DOCSLIB.ORG

Structural and Regulatory Genes Controlling the Biosynthesis of Essential Oil Constituents in Lavender

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

STRUCTURAL AND REGULATORY GENES CONTROLLING THE BIOSYNTHESIS OF ESSENTIAL OIL CONSTITUENTS IN LAVENDER By Lukman Syed Sarker M.Sc., University of British Columbia, 2013 M.Sc., University of Dhaka, 2009 B.Sc., University of Dhaka, 2007 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OFTHE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE COLLEGE OF GRADUATE STUDIES (Biology) THE UNIVERSITY OF BRITISH COLUMBIA April 2020 © Lukman Sarker, 2020 i The following individuals certify that they have read, and recommend to the College of Graduate Studies for acceptance, a thesis/dissertation entitled: Structural and regulatory genes controlling the biosynthesis of essential oil constituents in lavender Submitted by Lukman Sarker in partial fulfillment of the requirements of the degree of Doctor of Philosophy Dr. Soheil S. Mahmoud, Biology, Irving K. Barber School of Arts and Sciences, UBC Supervisor Dr. Michael Deyholos, Biology, Irving K. Barber School of Arts and Sciences, UBC Supervisory Committee Member Dr. Mark Rheault, Biology, Irving K. Barber School of Arts and Sciences, UBC Supervisory Committee Member Dr. Frederic Menard, Chemistry, Irving K. Barber School of Arts and Sciences, UBC University Examiner Dr. Philipp Zerbe, Department of Plant Biology, University of California External Examiner Additional Committee Members include: Dr. Thu-Thuy Dang, Chemistry, Irving K. Barber School of Arts and Sciences, UBC Supervisory Committee Member ii Abstract This thesis describes research conducted to enhance our understanding of essential oil (EO) metabolism in lavender (Lavandula). Specific experiments were carried out in three areas. First, we developed a comprehensive transcriptomic database to facilitate the discovery of novel structural and regulatory essential oil biosynthetic genes in lavender. The database includes 101,618 contigs (N50 = 831 bp), over 75% of which were successfully annotated. Annotated sequences include full length transcripts for all previously reported genes involved in the MVA and MEP pathways of isoprenoid metabolism, all prenyltransferases involved in the isoprenoid biosynthesis, and all terpene synthase genes cloned from various lavender species. They also contain novel EO-related genes, as exemplified by the S-linalool synthase (Li(S)-LINS) gene we cloned using this database. Further, the database contains 1633 TFs, representing 2.1% of the lavenders' transcriptome, some of which have been shown to regulate secondary metabolism in plants. The most abundant TF families were bHLH (209), WRKY (190), and MYB (189) followed by AP2 (79), bZIP (77), and zinc finger (19), NAC (13), and MYC (9). Second, we isolated the 5' upstream genomic DNA (promoter) sequences for linalool synthase (LiLINS) and 1,8-cineole synthase (LiCINS) genes from L. x intermedia and used them to conduct a Yeast One-Hybrid Assay in order to identify TFs that regulate the expression of LiLINS and LiCINS genes in this plant. The assay identified 96 proteins that interacted with one or both promoters. To elucidate the nature of this interaction further, the LiLINS and LiCINS promoter fragments were each fused to the E. coli gusA (GUS) reporter gene. The constructs were separately transformed into tobacco (Nicotiana benthamiana) leaves, co-expressing individually a subset of ten representative transcription factors. Six TFs iii induced expression from both promoters, two activated LiCINS promoter alone, and two did not induce expression from either promoter. Finally, we isolated and functionally characterized genes for two acetyltransferases, LiLAT-3 & LiLAT-4, which convert some of the monoterpene EO constituents into their respective esters in lavender. Our results, which have enhanced our understanding of EO biosynthesis in plants, will help improve EO yield and composition in lavender and other plants through plant breeding and biotechnology. iv Lay Summary Lavender is an economically important plant known for its essential oils (EO), which is dominated by a group of small, volatile biochemical compounds known as monoterpenoids. To understand the genetic basis of lavender EO constituent production, we developed a comprehensive transcriptome database, which facilitates the discovery of structural and regulatory genes involved in terpenoids biosynthesis, as well as other important processes such as defense against pest and herbivores. Further, we employed a Yeast One-Hybrid Assay to identify transcription factors that control the expression of two important genes responsible for the production of linalool and cineole in lavenders. Finally, we cloned genes for two acetyltransferase enzymes involved in the conversion of monoterpenes to their corresponding esters in lavender plants. v Preface Chapter 2 has been published in a journal Planta and the contents were reprinted/ adapted by permission from Springer Nature: Planta, 249(1):271–290, RNA-Seq in the discovery of a sparsely expressed scent-determining monoterpene synthase in lavender (Lavandula), Ayelign M. Adal, Lukman S. Sarker, Radesh PN Malli, Ping Liang and Soheil S. Mahmoud, © 2018, License # 4718011260334. I designed the experiment to develop the lavender transcriptomic database. I also helped Ayelign Adal to clone the S-linalool synthase. I helped in the writing procedure; however, Ayelign Adal led the manuscript preparation with the guidance of Dr. Soheil Mahmoud. Both Lukman Sarker and Ayelign Adal share an equal contribution in publishing this manuscript. Mr. Radesh PN Malli and Dr. Ping Liang analyzed genomic seq and copy numbers of S-linalool synthase in the genome. Chapter 3 has been published in Planta, and the contents were reprinted/ adapted by permission from Springer Nature: Planta, (2020) 251: 5 (online version), Diverse transcription factors control monoterpene synthase expression in lavender (Lavandula). Lukman S. Sarker, Ayelign M. Adal, and Soheil S. Mahmoud, © 2019, License # 4718020130702. I have designed and conducted the experiment. Ayelign Adal took the lead to write the manuscript with the help of myself and Dr. Soheil Mahmoud. Chapter 4 has been published in Planta, and the contents were reprinted/ adapted by permission from Springer Nature: Planta, 242 (3): 709-19. Cloning and functional characterization of two monoterpene acetyltransferases from glandular trichomes of L. x intermedia. Lukman S. Sarker and Soheil S. Mahmoud, © 2015, License vi #4718020297429. I have designed and conducted the experiments and wrote the manuscript with the guidance of Dr. Soheil Mahmoud. During my Ph.D. thesis work, I also co-authored the following manuscripts: a) Malli RPN, Adal AM, Sarker LS, Liang P, and Mahmoud SS (2019) De novo sequencing of the Lavandula angustifolia genome reveals highly duplicated and optimized features for essential oil production, Planta, 249(1):251–256. (I collected leaf tissues, prepared genomic DNA for sequencing and provided ESTs and transcriptomes for annotation). b) Wells R, Truong F, Adal AM, Sarker LS, and Mahmoud SS (2018) Lavandula essential oils: a current review of applications in medicinal, food, and cosmetic industries of lavender. Natural Product Communications, 13(10): 1403-1417. (I wrote a section of the review and helped with reference management and manuscript preparation). c) Adal AM, Sarker LS, Lemke A, Mahmoud SS (2017) Isolation and functional characterization of a methyl jasmonate-responsive 3-carene synthase from Lavandula x intermedia. Plant Molecular Biology, 93: 641-657. I helped Ayelign Adal with qPCR experimentation and writing the manuscript. vii Table of Contents Abstract ................................................................................................................................... iii Lay Summary .......................................................................................................................... v List of Tables .......................................................................................................................... xi Table of Figures..................................................................................................................... xii List of Symbols ..................................................................................................................... xiv Acknowledgments ................................................................................................................ xvi Dedication............................................................................................................................ xviii 1 Chapter: Introduction ...................................................................................................... 1 1.1 Biosynthesis of lavender terpenoids .......................................................................................... 3 1.1.1 Isoprene biosynthesis ...................................................................................................... 4 1.1.2 Mono- and sesquiterpene synthesis ................................................................................. 7 1.1.2.1 Mono and sesquiterpene synthases .......................................................................... 8 1.1.2.2 EO Esters and ketones in lavender ......................................................................... 10 1.2 Storage and secretion of volatile terpenoids ............................................................................ 11 1.3 Regulation of terpenoid synthesis ...........................................................................................
Recommended publications
  • Markedly Inhibited 7-Dehydrocholesterol-Delta 7-Reductase Activity in Liver Microsomes from Smith-Lemli-Opitz Homozygotes

    Markedly Inhibited 7-Dehydrocholesterol-Delta 7-Reductase Activity in Liver Microsomes from Smith-Lemli-Opitz Homozygotes

    Markedly inhibited 7-dehydrocholesterol-delta 7-reductase activity in liver microsomes from Smith-Lemli-Opitz homozygotes. S Shefer, … , T C Chen, M F Holick J Clin Invest. 1995;96(4):1779-1785. https://doi.org/10.1172/JCI118223. Research Article We investigated the enzyme defect in late cholesterol biosynthesis in the Smith-Lemli-Opitz syndrome, a recessively inherited developmental disorder characterized by facial dysmorphism, mental retardation, and multiple organ congenital anomalies. Reduced plasma and tissue cholesterol with increased 7-dehydrocholesterol concentrations are biochemical features diagnostic of the inherited enzyme defect. Using isotope incorporation assays, we measured the transformation of the precursors, [3 alpha- 3H]lathosterol and [1,2-3H]7-dehydrocholesterol into cholesterol by liver microsomes from seven controls and four Smith-Lemli-Opitz homozygous subjects. The introduction of the double bond in lathosterol at C- 5[6] to form 7-dehydrocholesterol that is catalyzed by lathosterol-5-dehydrogenase was equally rapid in controls and homozygotes liver microsomes (120 +/- 8 vs 100 +/- 7 pmol/mg protein per min, P = NS). In distinction, the reduction of the double bond at C-7 [8] in 7-dehydrocholesterol to yield cholesterol catalyzed by 7-dehydrocholesterol-delta 7- reductase was nine times greater in controls than homozygotes microsomes (365 +/- 23 vs 40 +/- 4 pmol/mg protein per min, P < 0.0001). These results demonstrate that the pathway of lathosterol to cholesterol in human liver includes 7- dehydrocholesterol as a key intermediate. In Smith-Lemli-Opitz homozygotes, the transformation of 7-dehydrocholesterol to cholesterol by hepatic microsomes was blocked although 7-dehydrocholesterol was produced abundantly from lathosterol.
  • Other Roles of Euap2 Genes in Plant Development Charles U

    Other Roles of Euap2 Genes in Plant Development Charles U

    Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 24 October 2019 doi:10.20944/preprints201901.0035.v3 Review Besides and Beyond Flowering: Other roles of euAP2 genes in plant development Charles U. Solomon1, 2* and Sinead Drea1 1Department of Genetics and Genome Biology, University of Leicester, UK; [email protected]; [email protected] 2Department of Plant Science and Biotechnology, Abia State University, Uturu, Nigeria *Correspondence: [email protected] Abstract: EuAP2 genes are famous for their role in flower development. A legacy of the founding member of this subfamily of transcription factors, whose mutants lacked petals in Arabidopsis. However, studies of euAP2 genes in several species have accumulated evidence highlighting the diverse roles of euAP2 genes in other aspects of plant development. Here, we emphasize other developmental roles of euAP2 genes in various species and suggest a shift from regarding euAP2 genes as just flowering genes to consider the global role they may be playing in plant development. We hypothesize that their almost universal expression profile and pleiotropic effects of their mutation suggest their involvement in fundamental plant development processes. Keywords: EuAP2 genes; Flowering; Plant Development Introduction APETALA 2 (AP2) genes are named after a series of Arabidopsis mutants characterized by homeotic transformations of their sepals to leaves and petals to staminoid petals. Analysis of the ap2 mutants along with other floral mutants gave birth to the ABC model of flower development where AP2 is classified as an A-class gene [1, 2]. The forerunner AP2 protein was cloned and characterized in Arabidopsis [3]. The Arabidopsis AP2 protein comprising 432 amino acids (aa) is mainly characterized by the possession of two AP2 domains, each made up of 68-aa with an 18-aa core conserved section that forms an amphipathic -훼–helix .
  • Pollination-Induced Gene Changes That Lead to Senescence in Petunia × Hybrida

    Pollination-Induced Gene Changes That Lead to Senescence in Petunia × Hybrida

    Pollination-Induced Gene Changes That Lead to Senescence in Petunia × hybrida DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Shaun Robert Broderick, M.S. Graduate Program in Horticulture and Crop Science The Ohio State University 2014 Dissertation Committee: Michelle L. Jones, Advisor Feng Qu Eric J. Stockinger Esther van der Knaap Copyrighted by Shaun Robert Broderick 2014 Abstract Flower longevity is a genetically programmed event that ends in flower senescence. Flowers can last from several hours to several months, based on flower type and environmental factors. For many flowers, particularly those that are ethylene- sensitive, longevity is greatly reduced after pollination. Cellular components are disassembled and nutrients are remobilized during senescence, which reduces the net energy expenditures of floral structures. The goal of this research is to identify the genes that can be targeted to extent shelf life by inhibiting pollination-induced senescence. Identifying and characterizing regulatory shelf-life genes will enable breeders to incorporate specific alleles that improve post production quality into ethylene-sensitive crops. Petunia × hybrida is particularly amenable to flower longevity studies because of its large floral organs, predictable flower senescence timing, and importance in the greenhouse industry. A general approach to gene functional analysis involves reducing gene expression and observing the resulting phenotype. Viruses, such as tobacco rattle virus (TRV), can be used to induce gene silencing in plants like petunia. We optimized several parameters that improved virus-induced gene silencing (VIGS) in petunia by increasing the consistency and efficiency of silencing.
  • The Effects of Phytosterols Present in Natural Food Matrices on Cholesterol Metabolism and LDL-Cholesterol: a Controlled Feeding Trial

    The Effects of Phytosterols Present in Natural Food Matrices on Cholesterol Metabolism and LDL-Cholesterol: a Controlled Feeding Trial

    European Journal of Clinical Nutrition (2010) 64, 1481–1487 & 2010 Macmillan Publishers Limited All rights reserved 0954-3007/10 www.nature.com/ejcn ORIGINAL ARTICLE The effects of phytosterols present in natural food matrices on cholesterol metabolism and LDL-cholesterol: a controlled feeding trial X Lin1, SB Racette2,1, M Lefevre3,5, CA Spearie4, M Most3,6,LMa1 and RE Ostlund Jr1 1Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA; 2Program in Physical Therapy, Washington University School of Medicine, St Louis, MO, USA; 3Pennington Biomedical Research Center, Baton Rouge, LA, USA and 4Center for Applied Research Sciences, Washington University School of Medicine, St Louis, MO, USA Background/Objectives: Extrinsic phytosterols supplemented to the diet reduce intestinal cholesterol absorption and plasma low-density lipoprotein (LDL)-cholesterol. However, little is known about their effects on cholesterol metabolism when given in native, unpurified form and in amounts achievable in the diet. The objective of this investigation was to test the hypothesis that intrinsic phytosterols present in unmodified foods alter whole-body cholesterol metabolism. Subjects/Methods: In all, 20 out of 24 subjects completed a randomized, crossover feeding trial wherein all meals were provided by a metabolic kitchen. Each subject consumed two diets for 4 weeks each. The diets differed in phytosterol content (phytosterol-poor diet, 126 mg phytosterols/2000 kcal; phytosterol-abundant diet, 449 mg phytosterols/2000 kcal), but were otherwise matched for nutrient content. Cholesterol absorption and excretion were determined by gas chromatography/mass spectrometry after oral administration of stable isotopic tracers.
  • A Latent Ability to Persist: Differentiation in Toxoplasma Gondii

    A Latent Ability to Persist: Differentiation in Toxoplasma Gondii

    View metadata, citation and similar papers at core.ac.uk brought to you by CORE HHS Public Access provided by IUPUIScholarWorks Author manuscript Author ManuscriptAuthor Manuscript Author Cell Mol Manuscript Author Life Sci. Author Manuscript Author manuscript; available in PMC 2019 July 01. Published in final edited form as: Cell Mol Life Sci. 2018 July ; 75(13): 2355–2373. doi:10.1007/s00018-018-2808-x. A Latent Ability to Persist: Differentiation in Toxoplasma gondii Victoria Jeffers1,*, Zoi Tampaki2, Kami Kim2,3, and William J. Sullivan Jr1,4 1Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA 2Departments of Medicine, Microbiology & Immunology, and Pathology; Albert Einstein College of Medicine, Bronx, NY 10461, USA 3Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA 4Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA Abstract A critical factor in the transmission and pathogenesis of Toxoplasma gondii is the ability to convert from an acute disease-causing, proliferative stage (tachyzoite), to a chronic, dormant stage (bradyzoite). The conversion of the tachyzoite-containing parasitophorous vacuole membrane into the less permeable bradyzoite cyst wall, allows the parasite to persist for years within the host to maximize transmissibility to both primary (felids) and secondary (virtually all other warm-blooded vertebrates) hosts. This review presents our current understanding of the latent stage, including the factors that are important in bradyzoite induction and maintenance. Also discussed are the recent studies that have begun to unravel the mechanisms behind stage switching. Keywords Toxoplasma; toxoplasmosis; differentiation; encystation; tachyzoite; bradyzoite; latency; gene regulation; epigenetics; immunity INTRODUCTION Toxoplasma gondii is an obligate intracellular protozoan parasite capable of infecting warm- blooded vertebrates world-wide [1].
  • Roles of Wrky Proteins in Mediating the Crosstalk of Hormone Signaling Pathways: an Approach Integrating Bioinformatics and Experimental Biology

    Roles of Wrky Proteins in Mediating the Crosstalk of Hormone Signaling Pathways: an Approach Integrating Bioinformatics and Experimental Biology

    UNLV Retrospective Theses & Dissertations 1-1-2006 Roles of Wrky proteins in mediating the crosstalk of hormone signaling pathways: An approach integrating bioinformatics and experimental biology Zhen Xie University of Nevada, Las Vegas Follow this and additional works at: https://digitalscholarship.unlv.edu/rtds Repository Citation Xie, Zhen, "Roles of Wrky proteins in mediating the crosstalk of hormone signaling pathways: An approach integrating bioinformatics and experimental biology" (2006). UNLV Retrospective Theses & Dissertations. 2711. http://dx.doi.org/10.25669/0cw1-sipg This Dissertation is protected by copyright and/or related rights. It has been brought to you by Digital Scholarship@UNLV with permission from the rights-holder(s). You are free to use this Dissertation in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s) directly, unless additional rights are indicated by a Creative Commons license in the record and/or on the work itself. This Dissertation has been accepted for inclusion in UNLV Retrospective Theses & Dissertations by an authorized administrator of Digital Scholarship@UNLV. For more information, please contact [email protected]. ROLES OF WRKY PROTEINS IN MEDIATING THE CROSSTALK OF HORMONE SIGNALING PATHWAYS: AN APPROACH INTEGRATING BIOINFORMATICS AND EXPERIMENTAL BIOLOGY by Zhen Xie Bachelor of Sciences Shandong Agricultural University 1998 Master of Sciences Shandong Agricultural University 2001 A dissertation submitted in partial fulfillment of the requirements for the Doctor of Philosophy Degree in Biological Sciences Department of Biological Sciences College of Sciences Graduate College University of Nevada, Las Vegas December 2006 Reproduced with permission of the copyright owner.
  • Lathosterol Oxidase (Sterol C-5 Desaturase) Deletion Confers Resistance to Amphotericin B and Sensitivity to Acidic Stress in Leishmania Major

    Lathosterol Oxidase (Sterol C-5 Desaturase) Deletion Confers Resistance to Amphotericin B and Sensitivity to Acidic Stress in Leishmania Major

    Washington University School of Medicine Digital Commons@Becker Open Access Publications 7-1-2020 Lathosterol oxidase (sterol C-5 desaturase) deletion confers resistance to amphotericin B and sensitivity to acidic stress in Leishmania major Yu Ning Cheryl Frankfater Fong-Fu Hsu Rodrigo P Soares Camila A Cardoso See next page for additional authors Follow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubs Authors Yu Ning, Cheryl Frankfater, Fong-Fu Hsu, Rodrigo P Soares, Camila A Cardoso, Paula M Nogueira, Noelia Marina Lander, Roberto Docampo, and Kai Zhang RESEARCH ARTICLE Molecular Biology and Physiology crossm Downloaded from Lathosterol Oxidase (Sterol C-5 Desaturase) Deletion Confers Resistance to Amphotericin B and Sensitivity to Acidic Stress in Leishmania major Yu Ning,a Cheryl Frankfater,b Fong-Fu Hsu,b Rodrigo P. Soares,c Camila A. Cardoso,c Paula M. Nogueira,c http://msphere.asm.org/ Noelia Marina Lander,d,e Roberto Docampo,d,e Kai Zhanga aDepartment of Biological Sciences, Texas Tech University, Lubbock, Texas, USA bMass Spectrometry Resource, Division of Endocrinology, Diabetes, Metabolism, and Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA cFundação Oswaldo Cruz-Fiocruz, Instituto René Rachou, Belo Horizonte, Minas Gerais, Brazil dCenter for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA eDepartment of Cellular Biology, University of Georgia, Athens, Georgia, USA ABSTRACT Lathosterol oxidase (LSO) catalyzes the formation of the C-5–C-6 double bond in the synthesis of various types of sterols in mammals, fungi, plants, and pro- on September 14, 2020 at Washington University in St.
  • The Pennsylvania State University the Graduate School College Of

    The Pennsylvania State University the Graduate School College Of

    The Pennsylvania State University The Graduate School College of Health and Human Development EFFECTS OF DIETS ENRICHED IN CONVENTIONAL AND HIGH-OLEIC ACID CANOLA OILS COMPARED TO A WESTERN DIET ON LIPIDS AND LIPOPROTEINS, GENE EXPRESSION, AND THE GUT ENVIRONMENT IN ADULTS WITH METABOLIC SYNDROME FACTORS A Dissertation in Nutritional Sciences by Kate Joan Bowen © 2018 Kate Joan Bowen Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy December 2018 The dissertation of Kate Joan Bowen was reviewed and approved* by the following: Penny Kris-Etherton Distinguished Professor of Nutritional Sciences Dissertation Advisor Chair of Committee Gregory Shearer Associate Professor of Nutritional Sciences Sheila West Professor of Biobehavioral Health Peter Jones Distinguished Professor of Human Nutritional Sciences and Food Sciences University of Manitoba Special Member Lavanya Reddivari Assistant Professor of Food Science Purdue University Laura E. Murray-Kolb Associate Professor of Nutritional Sciences Professor-in-Charge of the Graduate Program *Signatures are on file in the Graduate School ii ABSTRACT The premise of this dissertation was to investigate the effects of diets that differed only in fatty acid composition on biomarkers for cardiovascular disease (CVD) in individuals with metabolic syndrome risk factors, and to explore the mechanisms underlying the response. In a multi-site, double blind, randomized, controlled, three period crossover, controlled feeding study design, participants were fed an isocaloric, prepared, weight maintenance diet plus a treatment oil for 6 weeks with washouts of ≥ 4 weeks between diet periods. The treatment oils included conventional canola oil, high-oleic acid canola oil (HOCO), and a control oil (a blend of butter oil/ghee, flaxseed oil, safflower oil, and coconut oil).
  • Global Small RNA Analysis in Fast-Growing Arabidopsis Thaliana Title with Elevated Concentrations of ATP and Sugars

    Global Small RNA Analysis in Fast-Growing Arabidopsis Thaliana Title with Elevated Concentrations of ATP and Sugars

    Global small RNA analysis in fast-growing Arabidopsis thaliana Title with elevated concentrations of ATP and sugars Author(s) Liang, C; Liu, X; Sun, Y; Yiu, SM; Lim, BL Citation BMC Genomics, 2014, v. 15, article no. 116 Issued Date 2014 URL http://hdl.handle.net/10722/198225 Rights BMC Genomics. Copyright © BioMed Central Ltd. Liang et al. BMC Genomics 2014, 15:116 http://www.biomedcentral.com/1471-2164/15/116 RESEARCH ARTICLE Open Access Global small RNA analysis in fast-growing Arabidopsis thaliana with elevated concentrations of ATP and sugars Chao Liang1†, Xuan Liu2†, Yuzhe Sun1, Siu-Ming Yiu2 and Boon Leong Lim1,3* Abstract Background: In higher eukaryotes, small RNAs play a role in regulating gene expression. Overexpression (OE) lines of Arabidopsis thaliana purple acid phosphatase 2 (AtPAP2) were shown to grow faster and exhibit higher ATP and sugar contents. Leaf microarray studies showed that many genes involved in microRNAs (miRNAs) and trans-acting siRNAs (tasiRNAs) biogenesis were significantly changed in the fast-growing lines. In this study, the sRNA profiles of the leaf and the root of 20-day-old plants were sequenced and the impacts of high energy status on sRNA expression were analyzed. Results: 9-13 million reads from each library were mapped to genome. miRNAs, tasiRNAs and natural antisense transcripts-generated small interfering RNAs (natsiRNAs) were identified and compared between libraries. In the leaf of OE lines, 15 known miRNAs increased in abundance and 9 miRNAs decreased in abundance, whereas in the root of OE lines, 2 known miRNAs increased in abundance and 9 miRNAs decreased in abundance.
  • Steroidal Triterpenes of Cholesterol Synthesis

    Steroidal Triterpenes of Cholesterol Synthesis

    Molecules 2013, 18, 4002-4017; doi:10.3390/molecules18044002 OPEN ACCESS molecules ISSN 1420-3049 www.mdpi.com/journal/molecules Review Steroidal Triterpenes of Cholesterol Synthesis Jure Ačimovič and Damjana Rozman * Centre for Functional Genomics and Bio-Chips, Faculty of Medicine, Institute of Biochemistry, University of Ljubljana, Zaloška 4, Ljubljana SI-1000, Slovenia; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +386-1-543-7591; Fax: +386-1-543-7588. Received: 18 February 2013; in revised form: 19 March 2013 / Accepted: 27 March 2013 / Published: 4 April 2013 Abstract: Cholesterol synthesis is a ubiquitous and housekeeping metabolic pathway that leads to cholesterol, an essential structural component of mammalian cell membranes, required for proper membrane permeability and fluidity. The last part of the pathway involves steroidal triterpenes with cholestane ring structures. It starts by conversion of acyclic squalene into lanosterol, the first sterol intermediate of the pathway, followed by production of 20 structurally very similar steroidal triterpene molecules in over 11 complex enzyme reactions. Due to the structural similarities of sterol intermediates and the broad substrate specificity of the enzymes involved (especially sterol-Δ24-reductase; DHCR24) the exact sequence of the reactions between lanosterol and cholesterol remains undefined. This article reviews all hitherto known structures of post-squalene steroidal triterpenes of cholesterol synthesis, their biological roles and the enzymes responsible for their synthesis. Furthermore, it summarises kinetic parameters of enzymes (Vmax and Km) and sterol intermediate concentrations from various tissues. Due to the complexity of the post-squalene cholesterol synthesis pathway, future studies will require a comprehensive meta-analysis of the pathway to elucidate the exact reaction sequence in different tissues, physiological or disease conditions.
  • Supplementary Materials Modeling Cholesterol Metabolism by Gene Expression Profiling in the Hippocampus Christopher M

    Supplementary Materials Modeling Cholesterol Metabolism by Gene Expression Profiling in the Hippocampus Christopher M

    Supplementary Material (ESI) for Molecular BioSystems This journal is (c) The Royal Society of Chemistry, 2011 Supplementary Materials Modeling cholesterol metabolism by gene expression profiling in the hippocampus Christopher M. Valdez1, Clyde F. Phelix1, Mark A. Smith3, George Perry1,2, and Fidel Santamaria1,2 1Biology Department and 2Neurosciences Institute, The University of Texas at San Antonio, One UTSA circle, San Antonio, TX, 78249; 3Department of Pathology, Case Western Reserve University, Cleveland, Ohio 44106. Corresponding author: Fidel Santamaria, One UTSA circle, San Antonio, TX, 78249. Email: [email protected]. Table S1 Cholesterol metabolite index. Fifty one cholesterol metabolites were included in the brain cholesterol metabolism model, plus acetate (M1) and coenzyme A (M2). The index (M) is used to ease location of metabolites mentioned in the text. M1 acetate M28 4alpha-carboxy-5alpha-cholesta-8-en-3beta-ol M2 coenzyme A M29 5alpha-cholesta-8-en-3-one M3 acetyl-CoA M30 zymostenol M4 acetoacetyl-CoA M31 7-dehydrodesmosterol M5 3-hydroxy-3-methyl-glutaryl CoA M32 desmosterol M6 mevalonate M33 4,4-dimethyl-14alpha-hydroxymethyl-5alpha- cholesta-8,24-dien-3beta-ol M7 mevalonate-5 phosphate M34 4,4-dimethyl-14alpha-formyl-5alpha-cholesta-8,24- dien-3beta-ol M8 mevalonate-5-pyrophosphate M35 4,4-dimethyl-5alpha-cholesta-8,14,24-trien-3beta- ol M9 delta3-isopentenyl pyrophosphate M36 4,4-dimethyl-5alpha-cholesta-8,24-dien-3beta-ol M10 dimethylallyl pyrophosphate M37 4alpha-hydroxymethyl-4beta-methyl-5alpha- cholesta-8,24-dien-3beta-ol
  • Lipid Maps Mass Spectrometry Methods Chapters

    Lipid Maps Mass Spectrometry Methods Chapters

    LIPID MAPS MASS SPECTROMETRY METHODS CHAPTERS DISCLAIMER: These chapters were written for the sole purpose of guiding qualified, professional scientists in the indicated laboratory procedures. Some of the procedures involve the use of chemicals or equipment that may be dangerous, particularly if improperly performed or if carried out by personnel that are not appropriately trained in laboratory procedures. The authors, editors, institutions, publisher, and associated companies have no responsibility whatsoever for any injuries, harm, damage to property or any monetary losses associated with the use of the procedures described in these chapters. The end user accepts all responsibility for use of the procedures described in these chapters. This work is provided on the LIPID MAPS website with the written permission of the Publisher and the entire volume may be viewed from the website http://www.sciencedirect.com/science/bookseries/00766879. CHAPTER ONE Qualitative Analysis and Quantitative Assessment of Changes in Neutral Glycerol Lipid Molecular Species Within Cells Jessica Krank,* Robert C. Murphy,* Robert M. Barkley,* Eva Duchoslav,† and Andrew McAnoy* Contents 1. Introduction 2 2. Reagents 3 2.1. Cell culture 3 2.2. Standards 3 2.3. Extraction and purification 3 3. Methods 4 3.1. Cell culture 4 4. Results 7 4.1. Qualitative analysis 7 4.2. Quantitative analysis 11 5. Conclusions 19 Acknowledgments 19 References 19 Abstract Triacylglycerols (TAGs) and diacylglycerols (DAGs) are present in cells as a complex mixture of molecular species that differ in the nature of the fatty acyl groups esterified to the glycerol backbone. In some cases, the molecular weights of these species are identical, confounding assignments of identity and quantity by molecular weight.