99951
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Uchida D, Takaki A, Adachi T, Okada H. Beneficial and Paradoxical Roles of Anti-Oxidative Nutritional Support for Non-Alcoholic Fatty Liver Disease. Nutrients 2018; 10:E977. [PMID: 30060482 PMCID: PMC6116036 DOI: 10.3390/nu10080977] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 07/17/2018] [Accepted: 07/24/2018] [Indexed: 02/06/2023] Open
Abstract
Oxidative stress is being recognized as a key factor in the progression of chronic liver disease (CLD), especially non-alcoholic fatty liver disease (NAFLD). Many NAFLD treatment guidelines recommend the use of antioxidants, especially vitamin E. Many prospective studies have described the beneficial effects of such agents for the clinical course of NAFLD. However, as these studies are usually short-term evaluations, lasting only a few years, whether or not antioxidants continue to exert favorable long-term effects, including in cases of concomitant hepatocellular carcinoma, remains unclear. Antioxidants are generally believed to be beneficial for human health and are often commercially available as health-food products. Patients with lifestyle-related diseases often use such products to try to be healthier without practicing lifestyle intervention. However, under some experimental NAFLD conditions, antioxidants have been shown to encourage the progression of hepatocellular carcinoma, as oxidative stress is toxic for cancer cells, just as for normal cells. In this review, we will highlight the paradoxical effects of antioxidants against NAFLD and related hepatocellular carcinoma.
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Affiliation(s)
- Daisuke Uchida
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan.
| | - Akinobu Takaki
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan.
| | - Takuya Adachi
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan.
| | - Hiroyuki Okada
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan.
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99952
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Abstract
The spatial density of mitochondria was studied by thin-section electron microscopy in
smooth muscles of bladder, iris and gut in mice, rats, guinea-pigs and sheep. Morphometric
data included areas of muscle cell profiles (~6,000 muscle cells were measured) and areas
of their mitochondria (more than three times as many). The visual method delivers accurate
estimates of the extent of the chondrioma (the ensemble of mitochondria in a cell),
measuring all and only the mitochondria in each muscle cell and no other cells. The
digital records obtained can be used again for checks and new searches. Spatial density of
mitochondria varies between about 2 and 10% in different muscles in different species. In
contrast, there is consistency of mitochondrial density within a given muscle in a given
species. For each muscle in each species there is a characteristic mitochondrial density
with modest variation between experiments. On the basis of data from serial sections in
the rat detrusor muscle, mitochondrial density varies very little between the muscle
cells, each cell having a value close to that for the whole muscle. Mitochondrial density
is different in a given muscle, e.g., ileal circular muscle, from the four mammalian
species, with highest values in mouse and lowest in sheep; in mice the mitochondrial
density is nearly three time higher that in sheep. In a given species there are
characteristic variations between different muscles. For example, the bladder detrusor
muscle has markedly fewer mitochondria than the ileum, and the iris has markedly more.
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99953
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Abstract
T cells efficiently respond to foreign antigens to mediate immune responses against infections but are tolerant to self-tissues. Defect in T cell activation is associated with severe immune deficiencies, whereas aberrant T cell activation contributes to the pathogenesis of diverse autoimmune and inflammatory diseases. An emerging mechanism that regulates T cell activation and tolerance is ubiquitination, a reversible process of protein modification that is counter-regulated by ubiquitinating enzymes and deubiquitinases (DUBs). DUBs are isopeptidases that cleave polyubiquitin chains and remove ubiquitin from target proteins, thereby controlling the magnitude and duration of ubiquitin signaling. It is now well recognized that DUBs are crucial regulators of T cell responses and serve as potential therapeutic targets for manipulating immune responses in the treatment of immunological disorders and cancer. This review will discuss the recent progresses regarding the functions of DUBs in T cells.
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Affiliation(s)
- Xiao-Dong Yang
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Shao-Cong Sun
- Department of Immunology, The University of Texas MD Anderson Cancer Center, 7455 Fannin Street, Box 902, Houston, TX, 77030, USA. .,The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX, 77030, USA.
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99954
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Diament A, Tuller T. Modeling three-dimensional genomic organization in evolution and pathogenesis. Semin Cell Dev Biol 2018; 90:78-93. [PMID: 30030143 DOI: 10.1016/j.semcdb.2018.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/08/2018] [Indexed: 12/17/2022]
Abstract
The regulation of gene expression is mediated via the complex three-dimensional (3D) conformation of the genetic material and its interactions with various intracellular factors. Various experimental and computational approaches have been developed in recent years for understating the relation between the 3D conformation of the genome and the phenotypes of cells in normal condition and diseases. In this review, we will discuss novel approaches for analyzing and modeling the 3D genomic conformation, focusing on deciphering disease-causing mutations that affect gene expression. We conclude that as this is a very challenging mission, an important direction should involve the comparative analysis of various 3D models from various organisms or cells.
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Affiliation(s)
- Alon Diament
- Dept. of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tamir Tuller
- Dept. of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel; The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv 6997801, Israel.
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99955
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Reher R, Kuschak M, Heycke N, Annala S, Kehraus S, Dai HF, Müller CE, Kostenis E, König GM, Crüsemann M. Applying Molecular Networking for the Detection of Natural Sources and Analogues of the Selective Gq Protein Inhibitor FR900359. J Nat Prod 2018; 81:1628-1635. [PMID: 29943987 DOI: 10.1021/acs.jnatprod.8b00222] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The cyclic depsipeptide FR900359 (FR), isolated from the traditional Chinese medicine plant Ardisia crenata, is a potent Gq protein inhibitor and thus a valuable tool to study Gq-mediated signaling of G protein-coupled receptors. Two new FR analogues (3 and 4) were isolated from A. crenata together with the known analogues 1 and 2. The structures of compounds 3 and 4 were established by NMR spectroscopic data and MS-based molecular networking followed by in-depth LCMS2 analysis. The latter approach led to the annotation of further FR analogues 5-9. Comparative bioactivity tests of compounds 1-4 along with the parent molecule FR showed high-affinity binding to Gq proteins in the low nanomolar range (IC50 = 2.3-16.8 nM) for all analogues as well as equipotent inhibition of Gq signaling, which gives important SAR insights into this valuable natural product. Additionally, FR was detected from leaves of five other Ardisia species, among them the non-nodulated leaves of Ardisia lucida, implying a much broader distribution of FR than originally anticipated.
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Affiliation(s)
| | | | | | | | | | - Hao-Fu Dai
- Institute of Tropical Bioscience and Biotechnology , Chinese Academy of Tropical Agricultural Sciences , Haikou 571101 , Hainan , China
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99956
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99957
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Abstract
The rapidly expanding number of protein sequences found in public databases can improve our understanding of how protein functions evolve. However, our current knowledge of protein function likely represents a small fraction of the diverse repertoire that exists in nature. Integrative computational methods can facilitate the discovery of new protein functions and enzymatic reactions through the observation and investigation of the complex sequence-structure-function relationships within protein superfamilies. Here, we highlight the use of sequence similarity networks (SSNs) to identify previously unexplored sequence and function space. We exemplify this approach using the nitroreductase (NTR) superfamily. We demonstrate that SSN investigations can provide a rapid and effective means to classify groups of proteins, therefore exposing experimentally unexplored sequences that may exhibit novel functionality. Integration of such approaches with systematic experimental characterization will expand our understanding of the functional diversity of enzymes and their associated physiological roles.
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Affiliation(s)
- Janine N Copp
- Michael Smith Laboratories , University of British Columbia , 2185 East Mall , Vancouver , British Columbia V6T 1Z4 , Canada
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences , University of California , San Francisco , California 94158 , United States.,Quantitative Biosciences Institute , University of California , San Francisco , California 94143 , United States
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences , University of California , San Francisco , California 94158 , United States.,Quantitative Biosciences Institute , University of California , San Francisco , California 94143 , United States
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories , University of British Columbia , 2185 East Mall , Vancouver , British Columbia V6T 1Z4 , Canada
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99958
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diCenzo GC, Debiec K, Krzysztoforski J, Uhrynowski W, Mengoni A, Fagorzi C, Gorecki A, Dziewit L, Bajda T, Rzepa G, Drewniak L. Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14. Genes (Basel) 2018; 9:E379. [PMID: 30060533 PMCID: PMC6115938 DOI: 10.3390/genes9080379] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/22/2018] [Accepted: 07/25/2018] [Indexed: 12/23/2022] Open
Abstract
Ensifer (Sinorhizobium) sp. M14 is an efficient arsenic-oxidizing bacterium (AOB) that displays high resistance to numerous metals and various stressors. Here, we report the draft genome sequence and genome-guided characterization of Ensifer sp. M14, and we describe a pilot-scale installation applying the M14 strain for remediation of arsenic-contaminated waters. The M14 genome contains 6874 protein coding sequences, including hundreds not found in related strains. Nearly all unique genes that are associated with metal resistance and arsenic oxidation are localized within the pSinA and pSinB megaplasmids. Comparative genomics revealed that multiple copies of high-affinity phosphate transport systems are common in AOBs, possibly as an As-resistance mechanism. Genome and antibiotic sensitivity analyses further suggested that the use of Ensifer sp. M14 in biotechnology does not pose serious biosafety risks. Therefore, a novel two-stage installation for remediation of arsenic-contaminated waters was developed. It consists of a microbiological module, where M14 oxidizes As(III) to As(V) ion, followed by an adsorption module for As(V) removal using granulated bog iron ores. During a 40-day pilot-scale test in an abandoned gold mine in Zloty Stok (Poland), water leaving the microbiological module generally contained trace amounts of As(III), and dramatic decreases in total arsenic concentrations were observed after passage through the adsorption module. These results demonstrate the usefulness of Ensifer sp. M14 in arsenic removal performed in environmental settings.
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Affiliation(s)
- George C diCenzo
- Laboratory of Microbial Genetics, Department of Biology, University of Florence, via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
| | - Klaudia Debiec
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Jan Krzysztoforski
- Faculty of Chemical and Process Engineering, Warsaw University of Technology, Warynskiego 1, 00-645 Warsaw, Poland.
| | - Witold Uhrynowski
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Alessio Mengoni
- Laboratory of Microbial Genetics, Department of Biology, University of Florence, via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
| | - Camilla Fagorzi
- Laboratory of Microbial Genetics, Department of Biology, University of Florence, via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
| | - Adrian Gorecki
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Tomasz Bajda
- Department of Mineralogy, Petrography and Geochemistry, Faculty of Geology, Geophysics and Environmental Protection, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland.
| | - Grzegorz Rzepa
- Department of Mineralogy, Petrography and Geochemistry, Faculty of Geology, Geophysics and Environmental Protection, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland.
| | - Lukasz Drewniak
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
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99959
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Ku CA, Ryals RC, Jiang D, Coyner AS, Weller KK, Sinha W, Robb BM, Yang P, Pennesi ME. The Role of ERK1/2 Activation in Sarpogrelate-Mediated Neuroprotection. Invest Ophthalmol Vis Sci 2018; 59:462-471. [PMID: 29368005 PMCID: PMC5786286 DOI: 10.1167/iovs.17-23159] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Purpose To characterize the mediators of 5-HT2A serotonin receptor–driven retinal neuroprotection. Methods Albino mice were treated intraperitoneally with saline or sarpogrelate, a 5-HT2A antagonist, immediately before light exposure (LE). Following LE, retinas were harvested for a high-throughput phosphorylation microarray to quantify activated phosphorylated proteins in G protein–coupled receptor (GPCR) signaling. To confirm microarray results and define temporal changes, Western blots of select GPCR signaling proteins were performed. Since both methodologies implicated MAPK/ERK activation, the functional significance of sarpogrelate-mediated ERK1/2 activation was examined by inhibition of ERK1/2 phosphorylation via pretreatment with the MEK inhibitor (MEKi) PD0325901. The degree of neuroprotection was evaluated with spectral-domain optical coherence tomography (SD-OCT) and electroretinography (ERG). To determine the effects of sarpogrelate on gene expression, a qPCR array measuring the expression of 84 genes involved in oxidative stress and cell death was performed 48 hours post LE. Results Sarpogrelate led to an activation of the MAPK/ERK pathway. Temporal analysis further demonstrated a transient activation of ERK1/2, starting with an early inhibition 20 minutes into LE, a maximum activation at 3 hours post LE, and a return to baseline at 7 hours post LE. Inhibition of ERK1/2 with MEKi pretreatment led to attenuation of sarpogrelate-mediated neuroprotection. LE caused significant changes in the expression of genes involved in iron metabolism, oxidative stress, and apoptosis. These changes were prevented by sarpogrelate treatment. Conclusions Sarpogrelate-mediated retinal protection involves a transient activation of the MAPK/ERK pathway, although this pathway alone does not account for the full effect of neuroprotection.
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Affiliation(s)
- Cristy A Ku
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States
| | - Renee C Ryals
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States
| | - Dan Jiang
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States
| | - Aaron S Coyner
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States
| | - Kyle K Weller
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States
| | - Wrik Sinha
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States
| | - Bryan M Robb
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States
| | - Paul Yang
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States
| | - Mark E Pennesi
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States
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99960
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Nguyen KT, Mun SH, Lee CS, Hwang CS. Control of protein degradation by N-terminal acetylation and the N-end rule pathway. Exp Mol Med 2018; 50:1-8. [PMID: 30054456 PMCID: PMC6063864 DOI: 10.1038/s12276-018-0097-y] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 04/11/2018] [Indexed: 11/10/2022] Open
Abstract
Nα-terminal acetylation (Nt-acetylation) occurs very frequently and is found in most proteins in eukaryotes. Despite the pervasiveness and universality of Nt-acetylation, its general functions in terms of physiological outcomes remain largely elusive. However, several recent studies have revealed that Nt-acetylation has a significant impact on protein stability, activity, folding patterns, cellular localization, etc. In addition, Nt-acetylation marks specific proteins for degradation by a branch of the N-end rule pathway, a subset of the ubiquitin-mediated proteolytic system. The N-end rule associates a protein's in vivo half-life with its N-terminal residue or modifications on its N-terminus. This review provides a current understanding of intracellular proteolysis control by Nt-acetylation and the N-end rule pathway.
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Affiliation(s)
- Kha The Nguyen
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Sang-Hyeon Mun
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Chang-Seok Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Cheol-Sang Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea.
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99961
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Shoji T, Fukutomi H, Okada Y, Chiba K. Artificial bioconjugates with naturally occurring linkages: the use of phosphodiester. Beilstein J Org Chem 2018; 14:1946-1955. [PMID: 30112100 PMCID: PMC6071721 DOI: 10.3762/bjoc.14.169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 07/06/2018] [Indexed: 12/22/2022] Open
Abstract
Artificial orthogonal bond formations such as the alkyne–azide cycloaddition have enabled selective bioconjugations under mild conditions, yet naturally occurring linkages between native functional groups would be more straightforward to elaborate bioconjugates. Herein, we describe the use of a phosphodiester bond as a versatile option to access various bioconjugates. An opposite activation strategy, involving 5’-phosphitylation of the supported oligonucleotides, has allowed several biomolecules that possess an unactivated alcohol to be directly conjugated. It should be noted that there is no need to pre-install artificial functional groups and undesired and unpredictable perturbations possibly caused by bioconjugation can be minimized.
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Affiliation(s)
- Takao Shoji
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Hiroki Fukutomi
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Yohei Okada
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kazuhiro Chiba
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
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99962
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Abstract
SAM-V is one of the class of riboswitches that bind S-adenosylmethione, regulating gene expression by controlling translation. We have solved the crystal structure of the metY SAM-V riboswitch bound to its SAM ligand at 2.5 Å resolution. The RNA folds as an H-type pseudoknot, with a major-groove triple helix in which resides the SAM ligand binding site. The bound SAM adopts an elongated conformation aligned with the axis of the triple helix, and is held at either end by hydrogen bonding to the adenine and the amino acid moieties. The central sulfonium cation makes electrostatic interactions with an U:A.U base triple, so conferring specificity. We propose a model in which SAM binding leads to association of the triplex third strand that stabilizes a short helix and occludes the ribosome binding site. Thus the new structure explains both ligand specificity and the mechanism of genetic control.
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Affiliation(s)
- Lin Huang
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
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99963
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Khan R, Zeb A, Roy N, Thapa Magar R, Kim HJ, Lee KW, Lee SW. Biochemical and Structural Basis of Triclosan Resistance in a Novel Enoyl-Acyl Carrier Protein Reductase. Antimicrob Agents Chemother 2018; 62:e00648-18. [PMID: 29891603 DOI: 10.1128/AAC.00648-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/05/2018] [Indexed: 12/24/2022] Open
Abstract
Enoyl-acyl carrier protein reductases (ENR), such as FabI, FabL, FabK, and FabV, catalyze the last reduction step in bacterial type II fatty acid biosynthesis. Previously, we reported metagenome-derived ENR homologs resistant to triclosan (TCL) and highly similar to 7-α hydroxysteroid dehydrogenase (7-AHSDH). These homologs are commonly found in Epsilonproteobacteria, a class that contains several human-pathogenic bacteria, including the genera Helicobacter and Campylobacter Here we report the biochemical and predicted structural basis of TCL resistance in a novel 7-AHSDH-like ENR. The purified protein exhibited NADPH-dependent ENR activity but no 7-AHSDH activity, despite its high homology with 7-AHSDH (69% to 96%). Because this ENR was similar to FabL (41%), we propose that this metagenome-derived ENR be referred to as FabL2. Homology modeling, molecular docking, and molecular dynamic simulation analyses revealed the presence of an extrapolated six-amino-acid loop specific to FabL2 ENR, which prevented the entry of TCL into the active site of FabL2 and was likely responsible for TCL resistance. Elimination of this extrapolated loop via site-directed mutagenesis resulted in the complete loss of TCL resistance but not enzyme activity. Phylogenetic analysis suggested that FabL, FabL2, and 7-AHSDH diverged from a common short-chain dehydrogenase reductase family. This study is the first to report the role of the extrapolated loop of FabL2-type ENRs in conferring TCL resistance. Thus, the FabL2 ENR represents a new drug target specific for pathogenic Epsilonproteobacteria.
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99964
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99965
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Abstract
ABSTRACT
Although bacterial genomes are usually densely protein-coding, genome-wide mapping approaches of transcriptional start sites revealed that a significant fraction of the identified promoters drive the transcription of noncoding RNAs. These can be
trans
-acting RNAs, mainly originating from intergenic regions and, in many studied examples, possessing regulatory functions. However, a significant fraction of these noncoding RNAs consist of natural antisense transcripts (asRNAs), which overlap other transcriptional units. Naturally occurring asRNAs were first observed to play a role in bacterial plasmid replication and in bacteriophage λ more than 30 years ago. Today’s view is that asRNAs abound in all three domains of life. There are several examples of asRNAs in bacteria with clearly defined functions. Nevertheless, many asRNAs appear to result from pervasive initiation of transcription, and some data point toward global functions of such widespread transcriptional activity, explaining why the search for a specific regulatory role is sometimes futile. In this review, we give an overview about the occurrence of antisense transcription in bacteria, highlight particular examples of functionally characterized asRNAs, and discuss recent evidence pointing at global relevance in RNA processing and transcription-coupled DNA repair.
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99966
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Su X, Kong Y, Peng DQ. New insights into apolipoprotein A5 in controlling lipoprotein metabolism in obesity and the metabolic syndrome patients. Lipids Health Dis 2018; 17:174. [PMID: 30053818 PMCID: PMC6064078 DOI: 10.1186/s12944-018-0833-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 07/20/2018] [Indexed: 01/01/2023] Open
Abstract
Apolipoprotein A5 (apoA5) has been identified to play an important role in lipid metabolism, specifically in triglyceride (TG) and TG-rich lipoproteins (TRLs) metabolism. Numerous evidence has demonstrated for an association between apoA5 and the increased risk of obesity and metabolic syndrome, but the mechanism remains to be fully elucidated. Recently, several studies verified that apoA5 could significantly reduce plasma TG level by stimulating lipoprotein lipase (LPL) activity, and the intracellular role of apoA5 has also been proved since apoA5 is associated with cytoplasmic lipid droplets (LDs) and affects intrahepatic TG accumulation. Furthermore, since adipocytes provide the largest storage depot for TG and play a crucial role in the development of obesity, we could infer that apoA5 also acts as a novel regulator to modulate TG storage in adipocytes. In this review, we focus on the association of gene and protein of apoA5 with obesity and metabolic syndrome, and provide new insights into the physiological role of apoA5 in humans, giving a potential therapeutic target for obesity and associated disorders.
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Affiliation(s)
- Xin Su
- Department of Cardiovascular Medicine, the Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Yi Kong
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, the Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Dao-Quan Peng
- Department of Cardiovascular Medicine, the Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.
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99967
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Firmino M, Weis SN, Souza JMF, Gomes BRB, Mól AR, Mortari MR, Souza GEP, Coca GC, Williams TCR, Fontes W, Ricart CAO, de Sousa MV, Veiga-Souza FH. Label-free quantitative proteomics of rat hypothalamus under fever induced by LPS and PGE 2. J Proteomics 2018; 187:182-199. [PMID: 30056254 DOI: 10.1016/j.jprot.2018.07.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/13/2018] [Accepted: 07/24/2018] [Indexed: 12/21/2022]
Abstract
Fever is a brain-mediated increase in body temperature mainly during inflammatory or infectious challenges. Although there is considerable data regarding the inflammation pathways involved in fever, metabolic alterations necessary to orchestrate the complex inflammatory response are not totally understood. We performed proteomic analysis of rat hypothalamus using label-free LC-MS/MS in a model of fever induced by lipopolysaccharide (LPS) or prostaglandin E2 (PGE2). In total, 7021 proteins were identified. As far as we know, this is the largest rat hypothalamus proteome dataset available to date. Pathway analysis showed proteins from both stimuli associated with inflammatory and metabolic pathways. Concerning metabolic pathways, rats exposed to LPS or PGE2 presented lower relative abundance of proteins involved in glycolysis, pentose phosphate pathway and tricarboxylic acid cycle. Mitochondrial function may also be altered by both stimuli because significant downregulation of several proteins was found, mainly in complexes I and IV. LPS was able to induce downregulation of important proteins in the enzymatic antioxidant system, thereby contributing to oxidative stress. The results offered comprehensive information about fever responses and helped to reveal new insights into proteins potentially involved in inflammatory signaling and metabolic changes in the hypothalamus during systemic LPS and central PGE2 administration. SIGNIFICANCE The evolutionary persistence of fever, despite the elevated cost for maintenance of this response, suggests that elevation in core temperature may represent an interesting strategy for survival. Fever response is achieved through the integrated behavioral, physiological, immunological and biochemical processes that determine the balance between heat generation and elimination. The development of such complex response arouses interest in studying how the cell metabolism responds or even contributes to promote fever. Our results offered comprehensive information about fever responses, including metabolic and inflammatory pathways, providing new insights into candidate proteins potentially involved in inflammatory signaling and metabolic changes in the hypothalamus during fever induced by systemic LPS and central PGE2 perturbation.
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Affiliation(s)
- Marina Firmino
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, DF 70910-900, Brazil
| | - Simone N Weis
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, DF 70910-900, Brazil
| | - Jaques M F Souza
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, DF 70910-900, Brazil
| | - Bruna R B Gomes
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, DF 70910-900, Brazil
| | - Alan R Mól
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, DF 70910-900, Brazil
| | - Márcia R Mortari
- Laboratory of Neuropharmacology, Department of Physiological Sciences, Institute of Biological Sciences, University of Brasilia, Brasília, DF 70910-900, Brazil
| | - Gloria E P Souza
- Laboratory of Pharmacology, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP 14040-903, Brazil
| | - Guilherme C Coca
- Laboratory of Plant Biochemistry, Department of Botany, University of Brasilia, Brasília, DF 70910-900, Brazil
| | - Thomas C R Williams
- Laboratory of Plant Biochemistry, Department of Botany, University of Brasilia, Brasília, DF 70910-900, Brazil
| | - Wagner Fontes
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, DF 70910-900, Brazil
| | - Carlos André O Ricart
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, DF 70910-900, Brazil
| | - Marcelo V de Sousa
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, DF 70910-900, Brazil.
| | - Fabiane H Veiga-Souza
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, DF 70910-900, Brazil; School of Ceilandia, University of Brasilia, Brasília, DF 72220-275, Brazil.
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99968
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Stavropoulou DA, De Vuyst L, Leroy F. Nonconventional starter cultures of coagulase-negative staphylococci to produce animal-derived fermented foods, a SWOT analysis. J Appl Microbiol 2018; 125:1570-1586. [PMID: 30053335 DOI: 10.1111/jam.14054] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/15/2018] [Accepted: 07/17/2018] [Indexed: 01/03/2023]
Abstract
Coagulase-negative staphylococci (CNS) are ubiquitous micro-organisms that are commonly present on animal skin and animal-derived foods. They are members of the beneficial microbial consortia of several fermented food products where they contribute to quality. Currently, only a few CNS species are included in commercial starter cultures, although many other ones with promising properties have been isolated from diverse food ecosystems. In the present study, a Strengths-Weaknesses-Opportunities-Threats (SWOT) analysis of the potential use of unconventional CNS starter cultures for the fermentation of animal-derived foods is carried out. An overview of both their desirable and worrisome metabolic traits is given. In general, the application of innovative CNS-based starter cultures offers opportunities to modulate flavour, improve the safety and health aspects and develop novel colour development strategies for clean label products. Yet, their implementation is often not straightforward as nontrivial obstacles or threats are encountered, which relate to technological, food safety and legal concerns. As most of the desirable and undesirable characteristics of CNS species are strain dependent, a case-by-case evaluation is needed when evaluating specific strains for their potential use as novel starter cultures.
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Affiliation(s)
- D A Stavropoulou
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - L De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - F Leroy
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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99969
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Dubois C, Lecomte C, Ruys SPD, Kuzmic M, Della-Vedova C, Dubourg N, Galas S, Frelon S. Precoce and opposite response of proteasome activity after acute or chronic exposure of C. elegans to γ-radiation. Sci Rep 2018; 8:11349. [PMID: 30054490 PMCID: PMC6063909 DOI: 10.1038/s41598-018-29033-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 07/04/2018] [Indexed: 12/14/2022] Open
Abstract
Species are chronically exposed to ionizing radiation, a natural phenomenon which can be enhanced by human activities. The induced toxicity mechanisms still remain unclear and seem depending on the mode of exposure, i.e. acute and chronic. To better understand these phenomena, studies need to be conducted both at the subcellular and individual levels. Proteins, functional molecules in organisms, are the targets of oxidative damage (especially via their carbonylation (PC)) and are likely to be relevant biomarkers. After exposure of Caenorhabditis elegans to either chronic or acute γ rays we showed that hatching success is impacted after acute but not after chronic irradiation. At the molecular level, the carbonylated protein level in relation with dose was slightly different between acute and chronic exposure whereas the proteolytic activity is drastically modified. Indeed, whereas the 20S proteasome activity is inhibited by acute irradiation from 0.5 Gy, it is activated after chronic irradiation from 1 Gy. As expected, the 20S proteasome activity is mainly modified by irradiation whereas the 26S and 30S activity are less changed. This study provides preliminaries clues to understand the role of protein oxidation and proteolytic activity in the radiation-induced molecular mechanisms after chronic versus acute irradiation in C. elegans.
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Affiliation(s)
- Cécile Dubois
- IRSN/PSE-ENV/SRTE - Laboratoire d'ecotoxicologie des radionucléides - BP3, 13115, St Paul lez Durance Cedex, France
| | - Catherine Lecomte
- IRSN/PSE-ENV/SRTE - Laboratoire d'ecotoxicologie des radionucléides - BP3, 13115, St Paul lez Durance Cedex, France
| | - Sébastien Pyr Dit Ruys
- IRSN/PSE-ENV/SRTE - Laboratoire d'ecotoxicologie des radionucléides - BP3, 13115, St Paul lez Durance Cedex, France
| | - Mira Kuzmic
- IRSN/PSE-ENV/SRTE - Laboratoire d'ecotoxicologie des radionucléides - BP3, 13115, St Paul lez Durance Cedex, France
| | | | - Nicolas Dubourg
- IRSN/PSE-ENV/SRTE - Laboratoire d'ecotoxicologie des radionucléides - BP3, 13115, St Paul lez Durance Cedex, France
| | - Simon Galas
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | - Sandrine Frelon
- IRSN/PSE-ENV/SRTE - Laboratoire d'ecotoxicologie des radionucléides - BP3, 13115, St Paul lez Durance Cedex, France.
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99970
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Lenin R, Nagy PG, Alli S, Rao VR, Clauss MA, Kompella UB, Gangaraju R. Critical role of endoplasmic reticulum stress in chronic endothelial activation-induced visual deficits in tie2-tumor necrosis factor mice. J Cell Biochem 2018; 119:8460-8471. [PMID: 30054947 DOI: 10.1002/jcb.27072] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 04/26/2018] [Indexed: 12/15/2022]
Abstract
Diabetic retinopathy (DR) is the leading cause of vision loss among working-age adults. The interplay between hyperglycemia and endothelial activation in inducing endoplasmic reticulum (ER) stress pathways and visual deficits in DR is not fully understood. To address this, we used a mouse model of chronic vascular activation using endothelial-specific tumor necrosis factor-α (TNF-α)-expressing (tie2-TNF) mice to induce diabetes with streptozotocin. At 4 weeks post streptozotocin, a significant 2-fold to 10-fold increase in retinal neurovascular inflammatory gene transcript response in tie2-TNF mice was further increased in diabetic tie2-TNF mice. A decrease in visual acuity and scotopic b-wave amplitude in tie2-TNF mice was further accentuated in diabetic tie2-TNF mice and these changes correlated with a multi-fold increase in retinal ER stress markers and a reduction in adherens junctions. Cultured retinal endothelial cells showed a significant decrease in trans-endothelial resistance as well as VE-cadherin expression under TNF-α and high glucose stress. These changes were partly rescued by tauroursodeoxycholic acid, a potent ER stress inhibitor. Taken together, constant endothelial activation induced by TNF-α further exacerbated by hyperglycemia results in activation of ER stress and chronic proinflammation in a feed forward loop ultimately resulting in endothelial junction protein alterations leading to visual deficits in the retina. Inhibition of ER stress and endothelial activation may prove to be a novel therapeutic target in DR.
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Affiliation(s)
- Raji Lenin
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Peter G Nagy
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Shanta Alli
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Vidhya R Rao
- Department of Molecular Pharmacology and Experimental Therapeutics, Loyola University, Chicago, Illinois
| | - Matthias A Clauss
- Department of Cellular & Integrative Physiology, Indiana University, Indianapolis, Indiana
| | - Uday B Kompella
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, Colorado
| | - Rajashekhar Gangaraju
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee.,Department of Anatomy & Neurobiology, University of Tennessee Health Science Center, Memphis, Tennessee
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99971
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Anders F, Mann C, Liu A, Teister J, Funke S, Thanos S, Grus F, Pfeiffer N, Prokosch V. Correlation of Crystallin Expression and RGC Susceptibility in Experimental Glaucoma Rats of Different Ages. Curr Eye Res 2018; 43:1267-1273. [PMID: 29979889 DOI: 10.1080/02713683.2018.1485950] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
PURPOSE Glaucoma is one of the leading causes of blindness worldwide with age being an important risk factor. However, the pathogenesis remains poorly understood. Aim of this study was to focus on age-dependent molecular changes in an experimental animal model of glaucoma. METHODS Intraocular pressure was elevated in Sprague-Dawley rats aged 3, 14, and 47 weeks for a period of 7 weeks by episcleral vein cauterization. Ganglion cell loss was monitored by an immunohistochemical staining of the Brain-specific homeobox/POU (Pit-1, Oct-2, Unc-86) domain protein 3A positive cells in retinal flat-mounts and spectral-domain optical coherence tomography measuring the retinal nerve fiber layer thickness. Molecular protein alterations were analyzed using a comprehensive mass spectrometric proteomics approach of the retina and vitreous body. RESULTS While juvenile animals did not show a significant loss of retinal ganglion cells due to intraocular pressure elevation, adolescent animals showed a decrease up to 26% (p < 0.05). A shift of retinal crystallin protein expression levels within all protein-family subclasses (α, β, γ) could be observed in the youngest animal group (p < 0.05), while the upregulation of crystallin proteins in older animals was less striking. In addition, numerous crystallin proteins were also detected in the vitreous body. CONCLUSION These results provide insights of a potential correlation of age-related glaucomatous damage and the absence of crystallin proteins in the retina.
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Affiliation(s)
- Fabian Anders
- a Experimental Ophthalmology, Department of Ophthalmology , University Medical Center of the Johannes Gutenberg University Mainz , Mainz , Germany
| | - Carolina Mann
- a Experimental Ophthalmology, Department of Ophthalmology , University Medical Center of the Johannes Gutenberg University Mainz , Mainz , Germany
| | - Aiwei Liu
- a Experimental Ophthalmology, Department of Ophthalmology , University Medical Center of the Johannes Gutenberg University Mainz , Mainz , Germany
| | - Julia Teister
- a Experimental Ophthalmology, Department of Ophthalmology , University Medical Center of the Johannes Gutenberg University Mainz , Mainz , Germany
| | - Sebastian Funke
- a Experimental Ophthalmology, Department of Ophthalmology , University Medical Center of the Johannes Gutenberg University Mainz , Mainz , Germany
| | - Solon Thanos
- b Department of Experimental Ophthalmology, School of Medicine , University of Münster , Münster , Germany
| | - Franz Grus
- a Experimental Ophthalmology, Department of Ophthalmology , University Medical Center of the Johannes Gutenberg University Mainz , Mainz , Germany
| | - Norbert Pfeiffer
- a Experimental Ophthalmology, Department of Ophthalmology , University Medical Center of the Johannes Gutenberg University Mainz , Mainz , Germany
| | - Verena Prokosch
- a Experimental Ophthalmology, Department of Ophthalmology , University Medical Center of the Johannes Gutenberg University Mainz , Mainz , Germany
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99972
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Friis I, Solov’yov IA. Activation of the DNA-repair mechanism through NBS1 and MRE11 diffusion. PLoS Comput Biol 2018; 14:e1006362. [PMID: 30052627 PMCID: PMC6082579 DOI: 10.1371/journal.pcbi.1006362] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/08/2018] [Accepted: 07/12/2018] [Indexed: 12/27/2022] Open
Abstract
The non-homologous end joining of a DNA double strand break is initiated by the MRE11-NBS1-RAD50 complex whose subunits are the first three proteins to arrive to the breakage site thereby making the recruitment time of MRE11, NBS1 and RAD50 essential for cell survival. In the present investigation, the nature of MRE11 and NBS1 transportation from the cytoplasm to the nucleus, hosting the damaged DNA strand, is hypothesized to be a passive diffusive process. The feasibility of such a mechanism is addressed through theoretical and computational approaches which permit establishing the characteristic recruitment time of MRE11 and NBS1 by the nucleus. A computational model of a cell is constructed from a set of biological parameters and the kinetic Monte Carlo algorithm is used to simulate the diffusing MRE11 and NBS1 particles as a random walk process. To accurately describe the experimented data, it is discovered that MRE11 and NBS1 should start diffusion from significantly different starting positions which suggests that diffusion might not be the only transport mechanism of repair protein recruitment to the DNA break. The DNA repair mechanism is crucial for a cell to avoid apoptosis, and is a complicated process involving many different repair proteins. The mean of transportation of these repair proteins is largely unknown as their transportation mechanisms need clarification. We have focused on the transportation of some of the first proteins to arrive to the damaged DNA from the cytoplasm, namely the MRE11 and NBS1. Our hypothesis of diffusion as the transportation mechanism of MRE11 and NBS1 is tested against a theoretical model as well as simulation data and experiments, revealing a possibility for diffusion to be the method of recruiting MRE11 and NBS1 to the DNA break.
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Affiliation(s)
- Ida Friis
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
- * E-mail: (IF); (IAS)
| | - Ilia A. Solov’yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
- On leave from the Ioffe Institute, Politechnicheskaya Str. 26, 94021, St. Petersburg, Russia
- * E-mail: (IF); (IAS)
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99973
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Wang J, Cao P, Qi YY, Chen XP, Ma L, Deng RR, Zhang LL, Zhao Y. The relationship between cell apoptosis dysfunction and FEN1 E160D mutation in lupus nephritis patients. Autoimmunity 2018; 50:476-480. [PMID: 29239254 DOI: 10.1080/08916934.2017.1402302] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVE This study aims to evaluate the role of FEN1 E160D mutation in lupus nephritis (LN) patients with cell apoptosis dysfunction. METHODS (1) Cell apoptosis was detected from 50 paraffin samples obtained from renal biopsies of patients with Class IV LN by TUNEL method and the relationship of the systemic lupus erythematosus disease activity index 2000 (SLEDAI 2000) and renal tissue cell apoptotic index (AI) was discussed. (2) FEN1 gene 61563142-61563342 containing E160D were analysed by extracting genomic DNA from peripheral blood collected from the above 50 LN patients and 25 patients with nephrectomy caused by renal trauma. The difference between these two groups was statistically significant. RESULTS Cell apoptosis was detected in all patients with LN, and correlation analysis results revealed a positive relationship between SLEDAI 2000 and AI (r = 0.39, p = .032). The FEN1 gene 61563142-61563342 fragment had site mutations at C/- (+61563189), A/T (+61563198), A/- (+61563204), G/T (+61563303), and T/C (+61563304). However, no statistical significance was found between LN patients detected with cell apoptosis and healthy individuals. CONCLUSIONS This study revealed that cell apoptosis dysfunction plays a key role in the pathogenesis of LN, even though the difference in FEN1 gene 61563142-61563342 between LN patients and healthy individuals was not statistically significant. Larger sample size studies or genome-wide association studies are needed.
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Affiliation(s)
- Jing Wang
- a Department of Nephropathy , Lanzhou University Second Hospital , Lanzhou , PR China
| | - Ping Cao
- b Thinks People's Hospital , Gan Su , PR China
| | - Yuan-Yuan Qi
- a Department of Nephropathy , Lanzhou University Second Hospital , Lanzhou , PR China
| | - Xue-Ping Chen
- a Department of Nephropathy , Lanzhou University Second Hospital , Lanzhou , PR China
| | - Li Ma
- a Department of Nephropathy , Lanzhou University Second Hospital , Lanzhou , PR China
| | - Rong-Rong Deng
- a Department of Nephropathy , Lanzhou University Second Hospital , Lanzhou , PR China
| | - Li-Li Zhang
- a Department of Nephropathy , Lanzhou University Second Hospital , Lanzhou , PR China
| | - Yu Zhao
- a Department of Nephropathy , Lanzhou University Second Hospital , Lanzhou , PR China
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99974
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Abstract
Sepsis, defined as a “life-threatening organ dysfunction caused by a dysregulated host-response to infection” is a major health issue worldwide and still lacks a fully elucidated pathobiology and uniform diagnostic tests. The trace element zinc is known to be crucial to ensure an appropriate immune response. During sepsis a redistribution of zinc from serum into the liver has been observed and several studies imply a correlation between zinc and sepsis outcome. Therefore the alterations of zinc concentrations in different tissues might serve as one part of the host’s defense mechanism against pathogens during sepsis by diverse mechanisms. It has been suggested that zinc is involved in nutritional immunity, acts as a hepatoprotective agent, or a differentiation signal for innate immune cells, or supports the synthesis of acute phase proteins. Further knowledge about these events could help in the evaluation of how zinc could be optimally applied to improve treatment of septic patients. Moreover, the changes in zinc homeostasis are substantial and correlate with the severity of the disease, suggesting that zinc might also be useful as a diagnostic marker for evaluating the severity and predicting the outcome of sepsis.
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Affiliation(s)
- Wiebke Alker
- Department of Food Chemistry and Toxicology, Berlin Institute of Technology, 13355 Berlin, Germany.
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany.
| | - Hajo Haase
- Department of Food Chemistry and Toxicology, Berlin Institute of Technology, 13355 Berlin, Germany.
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany.
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99975
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Chan SN, Low END, Raja Ali RA, Mokhtar NM. Delineating inflammatory bowel disease through transcriptomic studies: current review of progress and evidence. Intest Res 2018; 16:374-383. [PMID: 30090036 PMCID: PMC6077315 DOI: 10.5217/ir.2018.16.3.374] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/23/2018] [Accepted: 01/29/2018] [Indexed: 12/13/2022] Open
Abstract
Inflammatory bowel disease (IBD), which comprises of Crohn's disease and ulcerative colitis, is an idiopathic relapsing and remitting disease in which the interplay of different environment, microbial, immunological and genetic factors that attribute to the progression of the disease. Numerous studies have been conducted in multiple aspects including clinical, endoscopy and histopathology for the diagnostics and treatment of IBD. However, the molecular mechanism underlying the aetiology and pathogenesis of IBD is still poorly understood. This review tries to critically assess the scientific evidence at the transcriptomic level as it would help in the discovery of RNA molecules in tissues or serum between the healthy and diseased or different IBD subtypes. These molecular signatures could potentially serve as a reliable diagnostic or prognostic biomarker. Researchers have also embarked on the study of transcriptome to be utilized in targeted therapy. We focus on the evaluation and discussion related to the publications reporting the different approaches and techniques used in investigating the transcriptomic changes in IBD with the intention to offer new perspectives to the landscape of the disease.
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Affiliation(s)
- Seow-Neng Chan
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | - Eden Ngah Den Low
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | - Raja Affendi Raja Ali
- Gastroenterology Unit, Department of Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | - Norfilza Mohd Mokhtar
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
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99976
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Pierson HE, Kaler M, O'Grady C, Uhlemann EE, Dmitriev OY. Engineered Protein Model of the ATP synthase H +- Channel Shows No Salt Bridge at the Rotor-Stator Interface. Sci Rep 2018; 8:11361. [PMID: 30054535 DOI: 10.1038/s41598-018-29693-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 07/17/2018] [Indexed: 12/12/2022] Open
Abstract
ATP synthase is powered by the flow of protons through the molecular turbine composed of two α-helical integral membrane proteins, subunit a, which makes a stator, and a cylindrical rotor assembly made of multiple copies of subunit c. Transient protonation of a universally conserved carboxylate on subunit c (D61 in E. coli) gated by the electrostatic interaction with arginine on subunit a (R210 in E. coli) is believed to be a crucial step in proton transfer across the membrane. We used a fusion protein consisting of subunit a and the adjacent helices of subunit c to test by NMR spectroscopy if cD61 and aR210 are involved in an electrostatic interaction with each other, and found no evidence of such interaction. We have also determined that R140 does not form a salt bridge with either D44 or D124 as was suggested previously by mutation analysis. Our results demonstrate the potential of using arginines as NMR reporter groups for structural and functional studies of challenging membrane proteins.
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99977
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Grossini E, Farruggio S, Raina G, Mary D, Deiro G, Gentilli S. Effects of Genistein on Differentiation and Viability of Human Visceral Adipocytes. Nutrients 2018; 10:E978. [PMID: 30060502 PMCID: PMC6115928 DOI: 10.3390/nu10080978] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/17/2018] [Accepted: 07/26/2018] [Indexed: 01/05/2023] Open
Abstract
Obesity can lead to pathological growth of adipocytes by inducing inflammation and oxidative stress. Genistein could be a potential candidate for the treatment of obesity due to its antioxidant properties. Specific kits were used to examine the effects of genistein vs adiponectin on human visceral pre-adipocytes differentiation, cell viability, mitochondrial membrane potential, and oxidative stress in pre-adipocytes and in white/brown adipocytes. Western Blot was performed to examine changes in protein activation/expression. Genistein increased human visceral pre-adipocytes differentiation and browning, and caused a dose-related improvement of cell viability and mitochondrial membrane potential. Similar effects were observed in brown adipocytes and in white adipocytes, although in white cells the increase of cell viability was inversely related to the dose. Moreover, genistein potentiated AMP-activated protein kinase (AMPK)/mitofusin2 activation/expression in pre-adipocytes and white/brown adipocytes and protected them from the effects of hydrogen peroxide. The effects caused by genistein were similar to those of adiponectin. The results obtained showed that genistein increases human visceral pre-adipocytes differentiation and browning, protected against oxidative stress in pre-adipocytes and white/brown adipocytes through mechanisms related to AMPK-signalling and the keeping of mitochondrial function.
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Affiliation(s)
- Elena Grossini
- Laboratory of Physiology, Department of Translational Medicine, University of Eastern Piedmont, Via Solaroli 17, 28100 Novara, Italy.
- Experimental Surgery, Azienda Ospedaliera Universitaria Maggiore della Carità, Corso Mazzini 36, 28100 Novara, Italy.
- AGING Project, Department of Translational Medicine, University of Eastern Piedmont, via Solaroli 17, 28100 Novara, Italy.
| | - Serena Farruggio
- Laboratory of Physiology, Department of Translational Medicine, University of Eastern Piedmont, Via Solaroli 17, 28100 Novara, Italy.
- AGING Project, Department of Translational Medicine, University of Eastern Piedmont, via Solaroli 17, 28100 Novara, Italy.
| | - Giulia Raina
- Laboratory of Physiology, Department of Translational Medicine, University of Eastern Piedmont, Via Solaroli 17, 28100 Novara, Italy.
- AGING Project, Department of Translational Medicine, University of Eastern Piedmont, via Solaroli 17, 28100 Novara, Italy.
| | - David Mary
- Laboratory of Physiology, Department of Translational Medicine, University of Eastern Piedmont, Via Solaroli 17, 28100 Novara, Italy.
| | - Giacomo Deiro
- General Surgery Unit, Department of Health Sciences, University of Eastern Piedmont, Via Solaroli 17, 28100 Novara, Italy.
| | - Sergio Gentilli
- General Surgery Unit, Department of Health Sciences, University of Eastern Piedmont, Via Solaroli 17, 28100 Novara, Italy.
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99978
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Borsetti F, Dal Piaz F, D'Alessio F, Stefan A, Brandimarti R, Sarkar A, Datta A, Montón Silva A, den Blaauwen T, Alberto M, Spisni E, Hochkoeppler A. Manganese is a Deinococcus radiodurans growth limiting factor in rich culture medium. Microbiology (Reading) 2018; 164:1266-1275. [PMID: 30052171 DOI: 10.1099/mic.0.000698] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
To understand the effects triggered by Mn2+ on Deinococcus radiodurans, the proteome patterns associated with different growth phases were investigated. In particular, under physiological conditions we tested the growth rate and the biomass yield of D. radiodurans cultured in rich medium supplemented or not with MnCl2. The addition of 2.5-5.0 µM MnCl2 to the medium neither altered the growth rate nor the lag phase, but significantly increased the biomass yield. When higher MnCl2 concentrations were used (10-250 µM), biomass was again found to be positively affected, although we did observe a concentration-dependent lag phase increase. The in vivo concentration of Mn2+ was determined in cells grown in rich medium supplemented or not with 5 µM MnCl2. By atomic absorption spectroscopy, we estimated 0.2 and 0.75 mM Mn2+ concentrations in cells grown in control and enriched medium, respectively. We qualitatively confirmed this observation using a fluorescent turn-on sensor designed to selectively detect Mn2+in vivo. Finally, we investigated the proteome composition of cells grown for 15 or 19 h in medium to which 5 µM MnCl2 was added, and we compared these proteomes with those of cells grown in the control medium. The presence of 5 µM MnCl2 in the culture medium was found to alter the pI of some proteins, suggesting that manganese affects post-translational modifications. Further, we observed that Mn2+ represses enzymes linked to nucleotide recycling, and triggers overexpression of proteases and enzymes linked to the metabolism of amino acids.
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Affiliation(s)
- Francesca Borsetti
- 1Department of Biology, Geology and Environmental Sciences, University of Bologna, Via Selmi 3, 40125 Bologna, Italy
| | - Fabrizio Dal Piaz
- 2Department of Medicine, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano SA, Italy
| | - Federico D'Alessio
- 3Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136 Bologna, Italy
| | - Alessandra Stefan
- 3Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136 Bologna, Italy.,4CSGI, University of Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino FI, Italy
| | - Renato Brandimarti
- 3Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136 Bologna, Italy
| | - Anindita Sarkar
- 5Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Ankona Datta
- 5Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Alejandro Montón Silva
- 6Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Tanneke den Blaauwen
- 6Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Mucchi Alberto
- 7Department of Industrial Chemistry "Toson Montanari", University of Bologna, Viale Risorgimento 4, 40136 Bologna, Italy
| | - Enzo Spisni
- 1Department of Biology, Geology and Environmental Sciences, University of Bologna, Via Selmi 3, 40125 Bologna, Italy
| | - Alejandro Hochkoeppler
- 4CSGI, University of Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino FI, Italy.,3Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136 Bologna, Italy
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99979
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Tegge AN, Rodrigues RR, Larkin AL, Vu L, Murali TM, Rajagopalan P. Transcriptomic Analysis of Hepatic Cells in Multicellular Organotypic Liver Models. Sci Rep 2018; 8:11306. [PMID: 30054499 PMCID: PMC6063915 DOI: 10.1038/s41598-018-29455-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 07/11/2018] [Indexed: 02/08/2023] Open
Abstract
Liver homeostasis requires the presence of both parenchymal and non-parenchymal cells (NPCs). However, systems biology studies of the liver have primarily focused on hepatocytes. Using an organotypic three-dimensional (3D) hepatic culture, we report the first transcriptomic study of liver sinusoidal endothelial cells (LSECs) and Kupffer cells (KCs) cultured with hepatocytes. Through computational pathway and interaction network analyses, we demonstrate that hepatocytes, LSECs and KCs have distinct expression profiles and functional characteristics. Our results show that LSECs in the presence of KCs exhibit decreased expression of focal adhesion kinase (FAK) signaling, a pathway linked to LSEC dedifferentiation. We report the novel result that peroxisome proliferator-activated receptor alpha (PPARα) is transcribed in LSECs. The expression of downstream processes corroborates active PPARα signaling in LSECs. We uncover transcriptional evidence in LSECs for a feedback mechanism between PPARα and farnesoid X-activated receptor (FXR) that maintains bile acid homeostasis; previously, this feedback was known occur only in HepG2 cells. We demonstrate that KCs in 3D liver models display expression patterns consistent with an anti-inflammatory phenotype when compared to monocultures. These results highlight the distinct roles of LSECs and KCs in maintaining liver function and emphasize the need for additional mechanistic studies of NPCs in addition to hepatocytes in liver-mimetic microenvironments.
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Affiliation(s)
- Allison N Tegge
- Department of Computer Science, Virginia Tech, Blacksburg, USA
- Department of Statistics, Virginia Tech, Blacksburg, USA
| | - Richard R Rodrigues
- Genetics, Bioinformatics, and Computational Biology Ph.D. Program, Virginia Tech, Blacksburg, USA
| | - Adam L Larkin
- Department of Chemical Engineering, Virginia Tech, Blacksburg, USA
| | - Lucas Vu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, USA
| | - T M Murali
- Department of Computer Science, Virginia Tech, Blacksburg, USA.
- ICTAS Center for Systems Biology of Engineered Tissues, Virginia Tech, Blacksburg, USA.
| | - Padmavathy Rajagopalan
- Department of Chemical Engineering, Virginia Tech, Blacksburg, USA.
- ICTAS Center for Systems Biology of Engineered Tissues, Virginia Tech, Blacksburg, USA.
- Virginia Tech-Wake Forest School of Biomedical Engineering and Sciences, Virginia Tech, Blacksburg, USA.
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99980
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Norman G, Campeau J, Sim VL. High Dose and Delayed Treatment with Bile Acids Ineffective in RML Prion-Infected Mice. Antimicrob Agents Chemother 2018; 62:e00222-18. [PMID: 29784843 DOI: 10.1128/AAC.00222-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 05/11/2018] [Indexed: 12/12/2022] Open
Abstract
Prion diseases are a group of neurodegenerative diseases associated with the misfolding of the cellular prion protein (PrPC) into the infectious form (PrPSc). There are currently no treatments for prion disease. Bile acids have the ability to protect hepatocytes from apoptosis and are neuroprotective in animal models of other protein-folding neurodegenerative diseases, including Huntington's, Parkinson's, and Alzheimer's disease. Importantly, bile acids are approved for clinical use in patients with cirrhosis and have recently been shown to be safe and possibly effective in pilot trials of patients with amyotrophic lateral sclerosis (ALS). We previously reported that the bile acid ursodeoxycholic acid (UDCA), given early in disease, prolonged incubation periods in male RML-infected mice. Here, we expand on this result to include tauro-ursodeoxycholic acid (TUDCA) treatment trials and delayed UDCA treatment. We demonstrate that despite a high dose of TUDCA given early in disease, there was no significant difference in incubation periods between treated and untreated cohorts, regardless of sex. In addition, delayed treatment with a high dose of UDCA resulted in a significant shortening of the average survival time for both male and female mice compared to their sex-matched controls, with evidence of increased BiP, a marker of apoptosis, in treated female mice. Our findings suggest that treatment with high-dose TUDCA provides no therapeutic benefit and that delayed treatment with high-dose UDCA is ineffective and could worsen outcomes.
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99981
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du Pré S, Beckmann N, Almeida MC, Sibley GEM, Law D, Brand AC, Birch M, Read ND, Oliver JD. Effect of the Novel Antifungal Drug F901318 (Olorofim) on Growth and Viability of Aspergillus fumigatus. Antimicrob Agents Chemother 2018; 62:e00231-18. [PMID: 29891595 DOI: 10.1128/AAC.00231-18] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 06/02/2018] [Indexed: 11/20/2022] Open
Abstract
F901318 (olorofim) is a novel antifungal drug that is highly active against Aspergillus species. Belonging to a new class of antifungals called the orotomides, F901318 targets dihydroorotate dehydrogenase (DHODH) in the de novo pyrimidine biosynthesis pathway. In this study, the antifungal effects of F901318 against Aspergillus fumigatus were investigated. Live cell imaging revealed that, at a concentration of 0.1 μg/ml, F901318 completely inhibited germination, but conidia continued to expand by isotropic growth for >120 h. When this low F901318 concentration was applied to germlings or vegetative hyphae, their elongation was completely inhibited within 10 h. Staining with the fluorescent viability dye bis-(1,3-dibutylbarbituric acid) trimethine oxonol (DiBAC) showed that prolonged exposure to F901318 (>24 h) led to vegetative hyphal swelling and a decrease in hyphal viability through cell lysis. The time-dependent killing of F901318 was further confirmed by measuring the fungal biomass and growth rate in liquid culture. The ability of hyphal growth to recover in drug-free medium after 24 h of exposure to F901318 was strongly impaired compared to that of the untreated control. A longer treatment of 48 h further improved the antifungal effect of F901318. Together, the results of this study indicate that F901318 initially has a fungistatic effect on Aspergillus isolates by inhibiting germination and growth, but prolonged exposure is fungicidal through hyphal swelling followed by cell lysis.
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99982
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Elango S, Samuel S, Khashim Z, Subbiah U. Selenium Influences Trace Elements Homeostasis, Cancer Biomarkers in Squamous Cell Carcinoma Patients Administered
with Cancerocidal Radiotherapy. Asian Pac J Cancer Prev 2018; 19:1785-1792. [PMID: 30049188 PMCID: PMC6165669 DOI: 10.22034/apjcp.2018.19.7.1785] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 06/16/2018] [Indexed: 11/27/2022] Open
Abstract
In the perspective of selenium as an antioxidant and anti-carcinogen, so far no strong intervention trials with selenium over radiation-treated oral squamous cell carcinoma cases have been conducted, to examine the response of the disease and the subsequent biochemical alterations. In the present study, untreated oral cancer cases (Gp II) were compared with radiation-treated groups with and without selenium (Gp IIa, IIb), forward to find the trace elements and cancer biomarkers status, at a follow-up of 6 months. Severe alteration in the trace elements levels of Se, Cu, Fe, Zn, Na, K, Ca, Cl, were noticed in Gp II. Though Gp IIa showed slight improvement, administration of selenium (Gp IIb) improved the level of all these elements to a greater extent (p<0.001). GpII and IIa showed increased level of bio markers 5’-nucleotidase, PschE, LAP, γ-GTP, LDH, SGOT, SGPT, ACP, ALP, CPK, TNF, CEA, AFP, Scc-Ag. The greater extent of restitution to near normalcy was observed in patients given selenium (Gp IIb) (p<0.001). Owing to the fact that selenium scavengers oxidants and hence decelerate carcinogenesis by eliminating tumors, so the tumor released constituents into the systemic circulation declined significantly. Therefore, the outcome of the study suggests selenium as a valuable therapeutic measure as adjuvant for oral cancer patients undergoing cancerocidal radiotherapy.
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Affiliation(s)
- Sonaa Elango
- Department of Life Science,School of Natural Sciences,Suwon University,312, Wau-ri, Bongdam -eup,Hwaseong-si,Gyeonggi - do, 445- 743., Republic of Korea.
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99983
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Hupfeld M, Trasanidou D, Ramazzini L, Klumpp J, Loessner MJ, Kilcher S. A functional type II-A CRISPR-Cas system from Listeria enables efficient genome editing of large non-integrating bacteriophage. Nucleic Acids Res 2018; 46:6920-6933. [PMID: 30053228 PMCID: PMC6061871 DOI: 10.1093/nar/gky544] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/30/2018] [Accepted: 06/01/2018] [Indexed: 12/31/2022] Open
Abstract
CRISPR-Cas systems provide bacteria with adaptive immunity against invading DNA elements including bacteriophages and plasmids. While CRISPR technology has revolutionized eukaryotic genome engineering, its application to prokaryotes and their viruses remains less well established. Here we report the first functional CRISPR-Cas system from the genus Listeria and demonstrate its native role in phage defense. LivCRISPR-1 is a type II-A system from the genome of L. ivanovii subspecies londoniensis that uses a small, 1078 amino acid Cas9 variant and a unique NNACAC protospacer adjacent motif. We transferred LivCRISPR-1 cas9 and trans-activating crRNA into Listeria monocytogenes. Along with crRNA encoding plasmids, this programmable interference system enables efficient cleavage of bacterial DNA and incoming phage genomes. We used LivCRISPR-1 to develop an effective engineering platform for large, non-integrating Listeria phages based on allelic replacement and CRISPR-Cas-mediated counterselection. The broad host-range Listeria phage A511 was engineered to encode and express lysostaphin, a cell wall hydrolase that specifically targets Staphylococcus peptidoglycan. In bacterial co-culture, the armed phages not only killed Listeria hosts but also lysed Staphylococcus cells by enzymatic collateral damage. Simultaneous killing of unrelated bacteria by a single phage demonstrates the potential of CRISPR-Cas-assisted phage engineering, beyond single pathogen control.
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Affiliation(s)
- Mario Hupfeld
- Institute of Food, Nutrition, and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Despoina Trasanidou
- Institute of Food, Nutrition, and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Livia Ramazzini
- Institute of Food, Nutrition, and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Jochen Klumpp
- Institute of Food, Nutrition, and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Martin J Loessner
- Institute of Food, Nutrition, and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Samuel Kilcher
- Institute of Food, Nutrition, and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
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99984
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Efremov AK, Yan J. Transfer-matrix calculations of the effects of tension and torque constraints on DNA-protein interactions. Nucleic Acids Res 2018; 46:6504-6527. [PMID: 29878241 PMCID: PMC6061897 DOI: 10.1093/nar/gky478] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 05/17/2018] [Indexed: 12/12/2022] Open
Abstract
Organization and maintenance of the chromosomal DNA in living cells strongly depends on the DNA interactions with a plethora of DNA-binding proteins. Single-molecule studies show that formation of nucleoprotein complexes on DNA by such proteins is frequently subject to force and torque constraints applied to the DNA. Although the existing experimental techniques allow to exert these type of mechanical constraints on individual DNA biopolymers, their exact effects in regulation of DNA-protein interactions are still not completely understood due to the lack of systematic theoretical methods able to efficiently interpret complex experimental observations. To fill this gap, we have developed a general theoretical framework based on the transfer-matrix calculations that can be used to accurately describe behaviour of DNA-protein interactions under force and torque constraints. Potential applications of the constructed theoretical approach are demonstrated by predicting how these constraints affect the DNA-binding properties of different types of architectural proteins. Obtained results provide important insights into potential physiological functions of mechanical forces in the chromosomal DNA organization by architectural proteins as well as into single-DNA manipulation studies of DNA-protein interactions.
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Affiliation(s)
- Artem K Efremov
- Mechanobiology Institute, National University of Singapore, 117411, Singapore
- Centre for Bioimaging Sciences, National University of Singapore, 117557, Singapore
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, 117411, Singapore
- Centre for Bioimaging Sciences, National University of Singapore, 117557, Singapore
- Department of Physics, National University of Singapore, 117551, Singapore
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99985
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Luhr M, Szalai P, Engedal N. The Lactate Dehydrogenase Sequestration Assay - A Simple and Reliable Method to Determine Bulk Autophagic Sequestration Activity in Mammalian Cells. J Vis Exp 2018:57971. [PMID: 30102280 PMCID: PMC6126555 DOI: 10.3791/57971] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Bulk autophagy is characterized by the sequestration of large portions of cytoplasm into double/multi-membrane structures termed autophagosomes. Here a simple protocol to monitor this process is described. Moreover, typical results and experimental validation of the method under autophagy-inducing conditions in various types of cultured mammalian cells are provided. During bulk autophagy, autophagosomes sequester cytosol, and thereby also soluble cytosolic proteins, alongside other autophagic cargo. LDH is a stable and highly abundant, soluble cytosolic enzyme that is non-selectively sequestered into autophagosomes. The amount of LDH sequestration therefore reflects the amount of bulk autophagic sequestration. To efficiently and accurately determine LDH sequestration in cells, we employ an electrodisruption-based fractionation protocol that effectively separates sedimentable from cytosolic LDH, followed by measurement of enzymatic activity in sedimentable fractions versus whole-cell samples. Autophagic sequestration is determined by subtracting the proportion of sedimentable LDH in untreated cells from that in treated cells. The advantage of the LDH sequestration assay is that it gives a quantitative measure of the autophagic sequestration of endogenous cargo, as opposed to other methods that either involve ectopic expression of sequestration probes or semi-quantitative protease protection analyses of autophagy markers or receptors.
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Affiliation(s)
- Morten Luhr
- The Autophagy Team, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo
| | - Paula Szalai
- The Autophagy Team, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo
| | - Nikolai Engedal
- The Autophagy Team, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo;
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99986
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Naveen Kumar M, Babu RL, Patil RH, Kiran Kumar KM, Hegde SM, Nagesh R, Kavya K, Ramesh GT, Sharma SC, Srinivas C. Protein kinases orchestrate cell cycle regulators in differentiating BeWo choriocarcinoma cells. Mol Cell Biochem 2019; 452:1-15. [PMID: 30051305 DOI: 10.1007/s11010-018-3407-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 07/13/2018] [Indexed: 01/17/2023]
Abstract
Choriocarcinoma, a trophoblastic neoplasia, occurs in women as an incidence of abnormal pregnancy. BeWo choriocarcinoma cells derived from the abnormal placentation are a suitable model system to study the factors associated with differentiation, invasion and other cellular events as an alternative to clinical samples. Many protein kinases orchestrate the complex events of cell cycle and in case of malignancy such regulators are found to be mutated. In the present study, BeWo cells treated with forskolin (Fo) and phorbol 12-myristate 13-acetate (PMA) were used to study the role of PKA (protein kinase A) and PKC (protein kinase C), respectively, on the expression pattern of differentiation-related genes, membrane markers, PKC isoforms and cell cycle regulators. The effect of Fo and PMA on the cell proliferation was assessed. Progressive induction of alkaline phosphatase level and formation of multinucleated differentiated cells were observed in the cells treated with Fo. Exposure of cells to Fo and PMA induced the mRNA transcripts of α-hCG, β-hCG and endoglin and down-regulates E-cadherin at mRNA and protein levels. Synergistic levels of both up- and down-regulated genes/proteins were observed when cells were treated with the combination of Fo and PMA. The mRNA levels of cyclin D1, cyclin E1, p21, Rb, p53, caspase-3 and caspase-8 decreased gradually during differentiation. Fo significantly inhibited the protein levels of PCNA, Rb, PKC-α and PMA stimulated mRNA expression of PKC-ε and PKC-δ. Further, failure in the activation of essential components of the cell cycle machinery caused G2/M phase arrest in differentiating BeWo cells.
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99987
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Abstract
Alternative splicing is an important mechanism used by the cell to generate greater transcriptomic and proteomic diversity from the genome. In the heart, alternative splicing is increasingly being recognised as an important layer of post-transcriptional gene regulation. Driven by rapidly evolving technologies in next-generation sequencing, alternative splicing has emerged as a crucial process governing complex biological processes during cardiac development and disease. The recent identification of several cardiac splice factors, such as RNA-binding motif protein 20 and 24, not only provided important insight into the mechanisms underlying alternative splicing but also revealed how these splicing factors impact functional properties of the heart. Here, we review our current knowledge of alternative splicing in the heart, with a particular focus on the factors controlling cardiac alternative splicing and their role in cardiomyopathies and subsequent heart failure.
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99988
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Mata-Garrido J, Tapia O, Casafont I, Berciano MT, Cuadrado A, Lafarga M. Persistent accumulation of unrepaired DNA damage in rat cortical neurons: nuclear organization and ChIP-seq analysis of damaged DNA. Acta Neuropathol Commun 2018; 6:68. [PMID: 30049290 PMCID: PMC6062993 DOI: 10.1186/s40478-018-0573-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 07/19/2018] [Indexed: 01/09/2023] Open
Abstract
Neurons are highly vulnerable to DNA damage induced by genotoxic agents such as topoisomerase activity, oxidative stress, ionizing radiation (IR) and chemotherapeutic drugs. To avert the detrimental effects of DNA lesions in genome stability, transcription and apoptosis, neurons activate robust DNA repair mechanisms. However, defective DNA repair with accumulation of unrepaired DNA are at the basis of brain ageing and several neurodegenerative diseases. Understanding the mechanisms by which neurons tolerate DNA damage accumulation as well as defining the genomic regions that are more vulnerable to DNA damage or refractory to DNA repair and therefore constitute potential targets in neurodegenerative diseases are essential issues in the field. In this work we investigated the nuclear topography and organization together with the genome-wide distribution of unrepaired DNA in rat cortical neurons 15 days upon IR. About 5% of non-irradiated and 55% of irradiated cells accumulate unrepaired DNA within persistent DNA damage foci (PDDF) of chromatin. These PDDF are featured by persistent activation of DNA damage/repair signaling, lack of transcription and localization in repressive nuclear microenvironments. Interestingly, the chromatin insulator CTCF is concentrated at the PDDF boundaries, likely contributing to isolate unrepaired DNA from intact transcriptionally active chromatin. By confining damaged DNA, PDDF would help preserving genomic integrity and preventing the production of aberrant proteins encoded by damaged genes. ChIP-seq analysis of genome-wide γH2AX distribution revealed a number of genomic regions enriched in γH2AX signal in IR-treated cortical neurons. Some of these regions are in close proximity to genes encoding essential proteins for neuronal functions and human neurodegenerative disorders such as epm2a (Lafora disease), serpini1 (familial encephalopathy with neuroserpin inclusion bodies) and il1rpl1 (mental retardation, X-linked 21). Persistent γH2AX signal close to those regions suggests that nearby genes could be either more vulnerable to DNA damage or more refractory to DNA repair.
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99989
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Abstract
Mitochondria are sensitive to numerous environmental stresses, which can lead to activation of mitochondrial stress responses (MSRs). Of particular recent interest has been the mitochondrial unfolded protein response (UPRmt), activated to restore protein homeostasis (proteostasis) upon mitochondrial protein misfolding. Several axes of the UPRmt have been described, creating some confusion as to the nature of the different responses. While distinct molecularly, these different axes are likely mutually beneficial and activated in parallel. This review aims at describing and distinguishing the different mammalian MSR/UPRmt axes to define key processes and members and to examine the involvement of protein misfolding.
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Affiliation(s)
- Christian Münch
- Institute of Biochemistry II, Goethe University - Medical Faculty, University Hospital, Frankfurt am Main, Germany.
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99990
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Eid AH, El-Yazbi AF, Zouein F, Arredouani A, Ouhtit A, Rahman MM, Zayed H, Pintus G, Abou-Saleh H. Inositol 1,4,5-Trisphosphate Receptors in Hypertension. Front Physiol 2018; 9:1018. [PMID: 30093868 PMCID: PMC6071574 DOI: 10.3389/fphys.2018.01018] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 07/09/2018] [Indexed: 12/21/2022] Open
Abstract
Chronic hypertension remains a major cause of global mortality and morbidity. It is a complex disease that is the clinical manifestation of multiple genetic, environmental, nutritional, hormonal, and aging-related disorders. Evidence supports a role for vascular aging in the development of hypertension involving an impairment in endothelial function together with an alteration in vascular smooth muscle cells (VSMCs) calcium homeostasis leading to increased myogenic tone. Changes in free intracellular calcium levels ([Ca2+] i ) are mediated either by the influx of Ca2+ from the extracellular space or release of Ca2+ from intracellular stores, mainly the sarcoplasmic reticulum (SR). The influx of extracellular Ca2+ occurs primarily through voltage-gated Ca2+ channels (VGCCs), store-operated Ca2+ channels (SOC), and Ca2+ release-activated channels (CRAC), whereas SR-Ca2+ release occurs through inositol trisphosphate receptor (IP3R) and ryanodine receptors (RyRs). IP3R-mediated SR-Ca2+ release, in the form of Ca2+ waves, not only contributes to VSMC contraction and regulates VGCC function but is also intimately involved in structural remodeling of resistance arteries in hypertension. This involves a phenotypic switch of VSMCs as well as an alteration of cytoplasmic Ca2+ signaling machinery, a phenomena tightly related to the aging process. Several lines of evidence implicate changes in expression/function levels of IP3R isoforms in the development of hypertension, VSMC phenotypic switch, and vascular aging. The present review discusses the current knowledge of these mechanisms in an integrative approach and further suggests potential new targets for hypertension management and treatment.
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Affiliation(s)
- Ali H Eid
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.,Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Ahmed F El-Yazbi
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.,Department of Pharmacology and Toxicology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Fouad Zouein
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Abdelilah Arredouani
- Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Allal Ouhtit
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Md M Rahman
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha, Qatar
| | - Gianfranco Pintus
- Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha, Qatar
| | - Haissam Abou-Saleh
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
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99991
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Zhang L, Serra-Cardona A, Zhou H, Wang M, Yang N, Zhang Z, Xu RM. Multisite Substrate Recognition in Asf1-Dependent Acetylation of Histone H3 K56 by Rtt109. Cell 2018; 174:818-830.e11. [PMID: 30057113 DOI: 10.1016/j.cell.2018.07.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/08/2018] [Accepted: 07/03/2018] [Indexed: 12/19/2022]
Abstract
Rtt109 is a unique histone acetyltransferase acetylating histone H3 lysine 56 (H3K56), a modification critical for DNA replication-coupled nucleosome assembly and genome stability. In cells, histone chaperone Asf1 is essential for H3K56 acetylation, yet the mechanisms for H3K56 specificity and Asf1 requirement remain unknown. We have determined the crystal structure of the Rtt109-Asf1-H3-H4 complex and found that unwinding of histone H3 αN, where K56 is normally located, and stabilization of the very C-terminal β strand of histone H4 by Asf1 are prerequisites for H3K56 acetylation. Unexpectedly, an interaction between Rtt109 and the central helix of histone H3 is also required. The observed multiprotein, multisite substrate recognition mechanism among histone modification enzymes provides mechanistic understandings of Rtt109 and Asf1 in H3K56 acetylation, as well as valuable insights into substrate recognition by histone modification enzymes in general.
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Affiliation(s)
- Lin Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China; University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Albert Serra-Cardona
- Institute for Cancer Genetics, Departments of Pediatrics and Genetics and Development and Irving Cancer Research Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Hui Zhou
- Institute for Cancer Genetics, Departments of Pediatrics and Genetics and Development and Irving Cancer Research Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Mingzhu Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Na Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, 300353 Tianjin, China
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Departments of Pediatrics and Genetics and Development and Irving Cancer Research Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
| | - Rui-Ming Xu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China; University of Chinese Academy of Sciences, 100049 Beijing, China.
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99992
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Fiedorczuk K, Sazanov LA. Mammalian Mitochondrial Complex I Structure and Disease-Causing Mutations. Trends Cell Biol 2018; 28:835-867. [PMID: 30055843 DOI: 10.1016/j.tcb.2018.06.006] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 06/14/2018] [Accepted: 06/22/2018] [Indexed: 12/31/2022]
Abstract
Complex I has an essential role in ATP production by coupling electron transfer from NADH to quinone with translocation of protons across the inner mitochondrial membrane. Isolated complex I deficiency is a frequent cause of mitochondrial inherited diseases. Complex I has also been implicated in cancer, ageing, and neurodegenerative conditions. Until recently, the understanding of complex I deficiency on the molecular level was limited due to the lack of high-resolution structures of the enzyme. However, due to developments in single particle cryo-electron microscopy (cryo-EM), recent studies have reported nearly atomic resolution maps and models of mitochondrial complex I. These structures significantly add to our understanding of complex I mechanism and assembly. The disease-causing mutations are discussed here in their structural context.
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Affiliation(s)
- Karol Fiedorczuk
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria; Present address: The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Leonid A Sazanov
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria.
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99993
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Kristoffersen AS, Erga SR, Hamre B, Frette Ø. Testing Fluorescence Lifetime Standards using Two-Photon Excitation and Time-Domain Instrumentation: Fluorescein, Quinine Sulfate and Green Fluorescent Protein. J Fluoresc 2018; 28:1065-1073. [PMID: 30046998 PMCID: PMC6153725 DOI: 10.1007/s10895-018-2270-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 07/20/2018] [Indexed: 11/30/2022]
Abstract
It is essential for everyone working with experimental science to be certain that their instruments produce reliable results, and for fluorescence lifetime experiments, information about fluorescence lifetime standards is crucial. A large part of the literature on lifetime standards dates back to the 1970s and 1980s, and the use of newer and faster measuring devices may deem these results unreliable. We have tested the three commonly used fluorophores fluorescein, quinine sulfate and green fluorescent protein for their suitability to serve as lifetime standards, especially to be used with two-photon excitation measurements in the time-domain. We measured absorption and emission spectra for the fluorophores to determine optimal wavelengths to use for excitation and detector settings. Fluorescence lifetimes were measured for different concentrations, ranging from 10− 3 − 10− 5 M, as well as for various solvents. Fluorescein was soluble in both ethanol, methanol and sulfuric acid, while quinine sulfate was only soluble in sulfuric acid. Green fluorescent protein was prepared in a commercial Tris-HCl, EDTA solution, and all three fluorophores produced stable lifetime results with low uncertainties. No siginificant variation with concentration was measured for any of the fluorophores, and all showed single-exponential decays. All lifetime measurements were carried out using two-photon excitation and lifetime data was obtained in the time-domain using time-correlated single-photon counting.
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Affiliation(s)
- Arne S Kristoffersen
- Department of Physics and Technology, University of Bergen, P.O. Box 7803, Bergen, N-5020, Norway.
| | - Svein R Erga
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, Bergen, N-5020, Norway
| | - Børge Hamre
- Department of Physics and Technology, University of Bergen, P.O. Box 7803, Bergen, N-5020, Norway
| | - Øyvind Frette
- Department of Physics and Technology, University of Bergen, P.O. Box 7803, Bergen, N-5020, Norway
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99994
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Yordanova Y, Vanderlinden W, Stoll R, Rüdiger D, Tosstorff A, Zaremba W, Winter G, Zahler S, Friess W. Zn 2+-triggered self-assembly of Gonadorelin [6-D-Phe] to produce nanostructures and fibrils. Sci Rep 2018; 8:11280. [PMID: 30050082 DOI: 10.1038/s41598-018-29529-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 07/12/2018] [Indexed: 12/23/2022] Open
Abstract
A synthetic derivative, GnRH [6-D-Phe], stable against enzymatic degradation, self-assembles and forms nanostructures and fibrils upon a pH shift in the presence of different concentrations of Zn2+in vitro. Attenuated Total Reflection Fourier Transform Infrared spectroscopy (ATR–FTIR) revealed the existence of higher order assembly of Zn2+: GnRH [6-D-Phe]. Nuclear Magnetic Resonance spectroscopy (NMR) indicated a weak interaction between Zn2+ and GnRH [6-D-Phe]. Atomic Force Microscopy (AFM) showed the existence of GnRH [6-D-Phe] oligomers and fibrils. Molecular Dynamic (MD) simulation of the 10:1 Zn2+: GnRH [6-D-Phe] explored the interaction and dimerization processes. In contrast to already existing short peptide fibrils, GnRH [6-D-Phe] nanostructures and fibrils form in a Tris-buffered pH environment in a controlled manner through a temperature reduction and a pH shift. The lyophilized Zn2+: GnRH [6-D-Phe] assembly was tested as a platform for the sustained delivery of GnRH [6-D-Phe] and incorporated into two different oil vehicle matrices. The in vitro release was slow and continuous over 14 days and not influenced by the oil matrix.
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99995
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Tanaka K, Goto H, Nishimura Y, Kasahara K, Mizoguchi A, Inagaki M. Tetraploidy in cancer and its possible link to aging. Cancer Sci 2018; 109:2632-2640. [PMID: 29949679 PMCID: PMC6125447 DOI: 10.1111/cas.13717] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 06/26/2018] [Indexed: 12/23/2022] Open
Abstract
Tetraploidy, a condition in which a cell has four homologous sets of chromosomes, is often seen as a natural physiological condition but is also frequently seen in pathophysiological conditions such as cancer. Tetraploidy facilitates chromosomal instability (CIN), which is an elevated level of chromosomal loss and gain that can cause production of a wide variety of aneuploid cells that carry structural and numerical aberrations of chromosomes. The resultant genomic heterogeneity supposedly expedites karyotypic evolution that confers oncogenic potential in spite of the reduced cellular fitness caused by aneuploidy. Recent studies suggest that tetraploidy might also be associated with aging; mice with mutations in an intermediate filament protein have revealed that these tetraploidy‐prone mice exhibit tissue disorders associated with aging. Cellular senescence and its accompanying senescence‐associated secretory phenotype have now emerged as critical factors that link tetraploidy and tetraploidy‐induced CIN with cancer, and possibly with aging. Here, we review recent findings about how tetraploidy is related to cancer and possibly to aging, and discuss underlying mechanisms of the relationship, as well as how we can exploit the properties of cells exhibiting tetraploidy‐induced CIN to control these pathological conditions.
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Affiliation(s)
- Kozo Tanaka
- Department of Molecular Oncology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Hidemasa Goto
- Department of Neural Regeneration and Cell Communication, Mie University Graduate School of Medicine, Tsu, Japan
| | - Yuhei Nishimura
- Department of Integrative Pharmacology, Mie University Graduate School of Medicine, Tsu, Japan
| | - Kousuke Kasahara
- Department of Physiology, Mie University Graduate School of Medicine, Tsu, Japan
| | - Akira Mizoguchi
- Department of Neural Regeneration and Cell Communication, Mie University Graduate School of Medicine, Tsu, Japan
| | - Masaki Inagaki
- Department of Physiology, Mie University Graduate School of Medicine, Tsu, Japan
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99996
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Yang S, Sun Z, Zhou Q, Wang W, Wang G, Song J, Li Z, Zhang Z, Chang Y, Xia K, Liu J, Yuan W. MicroRNAs, long noncoding RNAs, and circular RNAs: potential tumor biomarkers and targets for colorectal cancer. Cancer Manag Res 2018; 10:2249-2257. [PMID: 30100756 PMCID: PMC6065600 DOI: 10.2147/cmar.s166308] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Noncoding RNAs (ncRNAs) can be divided into microRNAs (miRNAs), long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), pRNAs, and tRNAs. Traditionally, miRNAs exert their biological function mainly through the inhibition of translation via the induction of target RNA transcript degradation. lncRNAs and circRNAs were once considered to have no potential to code proteins. Here, we will review the current knowledge on ncRNAs in relation to their origins, characteristics, and functions. We will also review how ncRNAs work as competitive endogenous RNA, gene transcription and expression regulators, and RNA-binding protein sponges in colorectal cancer (CRC). Notably, except for the abovementioned mechanisms, recent advances revealed that lncRNAs can also act as the precursor of miRNAs, and a small portion of lncRNAs and circRNAs was verified to have the potential to code proteins, providing new evidence for the significance of ncRNAs in CRC tumorigenesis and development.
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Affiliation(s)
- Shuaixi Yang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Zhenqiang Sun
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Quanbo Zhou
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Weiwei Wang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, People's Republic of China.,Department of Pathology, School of Basic Medicine, Zhengzhou University, Zhengzhou, Henan 450002, People's Republic of China
| | - Guixian Wang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Junmin Song
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Zhen Li
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Zhiyong Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Yuan Chang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Kunkun Xia
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Jinbo Liu
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
| | - Weitang Yuan
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, People's Republic of China, ;
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99997
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Trinh MN, Brown MS, Seemann J, Goldstein JL, Lu F. Lysosomal cholesterol export reconstituted from fragments of Niemann-Pick C1. eLife 2018; 7:e38564. [PMID: 30047864 PMCID: PMC6062155 DOI: 10.7554/elife.38564] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/17/2018] [Indexed: 12/25/2022] Open
Abstract
Niemann-Pick C1 (NPC1) is a polytopic membrane protein with 13 transmembrane helices that exports LDL-derived cholesterol from lysosomes by carrying it through the 80 Å glycocalyx and the 40 Å lipid bilayer. Transport begins when cholesterol binds to the N-terminal domain (NTD) of NPC1, which projects to the surface of the glycocalyx. Here, we reconstitute cholesterol transport by expressing the NTD as a fragment separate from the remaining portion of NPC1. When co-expressed, the two NPC1 fragments reconstitute cholesterol transport, indicating that the NTD has the flexibility to interact with the remaining parts of NPC1 even when not covalently linked. We also show that cholesterol can be transferred from the NTD of one full-length NPC1 to another NPC1 molecule that lacks the NTD. These data support the hypothesis that cholesterol is transported through interactions between two or more NPC1 molecules.
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Affiliation(s)
- Michael Nguyen Trinh
- Departments of Molecular GeneticsUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Michael S Brown
- Departments of Molecular GeneticsUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Joachim Seemann
- Cell BiologyUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Joseph L Goldstein
- Departments of Molecular GeneticsUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Feiran Lu
- Departments of Molecular GeneticsUniversity of Texas Southwestern Medical CenterDallasUnited States
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99998
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Ding L, Yang X, Tian H, Liang J, Zhang F, Wang G, Wang Y, Ding M, Shui G, Huang X. Seipin regulates lipid homeostasis by ensuring calcium-dependent mitochondrial metabolism. EMBO J 2018; 37:embj.201797572. [PMID: 30049710 DOI: 10.15252/embj.201797572] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/05/2018] [Accepted: 07/09/2018] [Indexed: 02/06/2023] Open
Abstract
Seipin, the gene that causes Berardinelli-Seip congenital lipodystrophy type 2 (BSCL2), is important for adipocyte differentiation and lipid homeostasis. Previous studies in Drosophila revealed that Seipin promotes ER calcium homeostasis through the Ca2+-ATPase SERCA, but little is known about the events downstream of perturbed ER calcium homeostasis that lead to decreased lipid storage in Drosophila dSeipin mutants. Here, we show that glycolytic metabolites accumulate and the downstream mitochondrial TCA cycle is impaired in dSeipin mutants. The impaired TCA cycle further leads to a decreased level of citrate, a critical component of lipogenesis. Mechanistically, Seipin/SERCA-mediated ER calcium homeostasis is important for maintaining mitochondrial calcium homeostasis. Reduced mitochondrial calcium in dSeipin mutants affects the TCA cycle and mitochondrial function. The lipid storage defects in dSeipin mutant fat cells can be rescued by replenishing mitochondrial calcium or by restoring the level of citrate through genetic manipulations or supplementation with exogenous metabolites. Together, our results reveal that Seipin promotes adipose tissue lipid storage via calcium-dependent mitochondrial metabolism.
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Affiliation(s)
- Long Ding
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiao Yang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - He Tian
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jingjing Liang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Fengxia Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Guodong Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mei Ding
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xun Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China .,University of Chinese Academy of Sciences, Beijing, China
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99999
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Luo W, Guo F, McMahon A, Couvertier S, Jin H, Diaz M, Fieldsend A, Weerapana E, Rosbash M. NonA and CPX Link the Circadian Clockwork to Locomotor Activity in Drosophila. Neuron 2018; 99:768-780.e3. [PMID: 30057203 DOI: 10.1016/j.neuron.2018.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 04/27/2018] [Accepted: 07/01/2018] [Indexed: 11/20/2022]
Abstract
Drosophila NonA and its mammalian ortholog NONO are members of the Drosophila behavior and human splicing (DBHS) family. NONO also has a strong circadian connection: it associates with the circadian repressor protein PERIOD (PER) and contributes to circadian timekeeping. Here, we investigate NonA, which is required for proper levels of evening locomotor activity as well as a normal free-running period in Drosophila. NonA is associated with the positive transcription factor CLOCK/CYCLE (CLK/CYC), interacts directly with complexin (cpx) pre-mRNA, and upregulates gene expression, including the gene cpx. Downregulation of cpx expression in circadian neurons phenocopies NonA downregulation, whereas cpx overexpression rescues the nonA RNAi phenotypes, indicating that cpx is an important NonA target gene. As the cpx protein contributes to proper neurotransmitter and neuropeptide release in response to calcium, these results and others indicate that this control is important for the normal circadian regulation of locomotor activity.
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100000
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Gabizon R, Lee A, Vahedian-Movahed H, Ebright RH, Bustamante CJ. Pause sequences facilitate entry into long-lived paused states by reducing RNA polymerase transcription rates. Nat Commun 2018; 9:2930. [PMID: 30050038 PMCID: PMC6062546 DOI: 10.1038/s41467-018-05344-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/21/2018] [Indexed: 11/25/2022] Open
Abstract
Transcription by RNA polymerase (RNAP) is interspersed with sequence-dependent pausing. The processes through which paused states are accessed and stabilized occur at spatiotemporal scales beyond the resolution of previous methods, and are poorly understood. Here, we combine high-resolution optical trapping with improved data analysis methods to investigate the formation of paused states at enhanced temporal resolution. We find that pause sites reduce the forward transcription rate of nearly all RNAP molecules, rather than just affecting the subset of molecules that enter long-lived pauses. We propose that the reduced rates at pause sites allow time for the elongation complex to undergo conformational changes required to enter long-lived pauses. We also find that backtracking occurs stepwise, with states backtracked by at most one base pair forming quickly, and further backtracking occurring slowly. Finally, we find that nascent RNA structures act as modulators that either enhance or attenuate pausing, depending on the sequence context.
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Affiliation(s)
- Ronen Gabizon
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, CA, 94720, USA
| | - Antony Lee
- Department of Physics, University of California, Berkeley, CA, 94720, USA
| | - Hanif Vahedian-Movahed
- Department of Chemistry and Waksman Institute, Rutgers University, Piscataway, NJ, 08854, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Richard H Ebright
- Department of Chemistry and Waksman Institute, Rutgers University, Piscataway, NJ, 08854, USA
| | - Carlos J Bustamante
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, CA, 94720, USA.
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.
- Department of Molecular and Cell Biology, and Kavli Energy Nanoscience Institute, University of California, Berkeley, CA, 94720, USA.
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