DOCSLIB.ORG

Reconstructing the Evolution of Xylose Fermentation in Scheffersomyces Stipitis by Kevin Correia a Thesis Submitted in Conformit

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Reconstructing the evolution of xylose fermentation in Scheffersomyces stipitis by Kevin Correia A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Graduate Department of Chemical Engineering and Applied Chemistry University of Toronto © Copyright 2019 by Kevin Correia Abstract Reconstructing the evolution of xylose fermentation in Scheffersomyces stipitis Kevin Correia Doctor of Philosophy Graduate Department of Chemical Engineering and Applied Chemistry University of Toronto 2019 Lignocellulose is a renewable feedstock that can be fermented to biofuels and biochemicals, but its use is limited by several techno-economic challenges, including xylose fermentation. Scheffersomyces stipitis has been identified as an efficient xylose fermenter, but does not ferment well in industrial conditions. The scientific community has been engineering Saccharomyces cerevisiae, the preferred yeast for industrial biotechnology, to ferment xylose to ethanol with the xylose reductase (XR)-xylitol dehydrogenase (XDH) genes from Sch. stipitis for 30 years; however, recombinant Sac. cerevisiae’s titres, rates, and yields for ethanol from xylose lags Sch. stipitis. This performance gap may be due to aspects of Sac. cerevisiae’s metabolism that hinders xylose fermentation, aspects of Sch. stipitis’ metabolism that enables xylose fermentation, or a combination of both. The focus of this thesis is to improve our understanding of budding yeast metabolism beyond Sac. cerevisiae, and ultimately reverse engineer how Sch. stipitis’ metabolism has evolved to ferment xylose to ethanol efficiently with improved genome annotations and metabolic modelling. To obtain higher-quality genome annotations, ortholog groups in 33 yeasts and fungi spanning 600 million years in Dikarya were predicted using OrthoMCL. Over 500 enzyme families were curated with phylogenetic reconstruction to resolve inconsistencies. These ortholog assignments are more accurate than existing ortholog databases, and span diverse yeasts. Next, the gains and losses of metabolic genes were reviewed to identify important and reoccurring events in the evolution of metabolism in budding yeasts. Duplications were found to play an important role in the evolution of metabolism, including changes in enzyme cofactor preference and localization. The curated pan-genome and functional annotations were used to reconstruct genome-scale metabolic networks of the 33 species; the reconstructions have more genomic and metabolic coverage than those made with previous methods. Finally, the Sch. stipitis metabolic network was used to simulate xylose fermentation. NADH kinase and NADP phosphatase (NADPase), an orphan enzyme in eukaryotes, were found to be critical to xylose fermentation in these metabolic flux simulations. Pho3.2p was the sole NADPase candidate showing expression during xylose fermentation; its activity was confirmed in vitro. Xylose fermentation evolved in the Scheffersomyces-Spathaspora clade following genes duplications for XR and an acid phosphatase. This thesis provides a foundation for unravelling how metabolism has evolved in the yeast pan-genome. ii Dedicated to my family, and especially to my late father, who was my first math and science teacher. Luis da Costa Correia (December 12, 1959-December 29, 2014) iii Acknowledgements My doctoral experience has been one of the most rewarding experiences in my life. I have been amazed at how much I have been able to learn during my time at the University of Toronto. First and foremost, I would like to thank Prof. Radhakrishnan Mahadevan for taking me on as a Masters student and eventually allowing me to bypass to the Ph.D. program. I am thankful for the freedom he gave me to pursue my research interests. I also thank my reading committee for guiding me throughout my doctoral research. Prof. Grant Allen for challenging me to make my research more accessible, Prof. Amy Caudy for inviting me to her lab meetings, Prof. Elizabeth Edwards for sitting as an examiner in my defences, and Prof. Jack Pronk for sitting as my external examiner and his helpful suggestions to improve my thesis. My labmates in the Laboratory for Metabolic Systems Engineering have been a great source of friendship and learning, including Peter Li, Pratish Gawand, Patrick Hyland, Chris Gowen, Kayla Nemr, Naveen Venayak, Shyam Srinivasan, Jeong Chan Joo, and Taeho Kim. Prof. Alexander F. Yakunin and Anna Khusnutdinova for their help and guidance with enzymology. Prof. Hung Lee, Xin Wen, and Mehdi Dashtban for their help with Scheffersomyces stipitis genetics. Dean Robson, Weijun Gao, Daniel Tomchyshyn for their help with IT. I thank my family and for their support throughout my Ph.D. It was surprising to hear my parents ask when I would graduate because when I was growing up they always told me to stay in school. They should have specified a time limit. Maiko Sugai, my better half and second brain, for her support. Pierre Sawtell for his sense of humour. I would also like to thank the taxpayers of Ontario and Canada who fund research programs across the country. Direct financial support was provided from Natural Sciences and Engineering Research Council of Canada from the Bioconversion project and the CREATE M3 scholarship. A special thanks to all the failures and rejections that brought me here. iv Contents List of Tables ix List of Figures xii 1 Abbreviations 1 2 Introduction 3 2.1 Motivation . .3 2.2 Challenges and Objectives . .5 2.3 Contributions . .6 2.3.1 Pan-genome creation . .6 2.3.2 Pan-genome analysis . .6 2.3.3 Pan-genome-scale metabolic network reconstruction . .6 2.3.4 Analysis of xylose fermentation in Sch. stipitis ....................7 2.3.5 Other contributions . .7 3 Literature review 9 3.1 History and physiology of xylose fermentation in yeasts . .9 3.1.1 Xylose catabolic pathways . .9 3.1.2 Native pentose fermentation by yeasts . 10 3.1.3 Engineering xylose fermentation in Saccharomyces cerevisiae ............ 15 3.1.4 Opportunities to improve our understanding of xylose fermentation . 18 3.2 Functional genome annotation . 19 3.2.1 Biology is technology . 19 3.2.2 Evolving machines with unknown origins . 19 3.2.3 Homology and analogy in biology . 21 3.2.4 Structural and functional genome annotation . 21 3.2.5 Identifying orthologous proteins . 23 3.2.6 Opportunities to improve functional genome annotation . 27 3.3 Reconstruction and analysis of metabolism in silico ...................... 27 3.3.1 The worm: the first full-scale reconstructed network of biology . 27 3.3.2 Genome-scale network reconstruction . 28 3.3.3 Flux balance analysis . 29 3.3.4 Scheffersomyces stipitis genome-scale network reconstruction and analysis . 30 v 3.3.5 Opportunities to improve genome-scale network reconstruction and analysis for Scheffersomyces stipitis ................................. 30 3.4 Summary of the literature and synthesis . 30 3.4.1 Xylose fermentation . 30 3.4.2 Functional genome annotation . 32 3.4.3 Genome-scale network reconstruction . 33 3.4.4 Synthesis of xylose fermentation in yeasts, genome annotations, and metabolic modelling . 34 3.5 Hypotheses, objectives, and organization of the thesis . 35 3.5.1 Curation of the yeast pan-genome . 35 3.5.2 Analysis of the yeast pan-genome . 35 3.5.3 In silico metabolic network reconstruction for the yeast pan-genome . 36 3.5.4 Reverse engineering xylose fermentation in Scheffersomyces stipitis ......... 36 4 AYbRAH: an open-source ortholog database for yeasts and fungi 38 4.1 Abstract . 38 4.2 Introduction . 39 4.3 Methods . 40 4.3.1 Initial construction of AYbRAH . 40 4.3.2 AYbRAH curation . 40 4.3.3 Annotating misidentified and unidentified proteins . 40 4.3.4 Comparison of AYbRAH to existing phylogenomic databases . 43 4.3.5 Subcellular localization prediction . 43 4.3.6 Literature references . 43 4.4 AYbRAH overview . 45 4.4.1 The AYbRAH web portal. 45 4.5 AYbRAH curation . 48 4.5.1 Over-clustering by OrthoMCL . 48 4.5.2 Under-clustering by OrthoMCL . 48 4.6 Comparison of AYbRAH to other ortholog identification methods. 48 4.6.1 BLASTP scoring metrics. 48 4.6.2 Comparison of AYbRAH to well-established phylogenomic databases. 51 4.7 Applications of a curated ortholog database. 53 4.8 Conclusion . 53 5 Reconstructing the evolution of metabolism in yeasts 54 5.1 Abstract . 54 5.2 Introduction . 55 5.3 Methods . 56 5.3.1 Refinement of the yeast species topology . 56 5.3.2 Reconstruction of gene duplications and losses . 56 5.3.3 Flux balance analysis . 56 5.4 Results & Discussion . 56 5.4.1 Refined yeast species tree topology . 56 vi 5.4.2 Evolution of the pyruvate dehydrogenase bypass . 60 5.4.3 Evolution of NADH dehydrogenase . 64 5.4.4 Heteromerization of enzyme complexes . 67 5.4.5 Ribosomal subunit duplications. 68 5.4.6 Changes in enzyme localization via gene duplications . 69 5.4.7 Redox cofactor changes in enzymes . 70 5.4.8 Horizontal gene transfer . 71 5.5 Conclusion . 71 6 Fungi pan-genome-scale network reconstruction 73 6.1 Abstract . 73 6.2 Introduction . 74 6.3 Methods . 76 6.3.1 Network reconstruction . 76 6.3.2 Biomass equation formulations . 78 6.3.3 Flux balance analysis . 79 6.4 Results . 79 6.4.1 Expanded genomic coverage in the fungal pan-GENRE . 79 6.4.2 Expanded metabolic coverage in the fungal pan-GENRE . 81 6.4.3 Amino acid yields vary across yeast strains . 81 6.4.4 Comparison.
Recommended publications
  • METACYC ID Description A0AR23 GO:0004842 (Ubiquitin-Protein Ligase

    METACYC ID Description A0AR23 GO:0004842 (Ubiquitin-Protein Ligase

    Electronic Supplementary Material (ESI) for Integrative Biology This journal is © The Royal Society of Chemistry 2012 Heat Stress Responsive Zostera marina Genes, Southern Population (α=0.
  • Expanding the Knowledge on the Skillful Yeast Cyberlindnera Jadinii

    Expanding the Knowledge on the Skillful Yeast Cyberlindnera Jadinii

    Journal of Fungi Review Expanding the Knowledge on the Skillful Yeast Cyberlindnera jadinii Maria Sousa-Silva 1,2 , Daniel Vieira 1,2, Pedro Soares 1,2, Margarida Casal 1,2 and Isabel Soares-Silva 1,2,* 1 Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; [email protected] (M.S.-S.); [email protected] (D.V.); [email protected] (P.S.); [email protected] (M.C.) 2 Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal * Correspondence: [email protected]; Tel.: +351-253601519 Abstract: Cyberlindnera jadinii is widely used as a source of single-cell protein and is known for its ability to synthesize a great variety of valuable compounds for the food and pharmaceutical industries. Its capacity to produce compounds such as food additives, supplements, and organic acids, among other fine chemicals, has turned it into an attractive microorganism in the biotechnology field. In this review, we performed a robust phylogenetic analysis using the core proteome of C. jadinii and other fungal species, from Asco- to Basidiomycota, to elucidate the evolutionary roots of this species. In addition, we report the evolution of this species nomenclature over-time and the existence of a teleomorph (C. jadinii) and anamorph state (Candida utilis) and summarize the current nomenclature of most common strains. Finally, we highlight relevant traits of its physiology, the solute membrane transporters so far characterized, as well as the molecular tools currently available for its genomic manipulation.
  • Ribonucleotides Incorporated by the Yeast Mitochondrial DNA Polymerase Are Not Repaired

    Ribonucleotides Incorporated by the Yeast Mitochondrial DNA Polymerase Are Not Repaired

    Ribonucleotides incorporated by the yeast mitochondrial DNA polymerase are not repaired Paulina H. Wanrooija,1, Martin K. M. Engqvistb,c,2, Josefin M. E. Forslunda,2, Clara Navarreteb, Anna Karin Nilssona, Juhan Sedmand, Sjoerd Wanrooija, Anders R. Clausenb, and Andrei Chabesa,e,1 aDepartment of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden; bInstitute of Biomedicine, University of Gothenburg, SE-405 30 Gothenburg, Sweden; cDepartment of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; dDepartment of Biochemistry, Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia; and eLaboratory for Molecular Infection Medicine Sweden, Umeå University, SE-901 87 Umeå, Sweden Edited by Philip C. Hanawalt, Stanford University, Stanford, CA, and approved October 17, 2017 (received for review July 25, 2017) Incorporation of ribonucleotides into DNA during genome replica- Mec1/Rad53 genome integrity checkpoint regulates yeast RNR tion is a significant source of genomic instability. The frequency activity through several different mechanisms (14). of ribonucleotides in DNA is determined by deoxyribonucleoside The incorporation of ribonucleotides (rNMPs) into the genome triphosphate/ribonucleoside triphosphate (dNTP/rNTP) ratios, by the during DNA replication has become recognized as a significant ability of DNA polymerases to discriminate against ribonucleotides, source of genomic instability. Given that the physiological con- and by the capacity of repair mechanisms to remove incorporated centrations of ribonucleoside triphosphates (rNTPs), the building ribonucleotides. To simultaneously compare how the nuclear and blocks of RNA, are one to two orders-of-magnitude higher than mitochondrial genomes incorporate and remove ribonucleotides, those of dNTPs, rNMPs are frequently incorporated into DNA we challenged these processes by changing the balance of cellular during replication (15, 16).
  • Table S1. List of Oligonucleotide Primers Used

    Table S1. List of Oligonucleotide Primers Used

    Table S1. List of oligonucleotide primers used. Cla4 LF-5' GTAGGATCCGCTCTGTCAAGCCTCCGACC M629Arev CCTCCCTCCATGTACTCcgcGATGACCCAgAGCTCGTTG M629Afwd CAACGAGCTcTGGGTCATCgcgGAGTACATGGAGGGAGG LF-3' GTAGGCCATCTAGGCCGCAATCTCGTCAAGTAAAGTCG RF-5' GTAGGCCTGAGTGGCCCGAGATTGCAACGTGTAACC RF-3' GTAGGATCCCGTACGCTGCGATCGCTTGC Ukc1 LF-5' GCAATATTATGTCTACTTTGAGCG M398Arev CCGCCGGGCAAgAAtTCcgcGAGAAGGTACAGATACGc M398Afwd gCGTATCTGTACCTTCTCgcgGAaTTcTTGCCCGGCGG LF-3' GAGGCCATCTAGGCCATTTACGATGGCAGACAAAGG RF-5' GTGGCCTGAGTGGCCATTGGTTTGGGCGAATGGC RF-3' GCAATATTCGTACGTCAACAGCGCG Nrc2 LF-5' GCAATATTTCGAAAAGGGTCGTTCC M454Grev GCCACCCATGCAGTAcTCgccGCAGAGGTAGAGGTAATC M454Gfwd GATTACCTCTACCTCTGCggcGAgTACTGCATGGGTGGC LF-3' GAGGCCATCTAGGCCGACGAGTGAAGCTTTCGAGCG RF-5' GAGGCCTGAGTGGCCTAAGCATCTTGGCTTCTGC RF-3' GCAATATTCGGTCAACGCTTTTCAGATACC Ipl1 LF-5' GTCAATATTCTACTTTGTGAAGACGCTGC M629Arev GCTCCCCACGACCAGCgAATTCGATagcGAGGAAGACTCGGCCCTCATC M629Afwd GATGAGGGCCGAGTCTTCCTCgctATCGAATTcGCTGGTCGTGGGGAGC LF-3' TGAGGCCATCTAGGCCGGTGCCTTAGATTCCGTATAGC RF-5' CATGGCCTGAGTGGCCGATTCTTCTTCTGTCATCGAC RF-3' GACAATATTGCTGACCTTGTCTACTTGG Ire1 LF-5' GCAATATTAAAGCACAACTCAACGC D1014Arev CCGTAGCCAAGCACCTCGgCCGAtATcGTGAGCGAAG D1014Afwd CTTCGCTCACgATaTCGGcCGAGGTGCTTGGCTACGG LF-3' GAGGCCATCTAGGCCAACTGGGCAAAGGAGATGGA RF-5' GAGGCCTGAGTGGCCGTGCGCCTGTGTATCTCTTTG RF-3' GCAATATTGGCCATCTGAGGGCTGAC Kin28 LF-5' GACAATATTCATCTTTCACCCTTCCAAAG L94Arev TGATGAGTGCTTCTAGATTGGTGTCggcGAAcTCgAGCACCAGGTTG L94Afwd CAACCTGGTGCTcGAgTTCgccGACACCAATCTAGAAGCACTCATCA LF-3' TGAGGCCATCTAGGCCCACAGAGATCCGCTTTAATGC RF-5' CATGGCCTGAGTGGCCAGGGCTAGTACGACCTCG
  • Evaluation of the Chitin-Binding Dye Congo Red As a Selection Agent for the Isolation, Classification, and Enumeration of Ascomycete Yeasts

    Evaluation of the Chitin-Binding Dye Congo Red As a Selection Agent for the Isolation, Classification, and Enumeration of Ascomycete Yeasts

    Archives of Microbiology (2018) 200:671–675 https://doi.org/10.1007/s00203-018-1498-y SHORT COMMUNICATION Evaluation of the chitin-binding dye Congo red as a selection agent for the isolation, classification, and enumeration of ascomycete yeasts Tomas Linder1 Received: 3 February 2018 / Revised: 19 February 2018 / Accepted: 21 February 2018 / Published online: 23 February 2018 © The Author(s) 2018. This article is an open access publication Abstract Thirty-nine strains of ascomycete yeasts representing 35 species and 33 genera were tested for their ability to grow on solid agar medium containing increasing concentrations of the chitin-binding dye Congo red. Six strains were classified as hyper- sensitive (weak or no growth at 10 mg/l Congo red), five were moderately sensitive (weak or no growth at 50 mg/l), three were moderately tolerant (weak or no growth at 100 mg/l), while the remaining 25 strains were classified as resistant (robust growth at ≥ 100 mg/l) with 20 of these strains classified as hyper-resistant (robust growth at 200 mg/l). Congo red growth phenotypes were consistent within some families but not others. The frequency of Congo red resistance among ascomycete yeasts was deemed too high for the practical use of Congo red as a selection agent for targeted isolation, but can be useful for identification and enumeration of yeasts. Keywords Antifungal · Cell wall · Phenotype · Yeast Introduction groups of yeasts. For example, chemically defined growth medium containing methanol as the sole carbon source is The development of genome sequencing over the past four commonly used to isolate species of methylotrophic yeasts decades has revolutionized yeast taxonomy and now enables (van Dijken and Harder 1974).
  • Comparative Genomics of Biotechnologically Important Yeasts Supplementary Appendix

    Comparative Genomics of Biotechnologically Important Yeasts Supplementary Appendix

    Comparative genomics of biotechnologically important yeasts Supplementary Appendix Contents Note 1 – Summary of literature on ascomycete yeasts used in this study ............................... 3 CUG-Ser yeasts ................................................................................................................................................................ 3 Other Saccharomycotina ............................................................................................................................................. 5 Taphrinomycotina ....................................................................................................................................................... 10 Note 2 – Genomes overview .................................................................................................11 Yeast culturing, identification, DNA and total RNA extraction ................................................................. 12 Genome sequencing and assembly ....................................................................................................................... 12 Transcriptome sequencing and assembly ......................................................................................................... 13 Table S1. Genome statistics ..................................................................................................................................... 14 Table S2. Annotation statistics ..............................................................................................................................
  • A Curated Ortholog Database for Yeasts and Fungi Spanning 600 Million Years of Evolution

    A Curated Ortholog Database for Yeasts and Fungi Spanning 600 Million Years of Evolution

    bioRxiv preprint doi: https://doi.org/10.1101/237974; this version posted October 8, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution Kevin Correia1, Shi M. Yu1, and Radhakrishnan Mahadevan1,2,* 1Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada, ON 2Institute of Biomaterials and Biomedical Engineering, University of Toronto, Ontario, Canada Corresponding author: Radhakrishnan Mahadevan∗ Email address: [email protected] ABSTRACT Budding yeasts inhabit a range of environments by exploiting various metabolic traits. The genetic bases for these traits are mostly unknown, preventing their addition or removal in a chassis organism for metabolic engineering. To help understand the molecular evolution of these traits in yeasts, we created Analyzing Yeasts by Reconstructing Ancestry of Homologs (AYbRAH), an open-source database of predicted and manually curated ortholog groups for 33 diverse fungi and yeasts in Dikarya, spanning 600 million years of evolution. OrthoMCL and OrthoDB were used to cluster protein sequence into ortholog and homolog groups, respectively; MAFFT and PhyML were used to reconstruct the phylogeny of all homolog groups. Ortholog assignments for enzymes and small metabolite transporters were compared to their phylogenetic reconstruction, and curated to resolve any discrepancies. Information on homolog and ortholog groups can be viewed in the AYbRAH web portal (https://kcorreia.github. io/aybrah/) to review ortholog groups, predictions for mitochondrial localization and transmembrane domains, literature references, and phylogenetic reconstructions.
  • Myconet Volume 14 Part One. Outine of Ascomycota – 2009 Part Two

    Myconet Volume 14 Part One. Outine of Ascomycota – 2009 Part Two

    (topsheet) Myconet Volume 14 Part One. Outine of Ascomycota – 2009 Part Two. Notes on ascomycete systematics. Nos. 4751 – 5113. Fieldiana, Botany H. Thorsten Lumbsch Dept. of Botany Field Museum 1400 S. Lake Shore Dr. Chicago, IL 60605 (312) 665-7881 fax: 312-665-7158 e-mail: [email protected] Sabine M. Huhndorf Dept. of Botany Field Museum 1400 S. Lake Shore Dr. Chicago, IL 60605 (312) 665-7855 fax: 312-665-7158 e-mail: [email protected] 1 (cover page) FIELDIANA Botany NEW SERIES NO 00 Myconet Volume 14 Part One. Outine of Ascomycota – 2009 Part Two. Notes on ascomycete systematics. Nos. 4751 – 5113 H. Thorsten Lumbsch Sabine M. Huhndorf [Date] Publication 0000 PUBLISHED BY THE FIELD MUSEUM OF NATURAL HISTORY 2 Table of Contents Abstract Part One. Outline of Ascomycota - 2009 Introduction Literature Cited Index to Ascomycota Subphylum Taphrinomycotina Class Neolectomycetes Class Pneumocystidomycetes Class Schizosaccharomycetes Class Taphrinomycetes Subphylum Saccharomycotina Class Saccharomycetes Subphylum Pezizomycotina Class Arthoniomycetes Class Dothideomycetes Subclass Dothideomycetidae Subclass Pleosporomycetidae Dothideomycetes incertae sedis: orders, families, genera Class Eurotiomycetes Subclass Chaetothyriomycetidae Subclass Eurotiomycetidae Subclass Mycocaliciomycetidae Class Geoglossomycetes Class Laboulbeniomycetes Class Lecanoromycetes Subclass Acarosporomycetidae Subclass Lecanoromycetidae Subclass Ostropomycetidae 3 Lecanoromycetes incertae sedis: orders, genera Class Leotiomycetes Leotiomycetes incertae sedis: families, genera Class Lichinomycetes Class Orbiliomycetes Class Pezizomycetes Class Sordariomycetes Subclass Hypocreomycetidae Subclass Sordariomycetidae Subclass Xylariomycetidae Sordariomycetes incertae sedis: orders, families, genera Pezizomycotina incertae sedis: orders, families Part Two. Notes on ascomycete systematics. Nos. 4751 – 5113 Introduction Literature Cited 4 Abstract Part One presents the current classification that includes all accepted genera and higher taxa above the generic level in the phylum Ascomycota.
  • Mitochondrial Uncoupling and the Reprograming of Intermediary Metabolism in Leukemia Cells

    Mitochondrial Uncoupling and the Reprograming of Intermediary Metabolism in Leukemia Cells

    REVIEW ARTICLE published: 02 April 2013 doi: 10.3389/fonc.2013.00067 Mitochondrial uncoupling and the reprograming of intermediary metabolism in leukemia cells Juliana Vélez 1, Numsen Hail Jr.2,3, Marina Konopleva2,3, Zhihong Zeng 2,3, Kensuke Kojima2,3, Ismael Samudio1* and Michael Andreeff 2,3* 1 Grupo de Terapia Celular y Molecular Laboratorio de Bioquimica, Pontificia Universidad Javeriana, Bogotá, Colombia 2 Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 3 Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA Edited by: Nearly 60 years ago Otto Warburg proposed, in a seminal publication, that an irreparable Jozsef Dudas, Medical University defect in the oxidative capacity of normal cells supported the switch to glycolysis for energy Innsbru, Austria generation and the appearance of the malignant phenotype (Warburg, 1956). Curiously, Reviewed by: Daniel Christian Hoessli, International this phenotype was also observed by Warburg in embryonic tissues, and recent research Center for Chemical and Biological demonstrated that normal stem cells may indeed rely on aerobic glycolysis – fermenting Sciences, Switzerland pyruvate to lactate in the presence of ample oxygen – rather than on the complete oxidation Jozsef Dudas, Medical University of pyruvate in the Krebs cycle – to generate cellular energy (Folmes et al., 2012). However, Innsbruck, Austria it remains to be determined whether this phenotype is causative for neoplastic develop- *Correspondence: Ismael Samudio, Laboratorio de ment, or rather the result of malignant transformation. In addition, in light of mounting Bioquimica #301, Edificio Jesús evidence demonstrating that cancer cells can carry out electron transport and oxidative Emilio Ramírez, Pontificia Universidad phosphorylation, although in some cases predominantly using electrons from non-glucose Javeriana, Cra 7 No.
  • Genome-Wide Investigation of Cellular Functions for Trna Nucleus

    Genome-Wide Investigation of Cellular Functions for Trna Nucleus

    Genome-wide Investigation of Cellular Functions for tRNA Nucleus- Cytoplasm Trafficking in the Yeast Saccharomyces cerevisiae DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Hui-Yi Chu Graduate Program in Molecular, Cellular and Developmental Biology The Ohio State University 2012 Dissertation Committee: Anita K. Hopper, Advisor Stephen Osmani Kurt Fredrick Jane Jackman Copyright by Hui-Yi Chu 2012 Abstract In eukaryotic cells tRNAs are transcribed in the nucleus and exported to the cytoplasm for their essential role in protein synthesis. This export event was thought to be unidirectional. Surprisingly, several lines of evidence showed that mature cytoplasmic tRNAs shuttle between nucleus and cytoplasm and their distribution is nutrient-dependent. This newly discovered tRNA retrograde process is conserved from yeast to vertebrates. Although how exactly the tRNA nuclear-cytoplasmic trafficking is regulated is still under investigation, previous studies identified several transporters involved in tRNA subcellular dynamics. At least three members of the β-importin family function in tRNA nuclear-cytoplasmic intracellular movement: (1) Los1 functions in both the tRNA primary export and re-export processes; (2) Mtr10, directly or indirectly, is responsible for the constitutive retrograde import of cytoplasmic tRNA to the nucleus; (3) Msn5 functions solely in the re-export process. In this thesis I focus on the physiological role(s) of the tRNA nuclear retrograde pathway. One possibility is that nuclear accumulation of cytoplasmic tRNA serves to modulate translation of particular transcripts. To test this hypothesis, I compared expression profiles from non-translating mRNAs and polyribosome-bound translating mRNAs collected from msn5Δ and mtr10Δ mutants and wild-type cells, in fed or acute amino acid starvation conditions.
  • Table S3 Abbreviations Variable Name in Program Definition Or Full

    Table S3 Abbreviations Variable Name in Program Definition Or Full

    Table S3 Abbreviations Variable name in program definition or full name tot_Glc_B total input glucose t_delay_Glc_B time delay of glucose release tot_TG_B total input TG t_delay_TG_B time dealy of TG release k_inssyn_B insulin base rate constant Vmax_inssyn_Glc_B insulin synthesis rate constant for plasma glucose Km_inssyn_Glc_B Michaelis constant for insulin synthesis n_inssyn_Glc_B Hill coefficient for insulin synthesis k_inssyn_FFA_B insulin synthesis rate constant for plasma FFA k_insdeg_Ins_B insulin degradation rate constant k_choluse_Chol_B cholesterol utilization rate constant in blood alpha_base_L insulin base factor in liver alpha_band_L insulin allowable width in liver Km_Ins_B_L Michaelis constant for insulin in liver n_Ins_B_L Hill coefficient for insulin in liver Vdif_glut2_Glc_B_L rate constant of glucose transporter type 2 in liver Kdif_glut2_Glc_B_L dissociation constant of glucose transporter type 2 for Glc_B in liver Kdif_glut2_Glc_L dissociation constant of glucose transporter type 2 in liver Vmax_hk_Glc_L reaction rate constant of hexiokinase for Glc in liver Km_hk_Glc_L Michaelis constant of hexiokinase for Glc in liver Ki_hk_G6p_L inhibition constant of hexiokinase for Glc in liver Km_hk_Atp_L Michaelis constant of hexiokinase for Atp in liver Ki_hk_Atp_L inhibition constant of hexiokinase for Atp in liver Vmax_ppp_G6p_L reaction rate constant of pentose phosphate pathway for G6p in liver Km_ppp_G6p_L Michaelis constant of pentose phosphate pathway for G6p in liver Km_ppp_Nadp_L Michaelis constant of pentose phosphate
  • Downloaded from by Lawrence Berkeley National Laboratory User on 13 May 2019

    Downloaded from by Lawrence Berkeley National Laboratory User on 13 May 2019

    Lawrence Berkeley National Laboratory Recent Work Title Physiological and comparative genomic analysis of new isolated yeasts Spathaspora sp. JA1 and Meyerozyma caribbica JA9 reveal insights into xylitol production. Permalink https://escholarship.org/uc/item/1r9258f1 Journal FEMS yeast research, 19(4) ISSN 1567-1356 Authors Trichez, Débora Steindorff, Andrei S Soares, Carlos EVF et al. Publication Date 2019-06-01 DOI 10.1093/femsyr/foz034 Peer reviewed eScholarship.org Powered by the California Digital Library University of California FEMS Yeast Research, 19, 2019, foz034 doi: 10.1093/femsyr/foz034 Advance Access Publication Date: 26 April 2019 Research Article Downloaded from https://academic.oup.com/femsyr/article-abstract/19/4/foz034/5480466 by Lawrence Berkeley National Laboratory user on 13 May 2019 RESEARCH ARTICLE Physiological and comparative genomic analysis of new isolated yeasts Spathaspora sp. JA1 and Meyerozyma caribbica JA9 reveal insights into xylitol production Debora´ Trichez1,AndreiS.Steindorff1,†,CarlosE.V.F.Soares1,2, Eduardo F. Formighieri 1 and Joao˜ R. M. Almeida1,2,* 1Embrapa Agroenergia. Parque Estac¸ao˜ Biologica,´ PqEB – W3 Norte Final, Postal code 70.770–901, Bras´ılia-DF, Brazil and 2Graduate Program in Chemical and Biological Technologies, Institute of Chemistry, University of Bras´ılia, Campus Darcy Ribeiro, Postal code 70.910-900, Bras´ılia-DF, Brazil ∗Corresponding author: Embrapa Agroenergia, Parque Estac¸ao˜ Biologica,´ PqEB – W3 Norte Final - s/n◦, 70.770-901 - Bras´ılia, DF – Brasil. Tel: +55 61 3448-2337; E-mail: [email protected] †Present address: U.S. Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, US.