Glucose Starvation to Rapid Death of Nrf1, but Not Nrf2, Deficient Hepatoma Cells from Its Fatal Defects in the Redox Metabolism Reprogramming
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The Switch from Fermentation to Respiration in Saccharomyces Cerevisiae Is Regulated by the Ert1 Transcriptional Activator/Repressor
INVESTIGATION The Switch from Fermentation to Respiration in Saccharomyces cerevisiae Is Regulated by the Ert1 Transcriptional Activator/Repressor Najla Gasmi,* Pierre-Etienne Jacques,† Natalia Klimova,† Xiao Guo,§ Alessandra Ricciardi,§ François Robert,†,** and Bernard Turcotte*,‡,§,1 ‡Department of Medicine, *Department of Biochemistry, and §Department of Microbiology and Immunology, McGill University Health Centre, McGill University, Montreal, QC, Canada H3A 1A1, †Institut de recherches cliniques de Montréal, Montréal, QC, Canada H2W 1R7, and **Département de Médecine, Faculté de Médecine, Université de Montréal, QC, Canada H3C 3J7 ABSTRACT In the yeast Saccharomyces cerevisiae, fermentation is the major pathway for energy production, even under aerobic conditions. However, when glucose becomes scarce, ethanol produced during fermentation is used as a carbon source, requiring a shift to respiration. This adaptation results in massive reprogramming of gene expression. Increased expression of genes for gluconeogenesis and the glyoxylate cycle is observed upon a shift to ethanol and, conversely, expression of some fermentation genes is reduced. The zinc cluster proteins Cat8, Sip4, and Rds2, as well as Adr1, have been shown to mediate this reprogramming of gene expression. In this study, we have characterized the gene YBR239C encoding a putative zinc cluster protein and it was named ERT1 (ethanol regulated transcription factor 1). ChIP-chip analysis showed that Ert1 binds to a limited number of targets in the presence of glucose. The strongest enrichment was observed at the promoter of PCK1 encoding an important gluconeogenic enzyme. With ethanol as the carbon source, enrichment was observed with many additional genes involved in gluconeogenesis and mitochondrial function. Use of lacZ reporters and quantitative RT-PCR analyses demonstrated that Ert1 regulates expression of its target genes in a manner that is highly redundant with other regulators of gluconeogenesis. -
The Thioredoxin Trx-1 Regulates the Major Oxidative Stress Response Transcription Factor, Skn-1, in Caenorhabditis Elegans
The Texas Medical Center Library DigitalCommons@TMC The University of Texas MD Anderson Cancer Center UTHealth Graduate School of The University of Texas MD Anderson Cancer Biomedical Sciences Dissertations and Theses Center UTHealth Graduate School of (Open Access) Biomedical Sciences 5-2016 THE THIOREDOXIN TRX-1 REGULATES THE MAJOR OXIDATIVE STRESS RESPONSE TRANSCRIPTION FACTOR, SKN-1, IN CAENORHABDITIS ELEGANS Katie C. McCallum Follow this and additional works at: https://digitalcommons.library.tmc.edu/utgsbs_dissertations Part of the Cellular and Molecular Physiology Commons, Medicine and Health Sciences Commons, Molecular Genetics Commons, and the Organismal Biological Physiology Commons Recommended Citation McCallum, Katie C., "THE THIOREDOXIN TRX-1 REGULATES THE MAJOR OXIDATIVE STRESS RESPONSE TRANSCRIPTION FACTOR, SKN-1, IN CAENORHABDITIS ELEGANS" (2016). The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access). 655. https://digitalcommons.library.tmc.edu/utgsbs_dissertations/655 This Dissertation (PhD) is brought to you for free and open access by the The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences at DigitalCommons@TMC. It has been accepted for inclusion in The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access) by an authorized administrator of DigitalCommons@TMC. For more information, please contact [email protected]. THE THIOREDOXIN TRX-1 REGULATES THE MAJOR OXIDATIVE STRESS RESPONSE TRANSCRIPTION FACTOR, SKN-1, IN CAENORHABDITIS ELEGANS A DISSERTATION Presented to the Faculty of The University of Texas Health Science Center at Houston and The University of Texas MD Anderson Cancer Center Graduate School of Biomedical Sciences in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY by Katie Carol McCallum, B.S. -
Analysis of Gene Expression Data for Gene Ontology
ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION A Thesis Presented to The Graduate Faculty of The University of Akron In Partial Fulfillment of the Requirements for the Degree Master of Science Robert Daniel Macholan May 2011 ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION Robert Daniel Macholan Thesis Approved: Accepted: _______________________________ _______________________________ Advisor Department Chair Dr. Zhong-Hui Duan Dr. Chien-Chung Chan _______________________________ _______________________________ Committee Member Dean of the College Dr. Chien-Chung Chan Dr. Chand K. Midha _______________________________ _______________________________ Committee Member Dean of the Graduate School Dr. Yingcai Xiao Dr. George R. Newkome _______________________________ Date ii ABSTRACT A tremendous increase in genomic data has encouraged biologists to turn to bioinformatics in order to assist in its interpretation and processing. One of the present challenges that need to be overcome in order to understand this data more completely is the development of a reliable method to accurately predict the function of a protein from its genomic information. This study focuses on developing an effective algorithm for protein function prediction. The algorithm is based on proteins that have similar expression patterns. The similarity of the expression data is determined using a novel measure, the slope matrix. The slope matrix introduces a normalized method for the comparison of expression levels throughout a proteome. The algorithm is tested using real microarray gene expression data. Their functions are characterized using gene ontology annotations. The results of the case study indicate the protein function prediction algorithm developed is comparable to the prediction algorithms that are based on the annotations of homologous proteins. -
Resveratrol Improves Glycemic Control in Insulin-Treated Diabetic Rats
Yonamine et al. Nutrition & Metabolism (2016) 13:44 DOI 10.1186/s12986-016-0103-0 RESEARCH Open Access Resveratrol improves glycemic control in insulin-treated diabetic rats: participation of the hepatic territory Caio Yogi Yonamine1†, Erika Pinheiro-Machado1†, Maria Luiza Michalani1, Helayne Soares Freitas1, Maristela Mitiko Okamoto1, Maria Lucia Corrêa-Giannella2 and Ubiratan Fabres Machado1* Abstract Background: Resveratrol is a natural polyphenol that has been proposed to improve glycemic control in diabetes, by mechanisms that involve improvement in insulin secretion and activity. In type 1 diabetes (T1D), in which insulin therapy is obligatory, resveratrol treatment has never been investigated. The present study aimed to evaluate resveratrol as an adjunctive agent to insulin therapy in a T1D-like experimental model. Methods: Rats were rendered diabetic by streptozotocin (STZ) treatment. Twenty days later, four groups of animals were studied: non-diabetic (ND); diabetic treated with placebo (DP); diabetic treated with insulin (DI) and diabetic treated with insulin plus resveratrol (DIR). After 30 days of treatment, 24-hour urine was collected; then, blood, soleus muscle, proximal small intestine, renal cortex and liver were sampled. Specific glucose transporter proteins were analyzed (Western blotting) in each territory of interest. Solute carrier family 2 member 2 (Slc2a2), phosphoenolpyruvate carboxykinase (Pck1) and glucose-6-phosphatase catalytic subunit (G6pc) mRNAs (qPCR), glycogen storage and sirtuin 1 (SIRT1) activity were analyzed in liver. Results: Diabetes induction increased blood glucose, plasma fructosamine concentrations, and glycosuria. Insulin therapy partially recovered the glycemic control; however, resveratrol as adjunctive therapy additionally improved glycemic control and restored plasma fructosamine concentration to values of non-diabetic rats. -
Domain Structure of the Glucocorticoid Receptor Protein
Proc. Nati. Acad. Sci. USA Vol. 84, pp. 4437-4440, July 1987 Biochemistry Domain structure of the glucocorticoid receptor protein (proteolysis/steroid binding/DNA binding/protein sequence) JAN CARLSTEDT-DUKE*, PER-ERIK STROMSTEDT*, ORJAN WRANGEt, TOMAS BERGMANt, JAN-AKE GuSTAFSSON*, AND HANS JORNVALLf *Department of Medical Nutrition, Karolinska Institute, Huddinge University Hospital, F69, S-141 86 Huddinge, Sweden; and Departments of tMedical Cell Genetics and tChemistry, Karolinska Institute, Box 60400, S-104 01 Stockholm, Sweden Communicated by Viktor Mutt, March 26, 1987 (receivedfor review December 1, 1986) ABSTRACT The purified rat liver glucocorticoid receptor GR was eluted with 27.5 mM MgCl2 and further purified by protein was analyzed by limited proteolysis and amino acid chromatography on DEAE-Sepharose, eluted with a linear sequence determination. The NH2 terminus appears to be NaCl gradient. The receptor was detected by analysis for 3H blocked. The steroid-binding domain, defined by a unique radioactivity. Each purification resulted in a yield of '50 ,g tryptic cleavage site, corresponds to the COOH-terminal part of GR, starting from eight rat livers. The purified prepara- of the protein with the domain border in the region of residue tions of GR contained the 94-kDa GR, the 72-kDa GR- 518. The DNA-binding domain, defined by a region with associated protein that is unrelated to GR (12, 13), as well as chymotryptic cleavage sites, is immediately adjacent to the very small amounts of proteolytic GR fragments (usually steroid-binding domain and reflects another domain border in <5% of total protein according to densitometric analysis of the region of residues 410-414. -
Role of Thioredoxin-Interacting Protein in Diseases and Its Therapeutic Outlook
International Journal of Molecular Sciences Review Role of Thioredoxin-Interacting Protein in Diseases and Its Therapeutic Outlook Naila Qayyum 1,†, Muhammad Haseeb 1,† , Moon Suk Kim 1 and Sangdun Choi 1,2,* 1 Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; [email protected] (N.Q.); [email protected] (M.H.); [email protected] (M.S.K.) 2 S&K Therapeutics, Woncheon Hall 135, Ajou University, Suwon 16499, Korea * Correspondence: [email protected] † These authors contributed equally to this work. Abstract: Thioredoxin-interacting protein (TXNIP), widely known as thioredoxin-binding protein 2 (TBP2), is a major binding mediator in the thioredoxin (TXN) antioxidant system, which involves a reduction-oxidation (redox) signaling complex and is pivotal for the pathophysiology of some diseases. TXNIP increases reactive oxygen species production and oxidative stress and thereby contributes to apoptosis. Recent studies indicate an evolving role of TXNIP in the pathogenesis of complex diseases such as metabolic disorders, neurological disorders, and inflammatory illnesses. In addition, TXNIP has gained significant attention due to its wide range of functions in energy metabolism, insulin sensitivity, improved insulin secretion, and also in the regulation of glucose and tumor suppressor activities in various cancers. This review aims to highlight the roles of TXNIP in the field of diabetology, neurodegenerative diseases, and inflammation. TXNIP is found to be a promising novel therapeutic target in the current review, not only in the aforementioned diseases but also in prolonged microvascular and macrovascular diseases. Therefore, TXNIP inhibitors hold promise for preventing the growing incidence of complications in relevant diseases. -
Role of RUNX1 in Aberrant Retinal Angiogenesis Jonathan D
Page 1 of 25 Diabetes Identification of RUNX1 as a mediator of aberrant retinal angiogenesis Short Title: Role of RUNX1 in aberrant retinal angiogenesis Jonathan D. Lam,†1 Daniel J. Oh,†1 Lindsay L. Wong,1 Dhanesh Amarnani,1 Cindy Park- Windhol,1 Angie V. Sanchez,1 Jonathan Cardona-Velez,1,2 Declan McGuone,3 Anat O. Stemmer- Rachamimov,3 Dean Eliott,4 Diane R. Bielenberg,5 Tave van Zyl,4 Lishuang Shen,1 Xiaowu Gai,6 Patricia A. D’Amore*,1,7 Leo A. Kim*,1,4 Joseph F. Arboleda-Velasquez*1 Author affiliations: 1Schepens Eye Research Institute/Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, 20 Staniford St., Boston, MA 02114 2Universidad Pontificia Bolivariana, Medellin, Colombia, #68- a, Cq. 1 #68305, Medellín, Antioquia, Colombia 3C.S. Kubik Laboratory for Neuropathology, Massachusetts General Hospital, 55 Fruit St., Boston, MA 02114 4Retina Service, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, 243 Charles St., Boston, MA 02114 5Vascular Biology Program, Boston Children’s Hospital, Department of Surgery, Harvard Medical School, 300 Longwood Ave., Boston, MA 02115 6Center for Personalized Medicine, Children’s Hospital Los Angeles, Los Angeles, 4650 Sunset Blvd, Los Angeles, CA 90027, USA 7Department of Pathology, Harvard Medical School, 25 Shattuck St., Boston, MA 02115 Corresponding authors: Joseph F. Arboleda-Velasquez: [email protected] Ph: (617) 912-2517 Leo Kim: [email protected] Ph: (617) 912-2562 Patricia D’Amore: [email protected] Ph: (617) 912-2559 Fax: (617) 912-0128 20 Staniford St. Boston MA, 02114 † These authors contributed equally to this manuscript Word Count: 1905 Tables and Figures: 4 Diabetes Publish Ahead of Print, published online April 11, 2017 Diabetes Page 2 of 25 Abstract Proliferative diabetic retinopathy (PDR) is a common cause of blindness in the developed world’s working adult population, and affects those with type 1 and type 2 diabetes mellitus. -
Protein Interactions in the Cancer Proteome† Cite This: Mol
Molecular BioSystems View Article Online PAPER View Journal | View Issue Small-molecule binding sites to explore protein– protein interactions in the cancer proteome† Cite this: Mol. BioSyst., 2016, 12,3067 David Xu,ab Shadia I. Jalal,c George W. Sledge Jr.d and Samy O. Meroueh*aef The Cancer Genome Atlas (TCGA) offers an unprecedented opportunity to identify small-molecule binding sites on proteins with overexpressed mRNA levels that correlate with poor survival. Here, we analyze RNA-seq and clinical data for 10 tumor types to identify genes that are both overexpressed and correlate with patient survival. Protein products of these genes were scanned for binding sites that possess shape and physicochemical properties that can accommodate small-molecule probes or therapeutic agents (druggable). These binding sites were classified as enzyme active sites (ENZ), protein–protein interaction sites (PPI), or other sites whose function is unknown (OTH). Interestingly, the overwhelming majority of binding sites were classified as OTH. We find that ENZ, PPI, and OTH binding sites often occurred on the same structure suggesting that many of these OTH cavities can be used for allosteric modulation of Creative Commons Attribution 3.0 Unported Licence. enzyme activity or protein–protein interactions with small molecules. We discovered several ENZ (PYCR1, QPRT,andHSPA6)andPPI(CASC5, ZBTB32,andCSAD) binding sites on proteins that have been seldom explored in cancer. We also found proteins that have been extensively studied in cancer that have not been previously explored with small molecules that harbor ENZ (PKMYT1, STEAP3,andNNMT) and PPI (HNF4A, MEF2B,andCBX2) binding sites. All binding sites were classified by the signaling pathways to Received 29th March 2016, which the protein that harbors them belongs using KEGG. -
Clinical and Molecular Characterization of Patients with Fructose 1,6-Bisphosphatase Deficiency
Article Clinical and Molecular Characterization of Patients with Fructose 1,6-Bisphosphatase Deficiency Niu Li 1,†, Guoying Chang 2,†, Yufei Xu 1, Yu Ding 2, Guoqiang Li 1, Tingting Yu 1, Yanrong Qing 1, Juan Li 2, Yiping Shen 1,3, Jian Wang 1,* and Xiumin Wang 2,* 1 Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, China; [email protected] (N.L.); [email protected] (Y.X.); [email protected] (G.L.); [email protected] (T.Y.); [email protected] (Y.Q.); [email protected] (Y.S.) 2 Department of Endocrinology and Metabolism, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, China; [email protected] (G.C.); [email protected] (Y.D.); [email protected] (J.L.) 3 Department of Laboratory Medicine, Boston Children’s Hospital, Boston, MA 02115, USA * Correspondence: [email protected] (J.W.); [email protected] (X.W.); Tel.: +86-21-3862-6161 (J.W. & X.W.); Fax: +86-21-5875-6923 (J.W. & X.W.) † These authors contributed equally to this work. Academic Editor: William Chi-shing Cho Received: 26 February 2017; Accepted: 17 April 2017; Published: 18 April 2017 Abstract: Fructose-1,6-bisphosphatase (FBPase) deficiency is a rare, autosomal recessive inherited disease caused by the mutation of the FBP1 gene, the incidence is estimated to be between 1/350,000 and 1/900,000. The symptoms of affected individuals are non-specific and are easily confused with other metabolic disorders. -
Role of PCK1 Gene on Oil Tea-Induced Glucose Homeostasis and Type 2
Hu et al. Nutrition & Metabolism (2019) 16:12 https://doi.org/10.1186/s12986-019-0337-8 RESEARCH Open Access Role of PCK1 gene on oil tea-induced glucose homeostasis and type 2 diabetes: an animal experiment and a case-control study Qiantu Hu1†, Huafeng Chen2†, Yanli Zuo3†, Qin He2, Xuan He2, Steve Simpson Jr4,5, Wei Huang2, Hui Yang2, Haiying Zhang1,6* and Rui Lin1,2,6* Abstract Background: Oil tea is a type of traditional tea beverage used for treating various ailments in minority population in Guangxi, China. Our previous study showed oil tea improved glucose and lipid levels in type 2 diabetic mice. Yet, the underling molecular mechanisms are still not understood. This study aimed at assessing the effect of oil tea on glucose homeostasis and elucidating the molecular mechanisms underlying the oil tea-induced antidiabetic effects. Methods: Twenty seven db/db mice were gavaged with saline, metformin and oil tea for 8 weeks with measurement of biochemical profiles. A real-time2 (RT2) profiler polymerase chain reaction (PCR) array comprising 84 genes involved in glucose metabolism was measured and validated by quantitative PCR (qPCR). The association between the candidate genes and type 2 diabetes were further analyzed in a case-control study in the Chinese minority population. Results: Oil tea treatment facilitated glucose homeostasis by decreasing fasting blood glucose and total cholesterol, and improving glucose tolerance. Suppressing phosphoenolpyruvate carboxykinase 1 (PCK1) expression was observed in the oil tea treatment group and the expression was significantly correlated with fasting blood glucose levels. Target prediction and functional annotation by WEB-based GEne SeT AnaLysis Toolkit (WebGestalt) revealed that PCK1 mainly involved in the glycolysis/gluconeogenesis pathway among the top Kyoto Encyclopedia of Genes and Genomes (KEGG) database pathways. -
B-Cell Translocation Gene 2 Regulates Hepatic Glucose Homeostasis Via Induction of Orphan Nuclear Receptor Nur77 in Diabetic Mouse Model
1870 Diabetes Volume 63, June 2014 Yong Deuk Kim,1 Sun-Gyun Kim,2 Seung-Lark Hwang,3 Hueng-Sik Choi,4 Jae-Hoon Bae,1 Dae-Kyu Song,1 and Seung-Soon Im1 B-Cell Translocation Gene 2 Regulates Hepatic Glucose Homeostasis via Induction of Orphan Nuclear Receptor Nur77 in Diabetic Mouse Model Diabetes 2014;63:1870–1880 | DOI: 10.2337/db13-1368 B-cell translocation gene 2 (BTG2) is a member of an might serve as a potential therapeutic target for com- emerging gene family that is involved in cellular func- bating metabolic dysfunction. tions. In this study, we demonstrate that BTG2 regu- lates glucose homeostasis via upregulation of Nur77 in diabetic mice. Hepatic BTG2 gene expression was The liver plays a crucial role in glucose homeostasis by elevated by fasting and forskolin. Overexpression of maintaining a balance between uptake and storage of Btg2 increased the expression of hepatic gluconeogenic glucose via glycogenesis and in the release of glucose by genes and blood glucose output and subsequently im- both glycogenolysis and gluconeogenesis (1,2). Gluconeo- paired glucose and insulin tolerance. Upregulation METABOLISM genesis is commonly triggered by key hormones including of the transcriptional activity of Nur77, gluconeogenic insulin, glucagon, and glucocorticoid, which contribute to genes, and glucose production by forskolin was ob- the expression of key metabolic enzymes, such as phospho- served by Btg2 transduction, but not in Btg2 knockdown. enolpyruvate carboxykinase (Pck1), fructose biphosphatase BTG2-stimulated glucose production and glucose-6- (Fbp) 1, and glucose-6-phosphatase (G6pc) (3). A variety phosphatase promoter activity were attenuated by of transcriptional factors and cofactors regulated by dominant-negative Nur77. -
Is Glyceraldehyde-3-Phosphate Dehydrogenase a Central Redox Mediator?
1 Is glyceraldehyde-3-phosphate dehydrogenase a central redox mediator? 2 Grace Russell, David Veal, John T. Hancock* 3 Department of Applied Sciences, University of the West of England, Bristol, 4 UK. 5 *Correspondence: 6 Prof. John T. Hancock 7 Faculty of Health and Applied Sciences, 8 University of the West of England, Bristol, BS16 1QY, UK. 9 [email protected] 10 11 SHORT TITLE | Redox and GAPDH 12 13 ABSTRACT 14 D-Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an immensely important 15 enzyme carrying out a vital step in glycolysis and is found in all living organisms. 16 Although there are several isoforms identified in many species, it is now recognized 17 that cytosolic GAPDH has numerous moonlighting roles and is found in a variety of 18 intracellular locations, but also is associated with external membranes and the 19 extracellular environment. The switch of GAPDH function, from what would be 20 considered as its main metabolic role, to its alternate activities, is often under the 21 influence of redox active compounds. Reactive oxygen species (ROS), such as 22 hydrogen peroxide, along with reactive nitrogen species (RNS), such as nitric oxide, 23 are produced by a variety of mechanisms in cells, including from metabolic 24 processes, with their accumulation in cells being dramatically increased under stress 25 conditions. Overall, such reactive compounds contribute to the redox signaling of the 26 cell. Commonly redox signaling leads to post-translational modification of proteins, 27 often on the thiol groups of cysteine residues. In GAPDH the active site cysteine can 28 be modified in a variety of ways, but of pertinence, can be altered by both ROS and 29 RNS, as well as hydrogen sulfide and glutathione.