Table S3.2 D13 Vs D6 Up-Regulated Genes
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MITOCHONDRIAL CREATINE KINASE Some Clinical, Biochemical and Morphological Aspects
PDF hosted at the Radboud Repository of the Radboud University Nijmegen The following full text is a publisher's version. For additional information about this publication click this link. http://hdl.handle.net/2066/114105 Please be advised that this information was generated on 2021-10-11 and may be subject to change. MITOCHONDRIAL CREATINE KINASE some clinical, biochemical and morphological aspects Jan A.M. Smeitink MITOCHONDRIAL CREATINE KINASE some clinical, biochemical and morphological aspects Jan A.M. Smeitink MITOCHONDRIAL CREATINE KINASE SOME CLINICAL, BIOCHEMICAL AND MORPHOLOGICAL ASPECTS EEN WETENSCHAPPELIJKE PROEVE OP HET GEBIED VAN DE MEDISCHE WETENSCHAPPEN, IN HET BIJZONDER DE GENEESKUNDE PROEFSCHRIFT TER VERKRIJGING VAN DE GRAAD VAN DOCTOR AAN DE KATHOLIEKE UNIVERSITEIT NIJMEGEN VOLGENS BESLUIT VAN HET COLLEGE VAN DECANEN IN HET OPENBAAR TE VERDEDIGEN OP DINSDAG 6 OKTOBER 1992, DES NAMIDDAGS TE 1.30 UUR PRECIES DOOR JOHANNES ALBERTUS MARIA SMEITINK GEBOREN OP 21 JUNI 1956 TE ARNHEM IV Promotores : Prof. Dr. R.C.A. Sengers Prof. Dr. J.M.F. Trijbels Co-Promotores : Dr. W. Ruitenbeek Dr. R.A. Wevers Aan mijn ouders AanWillemien en Mark CONTEN CHAPTER 1 Introduction and aim of the study CHAPTER 2 Mitochondrial creatine kinase: a key enzyme of aerobic energy metabolism Biochimica et Biophysica Acta (Reviews on Bioenergetics): in press I. Introduction II. Biochemical studies of Mi-CK ΠΙ. Functional studies of Mi-CK IV. Integration of Mi-CK in cellular energy metabolism V. Perspectives CHAPTER 3 A method for quantitative measurement -
(12) Patent Application Publication (10) Pub. No.: US 2010/0317005 A1 Hardin Et Al
US 20100317005A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2010/0317005 A1 Hardin et al. (43) Pub. Date: Dec. 16, 2010 (54) MODIFIED NUCLEOTIDES AND METHODS (22) Filed: Mar. 15, 2010 FOR MAKING AND USE SAME Related U.S. Application Data (63) Continuation of application No. 11/007,794, filed on Dec. 8, 2004, now abandoned, which is a continuation (75) Inventors: Susan H. Hardin, College Station, in-part of application No. 09/901,782, filed on Jul. 9, TX (US); Hongyi Wang, Pearland, 2001. TX (US); Brent A. Mulder, (60) Provisional application No. 60/527,909, filed on Dec. Sugarland, TX (US); Nathan K. 8, 2003, provisional application No. 60/216,594, filed Agnew, Richmond, TX (US); on Jul. 7, 2000. Tommie L. Lincecum, JR., Publication Classification Houston, TX (US) (51) Int. Cl. CI2O I/68 (2006.01) Correspondence Address: (52) U.S. Cl. ............................................................ 435/6 LIFE TECHNOLOGES CORPORATION (57) ABSTRACT CFO INTELLEVATE Labeled nucleotide triphosphates are disclosed having a label P.O. BOX S2OSO bonded to the gamma phosphate of the nucleotide triphos MINNEAPOLIS, MN 55402 (US) phate. Methods for using the gamma phosphate labeled nucleotide are also disclosed where the gamma phosphate labeled nucleotide are used to attach the labeled gamma phos (73) Assignees: LIFE TECHNOLOGIES phate in a catalyzed (enzyme or man-made catalyst) reaction to a target biomolecule or to exchange a phosphate on a target CORPORATION, Carlsbad, CA biomolecule with a labeled gamme phosphate. Preferred tar (US); VISIGEN get biomolecules are DNAs, RNAs, DNA/RNAs, PNA, BIOTECHNOLOGIES, INC. polypeptide (e.g., proteins enzymes, protein, assemblages, etc.), Sugars and polysaccharides or mixed biomolecules hav ing two or more of DNAs, RNAs, DNA/RNAs, polypeptide, (21) Appl. -
Identi Cation of Metabolic Reprogramming Related Gene
Identication of Metabolic Reprogramming Related Gene Signature to Predict the Prognosis of Bladder Cancer Patients Tinghao Li The First Aliated Hospital of Chongqing Medical University https://orcid.org/0000-0002-7980-6298 Hang Tong The First Aliated Hospital of Chongqing Medical University Hubin Yin The First Aliated Hospital of Chongqing Medical University Honghao Cao Rongchang tranditional Chinese medicine hospital Junlong Zhu the rst aiated hospital of Chongqing medical uiversity Zijia Qin The First Aliated Hospital of Chongqing Medical University Siwen Yin The First Aliated Hospital of Chongqing Medical University Weiyang He ( [email protected] ) The First Aliated Hospital of Chongqing Medical University https://orcid.org/0000-0002-7445-8781 Research article Keywords: Metabolic reprogramming, Prognosis, Bladder cancer, TCGA, GEO Posted Date: December 23rd, 2020 DOI: https://doi.org/10.21203/rs.3.rs-132465/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/20 Abstract Background: Different kinds of metabolic reprogramming have been widely researched in multifarious cancer types and show up as a guaranteed prognostic predictor, while bladder cancer (BLCA) is most frequent urothelium carcinoma but with poor prognosis despite there are emerging treatments, for lack of reliable predicting biomarkers to early predict the prognosis and delayed treatment options for patients in the terminal stage. Our study aims to explore new prognostic factors related to metabolism in BLCA and make these genes up as novel risk stratication. Methods: We selected a large number of samples downloaded from TCGA (The Cancer Genome Atlas) to nd out the possible glycolysis-related genes that correlated with differentiation from cancer sample to normal tissue, aimed to nd out a more credible model. -
Lombricine Kinase Structure and Substrate Specificity: a Paradigm for Elucidation of Substrate Specificity in Phosphagen Kinases D
Florida State University Libraries Electronic Theses, Treatises and Dissertations The Graduate School 2007 Lombricine Kinase Structure and Substrate Specificity: A Paradigm for Elucidation of Substrate Specificity in Phosphagen Kinases D. Jeffrey. Bush Follow this and additional works at the FSU Digital Library. For more information, please contact [email protected] THE FLORIDA STATE UNIVERSITY COLLEGE OF ARTS AND SCIENCES LOMBRICINE KINASE STRUCTURE AND SUBSTRATE SPECIFICITY: A PARADIGM FOR ELUCIDATION OF SUBSTRATE SPECIFICITY IN PHOSPHAGEN KINASES By D. JEFFREY BUSH A Dissertation submitted to the Department of Chemistry and Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy Degree Awarded: Spring Semester, 2007 The members of the Committee approve the Dissertation of D. Jeffrey Bush defended on February 20, 2007. Michael S. Chapman Professor Co-Directing Dissertation John Dorsey Professor Co-Directing Dissertation W. Ross Ellington Outside Committee Member Michael Blaber Committee Member Approved: ____________________________________________ Joseph Schlenoff, Department Chair, Department of Chemistry & Biochemistry ____________________________________________ Joseph Travis, Dean, College of Arts & Sciences The Office of Graduate Studies has verified and approved the above named committee members. ii To the late Clifford M. Bush, who with statements such as “A heterogeneous compound of two or more substances whose ray through certain limits is confined to a specific area…” fostered a strong interest of the author in science at a very young age, if only just to know more about what he spoke. iii ACKNOWLEDGEMENTS I wish to first convey my sincere gratitude to my parents, Donald and Roberta for raising me in the nurture and admonition of the Almighty God. -
Acidophilic Green Algal Genome Provides Insights Into Adaptation to an Acidic Environment
Acidophilic green algal genome provides insights into adaptation to an acidic environment Shunsuke Hirookaa,b,1, Yuu Hirosec, Yu Kanesakib,d, Sumio Higuchie, Takayuki Fujiwaraa,b,f, Ryo Onumaa, Atsuko Eraa,b, Ryudo Ohbayashia, Akihiro Uzukaa,f, Hisayoshi Nozakig, Hirofumi Yoshikawab,h, and Shin-ya Miyagishimaa,b,f,1 aDepartment of Cell Genetics, National Institute of Genetics, Shizuoka 411-8540, Japan; bCore Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama 332-0012, Japan; cDepartment of Environmental and Life Sciences, Toyohashi University of Technology, Aichi 441-8580, Japan; dNODAI Genome Research Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan; eResearch Group for Aquatic Plants Restoration in Lake Nojiri, Nojiriko Museum, Nagano 389-1303, Japan; fDepartment of Genetics, Graduate University for Advanced Studies, Shizuoka 411-8540, Japan; gDepartment of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan; and hDepartment of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan Edited by Krishna K. Niyogi, Howard Hughes Medical Institute, University of California, Berkeley, CA, and approved August 16, 2017 (received for review April 28, 2017) Some microalgae are adapted to extremely acidic environments in pumps that biotransform arsenic and archaeal ATPases, which which toxic metals are present at high levels. However, little is known probably contribute to the algal heat tolerance (8). In addition, the about how acidophilic algae evolved from their respective neutrophilic reduction in the number of genes encoding voltage-gated ion ancestors by adapting to particular acidic environments. To gain channels and the expansion of chloride channel and chloride car- insights into this issue, we determined the draft genome sequence rier/channel families in the genome has probably contributed to the of the acidophilic green alga Chlamydomonas eustigma and per- algal acid tolerance (8). -
Some Catalytic and Regulatory Properties of Pyruvate Kinase from the Spadix and Retractor Muscles of Nautilus Pompilius1
Pacific Science (1982), vol. 36, no. 3 © 1983 by the University of Hawaii Press. All rights reserved Some Catalytic and Regulatory Properties of Pyruvate Kinase from the Spadix and Retractor Muscles of Nautilus pompilius1 JEREMY H. A. FIELDS 2 ABSTRACT: Pyruvate kinase was partially purified from the spadix and retrac tor muscles of Nautilus pompilius. In both cases, the enzyme was activated by magnesium and potassium ions with similar affinities (apparent Ka values were 0.63 ± 0.04 mM and 5.8 ± 0.4 mM, respectively, for the enzyme from the spadix; and 0.77 ± 0.06 mM and 6.7 ± 0.8 mM, respectively, for the enzyme from the retractor muscle). The enzymes showed normal hyperbolic saturation kinetics for the substrates adenosine Y-diphosphate and phosphoenolpyruvate, and the apparent Km values were identical when measured at saturating concen trations of the cosubstrate (apparent Km values were 0.28 ± 0.01 mM and 0.063 ± 0.005 mM, respectively, for the spadix). Adenosine 5'-triphosphate, alanine, and citrate were found to be inhibitors. The enzyme from the spadix was more susceptible to inhibition by alanine than that from the retractor muscle. For the latter enzyme, inhibition by alanine was noncompetitive with respect to phosphoenolpyruvate, but the inhibition was nonlinear; it also decreased the affinity for Mg2+. For the enzyme from the spadix, inhibition by alanine changed the saturation kinetics for phosphoenolpyruvate to sigmoidal form. The affinity for Mg2+ was also decreased by alanine. For both enzymes, fructose-I, 6-bisphosphate at a concentration of 0.05 mM partially reversed the inhibition by alanine, but not that by adenosine Y-triphosphate. -
S42003-020-01354-W.Pdf
ARTICLE https://doi.org/10.1038/s42003-020-01354-w OPEN Broad-complex transcription factor mediates opposing hormonal regulation of two phylogenetically distant arginine kinase genes in Tribolium castaneum 1234567890():,; Nan Zhang1, Heng Jiang1, Xiangkun Meng1, Kun Qian1, Yaping Liu1, Qisheng Song 2, David Stanley3, Jincai Wu1, ✉ Yoonseong Park4 & Jianjun Wang1 The phosphoarginine-arginine kinase shuttle system plays a critical role in maintaining insect cellular energy homeostasis. Insect molting and metamorphosis are coordinated by fluc- tuations of the ecdysteroid and juvenile hormone. However, the hormonal regulation of insect arginine kinases remain largely elusive. In this report, we comparatively characterized two arginine kinase genes, TcAK1 and TcAK2,inTribolium castaneum. Functional analysis using RNAi showed that TcAK1 and TcAK2 play similar roles in adult fertility and stress response. TcAK1 was detected in cytoplasm including mitochondria, whereas TcAK2 was detected in cytoplasm excluding mitochondria. Interestingly, TcAK1 expression was negatively regulated by 20-hydroxyecdysone and positively by juvenile hormone, whereas TcAK2 was regulated by the opposite pattern. RNAi, dual-luciferase reporter assays and electrophoretic mobility shift assay further revealed that the opposite hormonal regulation of TcAK1 and TcAK2 was mediated by transcription factor Broad-Complex. Finally, relatively stable AK activities were observed during larval-pupal metamorphosis, which was generally consistent with the con- stant ATP levels. These results provide new insights into the mechanisms underlying the ATP homeostasis in insects by revealing opposite hormonal regulation of two phylogenetically distant arginine kinase genes. 1 College of Horticulture and Plant Protection, Yangzhou University, 225009 Yangzhou, China. 2 Division of Plant Sciences, University of Missouri, Columbia, MO, USA. -
Natural Products Containing 'Rare'
molecules Review Natural Products Containing ‘Rare’ Organophosphorus Functional Groups Janusz J. Petkowski 1,* , William Bains 2 and Sara Seager 1,3,4 1 Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA; [email protected] 2 Rufus Scientific, 37 The Moor, Melbourn, Royston, Herts SG8 6ED, UK; [email protected] 3 Department of Physics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA 4 Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA * Correspondence: [email protected] Received: 21 January 2019; Accepted: 22 February 2019; Published: 28 February 2019 Abstract: Phosphorous-containing molecules are essential constituents of all living cells. While the phosphate functional group is very common in small molecule natural products, nucleic acids, and as chemical modification in protein and peptides, phosphorous can form P–N (phosphoramidate), P–S (phosphorothioate), and P–C (e.g., phosphonate and phosphinate) linkages. While rare, these moieties play critical roles in many processes and in all forms of life. In this review we thoroughly categorize P–N, P–S, and P–C natural organophosphorus compounds. Information on biological source, biological activity, and biosynthesis is included, if known. This review also summarizes the role of phosphorylation on unusual amino acids in proteins (N- and S-phosphorylation) and reviews the natural phosphorothioate (P–S) and phosphoramidate (P–N) modifications of DNA and nucleotides with an emphasis on their role in the metabolism of the cell. We challenge the commonly held notion that nonphosphate organophosphorus functional groups are an oddity of biochemistry, with no central role in the metabolism of the cell. -
Design and Evaluation of Hmp Kinase Analogs As Thiamine
DESIGN AND EVALUATION OF HMP KINASE ANALOGS AS THIAMINE PATHWAY INHIBITORS by DIEGO A. LOPEZ Presented to the Faculty of the Graduate School of The University of Texas at Arlington in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY THE UNIVERSITY OF TEXAS AT ARLINGTON Summer 2016 Copyright © by Diego A. Lopez 2016 All Rights Reserved ii Acknowledgements This work would not have been possible without the help, support, and motivation of many people. First and foremost, I would like to thank Dr. Frank W. Foss Jr. for his mentorship, guidance, and amazing contribution into my life as a young scientist. I will always look up to him with admiration and follow his academic lessons and life teachings wherever I go. I would like to express my sincere gratitude to my committee members, Dr. Jeon and Dr. Mandal for their continuous support throughout the years and for their insightful suggestions towards the development of the project. In addition, I would like to thank the Organic division professors, Dr. Lovely, Dr. Bugarin, and Dr. Pierce for always being cordial and supportive both inside and outside of the chemistry field. I would also like to thank the numerous people who have contributed into the project, specially Dr. Sumit Bhawal who started the HMP project and developed most of the syntheses present in this study. His hard-work, passion for chemistry, and strive for success will always be remembered by this colleague and friend. I thank all my undergraduate students and members of the Foss’ lab for all the hard work, merit, and joy that have brought into my academic career: Aaron, Andra, Mohammad “Mu”, Pawan, Shakar, Johny, Twi, Nicky, Kevin and Caitlynn. -
Natural Products Containing 'Rare'
Natural Products Containing ‘Rare’ Organophosphorus Functional Groups The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Petkowski, Janusz, et al. “Natural Products Containing ‘Rare’ Organophosphorus Functional Groups.” Molecules, vol. 24, no. 5, Feb. 2019, p. 866. As Published http://dx.doi.org/10.3390/molecules24050866 Publisher Multidisciplinary Digital Publishing Institute Version Final published version Citable link http://hdl.handle.net/1721.1/120918 Terms of Use Creative Commons Attribution Detailed Terms https://creativecommons.org/licenses/by/4.0/ molecules Review Natural Products Containing ‘Rare’ Organophosphorus Functional Groups Janusz J. Petkowski 1,* , William Bains 2 and Sara Seager 1,3,4 1 Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA; [email protected] 2 Rufus Scientific, 37 The Moor, Melbourn, Royston, Herts SG8 6ED, UK; [email protected] 3 Department of Physics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA 4 Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA * Correspondence: [email protected] Received: 21 January 2019; Accepted: 22 February 2019; Published: 28 February 2019 Abstract: Phosphorous-containing molecules are essential constituents of all living cells. While the phosphate functional group is very common in small molecule natural products, nucleic acids, and as chemical modification in protein and peptides, phosphorous can form P–N (phosphoramidate), P–S (phosphorothioate), and P–C (e.g., phosphonate and phosphinate) linkages. While rare, these moieties play critical roles in many processes and in all forms of life. -
Acidophilic Green Algal Genome Provides Insights Into Adaptation To
Acidophilic green algal genome provides insights into PNAS PLUS adaptation to an acidic environment Shunsuke Hirookaa,b,1, Yuu Hirosec, Yu Kanesakib,d, Sumio Higuchie, Takayuki Fujiwaraa,b,f, Ryo Onumaa, Atsuko Eraa,b, Ryudo Ohbayashia, Akihiro Uzukaa,f, Hisayoshi Nozakig, Hirofumi Yoshikawab,h, and Shin-ya Miyagishimaa,b,f,1 aDepartment of Cell Genetics, National Institute of Genetics, Shizuoka 411-8540, Japan; bCore Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama 332-0012, Japan; cDepartment of Environmental and Life Sciences, Toyohashi University of Technology, Aichi 441-8580, Japan; dNODAI Genome Research Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan; eResearch Group for Aquatic Plants Restoration in Lake Nojiri, Nojiriko Museum, Nagano 389-1303, Japan; fDepartment of Genetics, Graduate University for Advanced Studies, Shizuoka 411-8540, Japan; gDepartment of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan; and hDepartment of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan Edited by Krishna K. Niyogi, Howard Hughes Medical Institute, University of California, Berkeley, CA, and approved August 16, 2017 (received for review April 28, 2017) Some microalgae are adapted to extremely acidic environments in pumps that biotransform arsenic and archaeal ATPases, which which toxic metals are present at high levels. However, little is known probably contribute to the algal heat tolerance (8). In addition, the about how acidophilic algae evolved from their respective neutrophilic reduction in the number of genes encoding voltage-gated ion ancestors by adapting to particular acidic environments. To gain channels and the expansion of chloride channel and chloride car- insights into this issue, we determined the draft genome sequence rier/channel families in the genome has probably contributed to the of the acidophilic green alga Chlamydomonas eustigma and per- algal acid tolerance (8). -
Insight Into Structural Aspects of Histidine 284 of Daphnia Magna
Molecules and Cells Insight into Structural Aspects of Histidine 284 of Daphnia magna Arginine Kinase Zhili Rao1,4, So Young Kim1,4, Xiaotong Li1, Da Som Kim1, Yong Ju Kim2,3,*, and Jung Hee Park1,3,* 1Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea, 2Department of Herbal Medicine Resources, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan 54596, Korea, 3Advanced Institute of Environment and Bioscience, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea, 4These authors contributed equally to this work. *Correspondence: [email protected] (YJK); [email protected] (JHP) https://doi.org/10.14348/molcells.2020.0136 www.molcells.org Arginine kinase (AK), a bioenergy-related enzyme, is INTRODUCTION distributed widely in invertebrates. The role of highly conserved histidines in AKs is still unascertained. In this study, Phosphagen kinases (PKs) are a family of phosphotransfer- the highly conserved histidine 284 (H284) in AK of Daphnia ases that reversibly catalyze the delivery of high-energy phos- magna (DmAK) was replaced with alanine to elucidate the phoryl groups between ATP and guanidine derivatives. The role of H284. We examined the alteration of catalytic activity phosphorylated guanidines, also known as phosphagens, are and structural changes of H284A in DmAK. The catalytic a type of high-energy compounds that play an important role activity of H284A was reduced dramatically compared to in cellular energy homeostasis in both the muscles and the that in wild type (WT). Thus the crystal structure of H284A brain by providing a way to store high-energy phosphates displayed several structural changes, including the alteration as a metastable compound (Ellington, 2001).