DOCSLIB.ORG

(12) United States Patent (10) Patent No.: US 9,045,789 B2 Nishi0 Et Al

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
(12) United States Patent (10) Patent No.: US 9,045,789 B2 Nishi0 Et Al US009045789B2 (12) United States Patent (10) Patent No.: US 9,045,789 B2 Nishi0 et al. (45) Date of Patent: Jun. 2, 2015 (54) METHOD FOR PRODUCING ATARGET CI2Y 102/01026 (2013.01); C12Y-301/01068 SUBSTANCE BY FERMENTATION (2013.01); C12Y402/01082 (2013.01); CI2P 7/58 (2013.01); C12P 13/001 (2013.01); (71) Applicant: AJINOMOTO CO., INC., Tokyo (JP) (Continued) (72) Inventors: Yousuke Nishio, Kanagawa (JP); Youko (58) Field of Classification Search Yamamoto, Kanagawa (JP); Kazuteru None Yamada, Kanagawa (JP); Kosuke See application file for complete search history. Yokota, Kanagawa (JP) (56) References Cited (73) Assignee: AJINOMOTO CO., INC., Tokyo (JP) U.S. PATENT DOCUMENTS (*) Notice: Subject to any disclaimer, the term of this 5,977,331 A 11/1999 Asakura et al. patent is extended or adjusted under 35 6,197.559 B1 3/2001 Moriya et al. U.S.C. 154(b) by 0 days. (Continued) (21) Appl. No.: 13/914,872 FOREIGN PATENT DOCUMENTS (22) Filed: Jun. 11, 2013 EP 1577396 9, 2005 JP 2005-261433 9, 2005 (65) Prior Publication Data OTHER PUBLICATIONS US 2013/O295621 A1 Nov. 7, 2013 Weimberg, “Pentose oxidation by Pseudomonas fragi'. Journal of Related U.S. Application Data Biological Chemistry, vol. 236, No. 3, pp. 629-635, 1961.* (63) Continuation of application No. PCT/JP2012/078725, (Continued) filed on Nov. 6, 2012. (60) Provisional application No. 61/558,685, filed on Nov. Primary Examiner — Rebecca Prouty 11, 2011. Assistant Examiner — Richard Ekstrom (74) Attorney, Agent, or Firm — Shelly Guest Cermak; (30) Foreign Application Priority Data Cermak Nakajima & McGowan LLP Nov. 11, 2011 (JP) ................................. 2011-247031 (57) ABSTRACT A target Substance can be produced by culturing a bacterium (51) Int. C. having an ability to produce 2-ketoglutaric acidora derivative CI2PI3/4 (2006.01) thereof, and an ability to produce Xylonic acid from Xylose, CI2P 7/50 (2006.01) which is imparted with xylonate dehydratase activity, 2-keto (Continued) 3-deoxyXylonate dehydratase activity and 2-ketoglutaric semialdehyde dehydrogenase activity, or in which these (52) U.S. C. activities are enhanced, in a medium containing Xylose as a CPC, C12P 13/14 (2013.01); C12P 7/50 (2013.01); carbon Source to produce and accumulate the target Substance CI2N 15/52 (2013.01); C12N 9/0006 in the medium, and collecting the target Substance from the (2013.01); C12N 9/0008 (2013.01); C12N 9/16 medium. (2013.01); C12Y 103/05001 (2013.01); CI2N 9/88 (2013.01); CI2Y 101/01 113 (2013.01); 6 Claims, 4 Drawing Sheets (a) (b) Xylorate RSXylass) AH 30 Lu O.D. 600 "asucAMxy. A """ -o-MG1655alsucAvM119 -1sucAccrinXA513 -AdsucAMxylAlpMW119 s ... --alsucAMxylA2.pMW119 --alsucAasylA/ccrxNA2 --alsucAMylA/ccrxA4 s s s ac s : & W US 9,045,789 B2 Page 2 (51) Int. Cl. Hartman, A. L., et al., “The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon. PLoS ONE CI2N 15/52 (2006.01) 2010:5(3),e9605:1-20. CI2N 9/04 (2006.01) Hosoya, S., et al., “Identification and characterization of the Bacillus CI2N 9/02 (2006.01) subtilis D-glucarate?galactarate utilization operon yebCDEFGHJ.” CI2N 9/16 (2006.01) FEMS Microbiol. Lett. 2002:210:193-199. Johnsen, U., et al., “Novel Xylose Dehydrogenase in the Halophilic CI2N 9/88 (2006.01) Archaeon Haloarcula marismortui.’ J. Bacteriol. CI2P 7/58 (2006.01) 2004; 186(18):6198-6207. CI2PI3/00 (2006.01) Johnsen, U., et al., “D-Xylose Degradation Pathway in the Halophilic CI2PI3/04 (2006.01) Archaeon Haloferax volcanii.” J. Biol. Chem. 2009:284(40):27290 CI2PI3/10 (2006.01) 273O3. Kawaguchi, H., et al., “Engineering of a Xylose Metabolic Pathway CI2PI3/24 (2006.01) in Corynebacterium glutamicum.” Appl. Environmen. Microbiol. (52) U.S. Cl. 2006:72(5):3418-3428. CPC ................. CI2PI3/04 (2013.01): CI2P 13/10 Meijnen, J.-P. et al., “Establishment of Oxidative D-Xylose Metabo (2013.01); CI2P 13/24 (2013.01) lism in Pseudomonas putida S12.” Appl. Environmen. Microbiol. 2009;75(9):2784-2791. (56) References Cited Meisenzahl. A. C., et al., “Isolation and Characterization of a Xylose Dependent Promoter from Caulobacter crescentus.” J. Bacteriol. U.S. PATENT DOCUMENTS 1997; 179(3):592-600. Nichols, N. N., et al., “Use of catabolite repression mutants for 6,267,309 B1 7/2001 Chieffalo et al. fermentation of Sugar mixtures to ethanol. Appl. Microbiol. 6,331419 B1 12/2001 Moriya et al. Biotechnol. 2001:56:120-125. 6,682,912 B2 1/2004 Moriya et al. Nierman, W. C., et al., “Complete genome sequence of Caulobacter 6,962,805 B2 11/2005 Asakura et al. crescentus.” PNAS 2001:98(7):4136-4141. 7,037,690 B2 5, 2006 Hara et al. Nygård, Y, et al., “Bioconversion of D-xylose to D-xylonate with 7,090,998 B2 8/2006 Ishikawa et al. Kluyveromyces lactis.” Metabolic Engineering 2011:13:383-391. 7,205,132 B2 4/2007 Hirano et al. Sasaki, M., et al., “Engineering of pentose transport in 7,244,581 B2 * 7/2007 Sode ............................... 435/14 Corynebacterium glutamicum to improve simultaneous utilization of 7,344,874 B2 3/2008 Hara et al. mixed sugars.” Appl. Microbiol. Biotechnol. 2009:85:105-115. 7,695,946 B2 4/2010 USuda et al. Song, S., et al., “Organization and Regulation of the D-Xylose 7,696,315 B2 4/2010 USuda et al. Operons in Escherichia coli K-12: XylR Acts as a Transcriptional 7,785,845 B2 * 8/2010 Hara et al. .................... 435/110 Activator.” J. Bacteriol. 1997; 179(22):7025-7032. 7,785,858 B2 8, 2010 Kozlov et al. Stephens, C., et al., “Regulation of D-Xylose Metabolism in 7,794,989 B2 9/2010 Nakamura et al. Caulobacter crescentus by a Lacl-Type Repressor.” J. Bacteriol. 7,915,018 B2 3/2011 Rybak et al. 2007; 189(24):8828-8834. 7.923,226 B2 * 4/2011 Frost ............................. 435,158 Tao, H., et al., “Engineering a Homo-Ethanol Pathway in Escherichia 7,927,844 B2 4/2011 Nakamura et al. coli: Increased Glycolytic Flux and Levels of Expression of RE42,350 E 5, 2011 IZuiet al. Glycolytic Genes during Xylose Fermentation.” J. Bacteriol. 8,003,367 B2 8/2011 Marchenko et al. 2001; 183(10):2979-2988. 8,012,722 B2 9, 2011 Chinen et al. Toivari, M. H., et al., “Microbial D-xylonate production.” Appl. 8,058,035 B2 11/2011 Hara et al. Microbiol. Biotechnol. 2012.96:1-8. 8,129,151 B2 3/2012 Moriya et al. Toivari, M. H., et al., "Saccharomyces cerevisiae engineered to pro 8, 192,963 B2 6, 2012 Nishio et al. duce D-xylonate.” Appl. Microbiol. Biotechnol. 2010;88:751-760. 8,206,954 B2 6/2012 Takikawa et al. Watanabe, S., et al., “Enzyme Catalysis and Regulation: 8,222,007 B2 7, 2012 Hara et al. O-Ketoglutaric Semialdehyde Dehydrogenase Isozymes Involved in 8,278,074 B2 10/2012 Nakamura et al. Metabolic Pathways of D-Glucarate, D-Galactarate, and Hydroxy 2005/0214913 A1 9, 2005 Marchenko et al. L-proline: Molecular and Metabolic Convergent Evolution.” J. Biol. 2005/0233308 A1 10, 2005 Nishio et al. Chem. 2007:282:6685-6695. 2007,0004014 A1 1/2007 Tsuji et al. Thanbichler, M., et al., “A comprehensive set of plasmids for vanil 2009/0286290 A1* 11/2009 Hara et al. .................... 435/107 late- and xylose-inducible gene expression in Caulobacter 2010, O190217 A1 7, 2010 Doi et al. crescentus.” Nucl. Acids Res. 2007:35(20),e 137: 1-16. 2011/0076730 A1 3f2011 Frost et al. .................... 435/106 Aghaie, A., et al., “Metabolism and Bioenergetics: New Insights into 2012/0129233 A1 5/2012 Tajima et al. the Alternative d-Glucarate Degradation Pathway,” J. Biol. Chem. 2013/0217078 A1* 8/2013 Tang et al. ...................... 435/99 2008:283(23): 15638-15646. 2013/0260423 A1* 10, 2013 Knudsen et al. ................ 435/99 Watanabe, S., et al., “Enzyme Catalysis and Regulation: Identifica tion and Characterization of I-Arabonate Dehydratase, I-2-Keto-3- OTHER PUBLICATIONS deoxyarabonate Dehydratase, and I-Arabinolactonase Involved in an Alternative Pathway of I-Arabinose Metabolism: Novel Evolution Berghall, S., et al., “Identification in the mould Hypocreajecorina of ary Insight Into Sugar Metabolism.” J. Biol. Chem. a gene encoding an NADP+:D-xylose dehydrogenase.” FEMS 2006:281 (44):33521-33536. Microbiol. Lett., 2007:277:249-253. Gopinath, V., et al., “Amino acid production from rice Straw and Brouns, S. J. J., et al., “Identification of the Missing Links in wheat bran hydrolysates by recombinant pentose-utilizing Prokaryotic Pentose Oxidation Pathways: Evidence for Enzyme Corynebacterium glutamicum.” Appl. Microbiol. Biotechnol. Recruitment. J. Bio. Chem. 2006:281:27378-27388. 2011;92:985-996. Dahms, A. S., et al., “D-xylose Dehydrogenase.” Methods in Enzy Liu, H., et al., “High yield production of D-xylonic acid from mology 1982;89:226-228. D-xylose using engineered Escherichia coli,” Bioresource Technol. Ely, B., “Genetics of Caulobacter crescentus.” Methods in Enzymol 2012; 115:244-248. ogy 1991:204:372-384. Stephens, C., et al., “Genetic Analysis of a Novel Pathway for Fernandes, S., et al., “Xylose reductase from the thermophilic fungus D-Xylose Metabolism in Caulobacter crescentus.” J. Bacteriol. Talaromyces emersonii: cloning and heterologous expression of the 2007; 189(5): 218 1-2185. native gene (Texr) and a double mutant (TexrK271 R+N273DI) with International Search Report for PCT Patent App. No. PCT/JP2012/ altered coenzyme specificity.” J. Biosci. 2009:34(6):881-890. 078725 (Jan. 22, 2013). Gonzalez, R., et al., “Global Gene Expression Differences Associ International Preliminary Report on Patentability for PCT Patent ated with Changes in Glycolytic Flux and Growth Rate in App. No. PCT/JP2012/078725 (May 22, 2014). Escherichia coli during the Fermentation of Glucose and Xylose.” Biotechnol.
Load more

Recommended publications
  • Genome-Scale Fitness Profile of Caulobacter Crescentus Grown in Natural Freshwater
    Supplemental Material Genome-scale fitness profile of Caulobacter crescentus grown in natural freshwater Kristy L. Hentchel, Leila M. Reyes Ruiz, Aretha Fiebig, Patrick D. Curtis, Maureen L. Coleman, Sean Crosson Tn5 and Tn-Himar: comparing gene essentiality and the effects of gene disruption on fitness across studies A previous analysis of a highly saturated Caulobacter Tn5 transposon library revealed a set of genes that are required for growth in complex PYE medium [1]; approximately 14% of genes in the genome were deemed essential. The total genome insertion coverage was lower in the Himar library described here than in the Tn5 dataset of Christen et al (2011), as Tn-Himar inserts specifically into TA dinucleotide sites (with 67% GC content, TA sites are relatively limited in the Caulobacter genome). Genes for which we failed to detect Tn-Himar insertions (Table S13) were largely consistent with essential genes reported by Christen et al [1], with exceptions likely due to differential coverage of Tn5 versus Tn-Himar mutagenesis and differences in metrics used to define essentiality. A comparison of the essential genes defined by Christen et al and by our Tn5-seq and Tn-Himar fitness studies is presented in Table S4. We have uncovered evidence for gene disruptions that both enhanced or reduced strain fitness in lake water and M2X relative to PYE. Such results are consistent for a number of genes across both the Tn5 and Tn-Himar datasets. Disruption of genes encoding three metabolic enzymes, a class C β-lactamase family protein (CCNA_00255), transaldolase (CCNA_03729), and methylcrotonyl-CoA carboxylase (CCNA_02250), enhanced Caulobacter fitness in Lake Michigan water relative to PYE using both Tn5 and Tn-Himar approaches (Table S7).
    [Show full text]
  • Supplementary Informations SI2. Supplementary Table 1
    Supplementary Informations SI2. Supplementary Table 1. M9, soil, and rhizosphere media composition. LB in Compound Name Exchange Reaction LB in soil LBin M9 rhizosphere H2O EX_cpd00001_e0 -15 -15 -10 O2 EX_cpd00007_e0 -15 -15 -10 Phosphate EX_cpd00009_e0 -15 -15 -10 CO2 EX_cpd00011_e0 -15 -15 0 Ammonia EX_cpd00013_e0 -7.5 -7.5 -10 L-glutamate EX_cpd00023_e0 0 -0.0283302 0 D-glucose EX_cpd00027_e0 -0.61972444 -0.04098397 0 Mn2 EX_cpd00030_e0 -15 -15 -10 Glycine EX_cpd00033_e0 -0.0068175 -0.00693094 0 Zn2 EX_cpd00034_e0 -15 -15 -10 L-alanine EX_cpd00035_e0 -0.02780553 -0.00823049 0 Succinate EX_cpd00036_e0 -0.0056245 -0.12240603 0 L-lysine EX_cpd00039_e0 0 -10 0 L-aspartate EX_cpd00041_e0 0 -0.03205557 0 Sulfate EX_cpd00048_e0 -15 -15 -10 L-arginine EX_cpd00051_e0 -0.0068175 -0.00948672 0 L-serine EX_cpd00054_e0 0 -0.01004986 0 Cu2+ EX_cpd00058_e0 -15 -15 -10 Ca2+ EX_cpd00063_e0 -15 -100 -10 L-ornithine EX_cpd00064_e0 -0.0068175 -0.00831712 0 H+ EX_cpd00067_e0 -15 -15 -10 L-tyrosine EX_cpd00069_e0 -0.0068175 -0.00233919 0 Sucrose EX_cpd00076_e0 0 -0.02049199 0 L-cysteine EX_cpd00084_e0 -0.0068175 0 0 Cl- EX_cpd00099_e0 -15 -15 -10 Glycerol EX_cpd00100_e0 0 0 -10 Biotin EX_cpd00104_e0 -15 -15 0 D-ribose EX_cpd00105_e0 -0.01862144 0 0 L-leucine EX_cpd00107_e0 -0.03596182 -0.00303228 0 D-galactose EX_cpd00108_e0 -0.25290619 -0.18317325 0 L-histidine EX_cpd00119_e0 -0.0068175 -0.00506825 0 L-proline EX_cpd00129_e0 -0.01102953 0 0 L-malate EX_cpd00130_e0 -0.03649016 -0.79413596 0 D-mannose EX_cpd00138_e0 -0.2540567 -0.05436649 0 Co2 EX_cpd00149_e0
    [Show full text]
  • From Enzyme Cascades Towards Physiology and Application
    Sugar metabolism: from enzyme cascades towards physiology and application Dissertation zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften - Dr. rer. nat. - vorgelegt von Lu Shen Molekulare Enzymtechnologie und Biochemie Biofilm Centre Fachbereich Chemie der Universität Duisburg-Essen 2019 Die vorliegende Arbeit wurde im Zeitraum von Dezember 2013 bis April 2019 bei Prof. Dr. Bettina Siebers im Arbeitskreis für Molekulare Enzymtechnologie und Biochemie (Biofim Centre) der Universität Duisburg-Essen durchgeführt. Tag der Disputation: 05.11.2019 Gutachter: Prof. Dr. Bettina Siebers Prof. Dr. Peter Bayer Vorsitzender: Prof. Dr. Thomas Schrader Diese Dissertation wird über DuEPublico, dem Dokumenten- und Publikationsserver der Universität Duisburg-Essen, zur Verfügung gestellt und liegt auch als Print-Version vor. DOI: 10.17185/duepublico/70847 URN: urn:nbn:de:hbz:464-20201027-101056-7 Dieses Werk kann unter einer Creative Commons Namensnennung 4.0 Lizenz (CC BY 4.0) genutzt werden. Content 1 Introduction ...................................................................................................................... 1 1.1 Archaea ......................................................................................................................... 1 1.2 Sulfolobus spp. .............................................................................................................. 3 1.3 Hexose metabolism in Sulfolobus spp. .......................................................................... 4 1.3.1 The bifunctional
    [Show full text]
  • The Crystal Structure of D-Xylonate Dehydratase Reveals Functional Features of Enzymes from the Ilv/ED Dehydratase Family
    www.nature.com/scientificreports OPEN The crystal structure of D-xylonate dehydratase reveals functional features of enzymes from the Ilv/ED Received: 18 October 2017 Accepted: 22 December 2017 dehydratase family Published: xx xx xxxx Mohammad Mubinur Rahman1, Martina Andberg2, Anu Koivula2, Juha Rouvinen1 & Nina Hakulinen 1 The Ilv/ED dehydratase protein family includes dihydroxy acid-, gluconate-, 6-phosphogluconate- and pentonate dehydratases. The members of this family are involved in various biosynthetic and carbohydrate metabolic pathways. Here, we describe the frst crystal structure of D-xylonate dehydratase from Caulobacter crescentus (CcXyDHT) at 2.7 Å resolution and compare it with other available enzyme structures from the IlvD/EDD protein family. The quaternary structure of CcXyDHT is a tetramer, and each monomer is composed of two domains in which the N-terminal domain forms a binding site for a [2Fe-2S] cluster and a Mg2+ ion. The active site is located at the monomer-monomer interface and contains residues from both the N-terminal recognition helix and the C-terminus of the dimeric counterpart. The active site also contains a conserved Ser490, which probably acts as a base in catalysis. Importantly, the cysteines that participate in the binding and formation of the [2Fe-2S] cluster are not all conserved within the Ilv/ED dehydratase family, which suggests that some members of the IlvD/EDD family may bind diferent types of [Fe-S] clusters. Tere is increasing interest in developing economical and sustainable bioprocesses to convert biomass into valua- ble organic compounds. Metabolic engineering and synthetic biology have enabled the development of optimized microbial strains for the production of target compounds by taking advantage of known pathways and enzymes.
    [Show full text]
  • Downloading the Data Le and Mathematica Notebook in the Several Assays
    ARTICLE https://doi.org/10.1038/s41467-020-14830-y OPEN A combined experimental and modelling approach for the Weimberg pathway optimisation Lu Shen1, Martha Kohlhaas2, Junichi Enoki3, Roland Meier4, Bernhard Schönenberger4, Roland Wohlgemuth 4,5, Robert Kourist 3,6, Felix Niemeyer 2, David van Niekerk7, Christopher Bräsen1, ✉ ✉ ✉ Jochen Niemeyer 2 , Jacky Snoep 7,8 & Bettina Siebers 1 The oxidative Weimberg pathway for the five-step pentose degradation to α-ketoglutarate is 1234567890():,; a key route for sustainable bioconversion of lignocellulosic biomass to added-value products and biofuels. The oxidative pathway from Caulobacter crescentus has been employed in in-vivo metabolic engineering with intact cells and in in-vitro enzyme cascades. The performance of such engineering approaches is often hampered by systems complexity, caused by non-linear kinetics and allosteric regulatory mechanisms. Here we report an iterative approach to construct and validate a quantitative model for the Weimberg pathway. Two sensitive points in pathway performance have been identified as follows: (1) product inhibition of the dehy- drogenases (particularly in the absence of an efficient NAD+ recycling mechanism) and (2) balancing the activities of the dehydratases. The resulting model is utilized to design enzyme cascades for optimized conversion and to analyse pathway performance in C. cresensus cell- free extracts. 1 Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Universitaetsstrasse 5, 45141 Essen, Germany. 2 Institute of Organic Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitaetsstrasse 7, 45117 Essen, Germany. 3 Junior Research Group for Microbial Biotechnology, Ruhr-University Bochum, Universitaetsstrasse 150, 44780 Bochum, Germany.
    [Show full text]
  • Biotechnological Production of Glycolic Acid and Ethylene Glycol: Current State and Perspectives
    Applied Microbiology and Biotechnology https://doi.org/10.1007/s00253-019-09640-2 MINI-REVIEW Biotechnological production of glycolic acid and ethylene glycol: current state and perspectives Laura Salusjärvi1 & Sami Havukainen1 & Outi Koivistoinen1 & Mervi Toivari1 Received: 4 September 2018 /Revised: 8 January 2019 /Accepted: 9 January 2019 # The Author(s) 2019 Abstract Glycolic acid (GA) and ethylene glycol (EG) are versatile two-carbon organic chemicals used in multiple daily applications. GA and EG are currently produced by chemical synthesis, but their biotechnological production from renewable resources has received a substantial interest. Several different metabolic pathways by using genetically modified microorganisms, such as Escherichia coli, Corynebacterium glutamicum and yeast have been established for their production. As a result, the yield of GA and EG produced from sugars has been significantly improved. Here, we describe the recent advancement in metabolic engi- neering efforts focusing on metabolic pathways and engineering strategies used for GA and EG production. Keywords Glycolic acid . Ethylene glycol . D-xylose . Glyoxylate shunt . D-xylulose-1-phosphate pathway . D-ribulose-1-phosphate pathway . L-xylulose-1-phosphate pathway . Dahms pathway . Serine pathway . Metabolic engineering . Biotechnology . Biorefinery Introduction agents. The market is expected to reach US$415.0 million by 2024 (https://www.grandviewresearch.com/press-release/ Glycolic acid (GA) is a small two-carbon α-hydroxy acid global-glycolic-acid-market). (Fig. 1a) with both alcohol and acid groups (pKa 3.83). GA is naturally produced by some chemolithotrophic iron- Textile industry uses GA as a dyeing and tanning agent, in and sulphur-oxidizing bacteria (Nancucheo and Johnson food industry, it is used as a flavour and preservative and in the 2010) or from glycolonitrile by hydrolyzation by nitrilase en- pharmaceutical industry as a skin care agent.
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2012/0266329 A1 Mathur Et Al
    US 2012026.6329A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2012/0266329 A1 Mathur et al. (43) Pub. Date: Oct. 18, 2012 (54) NUCLEICACIDS AND PROTEINS AND CI2N 9/10 (2006.01) METHODS FOR MAKING AND USING THEMI CI2N 9/24 (2006.01) CI2N 9/02 (2006.01) (75) Inventors: Eric J. Mathur, Carlsbad, CA CI2N 9/06 (2006.01) (US); Cathy Chang, San Marcos, CI2P 2L/02 (2006.01) CA (US) CI2O I/04 (2006.01) CI2N 9/96 (2006.01) (73) Assignee: BP Corporation North America CI2N 5/82 (2006.01) Inc., Houston, TX (US) CI2N 15/53 (2006.01) CI2N IS/54 (2006.01) CI2N 15/57 2006.O1 (22) Filed: Feb. 20, 2012 CI2N IS/60 308: Related U.S. Application Data EN f :08: (62) Division of application No. 1 1/817,403, filed on May AOIH 5/00 (2006.01) 7, 2008, now Pat. No. 8,119,385, filed as application AOIH 5/10 (2006.01) No. PCT/US2006/007642 on Mar. 3, 2006. C07K I4/00 (2006.01) CI2N IS/II (2006.01) (60) Provisional application No. 60/658,984, filed on Mar. AOIH I/06 (2006.01) 4, 2005. CI2N 15/63 (2006.01) Publication Classification (52) U.S. Cl. ................... 800/293; 435/320.1; 435/252.3: 435/325; 435/254.11: 435/254.2:435/348; (51) Int. Cl. 435/419; 435/195; 435/196; 435/198: 435/233; CI2N 15/52 (2006.01) 435/201:435/232; 435/208; 435/227; 435/193; CI2N 15/85 (2006.01) 435/200; 435/189: 435/191: 435/69.1; 435/34; CI2N 5/86 (2006.01) 435/188:536/23.2; 435/468; 800/298; 800/320; CI2N 15/867 (2006.01) 800/317.2: 800/317.4: 800/320.3: 800/306; CI2N 5/864 (2006.01) 800/312 800/320.2: 800/317.3; 800/322; CI2N 5/8 (2006.01) 800/320.1; 530/350, 536/23.1: 800/278; 800/294 CI2N I/2 (2006.01) CI2N 5/10 (2006.01) (57) ABSTRACT CI2N L/15 (2006.01) CI2N I/19 (2006.01) The invention provides polypeptides, including enzymes, CI2N 9/14 (2006.01) structural proteins and binding proteins, polynucleotides CI2N 9/16 (2006.01) encoding these polypeptides, and methods of making and CI2N 9/20 (2006.01) using these polynucleotides and polypeptides.
    [Show full text]
  • All Enzymes in BRENDA™ the Comprehensive Enzyme Information System
    All enzymes in BRENDA™ The Comprehensive Enzyme Information System http://www.brenda-enzymes.org/index.php4?page=information/all_enzymes.php4 1.1.1.1 alcohol dehydrogenase 1.1.1.B1 D-arabitol-phosphate dehydrogenase 1.1.1.2 alcohol dehydrogenase (NADP+) 1.1.1.B3 (S)-specific secondary alcohol dehydrogenase 1.1.1.3 homoserine dehydrogenase 1.1.1.B4 (R)-specific secondary alcohol dehydrogenase 1.1.1.4 (R,R)-butanediol dehydrogenase 1.1.1.5 acetoin dehydrogenase 1.1.1.B5 NADP-retinol dehydrogenase 1.1.1.6 glycerol dehydrogenase 1.1.1.7 propanediol-phosphate dehydrogenase 1.1.1.8 glycerol-3-phosphate dehydrogenase (NAD+) 1.1.1.9 D-xylulose reductase 1.1.1.10 L-xylulose reductase 1.1.1.11 D-arabinitol 4-dehydrogenase 1.1.1.12 L-arabinitol 4-dehydrogenase 1.1.1.13 L-arabinitol 2-dehydrogenase 1.1.1.14 L-iditol 2-dehydrogenase 1.1.1.15 D-iditol 2-dehydrogenase 1.1.1.16 galactitol 2-dehydrogenase 1.1.1.17 mannitol-1-phosphate 5-dehydrogenase 1.1.1.18 inositol 2-dehydrogenase 1.1.1.19 glucuronate reductase 1.1.1.20 glucuronolactone reductase 1.1.1.21 aldehyde reductase 1.1.1.22 UDP-glucose 6-dehydrogenase 1.1.1.23 histidinol dehydrogenase 1.1.1.24 quinate dehydrogenase 1.1.1.25 shikimate dehydrogenase 1.1.1.26 glyoxylate reductase 1.1.1.27 L-lactate dehydrogenase 1.1.1.28 D-lactate dehydrogenase 1.1.1.29 glycerate dehydrogenase 1.1.1.30 3-hydroxybutyrate dehydrogenase 1.1.1.31 3-hydroxyisobutyrate dehydrogenase 1.1.1.32 mevaldate reductase 1.1.1.33 mevaldate reductase (NADPH) 1.1.1.34 hydroxymethylglutaryl-CoA reductase (NADPH) 1.1.1.35 3-hydroxyacyl-CoA
    [Show full text]
  • Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future Sharon A
    Addressing global ruminant agricultural challenges through understanding the rumen microbiome: Past, present, and future Sharon A. Huws, Christopher J. Creevey, Linda B. Oyama, Itzhak Mizrahi, Stuart E. Denman, Milka Popova, Rafael Munoz Tamayo, Evelyne Forano, Sinead M. Waters, Matthias Hess, et al. To cite this version: Sharon A. Huws, Christopher J. Creevey, Linda B. Oyama, Itzhak Mizrahi, Stuart E. Den- man, et al.. Addressing global ruminant agricultural challenges through understanding the ru- men microbiome: Past, present, and future. Frontiers in Microbiology, Frontiers Media, 2018, 9, 10.3389/fmicb.2018.02161. hal-01890696 HAL Id: hal-01890696 https://hal.archives-ouvertes.fr/hal-01890696 Submitted on 8 Oct 2018 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. Distributed under a Creative Commons Attribution| 4.0 International License REVIEW published: 25 September 2018 doi: 10.3389/fmicb.2018.02161 Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Edited by: Future Zhongtang Yu, The Ohio State University, Sharon A. Huws 1*, Christopher J. Creevey 1, Linda B. Oyama 1, Itzhak Mizrahi 2, United States Stuart E. Denman 3, Milka Popova 4, Rafael Muñoz-Tamayo 5, Evelyne Forano 6, Reviewed by: Sinead M.
    [Show full text]
  • Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future
    UC Davis UC Davis Previously Published Works Title Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future. Permalink https://escholarship.org/uc/item/0tj1z2z6 Journal Frontiers in microbiology, 9(SEP) ISSN 1664-302X Authors Huws, Sharon A Creevey, Christopher J Oyama, Linda B et al. Publication Date 2018 DOI 10.3389/fmicb.2018.02161 Peer reviewed eScholarship.org Powered by the California Digital Library University of California REVIEW published: 25 September 2018 doi: 10.3389/fmicb.2018.02161 Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Edited by: Future Zhongtang Yu, The Ohio State University, Sharon A. Huws 1*, Christopher J. Creevey 1, Linda B. Oyama 1, Itzhak Mizrahi 2, United States Stuart E. Denman 3, Milka Popova 4, Rafael Muñoz-Tamayo 5, Evelyne Forano 6, Reviewed by: Sinead M. Waters 7, Matthias Hess 8, Ilma Tapio 9, Hauke Smidt 10, Sophie J. Krizsan 11, Shengguo Zhao, David R. Yáñez-Ruiz 12, Alejandro Belanche 12, Leluo Guan 13, Robert J. Gruninger 14, Institute of Animal Sciences, Chinese Tim A. McAllister 14, C. Jamie Newbold 15, Rainer Roehe 15, Richard J. Dewhurst 15, Academy of Agricultural Sciences, 16 17 18 19 China Tim J. Snelling , Mick Watson , Garret Suen , Elizabeth H. Hart , 19 1 20 20 Suzanne Lynn Ishaq, Alison H. Kingston-Smith , Nigel D. Scollan , Rodolpho M. do Prado , Eduardo J. Pilau , 21 22 23 24 University of Oregon, United States Hilario C. Mantovani , Graeme T. Attwood , Joan E. Edwards , Neil R. McEwan , Steven Morrisson 25, Olga L. Mayorga 26, Christopher Elliott 1 and Diego P.
    [Show full text]
  • Comparing the Mechanisms of Metal Action in Bacteria: Insight Into Novel Genes Involved in Silver, Gallium and Copper Resistance and Toxicity in Escherichia Coli
    University of Calgary PRISM: University of Calgary's Digital Repository Graduate Studies The Vault: Electronic Theses and Dissertations 2019-07-25 Comparing the mechanisms of metal action in bacteria: insight into novel genes involved in silver, gallium and copper resistance and toxicity in Escherichia coli Gugala, Natalie Gugala, N. (2019). Comparing the mechanisms of metal action in bacteria: insight into novel genes involved in silver, gallium and copper resistance and toxicity in Escherichia coli (Unpublished doctoral thesis). University of Calgary, Calgary, AB. http://hdl.handle.net/1880/110682 doctoral thesis University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission. Downloaded from PRISM: https://prism.ucalgary.ca ID Name Description Score P-value JW0001 thrA Bifunctional aspartokinase/homoserine0.0472 dehydrogenase0.4974 1 JW0002 thrB Homoserine kinase 0.4535 0.0103 JW0003 thrC L-threonine synthase 0.0791 0.0185 JW0004 yaaX DUF2502 family putative periplasmic0.0959 protein 0.0095 JW0005 yaaA Peroxide resistance protein, lowers0.0345 intracellular 0.4262iron JW0006 yaaJ Putative transporter 0.0623 0.1141 JW0008 mog Molybdochelatase incorporating0.0269 molybdenum into0.1935 molybdopterin JW0009 yaaH Succinate-acetate transporter 0.0876 0.0017 JW0010
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2015/0240226A1 Mathur Et Al
    US 20150240226A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2015/0240226A1 Mathur et al. (43) Pub. Date: Aug. 27, 2015 (54) NUCLEICACIDS AND PROTEINS AND CI2N 9/16 (2006.01) METHODS FOR MAKING AND USING THEMI CI2N 9/02 (2006.01) CI2N 9/78 (2006.01) (71) Applicant: BP Corporation North America Inc., CI2N 9/12 (2006.01) Naperville, IL (US) CI2N 9/24 (2006.01) CI2O 1/02 (2006.01) (72) Inventors: Eric J. Mathur, San Diego, CA (US); CI2N 9/42 (2006.01) Cathy Chang, San Marcos, CA (US) (52) U.S. Cl. CPC. CI2N 9/88 (2013.01); C12O 1/02 (2013.01); (21) Appl. No.: 14/630,006 CI2O I/04 (2013.01): CI2N 9/80 (2013.01); CI2N 9/241.1 (2013.01); C12N 9/0065 (22) Filed: Feb. 24, 2015 (2013.01); C12N 9/2437 (2013.01); C12N 9/14 Related U.S. Application Data (2013.01); C12N 9/16 (2013.01); C12N 9/0061 (2013.01); C12N 9/78 (2013.01); C12N 9/0071 (62) Division of application No. 13/400,365, filed on Feb. (2013.01); C12N 9/1241 (2013.01): CI2N 20, 2012, now Pat. No. 8,962,800, which is a division 9/2482 (2013.01); C07K 2/00 (2013.01); C12Y of application No. 1 1/817,403, filed on May 7, 2008, 305/01004 (2013.01); C12Y 1 1 1/01016 now Pat. No. 8,119,385, filed as application No. PCT/ (2013.01); C12Y302/01004 (2013.01); C12Y US2006/007642 on Mar. 3, 2006.
    [Show full text]