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Takeuchi M, Amao Y. Biocatalytic fumarate synthesis from pyruvate and CO 2 as a feedstock. REACT CHEM ENG 2022. [DOI: 10.1039/d2re00039c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The biocatalytic synthesis of fumarate from CO2 and pyruvate vial-malate as an intermediate in an aqueous medium using a biocatalytic system consisting of malate dehydrogenase and fumarase in the presence of NADH is developed.
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Affiliation(s)
- Mika Takeuchi
- Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Yutaka Amao
- Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
- Research Centre of Artificial Photosynthesis (ReCAP), Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
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2
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Carbone A, Borok M, Damania B, Gloghini A, Polizzotto MN, Jayanthan RK, Fajgenbaum DC, Bower M. Castleman disease. Nat Rev Dis Primers 2021; 7:84. [PMID: 34824298 PMCID: PMC9584164 DOI: 10.1038/s41572-021-00317-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/06/2021] [Indexed: 01/02/2023]
Abstract
Castleman disease (CD), a heterogeneous group of disorders that share morphological features, is divided into unicentric CD and multicentric CD (MCD) according to the clinical presentation and disease course. Unicentric CD involves a solitary enlarged lymph node and mild symptoms and excision surgery is often curative. MCD includes a form associated with Kaposi sarcoma herpesvirus (KSHV) (also known as human herpesvirus 8) and a KSHV-negative idiopathic form (iMCD). iMCD can present in association with severe syndromes such as TAFRO (thrombocytopenia, ascites, fever, reticulin fibrosis and organomegaly) or POEMS (polyneuropathy, organomegaly, endocrinopathy, monoclonal plasma cell disorder and skin changes). KSHV-MCD often occurs in the setting of HIV infection or another cause of immune deficiency. The interplay between KSHV and HIV elevates the risk for the development of KSHV-induced disorders, including KSHV-MCD, KSHV-lymphoproliferation, KSHV inflammatory cytokine syndrome, primary effusion lymphoma and Kaposi sarcoma. A CD diagnosis requires a multidimensional approach, including clinical presentation and imaging, pathological features, and molecular virology. B cell-directed monoclonal antibody therapy is the standard of care in KSHV-MCD, and anti-IL-6 therapy is the recommended first-line therapy and only treatment of iMCD approved by the US FDA and EMA.
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Affiliation(s)
- Antonino Carbone
- Centro di Riferimento Oncologico (CRO), IRCCS, National Cancer Institute, Aviano, Italy.
- S. Maria degli Angeli Hospital, Pordenone, Italy.
| | - Margaret Borok
- Unit of Internal Medicine, University of Zimbabwe Faculty of Medicine and Health Sciences, Harare, Zimbabwe
| | - Blossom Damania
- Department of Microbiology and Immunology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Annunziata Gloghini
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Mark N Polizzotto
- Clinical Hub for Interventional Research, John Curtin School of Medical Research, The Australian National University, Canberra, NSW, Australia
| | - Raj K Jayanthan
- Castleman Disease Collaborative Network, Philadelphia, PA, USA
| | - David C Fajgenbaum
- Center for Cytokine Storm Treatment & Laboratory, University of Pennsylvania, Philadelphia, PA, USA
| | - Mark Bower
- National Centre for HIV Malignancy, Chelsea & Westminster Hospital, London, UK
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Zhang J, Zhao Y, Cao Y, Yu Z, Wang G, Li Y, Ye X, Li C, Lin X, Song H. sRNA-Based Screening Chromosomal Gene Targets and Modular Designing Escherichia coli for High-Titer Production of Aglycosylated Immunoglobulin G. ACS Synth Biol 2020; 9:1385-1394. [PMID: 32396719 DOI: 10.1021/acssynbio.0c00062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The production of the aglycosylated immunoglobulin G (IgG) in Escherichia coli has received wide interest for its analytical and therapeutic applications. To enhance the production titer of IgG, we first used synthetic sRNAs to perform a systematical analysis of the gene expression in the translational level in the glycolytic pathway (module 1) and the tricarboxylic acid (TCA) cycle (module 2) to reveal the critical genes for the efficient IgG production. Second, to provide sufficient amino acid precursors for the protein biosynthesis, amino acid biosynthesis pathways (module 3) were enhanced to facilitate the IgG production. Upon integrated engineering of these genes in the three modules (module 1, aceF; module 2, gltA and acnA; module 3, serB) and optimization of fermentation conditions, the recombinant E. coli enabled a titer of the full-assembled IgG of 4.5 ± 0.6 mg/L in flask cultures and 184 ± 9.2 mg/L in the 5 L high cell density fed-batch fermenter, which is, as far as we know, the highest reported titer of IgG production in recombinant E. coli.
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Affiliation(s)
- Jinhua Zhang
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Yanshu Zhao
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Yingxiu Cao
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Zhenpeng Yu
- Yangzhou Lianao Biopharmaceutical Co. Ltd. and Yangzhou Aurisco Pharmaceutical Co. Ltd., Wanmei Road No. 5, Hanjiang Economic Development Zone, Yangzhou City, Jiangsu Province 225100, P. R. China
| | - Guoping Wang
- Yangzhou Lianao Biopharmaceutical Co. Ltd. and Yangzhou Aurisco Pharmaceutical Co. Ltd., Wanmei Road No. 5, Hanjiang Economic Development Zone, Yangzhou City, Jiangsu Province 225100, P. R. China
| | - Yiqun Li
- Yangzhou Lianao Biopharmaceutical Co. Ltd. and Yangzhou Aurisco Pharmaceutical Co. Ltd., Wanmei Road No. 5, Hanjiang Economic Development Zone, Yangzhou City, Jiangsu Province 225100, P. R. China
| | - Xiaoqiong Ye
- Yangzhou Lianao Biopharmaceutical Co. Ltd. and Yangzhou Aurisco Pharmaceutical Co. Ltd., Wanmei Road No. 5, Hanjiang Economic Development Zone, Yangzhou City, Jiangsu Province 225100, P. R. China
| | - Congfa Li
- College of Food Science and Technology, Hainan University, Haikou 570228, P. R. China
| | - Xue Lin
- College of Food Science and Technology, Hainan University, Haikou 570228, P. R. China
| | - Hao Song
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
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Kronen M, Berg IA. Mesaconase/Fumarase FumD in Escherichia coli O157:H7 and Promiscuity of Escherichia coli Class I Fumarases FumA and FumB. PLoS One 2015; 10:e0145098. [PMID: 26658641 PMCID: PMC4682846 DOI: 10.1371/journal.pone.0145098] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/29/2015] [Indexed: 11/18/2022] Open
Abstract
Mesaconase catalyzes the hydration of mesaconate (methylfumarate) to (S)-citramalate. The enzyme participates in the methylaspartate pathway of glutamate fermentation as well as in the metabolism of various C5-dicarboxylic acids such as mesaconate or L-threo-β-methylmalate. We have recently shown that Burkholderia xenovorans uses a promiscuous class I fumarase to catalyze this reaction in the course of mesaconate utilization. Here we show that classical Escherichia coli class I fumarases A and B (FumA and FumB) are capable of hydrating mesaconate with 4% (FumA) and 19% (FumB) of the catalytic efficiency kcat/Km, compared to the physiological substrate fumarate. Furthermore, the genomes of 14.8% of sequenced Enterobacteriaceae (26.5% of E. coli, 90.6% of E. coli O157:H7 strains) possess an additional class I fumarase homologue which we designated as fumarase D (FumD). All these organisms are (opportunistic) pathogens. fumD is clustered with the key genes for two enzymes of the methylaspartate pathway of glutamate fermentation, glutamate mutase and methylaspartate ammonia lyase, converting glutamate to mesaconate. Heterologously produced FumD was a promiscuous mesaconase/fumarase with a 2- to 3-fold preference for mesaconate over fumarate. Therefore, these bacteria have the genetic potential to convert glutamate to (S)-citramalate, but the further fate of citramalate is still unclear. Our bioinformatic analysis identified several other putative mesaconase genes and revealed that mesaconases probably evolved several times from various class I fumarases independently. Most, if not all iron-dependent fumarases, are capable to catalyze mesaconate hydration.
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Affiliation(s)
- Miriam Kronen
- Mikrobiologie, Fakultät für Biologie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Ivan A. Berg
- Mikrobiologie, Fakultät für Biologie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
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Chen BS, Otten LG, Hanefeld U. Stereochemistry of enzymatic water addition to C=C bonds. Biotechnol Adv 2015; 33:526-46. [PMID: 25640045 DOI: 10.1016/j.biotechadv.2015.01.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 01/09/2015] [Accepted: 01/09/2015] [Indexed: 12/20/2022]
Abstract
Water addition to carbon-carbon double bonds using hydratases is attracting great interest in biochemistry. Most of the known hydratases are involved in primary metabolism and to a lesser extent in secondary metabolism. New hydratases have recently been added to the toolbox, both from natural sources or artificial metalloenzymes. In order to comprehensively understand how the hydratases are able to catalyse the water addition to carbon-carbon double bonds, this review will highlight the mechanistic and stereochemical studies of the enzymatic water addition to carbon-carbon double bonds, focusing on the syn/anti-addition and stereochemistry of the reaction.
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Affiliation(s)
- Bi-Shuang Chen
- Biokatalyse, Gebouw voor Scheikunde, Afdeling Biotechnologie, Technische Universiteit Delft, Julianalaan 136, 2628 BL Delft, The Netherlands
| | - Linda G Otten
- Biokatalyse, Gebouw voor Scheikunde, Afdeling Biotechnologie, Technische Universiteit Delft, Julianalaan 136, 2628 BL Delft, The Netherlands
| | - Ulf Hanefeld
- Biokatalyse, Gebouw voor Scheikunde, Afdeling Biotechnologie, Technische Universiteit Delft, Julianalaan 136, 2628 BL Delft, The Netherlands.
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Ito M, Baba T, Mori H, Mori H. Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab Eng 2005; 7:318-27. [PMID: 16095938 DOI: 10.1016/j.ymben.2005.06.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2005] [Revised: 06/03/2005] [Accepted: 06/21/2005] [Indexed: 11/19/2022]
Abstract
Escherichia coli is one of the best elucidated organisms. However, about 40% of E. coli genes have not been assigned to their function yet. We analyzed 1440 single gene knock-out mutants using the GN2-MicroPlate, which permits assay of 95 carbon-source utilizations simultaneously. In the knock-out library there are 1044 of so called y-genes with no apparent function. The raw dataset was analyzed and genes were interrelated by the clustering method of the GeneSpring software. In the resulted dendrogram of genes, a group of genes with known and related function tended to be assembled into a cluster. Our clustering method would be useful for functional assignment of so called y-genes with no apparent function, since the resulted dendrogram could connect y-genes to phenotype and function of well-studied genes.
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Affiliation(s)
- Mikito Ito
- Biofrontier Laboratories, Kyowa Hakko Kogyo Co. Ltd., Tokyo 194-8533, Japan
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Affiliation(s)
- Dennis H. Flint
- E. I. du Pont de Nemours and Co., Central Research and Development, Experimental Station, P.O. Box 80328, Wilmington, Delaware 19880-0328
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Yagi T, Yano T, Matsuno-Yagi A. Characteristics of the energy-transducing NADH-quinone oxidoreductase of Paracoccus denitrificans as revealed by biochemical, biophysical, and molecular biological approaches. J Bioenerg Biomembr 1993; 25:339-45. [PMID: 8226715 DOI: 10.1007/bf00762459] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A comparison of the mitochondrial NADH-ubiquinone oxidoreductase and the energy-transducing NADH-quinone oxidoreductase (NDH-1) of Paracoccus denitrificans revealed that both systems have similar electron-transfer and energy-transduction pathways. In addition, both complexes are sensitive to the same inhibitors and contain similar electron carriers, suggesting that the Paracoccus NDH-1 may serve as a useful model system for the study of the human enzyme complex. The gene cluster encoding the Paracoccus NDH-1 has been cloned and sequenced. It is composed of 18,106 base pairs and contains 14 structural genes and six unidentified reading frames (URFs). The structural genes, URFs, and their polypeptides have been characterized. We also discuss nucleotide sequences which are believed to play a role in the regulation of the NDH-1 gene cluster and Paracoccus NDH-1 subunits which may contain the binding sites of substrates and/or electron carriers.
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Affiliation(s)
- T Yagi
- Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, California 92037
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Flint DH. Escherichia coli fumarase A catalyzes the isomerization of enol and keto oxalacetic acid. Biochemistry 1993; 32:799-805. [PMID: 8422384 DOI: 10.1021/bi00054a009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Fumarase A, a product of the fumA gene of Escherichia coli, has been found to catalyze the isomerization of enol to keto oxalacetic acid (OAA) in addition to catalyzing the fumarase reaction. The kcat/Km for the isomerization is almost identical to that for the fumarase reaction. The isomerization reaction apparently takes place at the same active site as the fumarase reaction since both reactions show a similar sensitivity to inactivation by O2, both reactions are strongly inhibited by 2-hydroxy-3-nitropropionate, and the isomerization reaction is inhibited by fumarate and malate. The isomerization requires the presence of a [4Fe-4S] or [3Fe-4S] cluster, perhaps for structural rather than catalytic reasons. Hydration of enol OAA to the gem diol has been ruled out as a possible mechanism of isomerization on the basis of the preservation of the oxygen on carbon 2 and the position of protonation on carbon 3. The isomerization is not stereospecific in the position of protonation at carbon 3 but appears to be stereoselective, with protonation preferentially occurring in the 3-pro-S position. Porcine fumarase, isopropyl malate isomerase, and dihydroxyacid dehydratase do not catalyze this isomerization. Fumarase A and aconitase, two enzymes with 4Fe-4S clusters that bind a linear 4-carbon dicarboxylic acid moiety in the trans conformation during their normal hydro-lyase reaction, do catalyze this isomerization.
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Affiliation(s)
- D H Flint
- Central Research and Development Department, E. I. du Pont de Nemours and Company, Wilmington, Delaware 19880
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10
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Characterization of an Fe-S fumarase fromEscherichia coli. Protein J 1992. [DOI: 10.1007/bf01673765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Cammack R. Iron—Sulfur Clusters in Enzymes: Themes and Variations. ADVANCES IN INORGANIC CHEMISTRY 1992. [DOI: 10.1016/s0898-8838(08)60066-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Bell PJ, Andrews SC, Sivak MN, Guest JR. Nucleotide sequence of the FNR-regulated fumarase gene (fumB) of Escherichia coli K-12. J Bacteriol 1989; 171:3494-503. [PMID: 2656658 PMCID: PMC210076 DOI: 10.1128/jb.171.6.3494-3503.1989] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The nucleotide sequence of a 3,162-base-pair (bp) segment of DNA containing the FNR-regulated fumB gene, which encodes the anaerobic class I fumarase (FUMB) of Escherichia coli, was determined. The structural gene was found to comprise 1,641 bp, 547 codons (excluding the initiation and termination codons), and the gene product had a predicted Mr of 59,956. The amino acid sequence of FUMB contained the same number of residues as did that of the aerobic class I fumarase (FUMA), and there were identical amino acids at all but 56 positions (89.8% identity). There was no significant similarity between the class I fumarases and the class II enzyme (FUMC) except in one region containing the following consensus: Gly-Ser-Xxx-Ile-Met-Xxx-Xxx-Lys-Xxx-Asn. Some of the 56 amino acid substitutions must be responsible for the functional preferences of the enzymes for malate dehydration (FUMB) and fumarate hydration (FUMA). Significant similarities between the cysteine-containing sequence of the class I fumarases (FUMA and FUMB) and the mammalian aconitases were detected, and this finding further supports the view that these enzymes are all members of a family of iron-containing hydrolyases. The nucleotide sequence of a 1,142-bp distal sequence of an unidentified gene (genF) located upstream of fumB was also defined and found to encode a product that is homologous to the product of another unidentified gene (genA), located downstream of the neighboring aspartase gene (aspA).
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Affiliation(s)
- P J Bell
- Department of Microbiology, University of Sheffield, United Kingdom
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