Liver Mitochondrial Membrane Crosslinking and Destruction in a Rat
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A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Assembling the Mitochondrial ATP Synthase Jiyao Songa, Nikolaus Pfannera,B,1, and Thomas Beckera,B
COMMENTARY COMMENTARY Assembling the mitochondrial ATP synthase Jiyao Songa, Nikolaus Pfannera,b,1, and Thomas Beckera,b Mitochondria are known as the powerhouses of the of the ATP synthase (5–7). A recent high-resolution cell. The F1Fo-ATP synthase of the mitochondrial inner cryoelectron microscopic structure of the dimeric Fo membrane produces the bulk of cellular ATP. The re- region of yeast ATP synthase revealed that the subunits spiratory chain complexes pump protons across the Atp6 and i/j form the contact sites between two ATP inner membrane into the intermembrane space and synthase monomers, supported by interaction between thereby generate a proton-motive force that drives subunits e and k (8). In mitochondria, rows of ATP syn- the ATP synthase. In a fascinating molecular mecha- thase dimers localize to the rims of the cristae mem- nism, the ATP synthase couples the synthesis of ATP branes, which are invaginations of the inner membrane. to the transport of protons into the matrix (1–3). For- The ATP synthase dimers bend the inner membrane mation of the ATP synthase depends on the associa- and are crucial for forming the typical cristae shape (9, tion of 17 different structural subunits of dual genetic 10). The supernumerary subunits e and g, together with origin. Whereas a number of assembly factors and the N-terminal portion of the peripheral stalk subunit b, steps have been identified in the model organism affect the curvature of the inner membrane (8, 9, 11). baker’s yeast, little has been known about the assem- Thus, the ATP synthase not only synthesizes ATP but bly of the human ATP synthase. -
Difference Between Atpase and ATP Synthase Key Difference
Difference Between ATPase and ATP Synthase www.differencebetween.com Key Difference - ATPase vs ATP Synthase Adenosine triphosphate (ATP) is a complex organic molecule that participates in the biological reactions. It is known as “molecular unit of currency” of intracellular energy transfer. It is found in almost all forms of life. In the metabolism, ATP is either consumed or generated. When ATP is consumed, energy is released by converting into ADP (adenosine diphosphate) and AMP (adenosine monophosphate) respectively. The enzyme which catalyzes the following reaction is known as ATPase. ATP → ADP + Pi + Energy is released In other metabolic reactions which incorporate external energy, ATP is generated from ADP and AMP. The enzyme which catalyzes the below-mentioned reaction is called an ATP Synthase. ADP + Pi → ATP + Energy is consumed So, the key difference between ATPase and ATP Synthase is, ATPase is the enzyme that breaks down ATP molecules while the ATP Synthase involves in ATP production. What is ATPase? The ATPase or adenylpyrophosphatase (ATP hydrolase) is the enzyme which decomposes ATP molecules into ADP and Pi (free phosphate ion.) This decomposition reaction releases energy which is used by other chemical reactions in the cell. ATPases are the class of membrane-bound enzymes. They consist of a different class of members that possess unique functions such as Na+/K+-ATPase, Proton-ATPase, V-ATPase, Hydrogen Potassium–ATPase, F-ATPase, and Calcium-ATPase. These enzymes are integral transmembrane proteins. The transmembrane ATPases move solutes across the biological membrane against their concentration gradient typically by consuming the ATP molecules. So, the main functions of the ATPase enzyme family members are moving cell metabolites across the biological membrane and exporting toxins, waste and the solutes that can hinder the normal cell function. -
ATP Synthase K+- and H+-Flux Drive ATP Synthesis and Enable Mitochondrial K+-Uniporter Function
bioRxiv preprint doi: https://doi.org/10.1101/355776; this version posted April 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. ATP synthase K+- and H+-flux drive ATP synthesis and enable mitochondrial K+-uniporter function Magdalena Juhaszova,1,9 Evgeny Kobrinsky,1,9 Dmitry B. Zorov,1,5,9 H. Bradley Nuss,1† Yael Yaniv,1‡ Kenneth W. Fishbein,2 Rafael de Cabo,3 Lluis Montoliu,6 Sandra B. Gabelli,4,7,8 Miguel A. Aon,1 Sonia Cortassa,1 and Steven J. Sollott1,* 1Laboratories of Cardiovascular Science and 2Clinical Investigation, and 3Translational Gerontology Branch, National Institute on Aging, NIH, and 4Dept. Medicine, 7Dept. Oncology, 8Dept. Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA 5A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia 6Centro Nacional de Biotecnología, CSIC, Madrid, Spain Present address: †Center for Scientific Review, NIH, Bethesda, MD, USA ‡Biomedical Engineering Faculty, Technion-IIT, Haifa, Israel 9 Co-first author * Correspondence: [email protected] Running title: ATP synthase K+- and H+-flux drive ATP synthesis Lead Contact: Steven J. Sollott, M.D. Chief, Cardioprotection Section Laboratory of Cardiovascular Science Biomedical Research Center, Suite 100 National Institute on Aging, NIH 251 Bayview Blvd Baltimore, MD 21224-2816 USA TEL: 410-558-8657 FAX: 410-558-8150 bioRxiv preprint doi: https://doi.org/10.1101/355776; this version posted April 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Gene Expression Signatures and Biomarkers of Noninvasive And
Oncogene (2006) 25, 2328–2338 & 2006 Nature Publishing Group All rights reserved 0950-9232/06 $30.00 www.nature.com/onc ORIGINAL ARTICLE Gene expression signatures and biomarkers of noninvasive and invasive breast cancer cells: comprehensive profiles by representational difference analysis, microarrays and proteomics GM Nagaraja1, M Othman2, BP Fox1, R Alsaber1, CM Pellegrino3, Y Zeng2, R Khanna2, P Tamburini3, A Swaroop2 and RP Kandpal1 1Department of Biological Sciences, Fordham University, Bronx, NY, USA; 2Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI, USA and 3Bayer Corporation, West Haven, CT, USA We have characterized comprehensive transcript and Keywords: representational difference analysis; micro- proteomic profiles of cell lines corresponding to normal arrays; proteomics; breast carcinoma; biomarkers; breast (MCF10A), noninvasive breast cancer (MCF7) and copper homeostasis invasive breast cancer (MDA-MB-231). The transcript profiles were first analysed by a modified protocol for representational difference analysis (RDA) of cDNAs between MCF7 and MDA-MB-231 cells. The majority of genes identified by RDA showed nearly complete con- Introduction cordance withmicroarray results, and also led to the identification of some differentially expressed genes such The transformation of a normal cell into a cancer cell as lysyl oxidase, copper transporter ATP7A, EphB6, has been correlated to altered expression of a variety of RUNX2 and a variant of RUNX2. The altered transcripts genes (Perou et al., 2000; Becker et al., 2005). The identified by microarray analysis were involved in cell–cell expression of some of these genes is a direct result of or cell–matrix interaction, Rho signaling, calcium home- sequence mutation, whereas other changes occur due to ostasis and copper-binding/sensitive activities. -
PRICKLE3 Linked to Atpase Biogenesis Manifested Leber's Hereditary Optic Neuropathy
PRICKLE3 linked to ATPase biogenesis manifested Leber’s hereditary optic neuropathy Jialing Yu, … , Pingping Jiang, Min-Xin Guan J Clin Invest. 2020. https://doi.org/10.1172/JCI134965. Research In-Press Preview Genetics Ophthalmology Graphical abstract Find the latest version: https://jci.me/134965/pdf PRICKLE3 linked to ATPase biogenesis manifested Leber’s hereditary optic neuropathy Jialing Yu1,2,3#, Xiaoyang Liang2#, Yanchun Ji1,2 #, Cheng Ai2#, Junxia Liu2, Ling Zhu1,2, Zhipeng Nie2, Xiaofen Jin2,3, Chenghui Wang2, Juanjuan Zhang2,4, Fuxin Zhao4, Shuang Mei2, Xiaoxu Zhao1,2, Xiangtian Zhou4, Minglian Zhang5, Meng Wang1,2, Taosheng Huang6, Pingping Jiang1,2* and Min-Xin Guan1,2,3,7* 1The Children’s Hospital, Division of Medical Genetics and Genomics, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China 2Institute of Genetics and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China. 3Key Laboratory of Reproductive Genetics, Ministry of Education of PRC, Hangzhou, Zhejiang, China 4School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China 5Department of Ophthalmology, Hebei Provincial Eye Hospital, Xingtai, Hebei, China 6Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA 7Joint Institute of Genetics and Genomic Medicine between Zhejiang University and University of Toronto, Zhejiang University, Hangzhou, Zhejiang, China #The first four authors have equally contributed to the work. *Corresponding authors: Min-Xin Guan, Ph.D., Institute of Genetics, Zhejiang University School of Medicine, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China; Tel: 86-571-88206916; Fax: 86-571-88982377; E-mail: [email protected]; Pingping Jiang, Ph.D., Department of Human Genetics, Zhejiang University School of Medicine, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China; Tel: 86-571- 88208328; Fax: 86-571-88982356; E-mail: [email protected]. -
Interrelation Between ROS and Ca2+ in Aging and Age-Related Diseases
Research Collection Review Article Interrelation between ROS and Ca2+ in aging and age-related diseases Author(s): Madreiter-Sokolowski, Corina T.; Thomas, Carolin; Ristow, Michael Publication Date: 2020-09 Permanent Link: https://doi.org/10.3929/ethz-b-000432186 Originally published in: Redox Biology 36, http://doi.org/10.1016/j.redox.2020.101678 Rights / License: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library Redox Biology 36 (2020) 101678 Contents lists available at ScienceDirect Redox Biology journal homepage: www.elsevier.com/locate/redox Review article + Interrelation between ROS and Ca2 in aging and age-related diseases Corina T. Madreiter-Sokolowski a,b,*, Carolin Thomas a, Michael Ristow a a Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland b Holder of an Erwin Schroedinger Abroad Fellowship, Austrian Science Fund (FWF), Austria ARTICLE INFO ABSTRACT + Keywords: Calcium (Ca2 ) and reactive oxygen species (ROS) are versatile signaling molecules coordinating physiological + Aging and pathophysiological processes. While channels and pumps shuttle Ca2 ions between extracellular space, ROS homeostasis + cytosol and cellular compartments, short-lived and highly reactive ROS are constantly generated by various Ca2 homeostasis + production sites within the cell. Ca2 controls membrane potential, modulates mitochondrial adenosine Cardiovascular diseases triphosphate (ATP) production and affects proteins like calcineurin (CaN) or calmodulin (CaM), which, in turn, Type 2 diabetes mellitus 2+ Neurodegenerative diseases have a wide area of action. Overwhelming Ca levels within mitochondria efficiently induce and trigger cell Malignant diseases death. -
ATP Synthase: Structure,Abstract: Functionlet F Denote a Eld and and Let Inhibitionv Denote a Vector Space Over F with Nite Positive Dimension
Spec. Matrices 2019; 7:1–19 Research Article Open Access Kazumasa Nomura* and Paul Terwilliger BioMol Concepts 2019; 10: 1–10 Self-dual Leonard pairs Research Article Open Access https://doi.org/10.1515/spma-2019-0001 Prashant Neupane*, Sudina Bhuju, Nita Thapa,Received Hitesh May 8, 2018; Kumar accepted Bhattarai September 22, 2018 ATP Synthase: Structure,Abstract: FunctionLet F denote a eld and and let InhibitionV denote a vector space over F with nite positive dimension. Consider a pair A, A∗ of diagonalizable F-linear maps on V, each of which acts on an eigenbasis for the other one in an irreducible tridiagonal fashion. Such a pair is called a Leonard pair. We consider the self-dual case in which https://doi.org/10.1515/bmc-2019-0001 there exists an automorphism of the endomorphism algebra of V that swaps A and A∗. Such an automorphism phosphate (Pi), along with considerable release of energy. received September 18, 2018; accepted December 21, 2018. is unique, and called the duality A A∗. In the present paper we give a comprehensive description of this ADP can absorb energy and regain↔ the group to regenerate duality. In particular, we display an invertible F-linear map T on V such that the map X TXT− is the duality Abstract: Oxidative phosphorylation is carried out by an ATP molecule to maintain constant ATP concentration. → A A∗. We express T as a polynomial in A and A∗. We describe how T acts on ags, decompositions, five complexes, which are the sites for electron transport↔ Other than supporting almost all the cellular and ATP synthesis. -
Cryo-EM Structures of the Autoinhibited E. Coli ATP Synthase in Three Rotational States
RESEARCH ARTICLE Cryo-EM structures of the autoinhibited E. coli ATP synthase in three rotational states Meghna Sobti1, Callum Smits1, Andrew SW Wong2, Robert Ishmukhametov3, Daniela Stock1,4, Sara Sandin2,5, Alastair G Stewart1,4* 1Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, Australia; 2NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore; 3Department of Physics, Clarendon Laboratory, University of Oxford, Oxford, United Kingdom; 4Faculty of Medicine, The University of New South Wales, Sydney, Australia; 5School of Biological Sciences, Nanyang Technological University, Singapore, Singapore Abstract A molecular model that provides a framework for interpreting the wealth of functional information obtained on the E. coli F-ATP synthase has been generated using cryo-electron microscopy. Three different states that relate to rotation of the enzyme were observed, with the central stalk’s e subunit in an extended autoinhibitory conformation in all three states. The Fo motor comprises of seven transmembrane helices and a decameric c-ring and invaginations on either side of the membrane indicate the entry and exit channels for protons. The proton translocating subunit contains near parallel helices inclined by ~30˚ to the membrane, a feature now synonymous with rotary ATPases. For the first time in this rotary ATPase subtype, the peripheral stalk is resolved over its entire length of the complex, revealing the F1 attachment points and a coiled-coil that bifurcates toward the membrane with its helices separating to embrace subunit a from two sides. DOI: 10.7554/eLife.21598.001 *For correspondence: a.stewart@ victorchang.edu.au Competing interests: The Introduction authors declare that no In most cells, the bulk of ATP, the principal source of cellular energy, is synthesized by ATP synthase. -
Kidney V-Atpase-Rich Cell Proteome Database
A comprehensive list of the proteins that are expressed in V-ATPase-rich cells harvested from the kidneys based on the isolation by enzymatic digestion and fluorescence-activated cell sorting (FACS) from transgenic B1-EGFP mice, which express EGFP under the control of the promoter of the V-ATPase-B1 subunit. In these mice, type A and B intercalated cells and connecting segment principal cells of the kidney express EGFP. The protein identification was performed by LC-MS/MS using an LTQ tandem mass spectrometer (Thermo Fisher Scientific). For questions or comments please contact Sylvie Breton ([email protected]) or Mark A. Knepper ([email protected]). -
Structure of the Hexameric Hera Atpase Reveals a Mechanism of Translocation-Coupled DNA-End Processing in Archaea
ARTICLE Received 29 May 2014 | Accepted 7 Oct 2014 | Published 25 Nov 2014 DOI: 10.1038/ncomms6506 Structure of the hexameric HerA ATPase reveals a mechanism of translocation-coupled DNA-end processing in archaea Neil J. Rzechorzek1, John K. Blackwood1, Sian M. Bray1, Joseph D. Maman1, Luca Pellegrini1 & Nicholas P. Robinson1 The HerA ATPase cooperates with the NurA nuclease and the Mre11–Rad50 complex for the repair of double-strand DNA breaks in thermophilic archaea. Here we extend our structural knowledge of this minimal end-resection apparatus by presenting the first crystal structure of hexameric HerA. The full-length structure visualizes at atomic resolution the N-terminal HerA-ATP synthase domain and a conserved C-terminal extension, which acts as a physical brace between adjacent protomers. The brace also interacts in trans with nucleotide-binding residues of the neighbouring subunit. Our observations support a model in which the coaxial interaction of the HerA ring with the toroidal NurA dimer generates a continuous channel traversing the complex. HerA-driven translocation would propel the DNA towards the narrow annulus of NurA, leading to duplex melting and nucleolytic digestion. This system differs substantially from the bacterial end-resection paradigms. Our findings suggest a novel mode of DNA-end processing by this integrated archaeal helicase–nuclease machine. 1 Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK. Correspondence and requests for materials should be addressed to L.P. (email: [email protected]) or to N.P.R. (email: [email protected]). NATURE COMMUNICATIONS | 5:5506 | DOI: 10.1038/ncomms6506 | www.nature.com/naturecommunications 1 & 2014 Macmillan Publishers Limited.