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|HAI LUI AUN ACUTULUS010006055B2 LUNIIT MOONHITI (12 ) United States Patent (10 ) Patent No. : US 10 , 006 , 055 B2 Burk et al. (45 ) Date of Patent: Jun . 26 , 2018 ( 54 ) MICROORGANISMS FOR PRODUCING 2002/ 0168654 A1 11/ 2002 Maranas et al. 2003 / 0059792 Al 3 /2003 Palsson et al . BUTADIENE AND METHODS RELATED 2003 /0087381 A1 5 / 2003 Gokarn THERETO 2003 / 0224363 Al 12 /2003 Park et al . 2003 / 0233218 Al 12 /2003 Schilling (71 ) Applicant: Genomatica , Inc. , San Diego , CA (US ) 2004 / 0009466 AL 1 /2004 Maranas et al. 2004 / 0029149 Al 2 /2004 Palsson et al. ( 72 ) Inventors : Mark J . Burk , San Diego , CA (US ) ; 2004 / 0072723 A1 4 /2004 Palsson et al. Anthony P . Burgard , Bellefonte , PA 2004 / 0152159 Al 8 / 2004 Causey et al . 2005 /0042736 A1 2 / 2005 San et al . (US ) ; Robin E . Osterhout , San Diego , 2005 / 0079482 A1 4 / 2005 Maranas et al . CA (US ) ; Jun Sun , San Diego , CA 2006 / 0046288 Al 3 / 2006 Ka - Yiu et al. ( US ) ; Priti Pharkya , San Diego , CA 2006 / 0073577 A1 4 / 2006 Ka - Yiu et al . (US ) 2007 /0184539 Al 8 / 2007 San et al . 2009 / 0047718 Al 2 / 2009 Blaschek et al . 2009 / 0047719 Al 2 / 2009 Burgard et al . (73 ) Assignee : Genomatica , Inc ., San Diego , CA (US ) 2009 /0191593 A1 7 / 2009 Burk et al . 2010 / 0003716 A1 1 / 2010 Cervin et al. ( * ) Notice : Subject to any disclaimer , the term of this 2010 /0184171 Al 7 /2010 Jantama et al. patent is extended or adjusted under 35 2010 /0304453 Al 12 / 2010 Trawick et al . 2010 / 0330635 Al 12 / 2010 Burgard et al . U . S . C . 154 (b ) by 0 days . days . 2011 /0008858 AL 1 / 2011 Osterhout et al. 2011/ 0008861 A1 1 / 2011 Berry et al. ( 21) Appl. No. : 14 /869 , 872 2011 / 0045563 AL 2 / 2011 Melis 2011/ 0201089 Al * 8 / 2011 Burgard C12N 9 / 0006 ( 22 ) Filed : Sep . 29 , 2015 435 / 243 2011/ 0300597 A112 / 2011 Burk et al . (65 ) ) Prior Publication Data 2012 /0225466 AL 9 / 2012 Burk et al . US 2016 /0244786 A1 Aug . 25, 2016 2013 /0011891 A11 / 2013 Burk et al . FOREIGN PATENT DOCUMENTS Related U . S . Application Data WO WO 2002 /055995 7 / 2002 (62 ) Division of application No . 13/ 527 ,440 , filed on Jun . WO WO 2002 /061115 8 / 2002 WO WO 2003 / 106998 12 / 2003 19 , 2012 , now Pat . No . 9 , 169 ,486 . WO WO 2004 /018621 3 / 2004 (60 ) Provisional application No . 61/ 502 , 264, filed on Jun . WO WO 2005 /047498 5 /2005 28 , 2011 . (Continued ) ( 51 ) Int. Cl. OTHER PUBLICATIONS C12P 7 /04 ( 2006 .01 ) C12N 15 / 52 ( 2006 .01 ) Aberhart and Hsu , “ Stereospecific hydrogen loss in the conversion C12P 5 /02 ( 2006 . 01 ) of [2H7 ] isobutyrate to B -hydroxyisobutyrate in Pseudomonas C12N 15 / 70 ( 2006 .01 ) putida . The stereochemistry of B -hydroxyisobutyrate C12P 7 / 16 ( 2006 .01 ) dehydrogenase, ” J . Chem . Soc . [ Perkinl ] 6 ; 1404 - 1406 ( 1979 ) . (52 ) U . S . CI. Adams et al ., “ Oxidoreductase - Type Enzymes and Redox Proteins Involved in Fermentative Metabolisms of Hyperthermophilic CPC .. C12P 7704 ( 2013 .01 ) ; C12N 15 /52 Archaea ,” Archaea . Adv. Protein Chem . 48 : 101 - 180 ( 1996 ) . (2013 . 01 ) ; C12N 15 / 70 (2013 . 01 ) ; C12P 5 / 026 Ajjawi et al . , “ Thiamin pyrophosphokinase is required for thiamin ( 2013 .01 ) ; C12P 7 / 16 ( 2013 . 01 ) cofactor activation in Arabidopsis , ” Plant Mol. Biol. 65 ( 1 - 2 ) : 151 ( 58 ) Field of Classification Search 162 (2007 ) . (Epub Jul. 5 , 2007 ) . None Alber et al . , “Malonyl -Coenzyme A reductase in the modified See application file for complete search history. 3 -hydroxypropionate cycle for autotrophic carbon fixation in archaeal Metallosphaera and Sulfolobus spp ., " J . Bacteriol. References Cited 188 ( 24 ) : 8551 - 8559 ( 2006 ) . ( 56 ) Alber et al. , “ Study of an alternate glyoxylate cycle for acetate U . S . PATENT DOCUMENTS assimilation by Rhodobacter sphaeroides ,” Mol. Microbiol. 61 ( 2 ): 297 - 309 ( 2006 ) . 5 ,413 , 922 A 5 / 1995 Matsuyama et al . 5 , 830 ,716 A 11/ 1998 Kojima et al. (Continued ) 5 , 849 , 970 A 12 / 1998 Fall et al. 5 , 958 , 745 A 9 / 1999 Gruys et al. Primary Examiner — Iqbal H Chowdhury 6 , 117 ,658 A 9 / 2000 Dennis et al . ( 74 ) Attorney , Agent, or Firm — Jones Day 6 , 455 ,284 B1 9 / 2002 Gokarn et al . 7 , 127, 379 B2 10 / 2006 Palsson et al . ABSTRACT 7 , 223 , 567 B2 5 / 2007 Ka - Yiu et al. (57 ) 7 , 244 , 610 B2 7 / 2007 San et al. The invention provides non -naturally occurring microbial 7 , 256, 016 B2 8 / 2007 San et al. organisms having a butadiene or crotyl alcohol pathway . The 7 , 262 , 046 B2 8 / 2007 Ka - Yiu et al . 7 ,309 ,597 B2 12 / 2007 Liao et al. invention additionally provides methods of using such 7 , 718 , 417 B2 5 / 2010 Millis et al. organisms to produce butadiene or crotyl alcohol. 7 , 947, 483 B2 5 / 2011 Burgard et al . 2002 /0012939 AL 1 /2002 Palsson 14 Claims, 24 Drawing Sheets US 10 ,006 , 055 B2 Page 2 References Cited nucleatum ) . Comparison with the glutaconyl- CoA decarboxylases ( 56 ) from gram - positive bacteria , " Arch . Microbiol. 154 ( 4 ) : 362 - 369 ( 1990 ) . FOREIGN PATENT DOCUMENTS Bekal et al . , “ Purification of Leuconostoc mesenteroides Citrate WO WO 2006 /031424 3 / 2006 Lyase and Cloning and Characterization of the citCDEFG Gene WO WO 2006 / 034156 3 / 2006 Cluster, " J . Bacteriol. 180 :647 -654 ( 1998 ) . WO WO 2007 / 141208 12 / 2007 Berg et al. , “ A 3 -Hydroxypropionate / 4 -Hydroxybutyrate WO WO 2008 / 080124 7 / 2008 Autotrophic Carbon Dioxide Assimilation Pathway in Archaea, " WO WO 2008 / 115840 9 / 2008 Science 318 ( 5857 ) 1782 - 1786 (2007 ) . wo WO 2008 / 131286 10 / 2008 Bergquist and Gibbs, “ Degenerate oligonucleotide gene shuffling, " WO WO 2009 /076676 6 / 2009 Meth . Mol. Biol. 352 : 191 - 204 ( 2007 ) . WO WO 2009 /094485 7 / 2009 Bergquist et al ., “ Degenerate oligonucleotide gene shuffling WO WO 2009 / 111513 9 / 2009 (DOGS ) and random drift mutagenesis (RNDM ) : Two complemen WO WO 2010 / 031077 3 / 2010 tary techniques for enzyme evolution ,” Biomol. Eng . 22 :63 - 72 WO WO 2010 /031079 3 / 2010 ( 2005 ) . WO WO 2011 /052718 5 / 2011 Bernhard et al. , “ Functional and structural role of the cytochrome b wo WO 2011 / 140171 11 / 2011 subunit of the membrane -bound hydrogenase complex of Alcaligenes eutrophus H16 , ” Eur. J . Biochem . 248 , 179 - 186 ( 1997 ) . OTHER PUBLICATIONS Binstock and Schulz , “ Fatty acid oxidation complex from Escherichia coli ," Methods Enzymol. 71 ( Pt C ) :403 - 411 ( 1981 ) . Alber et al. , “ Malonyl- Coenzyme A Reductase in the Modified Bisswanger, “ Substrate Specificity of the Pyruvate Dehydrogenase 3 -Hydroxypropionate Cycle for Autotrophic Carbon Fixation in Complex from Escherichia coli ,” H . , J . Biol. Chem . 256 : 815 - 82 Archaeal Metallosphaera and Sulfolobus spp ., " J. Bacteriol. ( 1981 ) . Blaschkowski et al. , “ Routes of Flavodoxin and Ferredoxin Reduc 188 : 8551 - 8559 ( 2006 ) . tion in Escherichia coli, ” Eur. J . Biochem . 123 : 563 - 569 ( 1982 ) . Altincicek et al. , " LytB protein catalyzes the terminal step of the Blazquez et al. , “ Identification and analysis of a glutaryl - CoA 2 - C -methyl - D - erythritol- 4 -phosphate pathway of isoprenoid bio dehydrogenase- encoding gene and its cognate transcriptional regu synthesis , ” FEBS Lett . 532 ( 3 )437 -440 ( 2002 ) . lator from Azoarcus sp . CIB , " Environ . Microbiol. 10 ( 2 ): 474 -482 Anderson et al ., “ Isopentenyl diphosphate : dimethylallyl (2008 ). diphosphate isomerase . An improved purification of the enzyme and Bochar et al. , “ 3 -hydroxy - 3 -methylglutaryl coenzyme A reductase isolation of the gene from Saccharomyces cerevisiae, " J . Biol. of Sulfolobus solfataricus: DNA sequence, phylogeny, expression in Chem . 264 (32 ) : 19169 - 19175 ( 1989 ) . Escherichia coli of the hmgA gene , and purification and kinetic Andersson et al. , “ Effect of different carbon sources on the produc characterization of the gene product ,” J . Bacteriol. 179 ( 11 ) :3632 tion of succinic acid using metabolically engineered Escherichia 3638 ( 1997 ). coli, ” Biotechnol. Prog . 23 ( 2 ) : 381 - 388 ( 2007 ) . Bock et al. , “ Purification and Characterization of Two Extremely Aoshima and Igarashi, “ A novel oxalosuccinate - forming enzyme Thermostable Enzymes, Phosphate Acetyltransferase and Acetate involved in the reductive carboxylation of 2 - oxoglutarate in Kinase , from the Hyperthermophilic Eubacterium Thermotoga Hydrogenobacter thermophilus TK - 6 ," Mol. Microbiol. 62 :748 -759 maritime, " J . Bacteriol. 181: 1861- 1867 ( 1999 ) . (2006 ) . Boiangiu et al. , “ Sodium Ion Pumps and Hydrogen Production in Aoshima and Igarashi, “ Nondecarboxylating and Decarboxylating Glutamate Fermenting Anaerobic Bacteria , ” J . Mol. Microbiol. Isocitrate Dehydrogenases : Oxalosuccinate Reductase as an Ances Biotechnol . 10 : 105 - 119 ( 2005 ) . tral Form of Isocitrate Dehydrogenase, ” J . Bacteriol. 190 :2050 Bonner and Bloch , “ Purification and properties of fatty acyl 2055 ( 2008 ) . thioesterase I from Escherichia coli, ” J. Biol. Chem . 247 ( 10 ) :3123 Aoshima et al ., “ A novel biotin protein required for reductive 3133 ( 1972 ) . carboxylation of 2 -oxoglutarate by isocitrate dehydrogenase in Botella -Pavia et al. , “ Regulation of carotenoid biosynthesis in Hydrogenobacter thermophilus TK - 6 ," Mol. Microbiol. 51: 791 - 798 plants : evidence for a key role of hydroxymethylbutenyl ( 2004 ) . diphosphate reductase in controlling the supply of plastidial Aoshima et al ., “ A novel enzyme, citryl- CoA lyase , catalysing the isoprenoid precursors , ” Plant J . 40 ( 2 ) : 188 - 199 (2004 ) . second step of the citrate cleavage reaction
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  • Supplemental Figure S1. Principal Component Analysis (PCA) for the Leaf and Root Transcriptomes

    Supplemental Figure S1. Principal Component Analysis (PCA) for the Leaf and Root Transcriptomes

    Supplemental Figure S1. Principal component analysis (PCA) for the leaf and root transcriptomes. A ZT12 ZT18 ZT0 ZT6 ZT12 ZT18 ZT0 ZT6 → → → Pattern 1 ↗ ↘ ↗ ↘ ↘ ↘ ↘ → → → Pattern 2 ↗ ↘ ↗ ↘ ↘ ↘ ↘ → → → → Pattern 3 ↗ ↘ ↗ ↘ ↘ ↘ ↘ → → → → Pattern 4 ↘ ↗ ↘ ↘ ↘ ↘ ↘ ↗ → ↗ Pattern 5 ↗ ↘ ↗ ↘ → ↘ → → ↗ → ↗ Pattern 6 ↗ ↘ ↗ ↘ → ↘ → → ↗ → Pattern 7 ↘ ↗ ↘ ↗ ↘ → ↘ ↗ → ↗ → Pattern 8 ↘ ↗ ↘ → ↘ → ↘ ↗ ↗ ↗ ↗ Pattern 9 ↗ ↘ ↗ → → → → ↗ ↗ ↗ Pattern 10 ↘ ↗ ↘ ↗ → → → ↗ ↗ ↗ Pattern 11 ↘ ↗ ↘ ↗ → → → ↗ ↗ ↗ ↗ Pattern 12 ↘ ↗ ↘ → → → → Supplemental Figure S2. The 12 different diurnal patterns set for this study (A) and gene expression variations in the leaves (B) and roots (C). (B, C) The shaded areas show nighttime. The data points indicate the average of expression levels of five replicates. Figure S2 continued B Leaf - Pattern 1 Leaf - Pattern 2 Leaf - Pattern 3 400 2500 1200 350 1000 2000 300 800 250 1500 200 600 1000 150 400 100 Expression Level Level (TPM) Expression Expression Level Level Expression (TPM) 500 Expression Level Level (TPM) Expression 200 50 0 0 0 12 18 0 6 12 18 0 6 12 18 0 6 12 18 0 6 12 18 0 6 12 18 0 6 ZT ZT ZT Leaf - Pattern 4 Leaf - Pattern 5 Leaf - Pattern 6 3000 6000 20000 18000 2500 5000 16000 14000 2000 4000 12000 1500 3000 10000 8000 1000 2000 6000 Expression Level Level (TPM) Expression 4000 Expression Level Level Expression (TPM) 500 Level Expression (TPM) 1000 2000 0 0 0 12 18 0 6 12 18 0 6 12 18 0 6 12 18 0 6 12 18 0 6 12 18 0 6 ZT ZT ZT Leaf - Pattern 7 Leaf - Pattern 8 Leaf - Pattern 9 4500 400 2500 4000 350 2000 3500 300 3000 250
  • R Graphics Output

    R Graphics Output

    Figure S1. Multidimensional scaling analysis of the RNA-seq experiments. Samples are projected on the two first dimensions according to their gene expression profiles. Closeness between samples on the grid indicates a strong similarity. Figure S2. Similar tissue type are strongly correlated. Spearman's rho correlation was measured to check biological replicate homogeneity. Higher rho values indicate stronger similarities between pairs of samples. −log10(Pval) ● 5● 10● 15● 20 OL vs AR YL vs OL YL+YS+OL vs AR copper ion transport ● microtubule−based movement ● cyanate catabolic process ● establishment of protein localization ● DNA unwinding involved in DNA replication ● intracellular distribution of mitochondria ● regulation of root development ● DNA methylation on cytosine within a CG sequence ● carbon utilization ● glutamine biosynthetic process ● maintenance of DNA methylation ● photosystem II assembly ● response to singlet oxygen ● DNA replication initiation ● chlorophyll biosynthetic process ● specification of plant organ axis polarity ● mitotic cell cycle ● reductive pentose−phosphate cycle ● cellular response to nitrogen starvation ● double−strand break repair via homologous recombination ● photosynthesis, light harvesting in photosystem I ● cellular manganese ion homeostasis ● mitotic cell cycle phase transition ● protein−chromophore linkage ● cellular zinc ion homeostasis ● regulation of cyclin−dependent protein serine/threonine kinase activity ● response to light stimulus ● recognition of pollen ● cell division ● photosynthesis
  • Exchange of Nucleoside Monophosphate-Binding Domains in Adenylate Kinase and UMP/CMP Kinase1

    Exchange of Nucleoside Monophosphate-Binding Domains in Adenylate Kinase and UMP/CMP Kinase1

    J. Biochem. 124, 359-367 (1998) Exchange of Nucleoside Monophosphate-Binding Domains in Adenylate Kinase and UMP/CMP Kinase1 Toshihide Okajima,*"z Tamo Fukamizo,* Sachio Goto,* Toshio Fukui,t and Katsuyuki Tanizawa•õ *Faculty of Agriculture , Kinki University, 3327-204 Nakamachi, Nara 631-8505; and •õInstitute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047 Received for publication, March 6, 1998 Two types of active chimeric enzymes have been constructed by genetic engineering of chicken cytosolic adenylate kinase (AK) and porcine brain UMP/CMP kinase (UCK): one, designated as UAU, carries an AMP-binding domain of AK in the remaining body of UCK; and the other, designated as AUA, carries a UMP/CMP-binding domain of UCK in the remaining body of AK. Steady-state kinetic analysis of these chimeric enzymes revealed that UAU is 4-fold more active for AMP, 40-fold less active for UMP, and 4-fold less active for CMP than the parental UCK, although AUA has considerably lowered reactivity for both AMP and UMP. Circular dichroism spectra of the two chimeric enzymes suggest that UAU and AUA have similar folding structures to UCK and AK, respectively. Furthermore, proton NMR measurements of the UCK and UAU proteins indicate that significant differ ences in proton signals are limited to the aromatic region, where an imidazole C2H signal assigned to His31 shows a downfield shift upon conversion of UCK to UAU, and the signals assigned to Tyr49 and Tyr56 in the UMP/CMP-binding domain disappear in UAU. In contrast, AUA has a Tm value about 11•Ž lower than AK, whereas UAU and UCK have similar Tm values.