抑制剂的开发和生物活性。

IF 3.8 3区生物学

Biochemical Society transactions Pub Date : 2024-12-19 DOI: 10.1042/BST20231561

Jaroslav Nisler

{"title":"Beyond expectations: the development and biological activity of cytokinin oxidase/dehydrogenase inhibitors.","authors":"Jaroslav Nisler","doi":"10.1042/BST20231561","DOIUrl":"10.1042/BST20231561","url":null,"abstract":"Cytokinins are one of the main groups of plant hormones that regulate growth and development of plants. Cytokinin oxidase/dehydrogenase (CKX) is an enzyme that rapidly and irreversibly degrades cytokinins and thus directly affects their concentration and physiological effect. Genetically modified plants with reduced CKX activity in the shoot, i.e. with a higher concentration of cytokinins, showed e.g. increased tolerance to drought stress, formed larger inflorescences and had higher grain yield. For these reasons, chemical compounds capable of inhibiting the CKX activity (CKX inhibitors) were sought. First, they were identified among strong synthetic cytokinins, but their inhibitory activity was low. The trend has been to develop potent CKX inhibitors with minimal intrinsic cytokinin activity in the hope of avoiding the negative effect of cytokinins on root growth. Cloning CKX, production of key recombinant enzymes from Arabidopsis (AtCKX2) and maize (ZmCKX1 and ZmCKX4a), development of screening bioassays and progress in X-ray crystallography and synthetic organic chemistry led to extensive progress in the development of these compounds. Currently, the most suitable CKX inhibitors are seeking their application in research and the commercial sphere in two main areas - plant tissue cultures and agriculture. The key milestones that preceded it are summarized in this review.","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":" ","pages":"2297-2306"},"PeriodicalIF":3.8,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142602646","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

The expanding roles of myonuclei in adult skeletal muscle health and function. 肌核在成人骨骼肌健康和功能中的作用不断扩大。

IF 3.8 3区生物学

Biochemical Society transactions Pub Date : 2024-12-19 DOI: 10.1042/BST20241637

Agnieszka K Borowik, Kevin A Murach, Benjamin F Miller

{"title":"The expanding roles of myonuclei in adult skeletal muscle health and function.","authors":"Agnieszka K Borowik, Kevin A Murach, Benjamin F Miller","doi":"10.1042/BST20241637","DOIUrl":"10.1042/BST20241637","url":null,"abstract":"Skeletal muscle cells (myofibers) require multiple nuclei to support a cytoplasmic volume that is larger than other mononuclear cell types. It is dogmatic that mammalian resident myonuclei rely on stem cells (specifically satellite cells) for adding new DNA to muscle fibers to facilitate cytoplasmic expansion that occurs during muscle growth. In this review, we discuss the relationship between cell size and supporting genetic material. We present evidence that myonuclei may undergo DNA synthesis as a strategy to increase genetic material in myofibers independent from satellite cells. We then describe the details of our experiments that demonstrated that mammalian myonuclei can replicate DNA in vivo. Finally, we present our findings in the context of expanding knowledge about myonuclear heterogeneity, myonuclear mobility and shape. We also address why myonuclear replication is potentially important and provide future directions for remaining unknowns. Myonuclear DNA replication, coupled with new discoveries about myonuclear transcription, morphology, and behavior in response to stress, may provide opportunities to leverage previously unappreciated skeletal muscle biological processes for therapeutic targets that support muscle mass, function, and plasticity.","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":"52 6","pages":"1-14"},"PeriodicalIF":3.8,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142862926","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

Structural insights into the membrane-bound proteolytic machinery of bacterial protein quality control. 从结构上洞察细菌蛋白质质量控制的膜结合蛋白水解机制。

IF 3.8 3区生物学

Biochemical Society transactions Pub Date : 2024-10-30 DOI: 10.1042/BST20231250

Rya Ero, Zhu Qiao, Kwan Ann Tan, Yong-Gui Gao

{"title":"Structural insights into the membrane-bound proteolytic machinery of bacterial protein quality control.","authors":"Rya Ero, Zhu Qiao, Kwan Ann Tan, Yong-Gui Gao","doi":"10.1042/BST20231250","DOIUrl":"10.1042/BST20231250","url":null,"abstract":"In bacteria and eukaryotic organelles of prokaryotic origin, ATP-dependent proteases are crucial for regulating protein quality control through substrate unfolding and degradation. Understanding the mechanism and regulation of this key cellular process could prove instrumental in developing therapeutic strategies. Very recently, cryo-electron microscopy structural studies have shed light on the functioning of AAA+ proteases, including membrane-bound proteolytic complexes. This review summarizes the structure and function relationship of bacterial AAA+ proteases, with a special focus on the sole membrane-bound AAA+ protease in Escherichia coli, FtsH. FtsH substrates include both soluble cytoplasmic and membrane-incorporated proteins, highlighting its intricate substrate recognition and processing mechanisms. Notably, 12 copies of regulatory HflK and HflC proteins, arranged in a cage-like structure embedded in the bacterial inner membrane, can encase up to 4 FtsH hexamers, thereby regulating their role in membrane protein quality control. FtsH represents an intriguing example, highlighting both its similarity to cytosolic AAA+ proteases with respect to overall architecture and oligomerization as well as its unique features, foremost its incorporation into a membrane-bound complex formed by HflK and HflC to mediate its function in protein quality control.","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":" ","pages":"2077-2086"},"PeriodicalIF":3.8,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142457079","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

Understanding the role of ten-eleven translocation family proteins in kidney diseases. 了解十-十一转位家族蛋白在肾脏疾病中的作用。

IF 3.8 3区生物学

Biochemical Society transactions Pub Date : 2024-10-30 DOI: 10.1042/BST20240291

Yuelin Zhang, Jiahui Li, Li Tan, Jun Xue, Yujiang Geno Shi

{"title":"Understanding the role of ten-eleven translocation family proteins in kidney diseases.","authors":"Yuelin Zhang, Jiahui Li, Li Tan, Jun Xue, Yujiang Geno Shi","doi":"10.1042/BST20240291","DOIUrl":"10.1042/BST20240291","url":null,"abstract":"Epigenetic mechanisms play a critical role in the pathogenesis of human diseases including kidney disorders. As the erasers of DNA methylation, Ten-eleven translocation (TET) family proteins can oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), thus leading to passive or active DNA demethylation. Similarly, TET family proteins can also catalyze the same reaction on RNA. In addition, TET family proteins can also regulate chromatin structure and gene expression in a catalytic activity-independent manner through recruiting the SIN3A/HDAC co-repressor complex. In 2012, we reported for the first time that the genomic 5-hydroxymethylcytosine level and the mRNA levels of Tet1 and Tet2 were significantly downregulated in murine kidneys upon ischemia and reperfusion injury. Since then, accumulating evidences have eventually established an indispensable role of TET family proteins in not only acute kidney injury but also chronic kidney disease. In this review, we summarize the upstream regulatory mechanisms and the pathophysiological role of TET family proteins in major types of kidney diseases and discuss their potential values in clinical diagnosis and treatment.","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":" ","pages":"2203-2214"},"PeriodicalIF":3.8,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387606","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

Disruptions to protein kinase A localization in adrenal pathology. 肾上腺病理学中的蛋白激酶 A 定位紊乱。

IF 3.8 3区生物学

Biochemical Society transactions Pub Date : 2024-10-30 DOI: 10.1042/BST20240444

Mitchell H Omar

引用次数: 0

Calcium signaling in mitochondrial intermembrane space. 线粒体膜间隙中的钙信号传递。

IF 3.8 3区生物学

Biochemical Society transactions Pub Date : 2024-10-30 DOI: 10.1042/BST20240319

Shanikumar Goyani, Shatakshi Shukla, Pooja Jadiya, Dhanendra Tomar

{"title":"Calcium signaling in mitochondrial intermembrane space.","authors":"Shanikumar Goyani, Shatakshi Shukla, Pooja Jadiya, Dhanendra Tomar","doi":"10.1042/BST20240319","DOIUrl":"10.1042/BST20240319","url":null,"abstract":"The mitochondrial intermembrane space (IMS) is a highly protected compartment, second only to the matrix. It is a crucial bridge, coordinating mitochondrial activities with cellular processes such as metabolites, protein, lipid, and ion exchange. This regulation influences signaling pathways for metabolic activities and cellular homeostasis. The IMS harbors various proteins critical for initiating apoptotic cascades and regulating reactive oxygen species production by controlling the respiratory chain. Calcium (Ca2+), a key intracellular secondary messenger, enter the mitochondrial matrix via the IMS, regulating mitochondrial bioenergetics, ATP production, modulating cell death pathways. IMS acts as a regulatory site for Ca2+ entry due to the presence of different Ca2+ sensors such as MICUs, solute carriers (SLCs); ion exchangers (LETM1/SCaMCs); S100A1, mitochondrial glycerol-3-phosphate dehydrogenase, and EFHD1, each with unique Ca2+ binding motifs and spatial localizations. This review primarily emphasizes the role of these IMS-localized Ca2+ sensors concerning their spatial localization, mechanism, and molecular functions. Additionally, we discuss how these sensors contribute to the progression and pathogenesis of various human health conditions and diseases.","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":" ","pages":"2215-2229"},"PeriodicalIF":3.8,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11727339/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142399177","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

How does CHD4 slide nucleosomes? CHD4 如何滑动核糖体？

IF 3.8 3区生物学

Biochemical Society transactions Pub Date : 2024-10-30 DOI: 10.1042/BST20230070

Xavier J Reid, Yichen Zhong, Joel P Mackay

{"title":"How does CHD4 slide nucleosomes?","authors":"Xavier J Reid, Yichen Zhong, Joel P Mackay","doi":"10.1042/BST20230070","DOIUrl":"10.1042/BST20230070","url":null,"abstract":"Chromatin remodelling enzymes reposition nucleosomes throughout the genome to regulate the rate of transcription and other processes. These enzymes have been studied intensively since the 1990s, and yet the mechanism by which they operate has only very recently come into focus, following advances in cryoelectron microscopy and single-molecule biophysics. CHD4 is an essential and ubiquitous chromatin remodelling enzyme that until recently has received less attention than remodellers such as Snf2 and CHD1. Here we review what recent work in the field has taught us about how CHD4 reshapes the genome. Cryoelectron microscopy and single-molecule studies demonstrate that CHD4 shares a central remodelling mechanism with most other chromatin remodellers. At the same time, differences between CHD4 and other chromatin remodellers result from the actions of auxiliary domains that regulate remodeller activity by for example: (1) making differential interactions with nucleosomal epitopes such as the acidic patch and the N-terminal tail of histone H4, and (2) inducing the formation of distinct multi-protein remodelling complexes (e.g. NuRD vs ChAHP). Thus, although we have learned much about remodeller activity, there is still clearly much more waiting to be revealed.","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":" ","pages":"1995-2008"},"PeriodicalIF":3.8,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11555702/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103968","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 role of prokaryotic argonautes in resistance to type II topoisomerases poison ciprofloxacin. 原核生物箭毒在抗 II 型拓扑异构酶毒环丙沙星中的作用。

IF 3.8 3区生物学

Biochemical Society transactions Pub Date : 2024-10-30 DOI: 10.1042/BST20240094

Alina Galivondzhyan, Dmitry Sutormin, Vladimir Panteleev, Andrey Kulbachinskiy, Konstantin Severinov

{"title":"The role of prokaryotic argonautes in resistance to type II topoisomerases poison ciprofloxacin.","authors":"Alina Galivondzhyan, Dmitry Sutormin, Vladimir Panteleev, Andrey Kulbachinskiy, Konstantin Severinov","doi":"10.1042/BST20240094","DOIUrl":"10.1042/BST20240094","url":null,"abstract":"Argonaute proteins are programmable nucleases found in all domains of life. Eukaryotic argonautes (eAgos) participate in genetic regulation, antiviral response, and transposon silencing during RNA interference. Prokaryotic argonautes (pAgos) are much more diverse than eAgos and have been implicated in defense against invading genetic elements. Recently, it was shown that pAgos protect bacterial cells from a topoisomerase poison ciprofloxacin, raising a possibility that they may play a role in DNA replication and/or repair. Here, we discuss possible models of pAgo-mediated ciprofloxacin resistance. We propose that pAgos could (i) participate in chromosome decatenation as a backup to topoisomerases; (ii) participate in the processing of DNA repair intermediates formed after topoisomerase poisoning, or (iii) induce SOS response that generally affects DNA repair and antibiotic resistance. These hypotheses should guide future investigations of the involvement of pAgos in the emergence of resistance to ciprofloxacin and, possibly, other antibiotics.","PeriodicalId":8841,"journal":{"name":"Biochemical Society transactions","volume":" ","pages":"2157-2166"},"PeriodicalIF":3.8,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11555693/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142493946","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

Histone H3 mutations and their impact on genome stability maintenance. 组蛋白 H3 突变及其对维持基因组稳定性的影响。

IF 3.8 3区生物学

Biochemical Society transactions Pub Date : 2024-10-30 DOI: 10.1042/BST20240177

Lucas D Caeiro, Ramiro E Verdun, Lluis Morey

引用次数: 0