Biosynthesis of Poly(3-Hydroxypropionate) from Glycerol by Recombinant Escherichia Coli
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<I>Lactobacillus Reuteri</I>
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Faculty Publications in Food Science and Food Science and Technology Department Technology 2014 From prediction to function using evolutionary genomics: Human-specific ecotypes of Lactobacillus reuteri have diverse probiotic functions Jennifer K. Spinler Texas Children’s Hospital, [email protected] Amrita Sontakke Baylor College of Medicine Emily B. Hollister Baylor College of Medicine Susan F. Venable Baylor College of Medicine Phaik Lyn Oh University of Nebraska, Lincoln See next page for additional authors Follow this and additional works at: http://digitalcommons.unl.edu/foodsciefacpub Spinler, Jennifer K.; Sontakke, Amrita; Hollister, Emily B.; Venable, Susan F.; Oh, Phaik Lyn; Balderas, Miriam A.; Saulnier, Delphine M.A.; Mistretta, Toni-Ann; Devaraj, Sridevi; Walter, Jens; Versalovic, James; and Highlander, Sarah K., "From prediction to function using evolutionary genomics: Human-specific ce otypes of Lactobacillus reuteri have diverse probiotic functions" (2014). Faculty Publications in Food Science and Technology. 132. http://digitalcommons.unl.edu/foodsciefacpub/132 This Article is brought to you for free and open access by the Food Science and Technology Department at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Faculty Publications in Food Science and Technology by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Jennifer K. Spinler, Amrita Sontakke, Emily B. Hollister, -
Medium and Long-Term Opportunities and Risks of the Biotechnological Production of Bulk Chemicals from Renewable Resources
Medium and Long-term Opportunities and Risks of the Biotechnological Production of Bulk Chemicals from Renewable Resources - The Potential of White Biotechnology The BREW Project Final report Prepared under the European Commission’s GROWTH Programme (DG Research) Project team: Academy Utrecht University (UU), Dept. of Science, Technology and Society (STS), Utrecht, Netherlands Fraunhofer Institute for Systems and Innovation Research (FhG-ISI), Karlsruhe, Germany Universidad Complutense de Madrid (UCM), Dept. of Chemical Engineering, Madrid, Spain Plant Research International (PRI), Wageningen, Netherlands CERISS (Centro per l'Educazione, la Ricerca, l'Informazione su Scienza e Società), Milan, Italy A&F (Agrotechnology and Food Innovations) Wageningen, Netherlands Industry partners BP Chemicals, Hull, United Kingdom Degussa AG, Hanau, Germany DSM NV, Heerlen, Netherlands DuPont, Bad Homburg, Germany NatureWorks, Naarden, Netherlands Novozymes A/S, Bagsvaerd, Denmark Roquette Frères, Lestrem, France Shell International Chemicals BV, Amsterdam, Netherlands Uniqema, Wilton/Redcar, United Kingdom Utrecht, September 2006 Authors Dr. Martin Patel (project co-ordinator) Utrecht University (UU) Manuela Crank, BE Chem Department of Science, Technology Dr. Veronika Dornburg and Society (STS) Barbara Hermann, M.Sc. Heidelberglaan 2 Lex Roes, M.Sc. NL-3584 CS Utrecht, Netherlands Tel. +31 (0) 30 253-7600 Fax +31 (0) 30 253-7601 [email protected] Dr. Bärbel Hüsing Fraunhofer Institute for Systems and Innovation Research (FhG-ISI), Karlsruhe, Germany Dr. Leo Overbeek Plant Research International (PRI) Wageningen, Netherlands Dr. Fabio Terragni CERISS (Centro per l'Educazione, la Dr. Elena Recchia Ricerca, l'Informazione su Scienza e Società), Milan, Italy Contributors Academy Dr. Ruud Weusthuis A&F (Agrotechnology and Food Innovations) Wageningen, Netherlands Prof. -
Evolution of Coenzyme BI2 Synthesis Among Enteric Bacteria
Copyright 0 1996 by the Genetics Society of America Evolution of Coenzyme BI2Synthesis Among Enteric Bacteria: Evidence for Loss and Reacquisition of a Multigene Complex Jeffrey G. Lawrence and John R. Roth Department of Biology, University of Utah, Salt Lake City, Utah 84112 Manuscript received June 16, 1995 Accepted for publication October 4, 1995 ABSTRACT We have examined the distribution of cobalamin (coenzyme BI2) synthetic ability and cobalamin- dependent metabolism among entericbacteria. Most species of enteric bacteria tested synthesize cobala- min under both aerobic and anaerobic conditions and ferment glycerol in a cobalamindependent fashion. The group of species including Escha'chia coli and Salmonella typhimurium cannot ferment glyc- erol. E. coli strains cannot synthesize cobalamin de novo, and Salmonella spp. synthesize cobalamin only under anaerobic conditions. In addition, the cobalamin synthetic genes of Salmonella spp. (cob) show a regulatory pattern different from that of other enteric taxa tested. We propose that the cobalamin synthetic genes, as well asgenes providing cobalamindependent diol dehydratase, were lostby a common ancestor of E. coli and Salmonella spp. and were reintroduced as a single fragment into the Salmonella lineage from an exogenous source. Consistent with this hypothesis, the S. typhimurium cob genes do not hybridize with the genomes of other enteric species. The Salmonella cob operon may represent a class of genes characterized by periodic loss and reacquisition by host genomes. This process may be an important aspect of bacterial population genetics and evolution. OBALAMIN (coenzyme BIZ) is a large evolution- The cobalamin biosynthetic genes have been charac- C arily ancient molecule ( GEORGOPAPADAKOUand terized in S. -
Invasive Escherichia Colito Exposure to Bile Salts
www.nature.com/scientificreports OPEN Metabolic adaptation of adherent- invasive Escherichia coli to exposure to bile salts Received: 7 August 2018 Julien Delmas 1,2, Lucie Gibold1,2, Tiphanie Faïs1,2, Sylvine Batista1, Martin Leremboure4, Accepted: 13 December 2018 Clara Sinel3, Emilie Vazeille2,5, Vincent Cattoir3, Anthony Buisson2,5, Nicolas Barnich2,6, Published: xx xx xxxx Guillaume Dalmasso 2 & Richard Bonnet1,2 The adherent-invasive Escherichia coli (AIEC), which colonize the ileal mucosa of Crohn’s disease patients, adhere to intestinal epithelial cells, invade them and exacerbate intestinal infammation. The high nutrient competition between the commensal microbiota and AIEC pathobiont requires the latter to occupy their own metabolic niches to survive and proliferate within the gut. In this study, a global RNA sequencing of AIEC strain LF82 has been used to observe the impact of bile salts on the expression of metabolic genes. The results showed a global up-regulation of genes involved in degradation and a down-regulation of those implicated in biosynthesis. The main up-regulated degradation pathways were ethanolamine, 1,2-propanediol and citrate utilization, as well as the methyl-citrate pathway. Our study reveals that ethanolamine utilization bestows a competitive advantage of AIEC strains that are metabolically capable of its degradation in the presence of bile salts. We observed that bile salts activated secondary metabolism pathways that communicate to provide an energy beneft to AIEC. Bile salts may be used by AIEC as an environmental signal to promote their colonization. Te adherent-invasive Escherichia coli (AIEC) pathogroup was initially characterized in isolates from the ileal mucosa of Crohn’s disease (CD) patients1–5. -
J. Nutr. Sci. Vitaminol., 28, 225-236, 1982 the Mechanism of in Situ
J. Nutr. Sci. Vitaminol.,28, 225-236, 1982 The Mechanism of In Situ Reactivation of Glycerol Inactivated Coenzyme B12-Dependent Enzymes, Glycerol Dehydratase and Diol Dehydratasel Kazutoshi USHIO, Susumu HONDA, Tetsuo TORAYA,2 and Saburo FUKUI3 Laboratory of Industrial Biochemistry, Department of Industrial Chemistry, Faculty of Engineering, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606, Japan (Received September 28, 1981) Summary In the previous paper (S. Honda, T. Toraya, and S. Fukui, J. Bacteriol., 143, 1458-1465 (1980)), we reported that the glycerol inactivated holoenzymes of adenosylcobalamin-dependent glycerol dehy dratase and diol dehydratase are rapidly and continually reactivated in toluene-treated cells (in situ) by adenosine 5•L-triphosphate (ATP) and divalent metal ions in the presence of free adenosylcobalamin. To elucidate the mechanism of this in situ reactivation, the nature of the binding of various irreversible cobalamin inhibitors to the dehydratases in situ was investigated. In the presence of ATP and Mn2+, enzyme-bound hydroxocobalamin, cyanocobalamin and methylcobalamin were rapidly displaced by added adenosylcobalamin. Without ATP and Mn2+, such displacement did not take place. In contrast, enzyme-bound adeninyl butylcobalamin and adenosylethylcobalamin were essentially not displace able by the free coenzyme even in the presence of ATP and Mn2+. Inosylcobalamin was a very weak inhibitor irrespective of the presence of ATP and Mn2+ . These results indicate that the relative affinity of the enzymes in situ for the cobalamins with simple Cof ligands was markedly lowered in the presence of ATP and Mn2+, whereas that for the cobalamins with adenine-containing ligands was not. When the glycerol inactivated holoenzymes in situ were dialyzed against a buffer containing ATP and Mg2+, the inactivated coenzyme moiety dissociated from the enzymes leaving apoproteins. -
12) United States Patent (10
US007635572B2 (12) UnitedO States Patent (10) Patent No.: US 7,635,572 B2 Zhou et al. (45) Date of Patent: Dec. 22, 2009 (54) METHODS FOR CONDUCTING ASSAYS FOR 5,506,121 A 4/1996 Skerra et al. ENZYME ACTIVITY ON PROTEIN 5,510,270 A 4/1996 Fodor et al. MICROARRAYS 5,512,492 A 4/1996 Herron et al. 5,516,635 A 5/1996 Ekins et al. (75) Inventors: Fang X. Zhou, New Haven, CT (US); 5,532,128 A 7/1996 Eggers Barry Schweitzer, Cheshire, CT (US) 5,538,897 A 7/1996 Yates, III et al. s s 5,541,070 A 7/1996 Kauvar (73) Assignee: Life Technologies Corporation, .. S.E. al Carlsbad, CA (US) 5,585,069 A 12/1996 Zanzucchi et al. 5,585,639 A 12/1996 Dorsel et al. (*) Notice: Subject to any disclaimer, the term of this 5,593,838 A 1/1997 Zanzucchi et al. patent is extended or adjusted under 35 5,605,662 A 2f1997 Heller et al. U.S.C. 154(b) by 0 days. 5,620,850 A 4/1997 Bamdad et al. 5,624,711 A 4/1997 Sundberg et al. (21) Appl. No.: 10/865,431 5,627,369 A 5/1997 Vestal et al. 5,629,213 A 5/1997 Kornguth et al. (22) Filed: Jun. 9, 2004 (Continued) (65) Prior Publication Data FOREIGN PATENT DOCUMENTS US 2005/O118665 A1 Jun. 2, 2005 EP 596421 10, 1993 EP 0619321 12/1994 (51) Int. Cl. EP O664452 7, 1995 CI2O 1/50 (2006.01) EP O818467 1, 1998 (52) U.S. -
POLSKIE TOWARZYSTWO BIOCHEMICZNE Postępy Biochemii
POLSKIE TOWARZYSTWO BIOCHEMICZNE Postępy Biochemii http://rcin.org.pl WSKAZÓWKI DLA AUTORÓW Kwartalnik „Postępy Biochemii” publikuje artykuły monograficzne omawiające wąskie tematy, oraz artykuły przeglądowe referujące szersze zagadnienia z biochemii i nauk pokrewnych. Artykuły pierwszego typu winny w sposób syntetyczny omawiać wybrany temat na podstawie możliwie pełnego piśmiennictwa z kilku ostatnich lat, a artykuły drugiego typu na podstawie piśmiennictwa z ostatnich dwu lat. Objętość takich artykułów nie powinna przekraczać 25 stron maszynopisu (nie licząc ilustracji i piśmiennictwa). Kwartalnik publikuje także artykuły typu minireviews, do 10 stron maszynopisu, z dziedziny zainteresowań autora, opracowane na podstawie najnow szego piśmiennictwa, wystarczającego dla zilustrowania problemu. Ponadto kwartalnik publikuje krótkie noty, do 5 stron maszynopisu, informujące o nowych, interesujących osiągnięciach biochemii i nauk pokrewnych, oraz noty przybliżające historię badań w zakresie różnych dziedzin biochemii. Przekazanie artykułu do Redakcji jest równoznaczne z oświadczeniem, że nadesłana praca nie była i nie będzie publikowana w innym czasopiśmie, jeżeli zostanie ogłoszona w „Postępach Biochemii”. Autorzy artykułu odpowiadają za prawidłowość i ścisłość podanych informacji. Autorów obowiązuje korekta autorska. Koszty zmian tekstu w korekcie (poza poprawieniem błędów drukarskich) ponoszą autorzy. Artykuły honoruje się według obowiązujących stawek. Autorzy otrzymują bezpłatnie 25 odbitek swego artykułu; zamówienia na dodatkowe odbitki (płatne) należy zgłosić pisemnie odsyłając pracę po korekcie autorskiej. Redakcja prosi autorów o przestrzeganie następujących wskazówek: Forma maszynopisu: maszynopis pracy i wszelkie załączniki należy nadsyłać w dwu egzem plarzach. Maszynopis powinien być napisany jednostronnie, z podwójną interlinią, z marginesem ok. 4 cm po lewej i ok. 1 cm po prawej stronie; nie może zawierać więcej niż 60 znaków w jednym wierszu nie więcej niż 30 wierszy na stronie zgodnie z Normą Polską. -
Table 4.3 Enzyme Activities and Glycerol Utilization and Ethanol Synthesis Fluxes for Wild-Type MG1655 and Strains Overexpressing Glycerol Utilization Enzymes
Abstract Understanding Fermentative Glycerol Metabolism and its Application for the Production of Fuels and Chemicals by James M. Clomburg Due to its availability, low-price, and higher degree of reduction than lignocellulosic sugars, glycerol has become an attractive carbon source for the production of fuels and reduced chemicals. However, this high degree of reduction of carbon atoms in glycerol also results in significant challenges in regard to its utilization under fermentative conditions. Therefore, in order to unlock the full potential of microorganisms for the fermentative conversion of glycerol into fuels and chemicals, a detailed understanding of the anaerobic fermentation of glycerol is required. The work presented here highlights a comprehensive experimental investigation into fermentative glycerol metabolism in Escherichia coli, which has elucidated several key pathways and mechanisms. The activity of both the fermentative and respiratory glycerol dissimilation pathways was found to be important for maximum glycerol utilization, a consequence of the metabolic cycle and downstream effects created by the essential involvement of PEP-dependent dihydroxyacetone kinase (DHAK) in the fermentative glycerol dissimilation pathway. The decoupling of this cycle is of central importance during fermentative glycerol metabolism, and while multiple decoupling mechanisms were identified, their relative inefficiencies dictated not only their level of involvement, but also iii implicated the activity of other pathways/enzymes, including fumarate reductase and pyruvate kinase. The central role of the PEP-dependent DHAK, an enzyme whose transcription was found to be regulated by the cyclic adenosine monophosphate (cAMP) receptor protein (CRP)-cAMP complex, was also tied to the importance of multiple fructose 1,6-bisphosphotases (FBPases) encoded by fbp, glpX, and yggF. -
Discovery and Characterization of a Prominent Gut Microbial Glycyl Radical Enzyme Responsible for 4-Hydroxyproline Metabolism
Discovery and Characterization of a Prominent Gut Microbial Glycyl Radical Enzyme Responsible for 4-Hydroxyproline Metabolism The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Huang, Yue. 2019. Discovery and Characterization of a Prominent Gut Microbial Glycyl Radical Enzyme Responsible for 4- Hydroxyproline Metabolism. Doctoral dissertation, Harvard University, Graduate School of Arts & Sciences. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:41121269 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Discovery and characterization of a prominent gut microbial glycyl radical enzyme responsible for 4-hydroxyproline metabolism A dissertation presented by Yue Huang to the Committee on Higher Degrees in Chemical Biology in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Chemical Biology Harvard University Cambridge, Massachusetts October 2018 © 2018 – Yue Huang All rights reserved Dissertation advisor: Professor Emily P. Balskus Yue Huang Discovery and characterization of a prominent gut microbial glycyl radical enzyme responsible for 4-hydroxyproline metabolism Abstract The human gut is one of the most densely populated microbial habitat on Earth and the gut microbiota is extremely important in maintaining health and disease states. Advances in sequencing technologies have enabled us to gain a better understanding of microbiome compositions, but the majority of microbial genes are not functionally annotated. Therefore, the molecular basis by which gut microbes influence human health remains largely unknown. -
Roles of the Methylcitrate and Methylmalonyl-COA Pathways in Mycobacterial Metabolism and Pathogenesis" (2012)
Rockefeller University Digital Commons @ RU Student Theses and Dissertations 2012 Roles of the Methylcitrate and Methylmalonyl- COA Pathways in Mycobacterial Metabolism and Pathogenesis Manisha Ulhas Lotlikar Follow this and additional works at: http://digitalcommons.rockefeller.edu/ student_theses_and_dissertations Part of the Life Sciences Commons Recommended Citation Lotlikar, Manisha Ulhas, "Roles of the Methylcitrate and Methylmalonyl-COA Pathways in Mycobacterial Metabolism and Pathogenesis" (2012). Student Theses and Dissertations. Paper 245. This Thesis is brought to you for free and open access by Digital Commons @ RU. It has been accepted for inclusion in Student Theses and Dissertations by an authorized administrator of Digital Commons @ RU. For more information, please contact [email protected]. ROLES OF THE METHYLCITRATE AND METHYLMALONYL-COA PATHWAYS IN MYCOBACTERIAL METABOLISM AND PATHOGENESIS A Thesis Presented to the Faculty of The Rockefeller University in Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy by Manisha Ulhas Lotlikar June 2012 © Copyright by Manisha Ulhas Lotlikar 2012 ROLES OF THE METHYLCITRATE AND METHYLMALONYL-COA PATHWAYS IN MYCOBACTERIAL METABOLISM AND PATHOGENESIS Manisha Ulhas Lotlikar, Ph.D. The Rockefeller University 2012 Mycobacterium tuberculosis has been a human pathogen for the history of mankind, but we are only now beginning to understand how it is able to survive and persist indefinitely in the host. Understanding carbon metabolism of the pathogen during infection is key, not only as a source of potential drug targets, but also for elucidating the environment in vivo, so that drugs can be tested under relevant conditions. Studies have revealed that, during infection, M. tuberculosis relies on gluconeogenic carbon sources rather than sugars. -
Genome-Directed Analysis of Prophage Excision, Host Defence
www.nature.com/scientificreports OPEN Genome-directed analysis of prophage excision, host defence systems, and central fermentative Received: 02 December 2015 Accepted: 29 April 2016 metabolism in Clostridium Published: 19 September 2016 pasteurianum Michael E. Pyne1,†, Xuejia Liu1, Murray Moo-Young1, Duane A. Chung1,2,3 & C. Perry Chou1 Clostridium pasteurianum is emerging as a prospective host for the production of biofuels and chemicals, and has recently been shown to directly consume electric current. Despite this growing biotechnological appeal, the organism’s genetics and central metabolism remain poorly understood. Here we present a concurrent genome sequence for the C. pasteurianum type strain and provide extensive genomic analysis of the organism’s defence mechanisms and central fermentative metabolism. Next generation genome sequencing produced reads corresponding to spontaneous excision of a novel phage, designated ϕ6013, which could be induced using mitomycin C and detected using PCR and transmission electron microscopy. Methylome analysis of sequencing reads provided a near-complete glimpse into the organism’s restriction-modification systems. We also unveiled the chiefC. pasteurianum Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) locus, which was found to exemplify a Type I-B system. Finally, we show that C. pasteurianum possesses a highly complex fermentative metabolism whereby the metabolic pathways enlisted by the cell is governed by the degree of reductance of the substrate. Four distinct fermentation profiles, ranging from exclusively acidogenic to predominantly alcohologenic, were observed through redox consideration of the substrate. A detailed discussion of the organism’s central metabolism within the context of metabolic engineering is provided. Clostridium pasteurianum is an obligately anaerobic, endospore-forming soil bacterium that is emerging as an attractive industrial host owing to its unique fermentative metabolism1–3 and newfound capacity to directly con- sume electric current4. -
Key Enzymes Catalyzing Glycerol to 1,3-Propanediol
Jiang et al. Biotechnol Biofuels (2016) 9:57 DOI 10.1186/s13068-016-0473-6 Biotechnology for Biofuels REVIEW Open Access Key enzymes catalyzing glycerol to 1,3‑propanediol Wei Jiang1,2, Shizhen Wang1,2, Yuanpeng Wang1 and Baishan Fang1,2,3* Abstract Biodiesel can replace petroleum diesel as it is produced from animal fats and vegetable oils, and it produces about 10 % (w/w) glycerol, which is a promising new industrial microbial carbon, as a major by-product. One of the most potential applications of glycerol is its biotransformation to high value chemicals such as 1,3-propanediol (1,3-PD), dihydroxyacetone (DHA), succinic acid, etc., through microbial fermentation. Glycerol dehydratase, 1,3-propanediol dehydrogenase (1,3-propanediol-oxydoreductase), and glycerol dehydrogenase, which were encoded, respectively, by dhaB, dhaT, and dhaD and with DHA kinase are encompassed by the dha regulon, are the three key enzymes in glycerol bioconversion into 1,3-PD and DHA, and these are discussed in this review article. The summary of the main research direction of these three key enzyme and methods of glycerol bioconversion into 1,3-PD and DHA indicates their potential application in future enzymatic research and industrial production, especially in biodiesel industry. Keywords: Bioconversion, Biodiesel, Glycerol, Biocatalyst, GDHt, GDH, PDOR, Industrial enzyme, Multienzyme coupling, Renewable resources Background polytrimethylene terephthalate [16–24], as a monomer The demand for biofuels is increasing worldwide; as for cyclic compounds [25, 26], and as a polyglycol-type raw material, it is one of the most promising alternative lubricant. Besides, it may also serve as a solvent [27, 28].