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Sharma S, Patel SN, Singh SP. A novel thermotolerant L-rhamnose isomerase variant for biocatalytic conversion of D-allulose to D-allose. Appl Microbiol Biotechnol 2024; 108:279. [PMID: 38564031 PMCID: PMC10987364 DOI: 10.1007/s00253-024-13074-w] [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: 08/29/2023] [Revised: 01/24/2024] [Accepted: 02/13/2024] [Indexed: 04/04/2024]
Abstract
A novel L-rhamnose isomerase was identified and cloned from an extreme-temperature aquatic habitat metagenome. The deduced amino acid sequence homology suggested the possible source of this metagenomic sequence to be Chloroflexus islandicus. The gene expression was performed in a heterologous host, Escherichia coli, and the recombinant protein L-rhamnose isomerase (L-RIM) was extracted and purified. The catalytic function of L-RIM was characterized for D-allulose to D-allose bioconversion. D-Allose is a sweet, rare sugar molecule with anti-tumour, anti-hypertensive, cryoprotective, and antioxidative properties. The characterization experiments showed L-RIM to be a Co++- or Mn++-dependent metalloenzyme. L-RIM was remarkably active (~ 80%) in a broad spectrum of pH (6.0 to 9.0) and temperature (70 to 80 °C) ranges. Optimal L-RIM activity with D-allulose as the substrate occurred at pH 7.0 and 75 °C. The enzyme was found to be excessively heat stable, displaying a half-life of about 12 days and 5 days at 65 °C and 70 °C, respectively. L-RIM catalysis conducted at slightly acidic pH of 6.0 and 70 °C achieved biosynthesis of about 30 g L-1 from 100 g L-1 D-allulose in 3 h. KEY POINTS: • The present study explored an extreme temperature metagenome to identify a novel gene that encodes a thermostable l-rhamnose isomerase (L-RIM) • L-RIM exhibits substantial (80% or more) activity in a broad spectrum of pH (6.0 to 9.0) and temperature (70 to 80 °C) ranges • L-RIM is excessively heat stable, displaying a half-life of about 12 days and 5 days at 65 °C and 70 °C, respectively.
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Affiliation(s)
- Sweety Sharma
- Center of Innovative and Applied Bioprocessing, Biotechnology Research and Innovation Council (Department of Biotechnology, Government of India), NABI Campus, SAS Nagar, Sector 81, Mohali, India, 140306
- Indian Institute of Science Education and Research Mohali, SAS Nagar, Sector 81, Mohali, India, 140306
| | - Satya Narayan Patel
- Center of Innovative and Applied Bioprocessing, Biotechnology Research and Innovation Council (Department of Biotechnology, Government of India), NABI Campus, SAS Nagar, Sector 81, Mohali, India, 140306
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing, Biotechnology Research and Innovation Council (Department of Biotechnology, Government of India), NABI Campus, SAS Nagar, Sector 81, Mohali, India, 140306.
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2
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Yoshida H, Yamamoto N, Kurahara LH, Izumori K, Yoshihara A. X-ray structure and characterization of a probiotic Lactobacillus rhamnosus Probio-M9 L-rhamnose isomerase. Appl Microbiol Biotechnol 2024; 108:249. [PMID: 38430263 PMCID: PMC10908623 DOI: 10.1007/s00253-024-13075-9] [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: 07/31/2023] [Revised: 01/18/2024] [Accepted: 02/16/2024] [Indexed: 03/03/2024]
Abstract
A recombinant L-rhamnose isomerase (L-RhI) from probiotic Lactobacillus rhamnosus Probio-M9 (L. rhamnosus Probio-M9) was expressed. L. rhamnosus Probio-M9 was isolated from human colostrum and identified as a probiotic lactic acid bacterium, which can grow using L-rhamnose. L-RhI is one of the enzymes involved in L-rhamnose metabolism and catalyzes the reversible isomerization between L-rhamnose and L-rhamnulose. Some L-RhIs were reported to catalyze isomerization not only between L-rhamnose and L-rhamnulose but also between D-allulose and D-allose, which are known as rare sugars. Those L-RhIs are attractive enzymes for rare sugar production and have the potential to be further improved by enzyme engineering; however, the known crystal structures of L-RhIs recognizing rare sugars are limited. In addition, the optimum pH levels of most reported L-RhIs are basic rather than neutral, and such a basic condition causes non-enzymatic aldose-ketose isomerization, resulting in unexpected by-products. Herein, we report the crystal structures of L. rhamnosus Probio-M9 L-RhI (LrL-RhI) in complexes with L-rhamnose, D-allulose, and D-allose, which show enzyme activity toward L-rhamnose, D-allulose, and D-allose in acidic conditions, though the activity toward D-allose was low. In the complex with L-rhamnose, L-rhamnopyranose was found in the catalytic site, showing favorable recognition for catalysis. In the complex with D-allulose, D-allulofuranose and ring-opened D-allulose were observed in the catalytic site. However, bound D-allose in the pyranose form was found in the catalytic site of the complex with D-allose, which was unfavorable for recognition, like an inhibition mode. The structure of the complex may explain the low activity toward D-allose. KEY POINTS: • Crystal structures of LrL-RhI in complexes with substrates were determined. • LrL-RhI exhibits enzyme activity toward L-rhamnose, D-allulose, and D-allose. • The LrL-RhI is active in acidic conditions.
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Affiliation(s)
- Hiromi Yoshida
- Department of Basic Life Science, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-Cho, Kita-Gun, Kagawa, 761-0793, Japan.
- International Institute of Rare Sugar Research and Education, Kagawa University, Takamatsu, Kagawa, Japan.
| | - Naho Yamamoto
- Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki, Kagawa, 761-0795, Japan
| | - Lin Hai Kurahara
- Department of Cardiovascular Physiology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-Cho, Kita-Gun, Kagawa, 761-0793, Japan
| | - Ken Izumori
- International Institute of Rare Sugar Research and Education, Kagawa University, Takamatsu, Kagawa, Japan
- Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki, Kagawa, 761-0795, Japan
| | - Akihide Yoshihara
- International Institute of Rare Sugar Research and Education, Kagawa University, Takamatsu, Kagawa, Japan
- Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki, Kagawa, 761-0795, Japan
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Kamitori S. X-ray structures of Enterobacter cloacae allose-binding protein in complexes with monosaccharides demonstrate its unique recognition mechanism for high affinity to allose. Biochem Biophys Res Commun 2023; 682:187-192. [PMID: 37820454 DOI: 10.1016/j.bbrc.2023.10.016] [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: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023]
Abstract
d-Allose is an aldohexose of the C3-epimer of d-glucose, existing in very small amounts in nature, called a rare sugar. The operon responsible for d-allose metabolism, the allose operon, was found in several bacteria, which consists of seven genes: alsR, alsB, alsA, alsC, alsE, alsK, and rpiB. To understand the biological implication of the allose operon utilizing a rare sugar of d-allose as a carbon source, it is important to clarify whether the allose operon functions specifically for d-allose or also functions for other ligands. It was proposed that the allose operon can function for d-ribose, which is essential as a component of nucleotides and abundant in nature. Allose-binding protein, AlsB, coded in the allose operon, is thought to capture a ligand outside the cell, and is expected to show high affinity for the specific ligand. X-ray structure determinations of Enterobacter cloacae AlsB (EtcAlsB) in ligand-free form, and in complexes with d-allose, d-ribose, and d-allulose, and measurements of the thermal parameters of the complex formation using an isothermal titration calorimeter were performed. The results demonstrated that EtcAlsB has a unique recognition mechanism for high affinity to d-allose by changing its conformation from an open to a closed form depending on d-allose-binding, and that the binding of d-ribose to EtcAlsB could not induce a completely closed form but an intermediate form, explaining the low affinity for d-ribose.
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Affiliation(s)
- Shigehiro Kamitori
- Research Facility Center for Science & Technology and Faculty of Medicine, International Institute of Rare Sugar Research and Education, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan.
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4
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Duan S, Chen Y, Wang G, Li Z, Dong S, Wu Y, Wang Y, Ma C, Wang R. A study of targeted mutation of l-rhamnose isomerase to improve the conversion efficiency of D-allose. Enzyme Microb Technol 2023; 168:110259. [PMID: 37245327 DOI: 10.1016/j.enzmictec.2023.110259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/30/2023]
Abstract
D-Allose is a rare cis-caprose with a wide range of physiological functions, which has a wide range of applications in medicine, food, and other industries. L-Rhamnose isomerase (L-Rhi) is the earliest enzyme found to catalyze the production of D-allose from D-psicose. This catalyst has a high conversion rate, but its specificity for substrates is limited; thus, it cannot fulfill the requirements of industrial production of D-allose. In this study, L-Rhi derived from Bacillus subtilis was employed as the research subject, and D-psicose as the conversion substrate. Two mutant libraries were constructed through alanine scanning, saturation mutation, and rational design based on the analysis of the secondary structure, tertiary structure, and interactions with ligands of the enzyme. The yield of D-allose produced by these mutants was assessed; it was found that the conversion rate of mutant D325M to D-allose was increased by 55.73 %, and the D325S improved by 15.34 %, while mutant W184H increased by 10.37 % at 55 °C, respectively. According to modeling analysis, manganese (Mn2+) had no significant effect on the production of D-psicose from D-psicose by L-Rhi. The results of molecular dynamics simulation demonstrated that the mutants W184H, D325M, and D325S had more stable protein structures while binding with the substrate D-psicose, as evidenced by its root mean square deviation (RMSD), root mean square fluctuation (RMSF), and binding free energy values. It was more conducive to binding D-psicose and facilitating its conversion to D-allose, providing the basis for the production of D-allose.
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Affiliation(s)
- Shuangshuang Duan
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Science), Jinan 250353, PR China; Shandong Provincial Key Laboratory of Microbial Engineering, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Science) Jinan 250353, PR China
| | - Yonghua Chen
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Science), Jinan 250353, PR China; Shandong Provincial Key Laboratory of Microbial Engineering, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Science) Jinan 250353, PR China
| | - Guodong Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Science), Jinan 250353, PR China; Shandong Provincial Key Laboratory of Microbial Engineering, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Science) Jinan 250353, PR China
| | - Zebin Li
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Science), Jinan 250353, PR China; Shandong Provincial Key Laboratory of Microbial Engineering, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Science) Jinan 250353, PR China
| | - Shitong Dong
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Science), Jinan 250353, PR China; Shandong Provincial Key Laboratory of Microbial Engineering, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Science) Jinan 250353, PR China
| | - Yingshuai Wu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Science), Jinan 250353, PR China; Shandong Provincial Key Laboratory of Microbial Engineering, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Science) Jinan 250353, PR China
| | - Yuanwei Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Science), Jinan 250353, PR China; Shandong Provincial Key Laboratory of Microbial Engineering, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Science) Jinan 250353, PR China
| | - Chunling Ma
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Science), Jinan 250353, PR China; Shandong Provincial Key Laboratory of Microbial Engineering, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Science) Jinan 250353, PR China.
| | - Ruiming Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Science), Jinan 250353, PR China; Shandong Provincial Key Laboratory of Microbial Engineering, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Science) Jinan 250353, PR China.
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5
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Enzymatic approaches to rare sugar production. Biotechnol Adv 2017; 35:267-274. [DOI: 10.1016/j.biotechadv.2017.01.004] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 12/30/2016] [Accepted: 01/17/2017] [Indexed: 01/02/2023]
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6
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Yoshida H, Yoshihara A, Ishii T, Izumori K, Kamitori S. X-ray structures of the Pseudomonas cichorii D-tagatose 3-epimerase mutant form C66S recognizing deoxy sugars as substrates. Appl Microbiol Biotechnol 2016; 100:10403-10415. [PMID: 27368739 DOI: 10.1007/s00253-016-7673-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 06/02/2016] [Accepted: 06/08/2016] [Indexed: 12/18/2022]
Abstract
Pseudomonas cichorii D-tagatose 3-epimerase (PcDTE), which has a broad substrate specificity, efficiently catalyzes the epimerization of not only D-tagatose to D-sorbose but also D-fructose to D-psicose (D-allulose) and also recognizes the deoxy sugars as substrates. In an attempt to elucidate the substrate recognition and catalytic reaction mechanisms of PcDTE for deoxy sugars, the X-ray structures of the PcDTE mutant form with the replacement of Cys66 by Ser (PcDTE_C66S) in complexes with deoxy sugars were determined. These X-ray structures showed that substrate recognition by the enzyme at the 1-, 2-, and 3-positions is responsible for enzymatic activity and that substrate-enzyme interactions at the 4-, 5-, and 6-positions are not essential for the catalytic reaction of the enzyme leading to the broad substrate specificity of PcDTE. They also showed that the epimerization site of 1-deoxy 3-keto D-galactitol is shifted from C3 to C4 and that 1-deoxy sugars may bind to the catalytic site in the inhibitor-binding mode. The hydrophobic groove that acts as an accessible surface for substrate binding is formed through the dimerization of PcDTE. In PcDTE_C66S/deoxy sugar complex structures, bound ligand molecules in both the linear and ring forms were detected in the hydrophobic groove, while bound ligand molecules in the catalytic site were in the linear form. This result suggests that the sugar-ring opening of a substrate may occur in the hydrophobic groove and also that the narrow channel of the passageway to the catalytic site allows a substrate in the linear form to pass through.
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Affiliation(s)
- Hiromi Yoshida
- Life Science Research Center and Faculty of Medicine, Kagawa University, Ikenobe, Miki-cho, Kita-gun, Kagawa, Japan
| | - Akihide Yoshihara
- Rare Sugar Research Center and Faculty of Agriculture, Kagawa University, Miki-cho, Kita-gun, Kagawa, Japan
| | - Tomohiko Ishii
- Faculty of Engineering, Kagawa University, Hayashi-cho, Takamatsu, Kagawa, Japan
| | - Ken Izumori
- Rare Sugar Research Center and Faculty of Agriculture, Kagawa University, Miki-cho, Kita-gun, Kagawa, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, Kagawa University, Ikenobe, Miki-cho, Kita-gun, Kagawa, Japan.
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7
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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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8
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Sugrue E, Hartley CJ, Scott C, Jackson CJ. The Evolution of New Catalytic Mechanisms for Xenobiotic Hydrolysis in Bacterial Metalloenzymes. Aust J Chem 2016. [DOI: 10.1071/ch16426] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
An increasing number of bacterial metalloenzymes have been shown to catalyse the breakdown of xenobiotics in the environment, while others exhibit a variety of promiscuous xenobiotic-degrading activities. Several different evolutionary processes have allowed these enzymes to gain or enhance xenobiotic-degrading activity. In this review, we have surveyed the range of xenobiotic-degrading metalloenzymes, and discuss the molecular and catalytic basis for the development of new activities. We also highlight how our increased understanding of the natural evolution of xenobiotic-degrading metalloenzymes can be been applied to laboratory enzyme design.
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9
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Prabhu P, Doan TNT, Tiwari M, Singh R, Kim SC, Hong MK, Kang YC, Kang LW, Lee JK. Structure-based studies on the metal binding of two-metal-dependent sugar isomerases. FEBS J 2014; 281:3446-59. [PMID: 24925069 DOI: 10.1111/febs.12872] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Revised: 05/30/2014] [Accepted: 06/09/2014] [Indexed: 11/30/2022]
Abstract
UNLABELLED Two-metal-dependent sugar isomerases are important in the synthesis of rare sugars. Many of their properties, specifically their metal dependency, have not been sufficiently explored. Here we used X-ray crystallography, site-directed mutagenesis, isothermal titration calorimetry and electron paramagnetic resonance spectroscopy to investigate the molecular determinants of the metal-binding affinity of l-rhamnose isomerase, a two-Mn(2+) -dependent isomerase from Bacillus halodurans (BHRI). The crystal structure of BHRI confirmed the presence of two metal ion-binding sites: a structural metal ion-binding site for substrate binding, and a catalytic metal ion-binding site that catalyzes a hydride shift. One conserved amino acid, W38, in wild-type BHRI was identified as a critical residue for structural Mn(2+) binding and thus the catalytic efficiency of BHRI. This function of W38 was explored by replacing it with other amino acids. Substitution by Phe, His, Lys, Ile or Ala caused complete loss of catalytic activity. The role of W38 was further examined by analyzing the crystal structure of wild-type BHRI and two inactive mutants of BHRI (W38F and W38A) in complex with Mn(2+) . A structural comparison of the mutants and the wild-type revealed differences in their coordination of Mn(2+) , including changes in metal-ligand bond length and affinity for Mn(2+) . The role of W38 was further confirmed in another two-metal-dependent enzyme: xylose isomerase from Bacillus licheniformis. These data suggest that W38 stabilizes protein-metal complexes and in turn assists ligand binding during catalysis in two-metal-dependent isomerases. STRUCTURED DIGITAL ABSTRACT BHRI and BHRI bind by x-ray crystallography (View interaction).
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Affiliation(s)
- Ponnandy Prabhu
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Korea
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10
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Ben-David M, Wieczorek G, Elias M, Silman I, Sussman JL, Tawfik DS. Catalytic metal ion rearrangements underline promiscuity and evolvability of a metalloenzyme. J Mol Biol 2013; 425:1028-38. [PMID: 23318950 DOI: 10.1016/j.jmb.2013.01.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Revised: 01/03/2013] [Accepted: 01/07/2013] [Indexed: 11/16/2022]
Abstract
Although largely deemed as structurally conserved, catalytic metal ion sites can rearrange, thereby contributing to enzyme evolvability. Here, we show that in paraoxonase-1, a lipo-lactonase, catalytic promiscuity and divergence into an organophosphate hydrolase are correlated with an alternative mode of the catalytic Ca(2+). We describe the crystal structures of active-site mutants bearing mutations at position 115. The histidine at this position acts as a base to activate the lactone-hydrolyzing water molecule. Mutations to Trp or Gln indeed diminish paraoxonase-1's lactonase activity; however, the promiscuous organophosphate hydrolase activity is enhanced. The structures reveal a 1.8-Å upward displacement towards the enzyme's surface of the catalytic Ca(2+) in the His115 mutants and configurational changes in the ligating side chains and water molecules, relative to the wild-type enzyme. Biochemical analysis and molecular dynamics simulations suggest that this alternative, upward metal mode mediates the promiscuous hydrolysis of organophosphates. The upward Ca(2+) mode observed in the His115 mutants also appears to mediate the wild type's paraoxonase activity. However, whereas the upward mode dominates in the Trp115 mutant, it is scarcely populated in wild type. Thus, the plasticity of active-site metal ions may permit alternative, latent, promiscuous activities and also provide the basis for the divergence of new enzymatic functions.
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Affiliation(s)
- Moshe Ben-David
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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11
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Yoshida H, Yoshihara A, Teraoka M, Yamashita S, Izumori K, Kamitori S. Structure of l-rhamnose isomerase in complex with l-rhamnopyranose demonstrates the sugar-ring opening mechanism and the role of a substrate sub-binding site. FEBS Open Bio 2012; 3:35-40. [PMID: 23772372 PMCID: PMC3668531 DOI: 10.1016/j.fob.2012.11.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 11/30/2012] [Indexed: 11/26/2022] Open
Abstract
l-Rhamnose isomerase (l-RhI) catalyzes the reversible isomerization of l-rhamnose to l-rhamnulose. Previously determined X-ray structures of l-RhI showed a hydride-shift mechanism for the isomerization of substrates in a linear form, but the mechanism for opening of the sugar-ring is still unclear. To elucidate this mechanism, we determined X-ray structures of a mutant l-RhI in complex with l-rhamnopyranose and d-allopyranose. Results suggest that a catalytic water molecule, which acts as an acid/base catalyst in the isomerization reaction, is likely to be involved in pyranose-ring opening, and that a newly found substrate sub-binding site in the vicinity of the catalytic site may recognize different anomers of substrates.
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Key Words
- D327N, mutant P. stutzeril-RhI, with a substitution of Asp327 with Asn
- E. coli, Escherichia coli
- H101N, mutant P. stutzeril-RhI, with a substitution of H101 with Asn
- P. stutzeri, Pseudomonas stutzeri
- Pseudomonas stutzeri
- RNS, l-rhamnose in a linear form
- Rare sugar
- Sugar-ring opening mechanism
- X-ray structure
- l-RhI, l-rhamnose isomerase
- l-Rhamnose isomerase
- α-APS, α-d-allopyranose
- α-RPS, α-l-rhamnopyranose
- β-RPS, β-l-rhamnopyranose
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Affiliation(s)
- Hiromi Yoshida
- 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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12
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Fieseler L, Schmitter S, Teiserskas J, Loessner MJ. Rhamnose-inducible gene expression in Listeria monocytogenes. PLoS One 2012; 7:e43444. [PMID: 22927968 PMCID: PMC3425472 DOI: 10.1371/journal.pone.0043444] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 07/20/2012] [Indexed: 12/02/2022] Open
Abstract
Acid production from rhamnose is a characteristic phenotype of Listeria monocytogenes. We report the identification of the rhamnose transport and utilization operon located at lmo2846 to lmo2851, including the rhamnose-dependent promoter Prha. Expression of reporter genes under control of Prha on a single copy integration vector demonstrated its suitability for inducible gene expression in L. monocytogenes. Transcription initiation from Prha is dose dependent, and a concentration as low as 100 µM rhamnose was found sufficient for induction. Moreover, Prha is subject to glucose catabolite repression, which provides additional options for strict control of expression. Infection of human THP1 macrophages revealed that Prha is repressed in intracellular L. monocytogenes, which is explained by the absence of rhamnose in the cytosol and possible interference by catabolite repression. The Prha promoter provides a novel and useful tool for triggering gene expression in extracellular L. monocytogenes, whereas intracellular conditions prevent transcription from this promoter.
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Affiliation(s)
- Lars Fieseler
- Institute of Food, Nutrition, and Health, ETH Zurich, Zurich, Switzerland
| | - Sibylle Schmitter
- Institute of Food, Nutrition, and Health, ETH Zurich, Zurich, Switzerland
| | | | - Martin J. Loessner
- Institute of Food, Nutrition, and Health, ETH Zurich, Zurich, Switzerland
- * E-mail:
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Usvalampi A, Turunen O, Valjakka J, Pastinen O, Leisola M, Nyyssölä A. Production of l-xylose from l-xylulose using Escherichia coli l-fucose isomerase. Enzyme Microb Technol 2012; 50:71-6. [DOI: 10.1016/j.enzmictec.2011.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 09/11/2011] [Accepted: 09/19/2011] [Indexed: 10/17/2022]
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14
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Schulten J, Klüfers P. Dibutylsilylene–pentose bis-chelates: on the glycoses’ binding sites for strongly Lewis-acidic centres. Carbohydr Res 2011; 346:1767-75. [DOI: 10.1016/j.carres.2011.05.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 05/30/2011] [Accepted: 05/31/2011] [Indexed: 11/26/2022]
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Lin CJ, Tseng WC, Fang TY. Characterization of a thermophilic L-rhamnose isomerase from Caldicellulosiruptor saccharolyticus ATCC 43494. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:8702-8708. [PMID: 21761877 DOI: 10.1021/jf201428b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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 Caldicellulosiruptor saccharolyticus ATCC 43494 and then expressed in Escherichia coli. A high yield of active L-RhI, 3010 U/g of wet cells, was obtained after 20 °C induction for 20 h. The enzyme was purified sequentially using heat treatment, nucleic acid precipitation, and ion-exchange chromatography. The purified L-RhI showed an apparent optimal pH of 7 and an optimal temperature at 90 °C. The enzyme was stable at pH values ranging from 4 to 11 and retained >90% activity after a 6 h incubation at 80 °C and pH 7-8. Compared with other previously characterized L-RhIs, the L-RhI from C. saccharolyticus ATCC 43494 has a good thermostability, the widest pH-stable range, and the highest catalytic efficiencies (k(cat)/K(M)) against L-rhamnose, L-lyxose, L-mannose, D-allose, and D-ribose, suggesting that this enzyme has the potential to be applied 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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Kamitori S, Ueda A, Tahara Y, Yoshida H, Ishii T, Uenishi J. Crystal structures of rare disaccharides, α-d-glucopyranosyl β-d-psicofuranoside, and α-d-galactopyranosyl β-d-psicofuranoside. Carbohydr Res 2011; 346:1182-5. [DOI: 10.1016/j.carres.2011.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 03/24/2011] [Accepted: 04/03/2011] [Indexed: 11/24/2022]
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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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