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Mahmood S, Iqbal MW, Tang X, Zabed HM, Chen Z, Zhang C, Ravikumar Y, Zhao M, Qi X. A comprehensive review of recent advances in the characterization of L-rhamnose isomerase for the biocatalytic production of D-allose from D-allulose. Int J Biol Macromol 2024; 254:127859. [PMID: 37924916 DOI: 10.1016/j.ijbiomac.2023.127859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/05/2023] [Accepted: 11/01/2023] [Indexed: 11/06/2023]
Abstract
D-Allose and D-allulose are two important rare natural monosaccharides found in meager amounts. They are considered to be the ideal substitutes for table sugar (sucrose) for, their significantly lower calorie content with around 80 % and 70 % of the sweetness of sucrose, respectively. Additionally, both monosaccharides have gained much attention due to their remarkable physiological properties and excellent health benefits. Nevertheless, D-allose and D-allulose are rare in nature and difficult to produce by chemical methods. Consequently, scientists are exploring bioconversion methods to convert D-allulose into D-allose, with a key enzyme, L-rhamnose isomerase (L-RhIse), playing a remarkable role in this process. This review provides an in-depth analysis of the extractions, physiological functions and applications of D-allose from D-allulose. Specifically, it provides a detailed description of all documented L-RhIse, encompassing their biochemical properties including, pH, temperature, stabilities, half-lives, metal ion dependence, molecular weight, kinetic parameters, specific activities and specificities of the substrates, conversion ratio, crystal structure, catalytic mechanism as well as their wide-ranging applications across diverse fields. So far, L-RhIses have been discovered and characterized experimentally by numerous mesophilic and thermophilic bacteria. Furthermore, the crystal forms of L-RhIses from E. coli and Stutzerimonas/Pseudomonas stutzeri have been previously cracked, together with their catalytic mechanism. However, there is room for further exploration, particularly the molecular modification of L-RhIse for enhancing its catalytic performance and thermostability through the directed evolution or site-directed mutagenesis.
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Affiliation(s)
- Shahid Mahmood
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Muhammad Waheed Iqbal
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Xinrui Tang
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Hossain M Zabed
- School of Life Sciences, Guangzhou University, 230 Wai Huan Xi Road, Guangzhou 510006, Guangdong, China
| | - Ziwei Chen
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Cunsheng Zhang
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Yuvaraj Ravikumar
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Mei Zhao
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China.
| | - Xianghui Qi
- School of Food & Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China; School of Life Sciences, Guangzhou University, 230 Wai Huan Xi Road, Guangzhou 510006, Guangdong, China.
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Watanabe S, Fukumori F, Watanabe Y. Substrate and metabolic promiscuities of d-altronate dehydratase family proteins involved in non-phosphorylative d-arabinose, sugar acid, l-galactose and l-fucose pathways from bacteria. Mol Microbiol 2019; 112:147-165. [PMID: 30985034 DOI: 10.1111/mmi.14259] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2019] [Indexed: 11/29/2022]
Abstract
The gene context in microorganism genomes is of considerable help for identifying potential substrates. The C785_RS13685 gene in Herbaspirillum huttiense IAM 15032 is a member of the d-altronate dehydratase protein family, and which functions as a d-arabinonate dehydratase in vitro, is clustered with genes related to putative pentose metabolism. In the present study, further biochemical characterization and gene expression analyses revealed that l-xylonate is a physiological substrate that is ultimately converted to α-ketoglutarate via so-called Route II of a non-phosphorylative pathway. Several hexonates, including d-altronate, d-idonate and l-gluconate, which are also substrates of C785_RS13685, also significantly up-regulated the gene cluster containing C785_RS13685, suggesting a possibility that pyruvate and d- or l-glycerate were ultimately produced (novel Route III). On the contrary, ACAV_RS08155 of Acidovorax avenae ATCC 19860, a homologous gene to C785_RS13685, functioned as a d-altronate dehydratase in a novel l-galactose pathway, through which l-galactonate was epimerized at the C5 position by the sequential activity of two dehydrogenases, resulting in d-altronate. Furthermore, this pathway completely overlapped with Route III of the non-phosphorylative l-fucose pathway. The 'substrate promiscuity' of d-altronate dehydratase protein(s) is significantly expanded to 'metabolic promiscuity' in the d-arabinose, sugar acid, l-fucose and l-galactose pathways.
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Affiliation(s)
- Seiya Watanabe
- Department of Bioscience, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan.,Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan.,Center for Marine Environmental Studies, Ehime University, 2-5 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Fumiyasu Fukumori
- Faculty of Food and Nutritional Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Ora-gun, Gunma, 374-0193, Japan
| | - Yasuo Watanabe
- Department of Bioscience, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan.,Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan
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3
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Kerangart S, Cournoyer B, Loukiadis E. C-source metabolic profilings of foodborne Shiga-toxin producing E. coli match serogroup differentiations and highlight functional adaptations. Int J Food Microbiol 2017; 266:324-336. [PMID: 29217302 DOI: 10.1016/j.ijfoodmicro.2017.10.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/05/2017] [Accepted: 10/13/2017] [Indexed: 01/07/2023]
Abstract
The tropism of pathogenic STEC for foodstuffs and cattle reservoir is related to functional specializations. An investigation of C-source utilization patterns among and between STEC serogroups was performed using omnilog phenotypic microarrays (OM). OM functional groupings were compared with STEC phylogroups, seropathotypes, EFSA's molecular risk assessment groups and serogroups. OM INT reduction activities of 37 STEC strains growing on 190 C-substrates were compared. Each strain had its own specific C-utilization profile but 23% of the substrates was used by all strains, 47% by none, and 30% was variably metabolized. Galactose, mannose, N-acetyl-glucosamine (GlcNAc), and N-acetyl neuraminic acid (Neu5Ac) found in the mucus layer of the bovine small intestine were metabolized by all strains. The 56 most informative substrates divided the C-utilization patterns (CP) into three clusters with: (A) harboring all O157 and O145 strains; (B) all O26 strains, and (C) strains of the other serogroups. Significant correlations between INT reduction values of pair of strains per CP group supported these differentiations. CP of group A and B strains were respectively defective in the use of galactonic acid-γ-lactone and rhamnose. Most CP group C strains grew with l-lyxose. Adjusted Wallace coefficients analyses of the datasets indicated high probabilities for the prediction of the use of glycolic acid, β-hydroxybutyric acid, l-lyxose and d-galactonic acid-γ-lactone and 5-keto-d-gluconic acid by a serogroup. The use of a C-substrate could be predicted from the classification of a strain into a phylogroup or seropathotype. Significantly lower numbers of C-substrates were used by seropathotype A strains like O157 ones. Improvements of STEC identification keys were proposed using the most discriminant C-substrates found in this study.
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Affiliation(s)
- Stéphane Kerangart
- University of Lyon, Research group on "Bacterial Opportunistic Pathogens and Environment", UMR Ecologie Microbienne, CNRS 5557, INRA 1418, University Lyon 1, VetAgro Sup, 69280 Marcy L'Etoile, France
| | - Benoit Cournoyer
- University of Lyon, Research group on "Bacterial Opportunistic Pathogens and Environment", UMR Ecologie Microbienne, CNRS 5557, INRA 1418, University Lyon 1, VetAgro Sup, 69280 Marcy L'Etoile, France.
| | - Estelle Loukiadis
- University of Lyon, Research group on "Bacterial Opportunistic Pathogens and Environment", UMR Ecologie Microbienne, CNRS 5557, INRA 1418, University Lyon 1, VetAgro Sup, 69280 Marcy L'Etoile, France; University of Lyon, VetAgro Sup, LMAP, National Reference Laboratory for Escherichia coli (including VTEC), Marcy L'Etoile, France
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4
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Salusjärvi L, Toivari M, Vehkomäki ML, Koivistoinen O, Mojzita D, Niemelä K, Penttilä M, Ruohonen L. Production of ethylene glycol or glycolic acid from D-xylose in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2017; 101:8151-8163. [PMID: 29038973 DOI: 10.1007/s00253-017-8547-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 09/05/2017] [Accepted: 09/17/2017] [Indexed: 11/26/2022]
Abstract
The important platform chemicals ethylene glycol and glycolic acid were produced via the oxidative D-xylose pathway in the yeast Saccharomyces cerevisiae. The expression of genes encoding D-xylose dehydrogenase (XylB) and D-xylonate dehydratase (XylD) from Caulobacter crescentus and YagE or YjhH aldolase and aldehyde dehydrogenase AldA from Escherichia coli enabled glycolic acid production from D-xylose up to 150 mg/L. In strains expressing only xylB and xylD, 29 mg/L 2-keto-3-deoxyxylonic acid [(S)-4,5-dihydroxy-2-oxopentanoic acid] (2K3DXA) was produced and D-xylonic acid accumulated to ca. 9 g/L. A significant amount of D-xylonic acid (ca. 14%) was converted to 3-deoxypentonic acid (3DPA), and also, 3,4-dihydroxybutyric acid was formed. 2K3DXA was further converted to glycolaldehyde when genes encoding by either YagE or YjhH aldolase from E. coli were expressed. Reduction of glycolaldehyde to ethylene glycol by an endogenous aldo-keto reductase activity resulted further in accumulation of ethylene glycol of 14 mg/L. The possibility of simultaneous production of lactic and glycolic acids was evaluated by expression of gene encoding lactate dehydrogenase ldhL from Lactobacillus helveticus together with aldA. Interestingly, this increased the accumulation of glycolic acid to 1 g/L. The D-xylonate dehydratase activity in yeast was notably low, possibly due to inefficient Fe-S cluster synthesis in the yeast cytosol, and leading to D-xylonic acid accumulation. The dehydratase activity was significantly improved by targeting its expression to mitochondria or by altering the Fe-S cluster metabolism of the cells with FRA2 deletion.
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Affiliation(s)
- Laura Salusjärvi
- VTT Technical Research Centre of Finland Ltd., Solutions for Natural Resources and Environment, Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland.
| | - Mervi Toivari
- VTT Technical Research Centre of Finland Ltd., Solutions for Natural Resources and Environment, Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Maija-Leena Vehkomäki
- VTT Technical Research Centre of Finland Ltd., Solutions for Natural Resources and Environment, Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Outi Koivistoinen
- VTT Technical Research Centre of Finland Ltd., Solutions for Natural Resources and Environment, Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Dominik Mojzita
- VTT Technical Research Centre of Finland Ltd., Solutions for Natural Resources and Environment, Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Klaus Niemelä
- VTT Technical Research Centre of Finland Ltd., Solutions for Natural Resources and Environment, Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., Solutions for Natural Resources and Environment, Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Laura Ruohonen
- VTT Technical Research Centre of Finland Ltd., Solutions for Natural Resources and Environment, Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
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5
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Kim YS, Kim DY, Park CS. Production of l-rhamnulose, a rare sugar, from l-rhamnose using commercial immobilized glucose isomerase. BIOCATAL BIOTRANSFOR 2017. [DOI: 10.1080/10242422.2017.1388374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Yeong-Su Kim
- Division of Plant Resource Industry, Baekdudaegan National Arboretum, Bonghwa, South Korea
| | - Do-Yeon Kim
- Department of Convergence Industrialization, International Ginseng and Herb Research Institute, Geumsan, South Korea
| | - Chang-Su Park
- Department of Food Science and Technology, Catholic University of Daegu, Hayang, South Korea
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The aldehyde dehydrogenase, AldA, is essential for L-1,2-propanediol utilization in laboratory-evolved Escherichia coli. Microbiol Res 2017; 194:47-52. [DOI: 10.1016/j.micres.2016.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 10/29/2016] [Indexed: 11/19/2022]
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7
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Watanabe S, Utsumi Y, Sawayama S, Watanabe Y. Identification and characterization of d-arabinose reductase and d-arabinose transporters from Pichia stipitis. Biosci Biotechnol Biochem 2016; 80:2151-2158. [DOI: 10.1080/09168451.2016.1204221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Abstract
d-xylose and l-arabinose are the major constituents of plant lignocelluloses, and the related fungal metabolic pathways have been extensively examined. Although Pichia stipitis CBS 6054 grows using d-arabinose as the sole carbon source, the hypothetical pathway has not yet been clarified at the molecular level. We herein purified NAD(P)H-dependent d-arabinose reductase from cells grown on d-arabinose, and found that the enzyme was identical to the known d-xylose reductase (XR). The enzyme activity of XR with d-arabinose was previously reported to be only 1% that with d-xylose. The kcat/Km value with d-arabinose (1.27 min−1 mM−1), which was determined using the recombinant enzyme, was 13.6- and 10.5-fold lower than those with l-arabinose and d-xylose, respectively. Among the 34 putative sugar transporters from P. stipitis, only seven genes exhibited uptake ability not only for d-arabinose, but also for d-glucose and other pentose sugars including d-xylose and l-arabinose in Saccharomyces cerevisiae.
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Affiliation(s)
- Seiya Watanabe
- Department of Bioscience, Graduate School of Agriculture, Ehime University, Matsuyama, Japan
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Japan
| | - Yuki Utsumi
- Department of Bioscience, Graduate School of Agriculture, Ehime University, Matsuyama, Japan
| | | | - Yasuo Watanabe
- Department of Bioscience, Graduate School of Agriculture, Ehime University, Matsuyama, Japan
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8
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Pereira B, Li ZJ, De Mey M, Lim CG, Zhang H, Hoeltgen C, Stephanopoulos G. Efficient utilization of pentoses for bioproduction of the renewable two-carbon compounds ethylene glycol and glycolate. Metab Eng 2016; 34:80-87. [DOI: 10.1016/j.ymben.2015.12.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 12/05/2015] [Accepted: 12/12/2015] [Indexed: 10/22/2022]
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9
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Affiliation(s)
- Liuqing Wen
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Kenneth Huang
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Yunpeng Liu
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
- National
Glycoengineering Research Center, Shandong University, Jinan 250100, China
| | - Peng George Wang
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
- National
Glycoengineering Research Center, Shandong University, Jinan 250100, China
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10
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Wen L, Zang L, Huang K, Li S, Wang R, Wang PG. Efficient enzymatic synthesis of L-rhamnulose and L-fuculose. Bioorg Med Chem Lett 2016; 26:969-972. [PMID: 26778148 PMCID: PMC5984655 DOI: 10.1016/j.bmcl.2015.12.051] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/12/2015] [Accepted: 12/15/2015] [Indexed: 11/23/2022]
Abstract
L-Rhamnulose (6-deoxy-L-arabino-2-hexulose) and L-fuculose (6-deoxy-L-lyxo-2-hexulose) were prepared from L-rhamnose and L-fucose by a two-step strategy. In the first reaction step, isomerization of L-rhamnose to L-rhamnulose, or L-fucose to L-fuculose was combined with a targeted phosphorylation reaction catalyzed by L-rhamnulose kinase (RhaB). The by-products (ATP and ADP) were selectively removed by silver nitrate precipitation method. In the second step, the phosphate group was hydrolyzed to produce L-rhamnulose or L-fuculose with purity exceeding 99% in more than 80% yield (gram scale).
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Affiliation(s)
- Liuqing Wen
- Department of Chemistry and Center for Therapeutics and Diagnostics, Georgia State University, Atlanta, GA 30303, USA
| | - Lanlan Zang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Kenneth Huang
- Department of Chemistry and Center for Therapeutics and Diagnostics, Georgia State University, Atlanta, GA 30303, USA
| | - Shanshan Li
- Department of Chemistry and Center for Therapeutics and Diagnostics, Georgia State University, Atlanta, GA 30303, USA
| | - Runling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China.
| | - Peng George Wang
- Department of Chemistry and Center for Therapeutics and Diagnostics, Georgia State University, Atlanta, GA 30303, USA.
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11
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Aziz RK, Khaw VL, Monk JM, Brunk E, Lewis R, Loh SI, Mishra A, Nagle AA, Satyanarayana C, Dhakshinamoorthy S, Luche M, Kitchen DB, Andrews KA, Palsson BØ, Charusanti P. Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC. Front Microbiol 2015; 6:958. [PMID: 26441892 PMCID: PMC4585216 DOI: 10.3389/fmicb.2015.00958] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/28/2015] [Indexed: 11/13/2022] Open
Abstract
Mathematical models of biochemical networks form a cornerstone of bacterial systems biology. Inconsistencies between simulation output and experimental data point to gaps in knowledge about the fundamental biology of the organism. One such inconsistency centers on the gene aldA in Escherichia coli: it is essential in a computational model of E. coli metabolism, but experimentally it is not. Here, we reconcile this disparity by providing evidence that aldA and prpC form a synthetic lethal pair, as the double knockout could only be created through complementation with a plasmid-borne copy of aldA. Moreover, virtual and biological screening against the two proteins led to a set of compounds that inhibited the growth of E. coli and Salmonella enterica serovar Typhimurium synergistically at 100-200 μM individual concentrations. These results highlight the power of metabolic models to drive basic biological discovery and their potential use to discover new combination antibiotics.
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Affiliation(s)
- Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University Cairo, Egypt ; Department of Bioengineering, University of California, San Diego La Jolla, CA, USA
| | - Valerie L Khaw
- Department of Bioengineering, University of California, San Diego La Jolla, CA, USA
| | - Jonathan M Monk
- Department of Bioengineering, University of California, San Diego La Jolla, CA, USA
| | - Elizabeth Brunk
- Department of Bioengineering, University of California, San Diego La Jolla, CA, USA
| | - Robert Lewis
- Computer-Aided Drug Discovery, Albany Molecular Research, Inc., Albany NY, USA
| | - Suh I Loh
- Biology and Pharmacology, Albany Molecular Research Singapore Research Centre, Pte. Ltd., Singapore Singapore
| | - Arti Mishra
- Biology and Pharmacology, Albany Molecular Research Singapore Research Centre, Pte. Ltd., Singapore Singapore
| | - Amrita A Nagle
- Biology and Pharmacology, Albany Molecular Research Singapore Research Centre, Pte. Ltd., Singapore Singapore
| | - Chitkala Satyanarayana
- Biology and Pharmacology, Albany Molecular Research Singapore Research Centre, Pte. Ltd., Singapore Singapore
| | | | - Michele Luche
- Computer-Aided Drug Discovery, Albany Molecular Research, Inc., Albany NY, USA
| | - Douglas B Kitchen
- Computer-Aided Drug Discovery, Albany Molecular Research, Inc., Albany NY, USA
| | - Kathleen A Andrews
- Department of Bioengineering, University of California, San Diego La Jolla, CA, USA
| | - Bernhard Ø Palsson
- Department of Bioengineering, University of California, San Diego La Jolla, CA, USA
| | - Pep Charusanti
- Department of Bioengineering, University of California, San Diego La Jolla, CA, USA ; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark Hørsholm, Denmark
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Abdoul Zabar J, Lorillière M, Yi D, Saravanan T, Devamani T, Nauton L, Charmantray F, Hélaine V, Fessner WD, Hecquet L. Engineering a Thermostable Transketolase for Unnatural Conversion of (2S
)-Hydroxyaldehydes. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201500207] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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13
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The transport and mediation mechanisms of the common sugars in Escherichia coli. Biotechnol Adv 2014; 32:905-19. [DOI: 10.1016/j.biotechadv.2014.04.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 03/23/2014] [Accepted: 04/18/2014] [Indexed: 11/17/2022]
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14
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Characterization ofMesorhizobium lotiL-Rhamnose Isomerase and Its Application toL-Talose Production. Biosci Biotechnol Biochem 2014; 75:1006-9. [DOI: 10.1271/bbb.110018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Park CS. Characterization of a recombinant l-rhamnose isomerase from Bacillus subtilis and its application on production of l-lyxose and l-mannose. BIOTECHNOL BIOPROC E 2014. [DOI: 10.1007/s12257-013-0597-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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16
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Characterization of a recombinant L-rhamnose isomerase from Dictyoglomus turgidum and its application for L-rhamnulose production. Biotechnol Lett 2012; 35:259-64. [PMID: 23070627 DOI: 10.1007/s10529-012-1069-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 10/04/2012] [Indexed: 10/27/2022]
Abstract
A putative recombinant enzyme from Dictyoglomus turgidum was characterized and immobilized on Duolite A568 beads. The native enzyme was a 46 kDa tetramer. Its activity was highest for L-rhamnose, indicating that it is an L-rhamnose isomerase. The maximum activities of both the free and immobilized enzymes for L-rhamnose isomerization were at pH 8.0 and 75 °C in the presence of Mn(2+). Under these conditions, the half-lives of the free and immobilized enzymes were 28 and 112 h, respectively. In a packed-bed bioreactor, the immobilized enzyme produced an average of 130 g L-rhamnulose l(-1) from 300 g L-rhamnose l(-1) after 240 h at pH 8.0, 70 °C, and 0.6 h(-1), with a productivity of 78 g l(-1) h(-1) and a conversion yield of 43 %. To the best of our knowledge, this is the first report describing the enzymatic production of L-rhamnulose.
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17
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Microbial metabolism and biotechnological production of d-allose. Appl Microbiol Biotechnol 2011; 91:229-35. [DOI: 10.1007/s00253-011-3370-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2011] [Revised: 05/04/2011] [Accepted: 05/05/2011] [Indexed: 10/18/2022]
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18
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Patel DH, Wi SG, Lee SG, Lee DS, Song YH, Bae HJ. Substrate specificity of the Bacillus licheniformis lyxose isomerase YdaE and its application in in vitro catalysis for bioproduction of lyxose and glucose by two-step isomerization. Appl Environ Microbiol 2011; 77:3343-50. [PMID: 21421786 PMCID: PMC3126444 DOI: 10.1128/aem.02693-10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Accepted: 03/10/2011] [Indexed: 12/25/2022] Open
Abstract
Enzymatic processes are useful for industrially important sugar production, and in vitro two-step isomerization has proven to be an efficient process in utilizing readily available sugar sources. A hypothetical uncharacterized protein encoded by ydaE of Bacillus licheniformis was found to have broad substrate specificities and has shown high catalytic efficiency on D-lyxose, suggesting that the enzyme is D-lyxose isomerase. Escherichia coli BL21 expressing the recombinant protein, of 19.5 kDa, showed higher activity at 40 to 45°C and pH 7.5 to 8.0 in the presence of 1.0 mM Mn²+. The apparent K(m) values for D-lyxose and D-mannose were 30.4 ± 0.7 mM and 26 ± 0.8 mM, respectively. The catalytic efficiency (k(cat)/K(m)) for lyxose (3.2 ± 0.1 mM⁻¹ s⁻¹) was higher than that for D-mannose (1.6 mM⁻¹ s⁻¹). The purified protein was applied to the bioproduction of D-lyxose and D-glucose from d-xylose and D-mannose, respectively, along with the thermostable xylose isomerase of Thermus thermophilus HB08. From an initial concentration of 10 mM D-lyxose and D-mannose, 3.7 mM and 3.8 mM D-lyxose and D-glucose, respectively, were produced by two-step isomerization. This two-step isomerization is an easy method for in vitro catalysis and can be applied to industrial production.
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Affiliation(s)
- Darshan H. Patel
- Bio-energy Research Institute, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Seung Gon Wi
- Bio-energy Research Institute, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Seong-Gene Lee
- Department of Biotechnology, Bio-energy Research Center, Biotechnology Research Institute, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Dae-Seok Lee
- Bio-energy Research Institute, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Youn-ho Song
- Department of Biotechnology, Bio-energy Research Center, Biotechnology Research Institute, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Hyeun-Jong Bae
- Bio-energy Research Institute, Chonnam National University, Gwangju 500-757, Republic of Korea
- Department of Forest Products and Technology (BK21 Program), Chonnam National University, Gwangju 500-757, Republic of Korea
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju 500-757, Republic of Korea
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19
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Yoshida H, Takeda K, Izumori K, Kamitori S. Elucidation of the role of Ser329 and the C-terminal region in the catalytic activity of Pseudomonas stutzeri L-rhamnose isomerase. Protein Eng Des Sel 2010; 23:919-27. [PMID: 20977999 DOI: 10.1093/protein/gzq077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Pseudomonas stutzeri l-rhamnose isomerase (l-RhI) is capable of catalyzing the isomerization between various aldoses and ketoses, showing high catalytic activity with broad substrate-specificity compared with Escherichia coli l-RhI. In a previous study, the crystal structure of P. stutzeri l-RhI revealed an active site comparable with that of E. coli l-RhI and d-xylose isomerases (d-XIs) with structurally conserved amino acids, but also with a different residue seemingly responsible for the specificity of P. stutzeri l-RhI, though the residue itself does not interact with the bound substrate. This residue, Ser329, corresponds to Phe336 in E. coli l-RhI and Lys294 in Actinoplanes missouriensis d-XI. To elucidate the role of Ser329 in P. stutzeri l-RhI, we constructed mutants, S329F (E. coli l-RhI type), S329K (A. missouriensis d-XI type), S329L and S329A. Analyses of the catalytic activity and crystal structure of the mutants revealed a hydroxyl group of Ser329 to be crucial for catalytic activity via interaction with a water molecule. In addition, in complexes with substrate, the mutants S329F and S329L exhibited significant electron density in the C-terminal region not observed in the wild-type P. stutzeri l-RhI. The C-terminal region of P. stutzeri l-RhI has flexibility and shows a flip-flop movement at the inter-molecular surface of the dimeric form.
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Affiliation(s)
- Hiromi Yoshida
- Division of Structural Biology, Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
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20
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Lin CJ, Tseng WC, Lin TH, Liu SM, Tzou WS, Fang TY. Characterization of a thermophilic L-rhamnose isomerase from Thermoanaerobacterium saccharolyticum NTOU1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2010; 58:10431-10436. [PMID: 20822145 DOI: 10.1021/jf102063q] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
L-rhamnose isomerase (EC 5.3.1.14, L-RhI) catalyzes the reversible aldose-ketose isomerization between L-rhamnose and L-rhamnulose. In this study, the L-Rhi gene encoding L-Rhi was PCR-cloned from Thermoanaerobacterium saccharolyticum NTOU1 and then expressed in Escherichia coli. A high yield of the active L-RhI, 9780 U/g of wet cells, was obtained in the presence of 0.2 mM IPTG induction. L-RhI was purified sequentially using heat treatment, nucleic acid precipitation, and anion-exchange chromatography. The purified L-RhI showed an apparent optimal pH of 7 and an optimal temperature at 75 °C. The enzyme was stable at pH values ranging from 5 to 9, and the activity was fully retained after a 2 h incubation at 40-70 °C. L-RhI from T. saccharolyticum NTOU1 is the most thermostable L-RhI to date, and it has a high specific activity (163 U/mg) and an acceptable purity after heat treatment, suggesting that this enzyme has the potential to be used in rare sugar production.
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Affiliation(s)
- Chia-Jui Lin
- Department of Food Science, National Taiwan Ocean University, Keelung, Taiwan
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21
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Cloning and characterization of a rhamnose isomerase from Bacillus halodurans. Appl Microbiol Biotechnol 2010; 89:635-44. [DOI: 10.1007/s00253-010-2844-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 08/07/2010] [Accepted: 08/14/2010] [Indexed: 10/19/2022]
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22
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Characterization of a recombinant thermostable l-rhamnose isomerase from Thermotoga maritima ATCC 43589 and its application in the production of l-lyxose and l-mannose. Biotechnol Lett 2010; 32:1947-53. [PMID: 20809285 DOI: 10.1007/s10529-010-0385-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 08/18/2010] [Indexed: 10/19/2022]
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23
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Carbonell P, Faulon JL. Molecular signatures-based prediction of enzyme promiscuity. Bioinformatics 2010; 26:2012-9. [DOI: 10.1093/bioinformatics/btq317] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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24
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Transcriptional activation of the aldehyde reductase YqhD by YqhC and its implication in glyoxal metabolism of Escherichia coli K-12. J Bacteriol 2010; 192:4205-14. [PMID: 20543070 DOI: 10.1128/jb.01127-09] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The reactive alpha-oxoaldehydes such as glyoxal (GO) and methylglyoxal (MG) are generated in vivo from sugars through oxidative stress. GO and MG are believed to be removed from cells by glutathione-dependent glyoxalases and other aldehyde reductases. We isolated a number of GO-resistant (GO(r)) mutants from Escherichia coli strain MG1655 on LB plates containing 10 mM GO. By tagging the mutations with the transposon TnphoA-132 and determining their cotransductional linkages, we were able to identify a locus to which most of the GO(r) mutations were mapped. DNA sequencing of the locus revealed that it contains the yqhC gene, which is predicted to encode an AraC-type transcriptional regulator of unknown function. The GO(r) mutations we identified result in missense changes in yqhC and were concentrated in the predicted regulatory domain of the protein, thereby constitutively activating the product of the adjacent gene yqhD. The transcriptional activation of yqhD by wild-type YqhC and its mutant forms was established by an assay with a beta-galactosidase reporter fusion, as well as with real-time quantitative reverse transcription-PCR. We demonstrated that YqhC binds to the promoter region of yqhD and that this binding is abolished by a mutation in the potential target site, which is similar to the consensus sequence of its homolog SoxS. YqhD facilitates the removal of GO through its NADPH-dependent enzymatic reduction activity by converting it to ethadiol via glycolaldehyde, as detected by nuclear magnetic resonance, as well as by spectroscopic measurements. Therefore, we propose that YqhC is a transcriptional activator of YqhD, which acts as an aldehyde reductase with specificity for certain aldehydes, including GO.
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25
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Plantinga TH, Van Der Does C, Badia J, Aguilar J, Konings WN, Driessen AJM. Functional characterization of theEscherichia coliK-12 yiaMNO transport protein genes. Mol Membr Biol 2009; 21:51-7. [PMID: 14668138 DOI: 10.1080/09687680310001607369] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The yiaMNO genes of Escherichia coli K-12 encode a binding protein-dependent secondary, or tri-partite ATP-independent periplasmic (TRAP), transporter. Since only a few members of this family have been functionally characterized to date, we aimed to identify the substrate for this transporter. Cells that constitutively express the yiaK-S gene cluster metabolized the rare pentose L-xylulose, while deletion of the yiaMNO transporter genes reduced L-xylulose metabolism. The periplasmic substrate-binding protein YiaO was found to bind L-xylulose, and stimulated L-xylulose uptake by spheroplasts. These date indicate that the yiaMNO transporter mediates uptake of this rare pentose.
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Affiliation(s)
- Titia H Plantinga
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, P.O. Box 14, 9750 AA Haren, The Netherlands
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26
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Watanabe S, Saimura M, Makino K. Eukaryotic and bacterial gene clusters related to an alternative pathway of nonphosphorylated L-rhamnose metabolism. J Biol Chem 2008; 283:20372-82. [PMID: 18505728 DOI: 10.1074/jbc.m801065200] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Entner-Doudoroff (ED) pathway is a classic central pathway of d-glucose metabolism in all three phylogenetic domains. On the other hand, Archaea and/or bacteria possess several modified versions of the ED pathway, in which nonphosphorylated intermediates are involved. Several fungi, including Pichia stipitis and Debaryomyces hansenii, possess an alternative pathway of L-rhamnose metabolism, which is different from the known bacterial pathway. Gene cluster related to this hypothetical pathway was identified by bioinformatic analysis using the metabolic enzymes involved in analogous sugar pathways to the ED pathway. Furthermore, the homologous gene cluster was found not only in many other fungi but also several bacteria, including Azotobacter vinelandii. Four putative metabolic genes, LRA1-4, were cloned, overexpressed in Escherichia coli, and purified. Substrate specificity and kinetic analysis revealed that nonphosphorylated intermediates related to L-rhamnose are significant active substrates for the purified LRA1-4 proteins. Furthermore, L-2-keto-3-deoxyrhamnonate was structurally identified as both reaction products of dehydration by LRA3 and aldol condensation by LRA4. These results suggested that the LRA1-4 genes encode L-rhamnose 1-dehydrogenase, L-rhamnono-gamma-lactonase, L-rhamnonate dehydratase, and L-KDR aldolase, respectively, by which L-rhamnose is converted into pyruvate and L-lactaldehyde through analogous reaction steps to the ED pathway. There was no evolutionary relationship between L-KDR aldolases from fungi and bacteria.
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Affiliation(s)
- Seiya Watanabe
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, Japan.
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27
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Poonperm W, Takata G, Okada H, Morimoto K, Granström TB, Izumori K. Cloning, sequencing, overexpression and characterization of L-rhamnose isomerase from Bacillus pallidus Y25 for rare sugar production. Appl Microbiol Biotechnol 2007; 76:1297-307. [PMID: 17653540 DOI: 10.1007/s00253-007-1109-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Revised: 06/28/2007] [Accepted: 07/01/2007] [Indexed: 11/27/2022]
Abstract
The L-rhamnose isomerase gene (L-rhi) encoding for L-rhamnose isomerase (L-RhI) from Bacillus pallidus Y25, a facultative thermophilic bacterium, was cloned and overexpressed in Escherichia coli with a cooperation of the 6xHis sequence at a C-terminal of the protein. The open reading frame of L-rhi consisted of 1,236 nucleotides encoding 412 amino acid residues with a calculated molecular mass of 47,636 Da, showing a good agreement with the native enzyme. Mass-produced L-RhI was achieved in a large quantity (470 mg/l broth) as a soluble protein. The recombinant enzyme was purified to homogeneity by a single step purification using a Ni-NTA affinity column chromatography. The purified recombinant L-RhI exhibited maximum activity at 65 degrees C (pH 7.0) under assay conditions, while 90% of the initial enzyme activity could be retained after incubation at 60 degrees C for 60 min. The apparent affinity (K(m)) and catalytic efficiency (k(cat)/K(m)) for L-rhamnose (at 65 degrees C) were 4.89 mM and 8.36 x 10(5) M(-1) min(-1), respectively. The enzyme demonstrated relatively low levels of amino acid sequence similarity (42 and 12%), higher thermostability, and different substrate specificity to those of E. coli and Pseudomonas stutzeri, respectively. The enzyme has a good catalyzing activity at 50 degrees C, for D: -allose, L-mannose, D-ribulose, and L-talose from D-psicose, L-fructose, D-ribose and L-tagatose with a conversion yield of 35, 25, 16 and 10%, respectively, without a contamination of by-products. These findings indicated that the recombinant L-RhI from B. pallidus is appropriate for use as a new source of rare sugar producing enzyme on a mass scale production.
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Affiliation(s)
- Wayoon Poonperm
- Rare Sugar Research Center and Faculty of Agriculture, Kagawa University, Ikenobe 2393, Miki, Kagawa Prefecture 761-0795, Japan
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28
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Grueninger D, Schulz GE. Substrate spectrum of L-rhamnulose kinase related to models derived from two ternary complex structures. FEBS Lett 2007; 581:3127-30. [PMID: 17568582 DOI: 10.1016/j.febslet.2007.05.075] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2007] [Revised: 05/29/2007] [Accepted: 05/29/2007] [Indexed: 11/18/2022]
Abstract
The enzyme L-rhamnulose kinase from Escherichia coli participates in the degradation pathway of L-rhamnose, a common natural deoxy-hexose. The structure of the enzyme in a ternary complex with its substrates ADP and L-rhamnulose has been determined at 1.55A resolution and refined to R(cryst)/R(free) values of 0.179/0.209. The result was compared with the lower resolution structure of a corresponding complex containing L-fructose instead of L-rhamnulose. In light of the two established sugar positions and conformations, a number of rare sugars have been modeled into the active center of L-rhamnulose kinase and the model structures have been compared with the known enzymatic phosphorylation rates. Rare sugars are of rising interest for the synthesis of bioactive compounds.
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Affiliation(s)
- Dirk Grueninger
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany
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29
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Cho EA, Lee DW, Cha YH, Lee SJ, Jung HC, Pan JG, Pyun YR. Characterization of a novel D-lyxose isomerase from Cohnella laevoribosii RI-39 sp. nov. J Bacteriol 2006; 189:1655-63. [PMID: 17189362 PMCID: PMC1855708 DOI: 10.1128/jb.01568-06] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A newly isolated bacterium, Cohnella laevoribosii RI-39, could grow in a defined medium with L-ribose as the sole carbon source. A 21-kDa protein isomerizing L-ribose to L-ribulose, as well as D-lyxose to D-xylulose, was purified to homogeneity from this bacterium. Based on the N-terminal and internal amino acid sequences of the purified enzyme obtained by N-terminal sequencing and quantitative time of flight mass spectrometry-mass spectrometry analyses, a 549-bp gene (lyxA) encoding D-lyxose (L-ribose) isomerase was cloned and expressed in Escherichia coli. The purified endogenous enzyme and the recombinant enzyme formed homodimers that were activated by Mn(2+). C. laevoribosii D-lyxose (L-ribose) isomerase (CLLI) exhibits maximal activity at pH 6.5 and 70 degrees C in the presence of Mn(2+) for D-lyxose and L-ribose, and its isoelectric point (pI) is 4.2 (calculated pI, 4.9). The enzyme is specific for D-lyxose, L-ribose, and D-mannose, with apparent K(m) values of 22.4 +/- 1.5 mM, 121.7 +/- 10.8 mM, and 34.0 +/- 1.1 mM, respectively. The catalytic efficiencies (k(cat)/K(m)) of CLLI were 84.9 +/- 5.8 mM(-1) s(-1) for D-lyxose (V(max), 5,434.8 U mg(-1)), 0.2 mM(-1) s(-1) for L-ribose (V(max), 75.5 +/- 6.0 U mg(-1)), and 1.4 +/- 0.1 mM(-1) s(-1) for D-mannose (V(max), 131.8 +/- 7.4 U mg(-1)). The ability of lyxA to permit E. coli cells to grow on D-lyxose and L-ribose and homology searches of other sugar-related enzymes, as well as previously described sugar isomerases, suggest that CLLI is a novel type of rare sugar isomerase.
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Affiliation(s)
- Eun-Ah Cho
- Department of Biotechnology, Yonsei University, Seoul 120-749, Korea
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30
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Di Costanzo L, Gomez GA, Christianson DW. Crystal structure of lactaldehyde dehydrogenase from Escherichia coli and inferences regarding substrate and cofactor specificity. J Mol Biol 2006; 366:481-93. [PMID: 17173928 PMCID: PMC1866264 DOI: 10.1016/j.jmb.2006.11.023] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Revised: 11/03/2006] [Accepted: 11/04/2006] [Indexed: 11/18/2022]
Abstract
Aldehyde dehydrogenases catalyze the oxidation of aldehyde substrates to the corresponding carboxylic acids. Lactaldehyde dehydrogenase from Escherichia coli (aldA gene product, P25553) is an NAD(+)-dependent enzyme implicated in the metabolism of l-fucose and l-rhamnose. During the heterologous expression and purification of taxadiene synthase from the Pacific yew, lactaldehyde dehydrogenase from E. coli was identified as a minor (</=5%) side-product subsequent to its unexpected crystallization. Accordingly, we now report the serendipitous crystal structure determination of unliganded lactaldehyde dehydrogenase from E. coli determined by the technique of multiple isomorphous replacement using anomalous scattering at 2.2 A resolution. Additionally, we report the crystal structure of the ternary enzyme complex with products lactate and NADH at 2.1 A resolution, and the crystal structure of the enzyme complex with NADPH at 2.7 A resolution. The structure of the ternary complex reveals that the nicotinamide ring of the cofactor is disordered between two conformations: one with the ring positioned in the active site in the so-called hydrolysis conformation, and another with the ring extended out of the active site into the solvent region, designated the out conformation. This represents the first crystal structure of an aldehyde dehydrogenase-product complex. The active site pocket in which lactate binds is more constricted than that of medium-chain dehydrogenases such as the YdcW gene product of E. coli. The structure of the binary complex with NADPH reveals the first view of the structural basis of specificity for NADH: the negatively charged carboxylate group of E179 destabilizes the binding of the 2'-phosphate group of NADPH sterically and electrostatically, thereby accounting for the lack of enzyme activity with this cofactor.
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Affiliation(s)
- Luigi Di Costanzo
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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31
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Grabar TB, Zhou S, Shanmugam KT, Yomano LP, Ingram LO. Methylglyoxal bypass identified as source of chiral contamination in l(+) and d(-)-lactate fermentations by recombinant Escherichia coli. Biotechnol Lett 2006; 28:1527-35. [PMID: 16868860 DOI: 10.1007/s10529-006-9122-7] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Accepted: 05/30/2006] [Indexed: 11/30/2022]
Abstract
Two new strains of Escherichia coli B were engineered for the production of lactate with no detectable chiral impurity. All chiral impurities were eliminated by deleting the synthase gene (msgA) that converts dihydroxyacetone-phosphate to methylglyoxal, a precursor for both L: (+)- and D: (-)-lactate. Strain TG113 contains only native genes and produced optically pure D: (-)-lactate. Strain TG108 contains the ldhL gene from Pediococcus acidilactici and produced only L: (+)-lactate. In mineral salts medium containing 1 mM betaine, both strains produced over 115 g (1.3 mol) lactate from 12% (w/v) glucose, >95% theoretical yield.
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Affiliation(s)
- T B Grabar
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
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32
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Grueninger D, Schulz GE. Structure and reaction mechanism of L-rhamnulose kinase from Escherichia coli. J Mol Biol 2006; 359:787-97. [PMID: 16674975 DOI: 10.1016/j.jmb.2006.04.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Revised: 03/31/2006] [Accepted: 04/05/2006] [Indexed: 11/20/2022]
Abstract
Bacterial L-rhamnulose kinase participates in the degradation of L-rhamnose, which is ubiquitous and particularly abundant in some plants. The enzyme catalyzes the transfer of the gamma-phosphate group from ATP to the 1-hydroxyl group of L-rhamnulose. We determined the crystal structures of the substrate-free kinase and of a complex between the enzyme, ADP and L-fructose, which besides rhamnulose is also processed. According to its chainfold, the kinase belongs to the hexokinase-hsp70-actin superfamily. The closest structurally known homologue is glycerol kinase. The reported structures reveal a large conformational change on substrate binding as well as the key residues involved in catalysis. The substrates ADP and beta-L-fructose are in an ideal position to define a direct in-line phosphoryl transfer through a bipyramidal pentavalent intermediate. The enzyme contains one disulfide bridge at a position where two homologous glycerol kinases are regulated by phosphorylation and effector binding, respectively, and it has two more pairs of cysteine residues near the surface that are poised for bridging. However, identical catalytic rates were observed for the enzyme in reducing and oxidizing environments, suggesting that regulation by disulfide formation is unlikely.
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Affiliation(s)
- Dirk Grueninger
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstr. 21, 79104 Freiburg im Breisgau, Germany
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Abstract
Escherichia coli and Salmonella enterica serovar Typhimurium exhibit a remarkable versatility in the usage of different sugars as the sole source of carbon and energy, reflecting their ability to make use of the digested meals of mammalia and of the ample offerings in the wild. Degradation of sugars starts with their energy-dependent uptake through the cytoplasmic membrane and is carried on further by specific enzymes in the cytoplasm, destined finally for degradation in central metabolic pathways. As variant as the different sugars are, the biochemical strategies to act on them are few. They include phosphorylation, keto-enol isomerization, oxido/reductions, and aldol cleavage. The catabolic repertoire for using carbohydrate sources is largely the same in E. coli and in serovar Typhimurium. Nonetheless, significant differences are found, even among the strains and substrains of each species. We have grouped the sugars to be discussed according to their first step in metabolism, which is their active transport, and follow their path to glycolysis, catalyzed by the sugar-specific enzymes. We will first discuss the phosphotransferase system (PTS) sugars, then the sugars transported by ATP-binding cassette (ABC) transporters, followed by those that are taken up via proton motive force (PMF)-dependent transporters. We have focused on the catabolism and pathway regulation of hexose and pentose monosaccharides as well as the corresponding sugar alcohols but have also included disaccharides and simple glycosides while excluding polysaccharide catabolism, except for maltodextrins.
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Affiliation(s)
- Christoph Mayer
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
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34
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Leang K, Takada G, Ishimura A, Okita M, Izumori K. Cloning, nucleotide sequence, and overexpression of the L-rhamnose isomerase gene from Pseudomonas stutzeri in Escherichia coli. Appl Environ Microbiol 2004; 70:3298-304. [PMID: 15184124 PMCID: PMC427750 DOI: 10.1128/aem.70.6.3298-3304.2004] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gene encoding L-rhamnose isomerase (L-RhI) from Pseudomonas stutzeri was cloned into Escherichia coli and sequenced. A sequence analysis of the DNA responsible for the L-RhI gene revealed an open reading frame of 1,290 bp coding for a protein of 430 amino acid residues with a predicted molecular mass of 46,946 Da. A comparison of the deduced amino acid sequence with sequences in relevant databases indicated that no significant homology has previously been identified. An amino acid sequence alignment, however, suggested that the residues involved in the active site of L-RhI from E. coli are conserved in that from P. stutzeri. The L-RhI gene was then overexpressed in E. coli cells under the control of the T5 promoter. The recombinant clone, E. coli JM109, produced significant levels of L-RhI activity, with a specific activity of 140 U/mg and a volumetric yield of 20,000 U of soluble enzyme per liter of medium. This reflected a 20-fold increase in the volumetric yield compared to the value for the intrinsic yield. The recombinant L-RhI protein was purified to apparent homogeneity on the basis of three-step chromatography. The purified recombinant enzyme showed a single band with an estimated molecular weight of 42,000 in a sodium dodecyl sulfate-polyacrylamide gel. The overall enzymatic properties of the purified recombinant L-RhI protein were the same as those of the authentic one, as the optimal activity was measured at 60 degrees C within a broad pH range from 5.0 to 11.0, with an optimum at pH 9.0.
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Affiliation(s)
- Khim Leang
- Department of Biochemistry and Food Science, Faculty of Agriculture and Rare Sugar Research Center, Kagawa University, Miki-cho, Kagawa 761-0795, Japan
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Mahato S, De D, Dutta D, Kundu M, Bhattacharya S, Schiavone MT, Bhattacharya SK. Potential use of sugar binding proteins in reactors for regeneration of CO2 fixation acceptor D-Ribulose-1,5-bisphosphate. Microb Cell Fact 2004; 3:7. [PMID: 15175111 PMCID: PMC421735 DOI: 10.1186/1475-2859-3-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2004] [Accepted: 06/02/2004] [Indexed: 12/02/2022] Open
Abstract
Sugar binding proteins and binders of intermediate sugar metabolites derived from microbes are increasingly being used as reagents in new and expanding areas of biotechnology. The fixation of carbon dioxide at emission source has recently emerged as a technology with potentially significant implications for environmental biotechnology. Carbon dioxide is fixed onto a five carbon sugar D-ribulose-1,5-bisphosphate. We present a review of enzymatic and non-enzymatic binding proteins, for 3-phosphoglycerate (3PGA), 3-phosphoglyceraldehyde (3PGAL), dihydroxyacetone phosphate (DHAP), xylulose-5-phosphate (X5P) and ribulose-1,5-bisphosphate (RuBP) which could be potentially used in reactors regenerating RuBP from 3PGA. A series of reactors combined in a linear fashion has been previously shown to convert 3-PGA, (the product of fixed CO2 on RuBP as starting material) into RuBP (Bhattacharya et al., 2004; Bhattacharya, 2001). This was the basis for designing reactors harboring enzyme complexes/mixtures instead of linear combination of single-enzyme reactors for conversion of 3PGA into RuBP. Specific sugars in such enzyme-complex harboring reactors requires removal at key steps and fed to different reactors necessitating reversible sugar binders. In this review we present an account of existing microbial sugar binding proteins and their potential utility in these operations.
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Affiliation(s)
- Sourav Mahato
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Debojyoti De
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Debajyoti Dutta
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Moloy Kundu
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Sumana Bhattacharya
- Environmental Biotechnology Division, ABRD Company LLC, 1555 Wood Road, Cleveland, Ohio, 44121, USA
| | - Marc T Schiavone
- Environmental Biotechnology Division, ABRD Company LLC, 1555 Wood Road, Cleveland, Ohio, 44121, USA
| | - Sanjoy K Bhattacharya
- Department of Ophthalmic Research, Cleveland Clinic Foundation, Area I31, 9500 Euclid Avenue, Cleveland, Ohio, 44195, USA
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Ibañez E, Gimenez R, Pedraza T, Baldoma L, Aguilar J, Badia J. Role of the yiaR and yiaS genes of Escherichia coli in metabolism of endogenously formed L-xylulose. J Bacteriol 2000; 182:4625-7. [PMID: 10913097 PMCID: PMC94635 DOI: 10.1128/jb.182.16.4625-4627.2000] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genes yiaP and yiaR of the yiaKLMNOPQRS cluster of Escherichia coli are required for the metabolism of the endogenously formed L-xylulose, whereas yiaS is required for this metabolism only in araD mutants. Like AraD, YiaS was shown to have L-ribulose-5-phosphate 4-epimerase activity. Similarity of YiaR to several 3-epimerases suggested that this protein could catalyze the conversion of L-xylulose-5-phosphate into L-ribulose-5-phosphate, thus completing the pathway between L-xylulose and the general metabolism.
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Affiliation(s)
- E Ibañez
- Department of Biochemistry, School of Pharmacy, University of Barcelona, 08028 Barcelona, Spain
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Korndörfer IP, Fessner WD, Matthews BW. The structure of rhamnose isomerase from Escherichia coli and its relation with xylose isomerase illustrates a change between inter and intra-subunit complementation during evolution. J Mol Biol 2000; 300:917-33. [PMID: 10891278 DOI: 10.1006/jmbi.2000.3896] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Using a new expression construct, rhamnose isomerase from Escherichia coli was purified and crystallized. The crystal structure was solved by multiple isomorphous replacement and refined to a crystallographic residual of 17.4 % at 1.6 A resolution. Rhamnose isomerase is a tight tetramer of four (beta/alpha)(8)-barrels. A comparison with other known structures reveals that rhamnose isomerase is most similar to xylose isomerase. Alignment of the sequences of the two enzymes based on their structures reveals a hitherto undetected sequence identity of 13 %, suggesting that the two enzymes evolved from a common precursor. The structure and arrangement of the (beta/alpha)(8)-barrels of rhamnose isomerase are very similar to xylose isomerase. Each enzyme does, however, have additional alpha-helical domains, which are involved in tetramer association, and largely differ in structure. The structures of complexes of rhamnose isomerase with the inhibitor l-rhamnitol and the natural substrate l-rhamnose were determined and suggest that an extended loop, which is disordered in the native enzyme, becomes ordered on substrate binding, and may exclude bulk solvent during catalysis. Unlike xylose isomerase, this loop does not extend across a subunit interface but contributes to the active site of its own subunit. It illustrates how an interconversion between inter and intra-subunit complementation can occur during evolution. In the crystal structure (although not necessarily in vivo) rhamnose isomerase appears to bind Zn(2+) at a "structural" site. In the presence of substrate the enzyme also binds Mn(2+) at a nearby "catalytic" site. An array of hydrophobic residues, not present in xylose isomerase, is likely to be responsible for the recognition of l-rhamnose as a substrate. The available structural data suggest that a metal-mediated hydride-shift mechanism, which is generally favored for xylose isomerase, is also feasible for rhamnose isomerase.
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Affiliation(s)
- I P Korndörfer
- Institute of Molecular Biology Howard Hughes Medical Institute and Department of Physics, 1229 University of Oregon, Eugene, OR, 97403-1229, USA
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Hossain Bhuiyan S, Itami Y, Izumori K. Isolation of an l-rhamnose isomerase-constitutive mutant of Pseudomonas sp. strain LL172: Purification and characterization of the enzyme. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0922-338x(97)89251-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Sánchez JC, Gímenez R, Schneider A, Fessner WD, Baldomà L, Aguilar J, Badía J. Activation of a cryptic gene encoding a kinase for L-xylulose opens a new pathway for the utilization of L-lyxose by Escherichia coli. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)43932-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Fessner WD, Schneider A, Eyrisch O, Sinerius G, Badía J. 6-deoxy-L-lyxo- and 6-deoxy-L-arabino-hexulose 1-phosphates. Enzymatic syntheses by antagonistic metabolic pathways. ACTA ACUST UNITED AC 1993. [DOI: 10.1016/s0957-4166(00)80227-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Fessner WD, Badía J, Eyrisch O, Schneider A, Sinerius G. Enzymatic syntheses of rare ketose 1-phosphates. Tetrahedron Lett 1992. [DOI: 10.1016/s0040-4039(00)79140-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Tate C, Muiry J, Henderson P. Mapping, cloning, expression, and sequencing of the rhaT gene, which encodes a novel L-rhamnose-H+ transport protein in Salmonella typhimurium and Escherichia coli. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)50517-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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