1
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Han Z, Li N, Xu H, Xu Z. Improved thermostability and robustness of L-arabinose isomerase by C-terminal elongation and its application in rare sugar production. Biochem Biophys Res Commun 2022; 637:224-231. [DOI: 10.1016/j.bbrc.2022.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/04/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022]
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2
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Enhancement of L-ribulose Production from L-ribose Through Modification of Ochrobactrum sp. CSL1 Ribose-5-phosphate Isomerase A. Appl Biochem Biotechnol 2022; 194:4852-4866. [PMID: 35670905 DOI: 10.1007/s12010-022-04015-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2022] [Indexed: 11/02/2022]
Abstract
L-ribulose, a kind of high-value rare sugar, could be utilized to manufacture L-form sugars and antiviral drugs, generally produced from L-arabinose as a substrate. However, the production of L-ribulose from L-arabinose is limited by the equilibrium ratio of the catalytic reaction, hence, it is necessary to explore a new biological enzymatic method to produce L-ribulose. Ribose-5-phosphate isomerase (Rpi) is an enzyme that can catalyze the reversible isomerization between L-ribose and L-ribulose, which is of great significance for the preparation of L-ribulose. In order to obtain highly active ribose-5-phosphate isomerase to manufacture L-ribulose, ribose-5-phosphate isomerase A (OsRpiA) from Ochrobactrum sp. CSL1 was engineered based on structural and sequence analyses. Through a rational design strategy, a triple-mutant strain A10T/T32S/G101N with 160% activity was acquired. The enzymatic properties of the mutant were systematically investigated, and the optimum conditions were characterized to achieve the maximum yield of L-ribulose. Kinetic analysis clarified that the A10T/T32S/G101N mutant had a stronger affinity for the substrate and increased catalytic efficiency. Furthermore, molecular dynamics simulations indicated that the binding of the substrate to A10T/T32S/G101N was more stable than that of wild type. The shorter distance between the catalytic residues of A10T/T32S/G101N and L-ribose illuminated the increased activity. Overall, the present study provided a solid basis for demonstrating the complex functions of crucial residues in RpiAs as well as in rare sugar preparation.
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3
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Singh A, Rai SK, Manisha M, Yadav SK. Immobilized L-ribose isomerase for the sustained synthesis of a rare sugar D-talose. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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4
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A review on l-ribose isomerases for the biocatalytic production of l-ribose and l-ribulose. Food Res Int 2021; 145:110409. [PMID: 34112412 DOI: 10.1016/j.foodres.2021.110409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/08/2021] [Accepted: 05/06/2021] [Indexed: 11/21/2022]
Abstract
Presently, because of the extraordinary roles and potential applications, rare sugars turn into a focus point for countless researchers in the field of carbohydrates. l-ribose and l-ribulose are rare sugars and isomers of each other. This aldo and ketopentose are expensive but can be utilized as an antecedent for the manufacturing of various rare sugars and l-nucleoside analogue. The bioconversion approach turns into an excellent alternative method to l-ribulose and l-ribose production, as compared to the complex and lengthy chemical methods. The basic purpose of this research was to describe the importance of rare sugars in various fields and their easy production by using enzymatic methods. l-Ribose isomerase (L-RI) is an enzyme discovered by Tsuyoshi Shimonishi and Ken Izumori in 1996 from Acinetobacter sp. strain DL-28. L-RI structure was cupin-type-β-barrel shaped with a catalytic site between two β-sheets surrounded by metal ions. The crystal structures of the L-RI showed that it contains a homotetramer structure. Current review have concentrated on the sources, characteristics, applications, conclusions and future prospects including the potentials of l-ribose isomerase for the commercial production of l-ribose and l-ribulose. The MmL-RIse and CrL-RIse have the potential to produce the l-ribulose up to 32% and 31%, respectively. The CrL-RIse is highly stable as compared to other L-RIs. The results explained that the L-RIs have great potential in the production of rare sugars especially, l-ribose and l-ribulose, while the immobilization technique can enhance its functionality and properties. The present study precises the applications of L-RIs acquired from various sources for l-ribose and l-ribulose production.
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5
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Wang R, Xu X, Yao X, Tang H, Ju X, Li L. Enhanced isomerization of rare sugars by ribose-5-phosphate isomerase A from Ochrobactrum sp. CSL1. Enzyme Microb Technol 2021; 148:109789. [PMID: 34116752 DOI: 10.1016/j.enzmictec.2021.109789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 11/19/2022]
Abstract
Ribose-5-phosphate isomerase A (RpiA) is of great importance in biochemistry research, however its application in biotechnology has not been fully explored. In this study the activity of RpiA from Ochrobactrum sp. CSL1 (OsRpiA) towards D-allose was engineered based on sequential and structural analyses. Strategies of alanine scanning, rational design and saturated mutagenesis were employed to create three mutant libraries. A single mutant of K124A showed a 45 % activity improvement towards D-allose. The reaction properties of the mutant were analyzed, and a shift of optimal pH and higher thermal stability at low reaction temperatures were identified. The conversion of D-allose was also improved by 40 % using K124A, and higher activities on major substrates were found in the mutant's substrate scope, implying its application potential in rare sugar preparation. Kinetics analysis revealed that Km of K124A mutant decreased by 12 % and the catalytic efficiency increased by 65 % towards D-allose. Moreover, molecular dynamics simulation illustrated the binding of substrate and K124A was more stable than that of the wild-type. The shorter distance and more relax bond angle between the catalytic residue of K124A and D-allose explained the activity improvement in detail. This study highlights the potential of OsRpiA as a biocatalyst for rare sugar preparation, and provides distinct evidences for its catalytic mechanism.
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Affiliation(s)
- Rong Wang
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, 215009, PR China
| | - Xinqi Xu
- Fujian Key Laboratory of Marine Enzyme Engineering, College of Biosciences and Engineering, Fuzhou University, Fuzhou, 350116, PR China
| | - Xuemei Yao
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, 215009, PR China
| | - Hengtao Tang
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, 215009, PR China
| | - Xin Ju
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, 215009, PR China.
| | - Liangzhi Li
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, 215009, PR China.
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6
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Ruchala J, Sibirny AA. Pentose metabolism and conversion to biofuels and high-value chemicals in yeasts. FEMS Microbiol Rev 2020; 45:6034013. [PMID: 33316044 DOI: 10.1093/femsre/fuaa069] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
Pentose sugars are widespread in nature and two of them, D-xylose and L-arabinose belong to the most abundant sugars being the second and third by abundance sugars in dry plant biomass (lignocellulose) and in general on planet. Therefore, it is not surprising that metabolism and bioconversion of these pentoses attract much attention. Several different pathways of D-xylose and L-arabinose catabolism in bacteria and yeasts are known. There are even more common and really ubiquitous though not so abundant pentoses, D-ribose and 2-deoxy-D-ribose, the constituents of all living cells. Thus, ribose metabolism is example of endogenous metabolism whereas metabolism of other pentoses, including xylose and L-arabinose, represents examples of the metabolism of foreign exogenous compounds which normally are not constituents of yeast cells. As a rule, pentose degradation by the wild-type strains of microorganisms does not lead to accumulation of high amounts of valuable substances; however, productive strains have been obtained by random selection and metabolic engineering. There are numerous reviews on xylose and (less) L-arabinose metabolism and conversion to high value substances; however, they mostly are devoted to bacteria or the yeast Saccharomyces cerevisiae. This review is devoted to reviewing pentose metabolism and bioconversion mostly in non-conventional yeasts, which naturally metabolize xylose. Pentose metabolism in the recombinant strains of S. cerevisiae is also considered for comparison. The available data on ribose, xylose, L-arabinose transport, metabolism, regulation of these processes, interaction with glucose catabolism and construction of the productive strains of high-value chemicals or pentose (ribose) itself are described. In addition, genome studies of the natural xylose metabolizing yeasts and available tools for their molecular research are reviewed. Metabolism of other pentoses (2-deoxyribose, D-arabinose, lyxose) is briefly reviewed.
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Affiliation(s)
- Justyna Ruchala
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Andriy A Sibirny
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
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7
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Recent advances in properties, production, and applications of L-ribulose. Appl Microbiol Biotechnol 2020; 104:5663-5672. [PMID: 32372201 DOI: 10.1007/s00253-020-10637-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/15/2020] [Accepted: 04/20/2020] [Indexed: 12/31/2022]
Abstract
Currently, due to the special functions and potential application values, rare sugars become the hot topic in carbohydrate fields. L-Ribulose, an isomer of L-ribose, is an expensive rare ketopentose. As an important precursor for other rare sugars and L-nucleoside analogue synthesis, L-ribulose attracts more and more attention in recent days. Compared with complicated chemical synthesis, the bioconversion method becomes a good alternative approach to L-ribulose production. Generally, the bioconversion of L-ribulose was linked with ribitol, L-arabinose, L-ribose, L-xylulose, and L-arabitol. Herein, an overview of recent advances in the metabolic pathway, chemical synthesis, bioproduction of L-ribulose, and the potential application of L-ribulose is reviewed in detail in this paper. KEY POINTS: 1. L-Ribulose is a rare sugar and the key precursor for L-ribose production. 2. L-Ribulose is the starting material for L-nucleoside derivative synthesis. 3. Chemical synthesis, bioproduction, and applications of L-ribulose are reviewed.
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8
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Chen M, Wu H, Zhang W, Mu W. Microbial and enzymatic strategies for the production of L-ribose. Appl Microbiol Biotechnol 2020; 104:3321-3329. [PMID: 32088757 DOI: 10.1007/s00253-020-10471-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/09/2020] [Accepted: 02/13/2020] [Indexed: 10/24/2022]
Abstract
L-Ribose is a non-naturally occurring pentose that recently has become known for its potential application in the pharmaceutical industry, as it is an ideal starting material for use in synthesizing L-nucleosides analogues, an important class of antiviral drugs. In the past few decades, the synthesis of L-ribose has been mainly undertaken through the chemical route. However, chemical synthesis of L-ribose is difficult to achieve on an industrial scale. Therefore, the biotechnological production of L-ribose has gained considerable attention, as it exhibits many merits over the chemical approaches. The present review focuses on various biotechnological strategies for the production of L-ribose through microbial biotransformation and enzymatic catalysis, and in particular on an analysis and comparison of the synthetic methods and different enzymes. The physiological functions and applications of L-ribose are also elucidated. In addition, different sugar isomerases involved in the production of L-ribose from a number of sources are discussed in detail with regard to their biochemical properties. Furthermore, analysis of the separation issues of L-ribose from the reaction solution and different purification methods is presented.Key points • l -Arabinose, l -ribulose and ribitol can be used to produce l -ribose by enzymes. • Five enzymes are systematically introduced for production of l -ribose. • Microbial transformation and enzymatic methods are promising for yielding l -ribose.
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Affiliation(s)
- Ming Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Hao Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, Jiangsu, China
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9
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Mahmood S, Iqbal MW, Riaz T, Hassanin HA, Zhu Y, Ni D, Mu W. Characterization of a recombinant l-ribose isomerase from Mycetocola miduiensis and its application for the production of l-ribulose. Enzyme Microb Technol 2020; 135:109510. [DOI: 10.1016/j.enzmictec.2020.109510] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/08/2020] [Accepted: 01/12/2020] [Indexed: 11/30/2022]
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10
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Wu H, Huang J, Deng Y, Zhang W, Mu W. Production of l-ribose from l-arabinose by co-expression of l-arabinose isomerase and d-lyxose isomerase in Escherichia coli. Enzyme Microb Technol 2020; 132:109443. [DOI: 10.1016/j.enzmictec.2019.109443] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 12/16/2022]
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11
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Affiliation(s)
- Csaba Fehér
- Department of Applied Biotechnology and Food Science, Biorefinery Research Group, Budapest University of Technology and Economics, Budapest, Hungary
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12
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Turner TL, Kim H, Kong II, Liu JJ, Zhang GC, Jin YS. Engineering and Evolution of Saccharomyces cerevisiae to Produce Biofuels and Chemicals. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 162:175-215. [PMID: 27913828 DOI: 10.1007/10_2016_22] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
To mitigate global climate change caused partly by the use of fossil fuels, the production of fuels and chemicals from renewable biomass has been attempted. The conversion of various sugars from renewable biomass into biofuels by engineered baker's yeast (Saccharomyces cerevisiae) is one major direction which has grown dramatically in recent years. As well as shifting away from fossil fuels, the production of commodity chemicals by engineered S. cerevisiae has also increased significantly. The traditional approaches of biochemical and metabolic engineering to develop economic bioconversion processes in laboratory and industrial settings have been accelerated by rapid advancements in the areas of yeast genomics, synthetic biology, and systems biology. Together, these innovations have resulted in rapid and efficient manipulation of S. cerevisiae to expand fermentable substrates and diversify value-added products. Here, we discuss recent and major advances in rational (relying on prior experimentally-derived knowledge) and combinatorial (relying on high-throughput screening and genomics) approaches to engineer S. cerevisiae for producing ethanol, butanol, 2,3-butanediol, fatty acid ethyl esters, isoprenoids, organic acids, rare sugars, antioxidants, and sugar alcohols from glucose, xylose, cellobiose, galactose, acetate, alginate, mannitol, arabinose, and lactose.
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Affiliation(s)
- Timothy L Turner
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Heejin Kim
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - In Iok Kong
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jing-Jing Liu
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Guo-Chang Zhang
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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13
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Tseng WC, Wu TJ, Chang YJ, Cheng HW, Fang TY. Overexpression and characterization of a recombinant l -ribose isomerase from Actinotalea fermentans ATCC 43279. J Biotechnol 2017; 259:168-174. [DOI: 10.1016/j.jbiotec.2017.07.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/19/2017] [Accepted: 07/21/2017] [Indexed: 11/25/2022]
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14
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l-Ribose isomerase and mannose-6-phosphate isomerase: properties and applications for l-ribose production. Appl Microbiol Biotechnol 2016; 100:9003-9011. [DOI: 10.1007/s00253-016-7834-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/20/2016] [Accepted: 08/23/2016] [Indexed: 11/27/2022]
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15
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Xu W, Zhang W, Zhang T, Jiang B, Mu W. l-Rhamnose isomerase and its use for biotechnological production of rare sugars. Appl Microbiol Biotechnol 2016; 100:2985-92. [DOI: 10.1007/s00253-016-7369-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 01/27/2016] [Accepted: 01/30/2016] [Indexed: 10/22/2022]
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16
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Xu Z, Wang R, Liu C, Chi B, Gao J, Chen B, Xu H. A new l-arabinose isomerase with copper ion tolerance is suitable for creating protein–inorganic hybrid nanoflowers with enhanced enzyme activity and stability. RSC Adv 2016. [DOI: 10.1039/c5ra27035a] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Protein–inorganic hybrid nanoflowers were prepared using Cu2+, PBS buffer, and a copper ion tolerant l-arabinose isomerase that was derived from Paenibacillus polymyxa (PPAI).
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Affiliation(s)
- Zheng Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering
- Nanjing 210009
- PR China
- College of Food Science and Light Industry
- Nanjing Tech University
| | - Rui Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering
- Nanjing 210009
- PR China
- College of Food Science and Light Industry
- Nanjing Tech University
| | - Chao Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering
- Nanjing 210009
- PR China
- College of Food Science and Light Industry
- Nanjing Tech University
| | - Bo Chi
- State Key Laboratory of Materials-Oriented Chemical Engineering
- Nanjing 210009
- PR China
- College of Food Science and Light Industry
- Nanjing Tech University
| | - Jian Gao
- Yancheng Institute of Technology
- China
| | | | - Hong Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering
- Nanjing 210009
- PR China
- College of Food Science and Light Industry
- Nanjing Tech University
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17
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Lv Z, Li X, Chen Z, Chen J, Chen C, Xiong P, Sun T, Qing G. Surface Stiffness--a Parameter for Sensing the Chirality of Saccharides. ACS APPLIED MATERIALS & INTERFACES 2015; 7:27223-27233. [PMID: 26595648 DOI: 10.1021/acsami.5b08405] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Surface stiffness is considered a key parameter for designing high-performance implantable materials and artificial extracellular matrices because of its substantial effects on cell behavior. How to transform biomolecule recognition events, particularly chiral recognition, into stiffness change on material surfaces is biologically essential but very challenging for chemists. Here, we report a chirality-triggered stiffness transition on a smart polymer film, which consists of flexible polyethylenimine (PEI) main chains grafted with dipeptide units capable of discriminating chiral monosaccharides. The polymer film became substantially softer after interacting with L-ribose and became more rigid after interacting with D-ribose (the basic building block of DNA and RNA). This chiral effect provides a new method for determining the enantiomeric purity of an L/D-ribose mixture and facilitates the chiral separation of deoxyribose racemates as well as the separation of diverse mono-, di-, and oligosaccharides. These are three puzzle problems in carbohydrate chemistry. Furthermore, taking advantage of the significant differences in the surface stiffness, the proliferation of fibroblast cells on the polymeric surfaces can also be regulated by chiral biomolecules.
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Affiliation(s)
- Ziyu Lv
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology , 122 Luoshi Road, Wuhan, 430070, P. R. China
| | - Xiuling Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian, 116023, P. R. China
| | - Zhonghui Chen
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology , 122 Luoshi Road, Wuhan, 430070, P. R. China
| | - Ji Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan, 430072, P. R. China
| | - Cheng Chen
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian, 116023, P. R. China
| | - Peng Xiong
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology , 122 Luoshi Road, Wuhan, 430070, P. R. China
| | - Taolei Sun
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology , 122 Luoshi Road, Wuhan, 430070, P. R. China
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology , 122 Luoshi Road, Wuhan, 430070, P. R. China
| | - Guangyan Qing
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology , 122 Luoshi Road, Wuhan, 430070, P. R. China
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18
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López-López O, Cerdán ME, González-Siso MI. Thermus thermophilus as a Source of Thermostable Lipolytic Enzymes. Microorganisms 2015; 3:792-808. [PMID: 27682117 PMCID: PMC5023265 DOI: 10.3390/microorganisms3040792] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 10/14/2015] [Accepted: 11/02/2015] [Indexed: 01/09/2023] Open
Abstract
Lipolytic enzymes, esterases (EC 3.1.1.1) and lipases (EC 3.1.1.3), catalyze the hydrolysis of ester bonds between alcohols and carboxylic acids, and its formation in organic media. At present, they represent about 20% of commercialized enzymes for industrial use. Lipolytic enzymes from thermophilic microorganisms are preferred for industrial use to their mesophilic counterparts, mainly due to higher thermostability and resistance to several denaturing agents. However, the production at an industrial scale from the native organisms is technically complicated and expensive. The thermophilic bacterium Thermus thermophilus (T. thermophilus) has high levels of lipolytic activity, and its whole genome has been sequenced. One esterase from the T. thermophilus strain HB27 has been widely characterized, both in its native form and in recombinant forms, being expressed in mesophilic microorganisms. Other putative lipases/esterases annotated in the T. thermophilus genome have been explored and will also be reviewed in this paper.
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Affiliation(s)
- Olalla López-López
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, Campus de A Coruña, 15071 A Coruña, Spain.
| | - María-Esperanza Cerdán
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, Campus de A Coruña, 15071 A Coruña, Spain.
| | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, Campus de A Coruña, 15071 A Coruña, Spain.
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19
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Krause M, Neubauer P, Wierenga RK. Structure-based directed evolution of a monomeric triosephosphate isomerase: toward a pentose sugar isomerase. Protein Eng Des Sel 2015; 28:187-97. [PMID: 25767111 DOI: 10.1093/protein/gzv010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/03/2015] [Indexed: 11/13/2022] Open
Abstract
Through structure-based and directed evolution approaches, a new catalytic activity has been established on the (β/α)8 barrel enzyme triosephosphate isomerase (TIM). This work started from ml8bTIM, a monomeric variant of TIM, in which the phosphate-binding loop (loop-8) had been shortened. Structure analysis suggested an additional point mutation (V233A), converting ml8bTIM into A-TIM. A-TIM has no detectable TIM activity, but it binds the TIM transition state analog, 2-phosphoglycollate. In an in vivo selection approach, we aimed at transferring the activity of three sugar isomerases (L-arabinose isomerase (L-AI), D-xylose isomerase A (D-XI) and D-ribose-5-phosphate isomerase (D-RPI)) onto A-TIM. Escherichia coli knockout variants were constructed, lacking E. coli L-AI, D-XI and D-RPI activities, respectively. Through a systematic approach, new A-TIM variants were obtained only from selection experiments with the L-AI knockout strain. Selection for D-RPI activity was impossible because of an impaired strain due to the gene knockouts. The selection for D-XI activity was unsuccessful, showing the importance of the starting protein for obtaining new biocatalytic properties. The L-AI-directed evolution experiments show that A-TIM already has residual in vivo L-AI activity. Most of the mutations providing A-TIM with enhanced L-AI activity are located in the loops between β-strands and the subsequent α-helices.
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Affiliation(s)
- Mirja Krause
- Laboratory of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Insitute of Biotechnology, Ackerstr. 76, ACK 24, D-13355 Berlin, Germany
| | - Peter Neubauer
- Laboratory of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Insitute of Biotechnology, Ackerstr. 76, ACK 24, D-13355 Berlin, Germany
| | - Rik K Wierenga
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, FIN-90014 Oulu, Finland
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Xu Z, Li S, Liang J, Feng X, Xu H. Protein purification, crystallization and preliminary X-ray diffraction analysis of L-arabinose isomerase from Lactobacillus fermentum CGMCC2921. Acta Crystallogr F Struct Biol Commun 2015; 71:28-33. [PMID: 25615964 PMCID: PMC4304743 DOI: 10.1107/s2053230x14025321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 11/18/2014] [Indexed: 11/11/2022] Open
Abstract
L-Arabinose isomerase (AI) catalyzes the isomerization of L-arabinose to L-ribulose, as well as that of D-galactose to D-tagatose. A thermophilic AI derived from Lactobacillus fermentum CGMCC2921 (LFAI) was overexpressed in Escherichia coli BL21 (DE3). This enzyme was purified to over 95% purity by nickel affinity, Mono-Q ion-exchange and size-exclusion chromatography. The LFAI protein was crystallized from either 0.1 M bis-tris pH 6.5, 23% PEG 3350, 0.3 M NaCl (form 1 crystals) or 0.1 M bis-tris pH 6.0, 25% PEG monomethyl ether 5000 (form 2 crystals). Diffraction data from form 1 LFAI crystals were collected to 2.80 Å resolution using synchrotron radiation. The form 1 crystals belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a=85.11, b=184.57, c=186.26 Å, α=β=γ=90°. The asymmetric unit contained six LFAI subunits, corresponding to a calculated Matthews coefficient of 2.29 Å3 Da(-1) and a solvent content of 46.22%.
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Affiliation(s)
- Zheng Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing 210009, People’s Republic of China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, People’s Republic of China
| | - Sha Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing 210009, People’s Republic of China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, People’s Republic of China
| | - Jinfeng Liang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing 210009, People’s Republic of China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, People’s Republic of China
| | - Xiaohai Feng
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing 210009, People’s Republic of China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, People’s Republic of China
| | - Hong Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing 210009, People’s Republic of China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, People’s Republic of China
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Kim KR, Seo ES, Oh DK. L-Ribose production from L-arabinose by immobilized recombinant Escherichia coli co-expressing the L-arabinose isomerase and mannose-6-phosphate isomerase genes from Geobacillus thermodenitrificans. Appl Biochem Biotechnol 2014; 172:275-88. [PMID: 24078190 DOI: 10.1007/s12010-013-0547-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 09/18/2013] [Indexed: 11/24/2022]
Abstract
L-Ribose is an important precursor for antiviral agents, and thus its high-level production is urgently demanded. For this aim, immobilized recombinant Escherichia coli cells expressing the L-arabinose isomerase and variant mannose-6-phosphate isomerase genes from Geobacillus thermodenitrificans were developed. The immobilized cells produced 99 g/l L-ribose from 300 g/l L-arabinose in 3 h at pH 7.5 and 60 °C in the presence of 1 mM Co(2+), with a conversion yield of 33 % (w/w) and a productivity of 33 g/l/h. The immobilized cells in the packed-bed bioreactor at a dilution rate of 0.2 h(-1) produced an average of 100 g/l L-ribose with a conversion yield of 33 % and a productivity of 5.0 g/l/h for the first 12 days, and the operational half-life in the bioreactor was 28 days. Our study is first verification for L-ribose production by long-term operation and feasible for cost-effective commercialization. The immobilized cells in the present study also showed the highest conversion yield among processes from L-arabinose as the substrate.
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Xu Z, Li S, Feng X, Liang J, Xu H. L-Arabinose isomerase and its use for biotechnological production of rare sugars. Appl Microbiol Biotechnol 2014; 98:8869-78. [PMID: 25280744 DOI: 10.1007/s00253-014-6073-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 09/02/2014] [Accepted: 09/03/2014] [Indexed: 11/26/2022]
Abstract
L-Arabinose isomerase (AI), a key enzyme in the microbial pentose phosphate pathway, has been regarded as an important biological catalyst in rare sugar production. This enzyme could isomerize L-arabinose into L-ribulose, as well as D-galactose into D-tagatose. Both the two monosaccharides show excellent commercial values in food and pharmaceutical industries. With the identification of novel AI family members, some of them have exhibited remarkable potential in industrial applications. The biological production processes for D-tagatose and L-ribose (or L-ribulose) using AI have been developed and improved in recent years. Meanwhile, protein engineering techniques involving rational design has effectively enhanced the catalytic properties of various AIs. Moreover, the crystal structure of AI has been disclosed, which sheds light on the understanding of AI structure and catalytic mechanism at molecular levels. This article reports recent developments in (i) novel AI screening, (ii) AI-mediated rare sugar production processes, (iii) molecular modification of AI, and (iv) structural biology study of AI. Based on previous reports, an analysis of the future development has also been initiated.
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Affiliation(s)
- Zheng Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, 210009, People's Republic of China
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L-Arabinose Binding, Isomerization, and Epimerization by D-Xylose Isomerase: X-Ray/Neutron Crystallographic and Molecular Simulation Study. Structure 2014; 22:1287-1300. [DOI: 10.1016/j.str.2014.07.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 06/19/2014] [Accepted: 07/01/2014] [Indexed: 11/22/2022]
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Yoshida H, Yoshihara A, Teraoka M, Terami Y, Takata G, Izumori K, Kamitori S. X-ray structure of a novell-ribose isomerase acting on a non-natural sugarl-ribose as its ideal substrate. FEBS J 2014; 281:3150-64. [DOI: 10.1111/febs.12850] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 04/30/2014] [Accepted: 05/15/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Hiromi Yoshida
- Life Science Research Center and Faculty of Medicine; Kagawa University; Japan
| | | | - Misa Teraoka
- Life Science Research Center and Faculty of Medicine; Kagawa University; Japan
| | - Yuji Terami
- Rare Sugar Research Center; Kagawa University; Japan
| | - Goro Takata
- Rare Sugar Research Center; Kagawa University; Japan
| | - Ken Izumori
- Rare Sugar Research Center; Kagawa University; Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine; Kagawa University; Japan
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Gunther WR, Duong Q, Román-Leshkov Y. Catalytic consequences of borate complexation and pH on the epimerization of l-arabinose to l-ribose in water catalyzed by Sn-Beta zeolite with borate salts. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcata.2013.08.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Schouten S, Villareal TA, Hopmans EC, Mets A, Swanson KM, Sinninghe Damsté JS. Endosymbiotic heterocystous cyanobacteria synthesize different heterocyst glycolipids than free-living heterocystous cyanobacteria. PHYTOCHEMISTRY 2013; 85:115-121. [PMID: 23044080 DOI: 10.1016/j.phytochem.2012.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 08/24/2012] [Accepted: 09/10/2012] [Indexed: 06/01/2023]
Abstract
The heterocysts of limnetic nitrogen-fixing filamentous cyanobacteria contain unique glycolipids in their cell wall that create the distinctive gas impermeability of the heterocyst cell wall as well as serve as biomarker lipids for these microbes. It has been assumed that marine free-living and endosymbiotic cyanobacteria synthesize the same glycolipids although they have not been investigated in any detail. Here we report the glycolipid composition of several marine free-living heterocystous cyanobacteria as well as the heterocystous endosymbiont Richelia intracellularis found in the biogeochemically important diatoms Hemiaulus hauckii and Hemiaulus membranaceus. In the marine cyanobacteria Nostoc muscorum and Calothrix sp., we detected the same glycolipids as found in freshwater representatives of these genera. However, we did not detect these glycolipids in the Hemiaulus-Richelia association. Instead, we identified glycolipids which comprised a C₅ sugar, ribose, rather than the C₆ sugars normally encountered in glycolipids of free-living cyanobacteria. In addition, the glycolipids had slightly longer chain lengths (C₃₀ and C₃₂ versus C₂₆ and C₂₈) in the aglycone moiety. The different glycolipid composition of the marine endosymbotic heterocystous cyanobacteria compared to their free-living counterparts may be an adaptation to the high intracellular O₂ concentrations within their host. These glycolipids may provide unique tracers for the presence of these microbes in marine environments and permit exploration of the evolutionary origins of these symbioses.
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Affiliation(s)
- Stefan Schouten
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, Den Burg, The Netherlands.
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Mu W, Zhang W, Feng Y, Jiang B, Zhou L. Recent advances on applications and biotechnological production of D-psicose. Appl Microbiol Biotechnol 2012; 94:1461-7. [PMID: 22569636 DOI: 10.1007/s00253-012-4093-1] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 01/13/2012] [Accepted: 01/13/2012] [Indexed: 12/01/2022]
Abstract
D-Psicose is a hexoketose monosaccharide sweetener, which is a C-3 epimer of D-fructose and is rarely found in nature. It has 70 % relative sweetness but 0.3 % energy of sucrose, and is suggested as an ideal sucrose substitute for food products. It shows important physiological functions, such as blood glucose suppressive effect, reactive oxygen species scavenging activity, and neuroprotective effect. It also improves the gelling behavior and produces good flavor during food process. This article presents a review of recent studies on the properties, physiological functions, and food application of D-psicose. In addition, the biochemical properties of D-tagatose 3-epimerase family enzymes and the D-psicose-producing enzyme are compared, and the biotechnological production of D-psicose from D-fructose is reviewed.
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Affiliation(s)
- Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.
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