bioRxiv - Biochemistry最新文献_第9页

Sweet science: Exploring the impact of fructose and glucose on brown adipocyte differentiation using optical diffraction tomography 甜蜜科学利用光衍射断层扫描探索果糖和葡萄糖对棕色脂肪细胞分化的影响

bioRxiv - Biochemistry Pub Date : 2024-09-04 DOI: 10.1101/2024.09.04.611269

Pooja Anantha, Xiangdong Wu, Salaheldeen Elsaid, Piyush Raj, Ishan Barman, Sui Seng Tee

{"title":"Sweet science: Exploring the impact of fructose and glucose on brown adipocyte differentiation using optical diffraction tomography","authors":"Pooja Anantha, Xiangdong Wu, Salaheldeen Elsaid, Piyush Raj, Ishan Barman, Sui Seng Tee","doi":"10.1101/2024.09.04.611269","DOIUrl":"https://doi.org/10.1101/2024.09.04.611269","url":null,"abstract":"The thermogenic capacity of brown adipose tissue (BAT) has garnered much attention for its potential to regulate systemic energy balance. BAT depot size and function need to be tightly to prevent loss of metabolic homeostasis due to energy dissipation via non-shivering thermogenesis. While adipocyte-intrinsic mechanisms controlling thermogenesis are critical, an increasing appreciation for the role of the BAT microenvironment is emerging. For example, changes in circulating hexoses due to dietary intake have shown to impact BAT function. Here, we show that murine BAT preadipocytes metabolism is impacted when fructose is used as the sole carbon source. Similarly, differentiation medium containing only fructose yield mature adipocytes with fewer lipid droplets, with a concomitant decrease in adipogenic genes. These deficiencies are also observed in human BAT preadipocytes, where cutting-edge optical imaging modalities show a decrease in total cell mass and lipid mass in fructose only medium. Taken together, the metabolic microenvironment significantly impacts BAT growth and function, with implications for the role of diets potentially mitigating the efficacy of BAT-targeted therapies.","PeriodicalId":501147,"journal":{"name":"bioRxiv - Biochemistry","volume":"18 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142175860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mechanism of Co-Transcriptional Cap-Snatching by Influenza Polymerase 流感聚合酶的共转录捕盖机制

bioRxiv - Biochemistry Pub Date : 2024-08-11 DOI: 10.1101/2024.08.11.607481

Alexander Helmut Rotsch, Delong Li, Maud Dupont, Tim Krischuns, Christiane Oberthuer, Alice Stelfox, Maria Lukarska, Isaac Fianu, Michael Lidschreiber, Nadia Naffakh, Christian Dienemann, Stephen Cusack, Patrick Cramer

{"title":"Mechanism of Co-Transcriptional Cap-Snatching by Influenza Polymerase","authors":"Alexander Helmut Rotsch, Delong Li, Maud Dupont, Tim Krischuns, Christiane Oberthuer, Alice Stelfox, Maria Lukarska, Isaac Fianu, Michael Lidschreiber, Nadia Naffakh, Christian Dienemann, Stephen Cusack, Patrick Cramer","doi":"10.1101/2024.08.11.607481","DOIUrl":"https://doi.org/10.1101/2024.08.11.607481","url":null,"abstract":"Influenza virus mRNA is stable and competent for nuclear export and translation because it re-ceives a 5′ cap(1) structure in a process called cap-snatching1. During cap-snatching, the viral RNA-dependent RNA polymerase (FluPol) binds to host RNA polymerase II (Pol II) and the emerging transcript2,3. The FluPol endonuclease then cleaves a capped RNA fragment that sub-sequently acts as a primer for the transcription of viral genes4,5. Here, we present the cryo-EM structure of FluPol bound to a transcribing Pol II in complex with the elongation factor DSIF in the pre-cleavage state. The structure shows that FluPol directly interacts with both Pol II and DSIF, which position the FluPol endonuclease domain near the RNA exit channel of Pol II. These interactions are important for the endonuclease activity of FluPol and FluPol activity in cells. A second structure trapped after cap-snatching shows that cleavage rearranges the capped RNA primer within the FluPol, directing the capped RNA 3′-end towards the FluPol polymer-ase active site for viral transcription initiation. Altogether, our results provide the molecular mechanisms of co-transcriptional cap-snatching by FluPol.","PeriodicalId":501147,"journal":{"name":"bioRxiv - Biochemistry","volume":"198 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141944456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Characterization of a marine bacteria through a novel metabologenomics approach 通过新型代谢组学方法确定海洋细菌的特征

bioRxiv - Biochemistry Pub Date : 2024-08-11 DOI: 10.1101/2024.08.11.607463

Gabriel Arini, Tiago Cabral Borelli, Elthon Gois Ferreira, Rafael de Felicio, Paula Rezende-Teixeira, Matheus Pedrino Goncalves, Franciene Rabico Oliveira, Guilherme Viana de Siqueira, Luiz Gabriel Mencucini, Henrique Tsuji, Lucas Sousa Neves Andrade, Leandro Garrido, Gabriel Padilla, Alberto Gil-de-la-Fuentes, Mingxun Wang, Norberto Peporine Lopes, Daniela BB Trivella, Leticia V Costa-Lotufo, Maria-Eugenia Guazzaroni, Ricardo Roberto da Silva

{"title":"Characterization of a marine bacteria through a novel metabologenomics approach","authors":"Gabriel Arini, Tiago Cabral Borelli, Elthon Gois Ferreira, Rafael de Felicio, Paula Rezende-Teixeira, Matheus Pedrino Goncalves, Franciene Rabico Oliveira, Guilherme Viana de Siqueira, Luiz Gabriel Mencucini, Henrique Tsuji, Lucas Sousa Neves Andrade, Leandro Garrido, Gabriel Padilla, Alberto Gil-de-la-Fuentes, Mingxun Wang, Norberto Peporine Lopes, Daniela BB Trivella, Leticia V Costa-Lotufo, Maria-Eugenia Guazzaroni, Ricardo Roberto da Silva","doi":"10.1101/2024.08.11.607463","DOIUrl":"https://doi.org/10.1101/2024.08.11.607463","url":null,"abstract":"Exploiting microbial natural products is a key pursuit of the bioactive compound discovery field. Recent advances in modern analytical techniques have increased the volume of microbial genomes and their encoded biosynthetic products measured by mass spectrometry-based metabolomics. However, connecting multi-omics data to uncover metabolic processes of interest is still challenging. This results in a large portion of genes and metabolites remaining unannotated. Further exacerbating the annotation challenge, databases and tools for annotation and omics integration are scattered, requiring complex computations to annotate and integrate omics datasets. Here we performed a two-way integrative analysis combining genomics and metabolomics data to describe a new approach to characterize the marine bacterial isolate BRA006 and to explore its biosynthetic gene cluster (BGC) content as well as the bioactive compounds detected by metabolomics. We described BRA006 genomic content and structure by comparing Illumina and Oxford Nanopore MinION sequencing approaches. Digital DNA:DNA hybridization (dDDH) taxonomically assigned BRA006 as a potential new species of the Micromonospora genus. Starting from LC-ESI(+)-HRMS/MS data, and mapping the annotated enzymes and metabolites belonging to the same pathways, our integrative analysis allowed us to correlate the compound Brevianamide F to a new BGC, previously assigned to other function.","PeriodicalId":501147,"journal":{"name":"bioRxiv - Biochemistry","volume":"220 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141944461","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genesis and regulation of C-terminal cyclic imides from protein damage 来自蛋白质损伤的 C 端环状亚胺的生成和调节

bioRxiv - Biochemistry Pub Date : 2024-08-10 DOI: 10.1101/2024.08.09.606997

Wenqing Xu, Zhenguang Zhao, Matthew Su, Atul Jain, Hannah C. Lloyd, Ethan Yang Feng, Nick Cox, Christina M. Woo

{"title":"Genesis and regulation of C-terminal cyclic imides from protein damage","authors":"Wenqing Xu, Zhenguang Zhao, Matthew Su, Atul Jain, Hannah C. Lloyd, Ethan Yang Feng, Nick Cox, Christina M. Woo","doi":"10.1101/2024.08.09.606997","DOIUrl":"https://doi.org/10.1101/2024.08.09.606997","url":null,"abstract":"C-Terminal cyclic imides are post-translational modifications (PTMs) that can arise from spontaneous intramolecular cleavage of asparagine or glutamine residues resulting in a form of irreversible protein damage. These protein damage events are recognized and removed by the E3 ligase substrate adapter cereblon (CRBN), indicating that these aging-related modifications may require cellular quality control mechanisms to prevent deleterious effects. However, the factors that determine protein or peptide susceptibility to C-terminal cyclic imide formation or their effect on protein stability have not been explored in detail. Here, we characterize the primary and secondary structures of peptides and proteins that promote intrinsic formation of C-terminal cyclic imides in comparison to deamidation, a related form of protein damage. Extrinsic effects from solution properties and stressors on the cellular proteome additionally promote C-terminal cyclic imide formation on proteins like glutathione synthetase (GSS) that are susceptible to aggregation if the protein damage products are not removed by CRBN. This systematic investigation provides insight to the regions of the proteome that are prone to these unexpectedly frequent modifications, the effects of this form of protein damage on protein stability, and the biological role of CRBN.","PeriodicalId":501147,"journal":{"name":"bioRxiv - Biochemistry","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141944459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An asymmetric nautilus-like HflK/C assembly controls FtsH proteolysis of membrane proteins 类似鹦鹉螺的不对称 HflK/C 组装控制着膜蛋白的 FtsH 蛋白水解作用

bioRxiv - Biochemistry Pub Date : 2024-08-10 DOI: 10.1101/2024.08.09.604662

Alireza Ghanbarpour, Bertina Telusma, Barrett M. Powell, Jia Jia Zhang, Isabella Bolstad, Carolyn Vargas, Sandro Keller, Tania A. Baker, Robert T. Sauer, Joseph H. Davis

{"title":"An asymmetric nautilus-like HflK/C assembly controls FtsH proteolysis of membrane proteins","authors":"Alireza Ghanbarpour, Bertina Telusma, Barrett M. Powell, Jia Jia Zhang, Isabella Bolstad, Carolyn Vargas, Sandro Keller, Tania A. Baker, Robert T. Sauer, Joseph H. Davis","doi":"10.1101/2024.08.09.604662","DOIUrl":"https://doi.org/10.1101/2024.08.09.604662","url":null,"abstract":"FtsH, a AAA protease, associates with HflK/C subunits to form a megadalton complex that spans the inner membrane and extends into the periplasm of E. coli. How this complex and homologous assemblies in eukaryotic organelles recruit, extract, and degrade membrane-embedded substrates is unclear. Following overproduction of protein components, recent cryo-EM structures reveal symmetric HflK/C cages surrounding FtsH in a manner proposed to inhibit degradation of membrane-embedded substrates. Here, we present structures of native complexes in which HflK/C instead forms an asymmetric nautilus-like assembly with an entryway for membrane-embedded substrates to reach and be engaged by FtsH. Consistent with this nautilus-like structure, proteomic assays suggest that HflK/C enhances FtsH degradation of certain membrane-embedded substrates. Membrane curvature in our FtsH*HflK/C complexes is opposite that of surrounding membrane regions, a property that correlates with lipid-scramblase activity and possibly with FtsH's function in the degradation of membrane-embedded proteins.","PeriodicalId":501147,"journal":{"name":"bioRxiv - Biochemistry","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141944460","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A pan-variant miniprotein inhibitor protects against SARS-CoV-2 variants 一种泛变异小蛋白抑制剂可抵御 SARS-CoV-2 变异病毒

bioRxiv - Biochemistry Pub Date : 2024-08-10 DOI: 10.1101/2024.08.08.606885

Jimin Lee, James Brett Case, Rashmi Ravichandran, Daniel Asarnow, M. Alejandra Tortorici, Jack T Brown, Shilpa Sanapala, Lauren Carter, David Baker, Michael S Diamond, David Veesler

引用次数: 0

Biochemical and structural insights into the auto-inhibited state of Mical1 and its activation by Rab8 Mical1的自动抑制状态及其被Rab8激活的生化和结构见解

bioRxiv - Biochemistry Pub Date : 2024-08-10 DOI: 10.1101/2024.06.17.599268

Amrita Rai, Petra Janning, Ingrid R. Vetter, Roger S. Goody

{"title":"Biochemical and structural insights into the auto-inhibited state of Mical1 and its activation by Rab8","authors":"Amrita Rai, Petra Janning, Ingrid R. Vetter, Roger S. Goody","doi":"10.1101/2024.06.17.599268","DOIUrl":"https://doi.org/10.1101/2024.06.17.599268","url":null,"abstract":"Mical1 regulates F-actin dynamics through the reversible oxidation of actin, a process controlled by its interactions with various proteins. Upon binding to Rab8 family members, Mical1 links endosomes to the cytoskeleton, promoting F-actin disassembly. In the absence of Rab, Mical1 exists in an auto-inhibited state, but its biochemical characterization remains incomplete. Our study reveals that the N-terminal MO-CH-LIM domains of Mical1 form an intramolecular complex with its C-terminal bMERB domain. Mutational analysis, guided by the AlphaFold2 model, identifies critical residues at the binding interface. Additionally, we demonstrate that full-length Mical1 binds to Rab8 in a 1:2 stoichiometry, thereby releasing auto-inhibition. Through structure-based mutational studies, we uncover allostery between the N and C-terminal Rab binding sites. Notably, Rab binding at the high-affinity C-terminal site precedes binding at the N-terminal site, suggesting a sequential binding mode. These findings elucidate how Rab8 binding releases the MO-CH-LIM domains from the Mical1 bMERB domain, facilitating interactions with other proteins and the actin cytoskeleton, thereby modulating actin dynamics.","PeriodicalId":501147,"journal":{"name":"bioRxiv - Biochemistry","volume":"40 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141944463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Probing intracellular determinants of PARP inhibitor selectivity and pharmacology with CeTEAM 利用 CeTEAM 探究 PARP 抑制剂选择性和药理学的细胞内决定因素

bioRxiv - Biochemistry Pub Date : 2024-08-10 DOI: 10.1101/2024.08.09.607390

Maria J. Pires, Alen Lovric, Emanuele Fabbrizi, Dante Rotili, Mikael Altun, Nicholas C.K. Valerie

{"title":"Probing intracellular determinants of PARP inhibitor selectivity and pharmacology with CeTEAM","authors":"Maria J. Pires, Alen Lovric, Emanuele Fabbrizi, Dante Rotili, Mikael Altun, Nicholas C.K. Valerie","doi":"10.1101/2024.08.09.607390","DOIUrl":"https://doi.org/10.1101/2024.08.09.607390","url":null,"abstract":"PARP inhibitors (PARPi) predominantly targeting PARP1 and PARP2 have revolutionized cancer therapy by exploiting synthetic lethality and selectively killing cancer cells with defective DNA repair. However, achieving PARP1 or PARP2-selective inhibitors is difficult due to their close structural homology. Selectivity profiling is typically done with purified proteins, but these lack the complexity of intracellular environments and could therefore be inaccurate. The cellular target engagement by accumulation of mutant (CeTEAM) method provides insights into drug binding in cellulo by means of conditionally stabilized biosensors, thus offering a dynamic view of pharmacological events in living cells. Here, we duplex PARP1 L713F-GFP and PARP2 L269A-mCherry biosensors to systematically characterize potential PARPi binding and cell cycle alterations at the single cell level. Our results reveal that most PARPi are generally equipotent for both PARPs or have slight biases only towards PARP1, not PARP2. AZD5305, a reported PARP1-selective inhibitor, was the exception and appears ~1600-fold more potent towards PARP1. Surprisingly, niraparib was >10-fold more selective for PARP1, despite reported equipotent biochemical activity. Meanwhile, the next generation PARPi, senaparib, was a potent PARP1/2 binder and DNA trapper. We also assessed the effect of the PARP1/2 active site component, HPF1, on intracellular PARPi binding and see that HPF1 depletion elicits slight deviations in apparent binding potency, while contributing additively to PARP-DNA trapping. These results highlight that multiplexing CeTEAM biosensors and layered genetic perturbations can systematically profile determinants of intracellular drug selectivity. Furthermore, the PARP1/2 CeTEAM platform should facilitate the discovery of selective PARPi for better targeted therapies.","PeriodicalId":501147,"journal":{"name":"bioRxiv - Biochemistry","volume":"80 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141944457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The molecular structure of an axle-less F1-ATPase 无轴 F1-ATP 酶的分子结构

bioRxiv - Biochemistry Pub Date : 2024-08-09 DOI: 10.1101/2024.08.08.607276

Emily J. Furlong, Ian-Blaine P. Reininger-Chatzigiannakis, Yi C. Zeng, Simon H. J. Brown, Meghna Sobti, Alastair G. Stewart

引用次数: 0

Evidence for S331-G-S-L within the amyloid core of myocilin olfactomedin domain fibrils based on low-resolution 3D solid-state NMR spectra 基于低分辨率三维固态 NMR 光谱的肌球蛋白橄榄酰肌球蛋白结构域纤维淀粉样核心内 S331-G-S-L 的证据

bioRxiv - Biochemistry Pub Date : 2024-08-09 DOI: 10.1101/2024.08.09.606901

Emily G. Saccuzzo, Alicia S. Robang, Yuan Gao, Bo J Chen, Raquel L Lieberman, Anant Krishna Paravastu

{"title":"Evidence for S331-G-S-L within the amyloid core of myocilin olfactomedin domain fibrils based on low-resolution 3D solid-state NMR spectra","authors":"Emily G. Saccuzzo, Alicia S. Robang, Yuan Gao, Bo J Chen, Raquel L Lieberman, Anant Krishna Paravastu","doi":"10.1101/2024.08.09.606901","DOIUrl":"https://doi.org/10.1101/2024.08.09.606901","url":null,"abstract":"Myocilin-associated glaucoma is a protein-conformational disorder associated with formation of a toxic amyloid-like aggregate. Numerous destabilizing single point variants, distributed across the myocilin olfactomedin β-propeller (OLF, myocilin residues 245-504, 30 kDa) are associated with accelerated disease progression. In vitro, wild type (WT) OLF can be promoted to form thioflavin T (ThT)-positive fibrils under mildly destabilizing (37°C, pH 7.2) conditions. Consistent with the notion that only a small number of residues within a protein are responsible for amyloid formation, 3D 13C-13C solid-state NMR spectra show that OLF fibrils are likely to be composed of only about one third of the overall sequence. Here, we probe the residue composition of fibrils formed de novo from purified full-length OLF. We were able to make sequential assignments consistent with the sequence S331-G-S-L334. This sequence appears once within a previously identified amyloid-prone region (P1, G326AVVYSGSLYFQ) internal to OLF. Since nearly half of the pairs of adjacent residues (di-peptides) in OLF occur only once in the primary structure and almost all the 3-residue sequences (tri-peptides) are unique, remarkably few sequential assignments are necessary to uniquely identify specific regions of the amyloid core. This assignment approach could be applied to other systems to expand our molecular comprehension of how folded proteins undergo fibrillization.","PeriodicalId":501147,"journal":{"name":"bioRxiv - Biochemistry","volume":"198 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141944376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0