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WO 2018/009838 Al 11 January 2018 (11.01.2018) W !P O PCT
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2018/009838 Al 11 January 2018 (11.01.2018) W !P O PCT (51) International Patent Classification: Declarations under Rule 4.17: C12N 5/075 (2010.01) — as to applicant's entitlement to apply for and be granted a (21) International Application Number: patent (Rule 4.1 7(H)) PCT/US2017/041 155 — as to the applicant's entitlement to claim the priority of the earlier application (Rule 4.17(Hi)) (22) International Filing Date: 07 July 2017 (07.07.2017) Published: — with international search report (Art. 21(3)) (25) Filing Language: English — before the expiration of the time limit for amending the (26) Publication Langi English claims and to be republished in the event of receipt of amendments (Rule 48.2(h)) (30) Priority Data: — with sequence listing part of description (Rule 5.2(a)) 62/359,416 07 July 2016 (07.07.2016) US (71) Applicant: RUBIUS THERAPEUTICS, INC. [US/US]; 620 Memorial Dr #100W, Cambridge, MA 02139 (US). (72) Inventors; and (71) Applicants: HARANDI, Omid [US/US]; 39 Rowena Road, Newton, MA 02459 (US). KHANWALKAR, Ur- jeet [IN/US]; 2 11 Elm Street, Apt. 3, Cambridge, MA 02139 (US). HARIHARAN, Sneha [IN/US]; 18 Hamilton Road, Apt. 407, Arlington, MA 02472 (US). (72) Inventors: KAHVEJIAN, Avak; 2 Beverly Road, Arling ton, MA 02474 (US). MATA-FINK, Jordi; 8 Windsor Rd #1, Somerville, MA 02144 (US).DEANS, Robert, J.; 1609 Ramsgate Court, Riverside, CA 92506 (US). -
Redalyc.Microorganisms Screening for Limonene Oxidation
Ciência e Tecnologia de Alimentos ISSN: 0101-2061 [email protected] Sociedade Brasileira de Ciência e Tecnologia de Alimentos Brasil LERIN, Lindomar; TONIAZZO, Geciane; de OLIVEIRA, Débora; ROTTAVA, Leda; DARIVA, Cláudio; CANSIAN, Rogério Luis; TREICHEL, Helen; PADILHA, Francine; Ceva ANTUNES, Octávio Augusto Microorganisms screening for limonene oxidation Ciência e Tecnologia de Alimentos, vol. 30, núm. 2, abril-junio, 2010, pp. 399-405 Sociedade Brasileira de Ciência e Tecnologia de Alimentos Campinas, Brasil Available in: http://www.redalyc.org/articulo.oa?id=395940100017 How to cite Complete issue Scientific Information System More information about this article Network of Scientific Journals from Latin America, the Caribbean, Spain and Portugal Journal's homepage in redalyc.org Non-profit academic project, developed under the open access initiative Ciência e Tecnologia de Alimentos ISSN 0101-2061 Microorganisms screening for limonene oxidation Seleção de microrganismos para oxidação de limoneno Original Lindomar LERIN1, Geciane TONIAZZO2, Débora de OLIVEIRA2*, Leda ROTTAVA1, Cláudio DARIVA3, Rogério Luis CANSIAN2, Helen TREICHEL2, Francine PADILHA3, Octávio Augusto Ceva ANTUNES1 Abstract Limonene is a monoterpene obtained in large amounts from essential oils and is used as a raw material for the synthesis of flavors and fine chemicals. Several pathways or routes for the microbial degradation of limonene making use of the cytochrome P450-dependent monooxygenases have been described. In this study, we present a fermentative screening of microorganisms in order to verify their ability to perform the desirable conversion. In parallel, the PCR technique was used to select the microorganisms that contain the limC gene, which is responsible for the conversion of carveol to carvone. -
Itraq-Based Quantitative Proteomics Analysis Reveals the Mechanism Underlying the Weakening of Carbon Metabolism in Chlorotic Tea Leaves
Article iTRAQ-Based Quantitative Proteomics Analysis Reveals the Mechanism Underlying the Weakening of Carbon Metabolism in Chlorotic Tea Leaves Fang Dong 1,2, Yuanzhi Shi 1,2, Meiya Liu 1,2, Kai Fan 1,2, Qunfeng Zhang 1,2,* and Jianyun Ruan 1,2 1 Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; [email protected] (F.D.); [email protected] (Y.S.); [email protected] (M.L.); [email protected] (K.F.); [email protected] (J.R.) 2 Key Laboratory for Plant Biology and Resource Application of Tea, the Ministry of Agriculture, Hangzhou 310008, China * Correspondence: [email protected]; Tel.: +86-571-8527-0665 Received: 7 November 2018; Accepted: 5 December 2018; Published: 7 December 2018 Abstract: To uncover mechanism of highly weakened carbon metabolism in chlorotic tea (Camellia sinensis) plants, iTRAQ (isobaric tags for relative and absolute quantification)-based proteomic analyses were employed to study the differences in protein expression profiles in chlorophyll-deficient and normal green leaves in the tea plant cultivar “Huangjinya”. A total of 2110 proteins were identified in “Huangjinya”, and 173 proteins showed differential accumulations between the chlorotic and normal green leaves. Of these, 19 proteins were correlated with RNA expression levels, based on integrated analyses of the transcriptome and proteome. Moreover, the results of our analysis of differentially expressed proteins suggested that primary carbon metabolism (i.e., carbohydrate synthesis and transport) was inhibited in chlorotic tea leaves. The differentially expressed genes and proteins combined with photosynthetic phenotypic data indicated that 4-coumarate-CoA ligase (4CL) showed a major effect on repressing flavonoid metabolism, and abnormal developmental chloroplast inhibited the accumulation of chlorophyll and flavonoids because few carbon skeletons were provided as a result of a weakened primary carbon metabolism. -
The Role of Protein Crystallography in Defining the Mechanisms of Biogenesis and Catalysis in Copper Amine Oxidase
Int. J. Mol. Sci. 2012, 13, 5375-5405; doi:10.3390/ijms13055375 OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 www.mdpi.com/journal/ijms Review The Role of Protein Crystallography in Defining the Mechanisms of Biogenesis and Catalysis in Copper Amine Oxidase Valerie J. Klema and Carrie M. Wilmot * Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-612-624-2406; Fax: +1-612-624-5121. Received: 6 April 2012; in revised form: 22 April 2012 / Accepted: 26 April 2012 / Published: 3 May 2012 Abstract: Copper amine oxidases (CAOs) are a ubiquitous group of enzymes that catalyze the conversion of primary amines to aldehydes coupled to the reduction of O2 to H2O2. These enzymes utilize a wide range of substrates from methylamine to polypeptides. Changes in CAO activity are correlated with a variety of human diseases, including diabetes mellitus, Alzheimer’s disease, and inflammatory disorders. CAOs contain a cofactor, 2,4,5-trihydroxyphenylalanine quinone (TPQ), that is required for catalytic activity and synthesized through the post-translational modification of a tyrosine residue within the CAO polypeptide. TPQ generation is a self-processing event only requiring the addition of oxygen and Cu(II) to the apoCAO. Thus, the CAO active site supports two very different reactions: TPQ synthesis, and the two electron oxidation of primary amines. Crystal structures are available from bacterial through to human sources, and have given insight into substrate preference, stereospecificity, and structural changes during biogenesis and catalysis. -
Rhodococcus Jostii Strain 8
Functional characterisation of alkane-degrading monooxygenases in Rhodococcus jostii strain 8 Jindarat Ekprasert A thesis submitted to the School of Environmental Sciences in fulfilment of the requirements for the degree of Doctor of Philosophy September 2014 University of East Anglia Norwich, UK i Contents List of figures viii List of tables xiii Declaration xv Acknowledgements xvi Abbreviations xvii Abstract xxi Chapter 1 introduction 1 1.1. Significance of alkanes in the environment 2 1.1.1. Chemistry of alkanes 2 1.2. The Rhodococcus genus 3 1.2.1. Common characteristics of Rhodococcus spp. 3 1.2.2. Rhodococcus spp. are capable of degrading gaseous alkanes 4 1.2.3. Potential applications of Rhodococcus in biotechnology 5 1.3. Bacterial enzymes responsible for alkane degradation 6 1.3.1. Integral membrane, non-heme iron alkane hydroxylases (AlkB) 6 1.3.2. Soluble di-iron monooxygenases (SDIMO) 8 1.3.2.1. SDIMO classification 10 1.3.2.2. Molecular genetics of SDIMOs 13 1.3.2.3. Mutagenesis of soluble methane monooxygenase 13 1.3.3. Cytochrome P450 alkane hydroxylases 14 3.3.1. Class I P450 14 3.3.2. Class II P450 (CYP52) 15 3.3.3. Class II P450 (CYP2E, CYP4B) 15 1.3.4. Membrane bound copper-containing (and possibly iron-containing) monooxygenases 15 1.4. Alkane metabolisms in Rhodococcus spp. 16 1.4.1. Aerobic metabolism of C2-C4 gaseous alkanes in bacteria 16 1.4.1.1. Ethane (C2H6) metabolism 16 1.4.1.2. Propane (C3H8) metabolism 17 ii 1.4.1.3. -
Adaptive Laboratory Evolution Enhances Methanol Tolerance and Conversion in Engineered Corynebacterium Glutamicum
ARTICLE https://doi.org/10.1038/s42003-020-0954-9 OPEN Adaptive laboratory evolution enhances methanol tolerance and conversion in engineered Corynebacterium glutamicum Yu Wang 1, Liwen Fan1,2, Philibert Tuyishime1, Jiao Liu1, Kun Zhang1,3, Ning Gao1,3, Zhihui Zhang1,3, ✉ ✉ 1234567890():,; Xiaomeng Ni1, Jinhui Feng1, Qianqian Yuan1, Hongwu Ma1, Ping Zheng1,2,3 , Jibin Sun1,3 & Yanhe Ma1 Synthetic methylotrophy has recently been intensively studied to achieve methanol-based biomanufacturing of fuels and chemicals. However, attempts to engineer platform micro- organisms to utilize methanol mainly focus on enzyme and pathway engineering. Herein, we enhanced methanol bioconversion of synthetic methylotrophs by improving cellular tolerance to methanol. A previously engineered methanol-dependent Corynebacterium glutamicum is subjected to adaptive laboratory evolution with elevated methanol content. Unexpectedly, the evolved strain not only tolerates higher concentrations of methanol but also shows improved growth and methanol utilization. Transcriptome analysis suggests increased methanol con- centrations rebalance methylotrophic metabolism by down-regulating glycolysis and up- regulating amino acid biosynthesis, oxidative phosphorylation, ribosome biosynthesis, and parts of TCA cycle. Mutations in the O-acetyl-L-homoserine sulfhydrylase Cgl0653 catalyzing formation of L-methionine analog from methanol and methanol-induced membrane-bound transporter Cgl0833 are proven crucial for methanol tolerance. This study demonstrates the importance of -
Induktion, Regulation Und Latenz Von
Organisation and transcriptional regulation of the polyphenol oxidase (PPO) multigene family of the moss Physcomitrella patens (Hedw.) B.S.G. and functional gene knockout of PpPPO1 Dissertation zur Erlangung des Doktorgrades - Dr. rer. nat. - im Department Biologie der Fakultät Mathematik, Informatik und Naturwissenschaften an der Universität Hamburg von Hanna Richter Hamburg, Januar 2009 TABLE OF CONTENTS TABLE OF CONTENTS SUMMARY...................................................................................................................5 ZUSAMMENFASSUNG...............................................................................................6 1. INTRODUCTION ................................................................................................. 8 1.1. Polyphenol oxidases ................................................................................................................ 8 1.2. Phenolic compounds ............................................................................................................. 14 1.3. The model plant Physcomitrella patens ............................................................................... 15 1.4. Aim of this research ............................................................................................................... 19 2. MATERIALS AND METHODS .......................................................................... 20 2.1. Chemicals ............................................................................................................................... -
Structure of Pigment Metabolic Pathways and Their Contributions to White Tepal Color Formation of Chinese Narcissus Tazetta Var
International Journal of Molecular Sciences Article Structure of Pigment Metabolic Pathways and Their Contributions to White Tepal Color Formation of Chinese Narcissus tazetta var. chinensis cv Jinzhanyintai Yujun Ren † ID , Jingwen Yang †, Bingguo Lu, Yaping Jiang, Haiyang Chen, Yuwei Hong, Binghua Wu and Ying Miao * Center for Molecular Cell and Systems Biology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; [email protected] (Y.R.); [email protected] (J.Y.); [email protected] (B.L.); [email protected] (Y.J.); [email protected] (H.C.); [email protected] (Y.H.); [email protected] (B.W.) * Correspondence: [email protected]; Tel.:/Fax: +86-591-8639-2987 † These authors contributed equally to this work. Received: 7 August 2017; Accepted: 4 September 2017; Published: 8 September 2017 Abstract: Chinese narcissus (Narcissus tazetta var. chinensis) is one of the ten traditional flowers in China and a famous bulb flower in the world flower market. However, only white color tepals are formed in mature flowers of the cultivated varieties, which constrains their applicable occasions. Unfortunately, for lack of genome information of narcissus species, the explanation of tepal color formation of Chinese narcissus is still not clear. Concerning no genome information, the application of transcriptome profile to dissect biological phenomena in plants was reported to be effective. As known, pigments are metabolites of related metabolic pathways, which dominantly decide flower color. In this study, transcriptome profile and pigment metabolite analysis methods were used in the most widely cultivated Chinese narcissus “Jinzhanyintai” to discover the structure of pigment metabolic pathways and their contributions to white tepal color formation during flower development and pigmentation processes. -
Flavonoid Glucodiversification with Engineered Sucrose-Active Enzymes Yannick Malbert
Flavonoid glucodiversification with engineered sucrose-active enzymes Yannick Malbert To cite this version: Yannick Malbert. Flavonoid glucodiversification with engineered sucrose-active enzymes. Biotechnol- ogy. INSA de Toulouse, 2014. English. NNT : 2014ISAT0038. tel-01219406 HAL Id: tel-01219406 https://tel.archives-ouvertes.fr/tel-01219406 Submitted on 22 Oct 2015 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Last name: MALBERT First name: Yannick Title: Flavonoid glucodiversification with engineered sucrose-active enzymes Speciality: Ecological, Veterinary, Agronomic Sciences and Bioengineering, Field: Enzymatic and microbial engineering. Year: 2014 Number of pages: 257 Flavonoid glycosides are natural plant secondary metabolites exhibiting many physicochemical and biological properties. Glycosylation usually improves flavonoid solubility but access to flavonoid glycosides is limited by their low production levels in plants. In this thesis work, the focus was placed on the development of new glucodiversification routes of natural flavonoids by taking advantage of protein engineering. Two biochemically and structurally characterized recombinant transglucosylases, the amylosucrase from Neisseria polysaccharea and the α-(1→2) branching sucrase, a truncated form of the dextransucrase from L. Mesenteroides NRRL B-1299, were selected to attempt glucosylation of different flavonoids, synthesize new α-glucoside derivatives with original patterns of glucosylation and hopefully improved their water-solubility. -
Biosynthesis of New Alpha-Bisabolol Derivatives Through a Synthetic Biology Approach Arthur Sarrade-Loucheur
Biosynthesis of new alpha-bisabolol derivatives through a synthetic biology approach Arthur Sarrade-Loucheur To cite this version: Arthur Sarrade-Loucheur. Biosynthesis of new alpha-bisabolol derivatives through a synthetic biology approach. Biochemistry, Molecular Biology. INSA de Toulouse, 2020. English. NNT : 2020ISAT0003. tel-02976811 HAL Id: tel-02976811 https://tel.archives-ouvertes.fr/tel-02976811 Submitted on 23 Oct 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE En vue de l’obtention du DOCTORAT DE L’UNIVERSITÉ DE TOULOUSE Délivré par l'Institut National des Sciences Appliquées de Toulouse Présentée et soutenue par Arthur SARRADE-LOUCHEUR Le 30 juin 2020 Biosynthèse de nouveaux dérivés de l'α-bisabolol par une approche de biologie synthèse Ecole doctorale : SEVAB - Sciences Ecologiques, Vétérinaires, Agronomiques et Bioingenieries Spécialité : Ingénieries microbienne et enzymatique Unité de recherche : TBI - Toulouse Biotechnology Institute, Bio & Chemical Engineering Thèse dirigée par Gilles TRUAN et Magali REMAUD-SIMEON Jury -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Supplementary Information
Supplementary Information Table S1. Pathway analysis of the 1246 dwf1-specific differentially expressed genes. Fold Change Fold Change Fold Change Gene ID Description (dwf1/WT) (XL-5/WT) (XL-6/WT) Carbohydrate Metabolism Glycolysis/Gluconeogenesis POPTR_0008s11770.1 Glucose-6-phosphate isomerase −1.7382 0.512146 0.168727 POPTR_0001s47210.1 Fructose-bisphosphate aldolase, class I 1.599591 0.044778 0.18237 POPTR_0011s05190.3 Probable phosphoglycerate mutase −2.11069 −0.34562 −0.9738 POPTR_0012s01140.1 Pyruvate kinase −1.25054 0.074697 −0.16016 POPTR_0016s12760.1 Pyruvate decarboxylase 2.664081 0.021062 0.371969 POPTR_0012s08010.1 Aldehyde dehydrogenase (NAD+) −1.41556 0.479957 −0.21366 POPTR_0014s13710.1 Acetyl-CoA synthetase −1.337 0.154552 −0.26532 POPTR_0017s11660.1 Aldose 1-epimerase 2.770518 0.016874 0.73016 POPTR_0010s11970.1 Phosphoglucomutase −1.25266 −0.35581 0.074064 POPTR_0012s14030.1 Phosphoglucomutase −1.15872 −0.68468 −0.93596 POPTR_0002s10850.1 Phosphoenolpyruvate carboxykinase (ATP) 1.489119 0.967284 0.821559 Citrate cycle (TCA cycle) 2-Oxoglutarate dehydrogenase E2 component POPTR_0014s15280.1 −1.63733 0.076435 0.170827 (dihydrolipoamide succinyltransferase) POPTR_0002s26120.1 Succinyl-CoA synthetase β subunit −1.29244 −0.38517 −0.3497 POPTR_0007s12750.1 Succinate dehydrogenase (ubiquinone) flavoprotein subunit −1.83751 0.519356 0.309149 POPTR_0002s10850.1 Phosphoenolpyruvate carboxykinase (ATP) 1.489119 0.967284 0.821559 Pentose phosphate pathway POPTR_0008s11770.1 Glucose-6-phosphate isomerase −1.7382 0.512146 0.168727 POPTR_0013s00660.1 Glucose-6-phosphate 1-dehydrogenase −1.26949 −0.18314 0.374822 POPTR_0015s00960.1 6-Phosphogluconolactonase 2.022223 0.168877 0.971431 POPTR_0010s11970.1 Phosphoglucomutase −1.25266 −0.35581 0.074064 POPTR_0012s14030.1 Phosphoglucomutase −1.15872 −0.68468 −0.93596 POPTR_0001s47210.1 Fructose-bisphosphate aldolase, class I 1.599591 0.044778 0.18237 S2 Table S1.