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Wang C, Mao L, Bao G, Zhu H. Pan-Genome Analyses of the Genus Cohnella and Proposal of the Novel Species Cohnella silvisoli sp. nov., Isolated from Forest Soil. Microorganisms 2023; 11:2726. [PMID: 38004738 PMCID: PMC10672984 DOI: 10.3390/microorganisms11112726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
Two strains, designated NL03-T5T and NL03-T5-1, were isolated from a soil sample collected from the Nanling National Forests, Guangdong Province, PR China. The two strains were Gram-stain-positive, aerobic, rod-shaped and had lophotrichous flagellation. Strain NL03-T5T could secrete extracellular mucus whereas NL03-T5-1 could not. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the two strains belong to the genus Cohnella, were most closely related to Cohnella lupini LMG 27416T (95.9% and 96.1% similarities), and both showed 94.0% similarity with Cohnella arctica NRRL B-59459T, respectively. The two strains showed 99.8% 16S rRNA gene sequence similarity between them. The draft genome size of strain NL03-T5T was 7.44 Mbp with a DNA G+C content of 49.2 mol%. The average nucleotide identities (ANI) and the digital DNA-DNA hybridization (dDDH) values between NL03-T5T and NL03-T5-1 were 99.98% and 100%, indicating the two strains were of the same species. Additionally, the ANI and dDDH values between NL03-T5T and C. lupini LMG 27416T were 76.1% and 20.4%, respectively. The major cellular fatty acids of strain NL03-T5T included anteiso-C15:0 and iso-C16:0. The major polar lipids and predominant respiratory quinone were diphosphatidylglycerol (DPG) and menaquinone-7 (MK-7). Based on phylogenetic analysis, phenotypic and chemotaxonomic characterization, genomic DNA G+C content, and ANI and dDDH values, strains NL03-T5T and NL03-T5-1 represent novel species in the genus Cohnella, for which the name Cohnella silvisoli is proposed. The type strain is NL03-T5T (=GDMCC 1.2294T = JCM 34999T). Furthermore, comparative genomics revealed that the genus Cohnella had an open pan-genome. The pan-genome of 29 Cohnella strains contained 41,356 gene families, and the number of strain-specific genes ranged from 6 to 1649. The results may explain the good adaptability of the Cohnella strains to different habitats at the genetic level.
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Affiliation(s)
- Chunling Wang
- College of Life Science, Huizhou University, Huizhou 516007, China; (C.W.); (L.M.)
| | - Lutian Mao
- College of Life Science, Huizhou University, Huizhou 516007, China; (C.W.); (L.M.)
| | - Gegen Bao
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China;
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510642, China
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De Rose SA, Kuprat T, Isupov MN, Reinhardt A, Schönheit P, Littlechild JA. Biochemical and Structural Characterisation of a Novel D-Lyxose Isomerase From the Hyperthermophilic Archaeon Thermofilum sp. Front Bioeng Biotechnol 2021; 9:711487. [PMID: 34422783 PMCID: PMC8378251 DOI: 10.3389/fbioe.2021.711487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/13/2021] [Indexed: 11/30/2022] Open
Abstract
A novel D-lyxose isomerase has been identified within the genome of a hyperthermophilic archaeon belonging to the Thermofilum species. The enzyme has been cloned and over-expressed in Escherichia coli and biochemically characterised. This enzyme differs from other enzymes of this class in that it is highly specific for the substrate D-lyxose, showing less than 2% activity towards mannose and other substrates reported for lyxose isomerases. This is the most thermoactive and thermostable lyxose isomerase reported to date, showing activity above 95°C and retaining 60% of its activity after 60 min incubation at 80°C. This lyxose isomerase is stable in the presence of 50% (v/v) of solvents ethanol, methanol, acetonitrile and DMSO. The crystal structure of the enzyme has been resolved to 1.4–1.7 A. resolution in the ligand-free form and in complexes with both of the slowly reacting sugar substrates mannose and fructose. This thermophilic lyxose isomerase is stabilised by a disulfide bond between the two monomers of the dimeric enzyme and increased hydrophobicity at the dimer interface. These overall properties of high substrate specificity, thermostability and solvent tolerance make this lyxose isomerase enzyme a good candidate for potential industrial applications.
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Affiliation(s)
- Simone Antonio De Rose
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Tom Kuprat
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Michail N Isupov
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Andreas Reinhardt
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Peter Schönheit
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Jennifer A Littlechild
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
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Comparative genomics and in silico gene evaluation involved in the probiotic potential of Bifidobacterium longum 5 1A. Gene 2021; 795:145781. [PMID: 34153410 DOI: 10.1016/j.gene.2021.145781] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 06/01/2021] [Accepted: 06/14/2021] [Indexed: 12/26/2022]
Abstract
The Bifidobacterium longum 51A strain of isolated from feces of a healthy child, has demonstrated probiotic properties by in vivo and in vitro studies, which may be assigned to its production of metabolites such as acetate. Thus, through the study of comparative genomics, the present work sought to identify unique genes that might be related to the production of acetate. To perform the study, the DNA strain was sequenced using Illumina HiSeq technology, followed by assembly and manual curation of coding sequences. Comparative analysis was performed including 19 complete B. longum genomes available in Genbank/NCBI. In the phylogenetic analysis, the CECT 7210 and 157F strains of B. longum subsp. infantis aggregated within the subsp. longum cluster, suggesting that their taxonomic classification should be reviewed. The strain 51A of B. longum has 26 unique genes, six of which are possibly related to carbohydrate metabolism and acetate production. The phosphoketolase pathway from B. longum 51A showed a difference in acetyl-phosphate production. This result seems to corroborate the analysis of their unique genes, whose presence suggests the strain may use different sources of carbohydrates that allow a greater production of acetate and consequently offer benefits to the host health.
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Wu H, Chen M, Guang C, Zhang W, Mu W. Identification of a novel recombinant D-lyxose isomerase from Thermoprotei archaeon with high thermostable, weak-acid and nickel ion dependent properties. Int J Biol Macromol 2020; 164:1267-1274. [PMID: 32750472 DOI: 10.1016/j.ijbiomac.2020.07.222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 07/16/2020] [Accepted: 07/24/2020] [Indexed: 10/23/2022]
Abstract
Recently, production of D-mannose becomes a hotspot owing to it exhibiting many physiological functions on people's health and wide applications in food and pharmaceutical field. The use of biological enzymes to production of D-mannose is of particular receiving considerable concerns due to it possessing many merits over chemical synthesis and plant extraction strategies. D-Lyxose isomerase (D-LIase) plays a pivotal role in preparation of D-mannose from d-fructose through isomerization reaction. Thus, a novel putative D-LIase from thermophiles strain Thermoprotei archaeon which was expressed in E. coli BL21(DE3) was first identified and biochemically characterized. The recombinant D-LIase showed an optimal temperature of 80 and 85 °C and pH of 6.5. It was highly thermostable at 70 °C and 80 °C after incubating for 48 h and 33 h, respectively, with retaining over 50% of the initial activity. A lower concentration of Ni2+ (0.5 mM) could greatly increase the activity by 25-fold, which was rare reported in other D-LIases. It was a dimer structure with melting temperature of 88.3 °C. Under the optimal conditions, 15.8 g L-1 of D-mannose and 33.8 g L-1 of D-xylulose were produced from 80 g L-1 of d-fructose and D-lyxose, respectively. This work provided a promising candidate sugar isomerase T. archaeon D-LIase for the production of D-mannose and D-xylulose.
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Affiliation(s)
- Hao Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Ming Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Cuie Guang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China
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Khayati K, Bhatt V, Hu ZS, Fahumy S, Luo X, Guo JY. Autophagy compensates for Lkb1 loss to maintain adult mice homeostasis and survival. eLife 2020; 9:62377. [PMID: 33236987 PMCID: PMC7714393 DOI: 10.7554/elife.62377] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022] Open
Abstract
Liver kinase B1 (LKB1), also known as serine/threonine kinase 11 (STK11) is the major energy sensor for cells to respond to metabolic stress. Autophagy degrades and recycles proteins, macromolecules, and organelles for cells to survive starvation. To assess the role and cross-talk between autophagy and Lkb1 in normal tissue homeostasis, we generated genetically engineered mouse models where we can conditionally delete Stk11 and autophagy essential gene, Atg7, respectively or simultaneously, throughout the adult mice. We found that Lkb1 was essential for the survival of adult mice, and autophagy activation could temporarily compensate for the acute loss of Lkb1 and extend mouse life span. We further found that acute deletion of Lkb1 in adult mice led to impaired intestinal barrier function, hypoglycemia, and abnormal serum metabolism, which was partly rescued by the Lkb1 loss-induced autophagy upregulation via inhibiting p53 induction. Taken together, we demonstrated that autophagy and Lkb1 work synergistically to maintain adult mouse homeostasis and survival.
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Affiliation(s)
- Khoosheh Khayati
- Rutgers Cancer Institute of New Jersey, New Brunswick, United States
| | - Vrushank Bhatt
- Rutgers Cancer Institute of New Jersey, New Brunswick, United States
| | | | - Sajid Fahumy
- Rutgers Cancer Institute of New Jersey, New Brunswick, United States
| | - Xuefei Luo
- Rutgers Cancer Institute of New Jersey, New Brunswick, United States
| | - Jessie Yanxiang Guo
- Rutgers Cancer Institute of New Jersey, New Brunswick, United States.,Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, United States.,Department of Chemical Biology, Rutgers Ernest Mario School of Pharmacy, Piscataway, United States
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6
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Wu H, Chen M, Guang C, Zhang W, Mu W. Characterization of a recombinant D-mannose-producing D-lyxose isomerase from Caldanaerobius polysaccharolyticus. Enzyme Microb Technol 2020; 138:109553. [DOI: 10.1016/j.enzmictec.2020.109553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 03/07/2020] [Accepted: 03/10/2020] [Indexed: 11/24/2022]
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7
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Phenotypic Response of Wolbachia pipientis in a Cell-Free Medium. Microorganisms 2020; 8:microorganisms8071060. [PMID: 32708688 PMCID: PMC7409048 DOI: 10.3390/microorganisms8071060] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/30/2020] [Accepted: 07/14/2020] [Indexed: 12/22/2022] Open
Abstract
Wolbachia, an obligate intracellular bacterium estimated to infect millions of arthropod species worldwide, is currently being utilized in novel control strategies to limit the transmission of Dengue and Zika viruses. A limitation for Wolbachia-based control approaches is the difficulty of transferring Wolbachia to novel hosts and the lack of tools for the genetic transformation of Wolbachia due to the inability to culture Wolbachia outside the insect host cell in an axenic media. Here, we applied extracellular Wolbachia to phenotypic microarrays to measure the metabolic response of Wolbachia in media formulations with different pH levels and supplementation with Casamino acids. Results suggested a pH of 6.5–6.8 and showed that the supplementation of 1 mg/mL casamino acids increased the survival and longevity of Wolbachia in an axenic medium. In addition, phenotypic microarrays are a useful tool to measure the phenotypic response of Wolbachia under different media conditions, as well as determine specific components that may be required for an axenic medium. This study is an initial step toward the development of a potential Wolbachia axenic culture system.
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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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9
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Recent studies on the biological production of D-mannose. Appl Microbiol Biotechnol 2019; 103:8753-8761. [DOI: 10.1007/s00253-019-10151-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/18/2019] [Accepted: 09/22/2019] [Indexed: 02/06/2023]
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10
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Guo Z, Long L, Ding S. Characterization of a D-lyxose isomerase from Bacillus velezensis and its application for the production of D-mannose and L-ribose. AMB Express 2019; 9:149. [PMID: 31529161 PMCID: PMC6746899 DOI: 10.1186/s13568-019-0877-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/09/2019] [Indexed: 11/10/2022] Open
Abstract
D-Mannose and L-ribose are two important monosaccharides, which have attracted public attention recently because of their great application potentials in food, cosmetic and pharmaceutical industries. Sugar isomerases catalyze the sugar isomerization and therefore can be used as the biocatalysts for production of the high-value sugars from inexpensive sugars. L-arabinose isomerase catalyzes the conversion of L-arabinose to L-ribulose, while D-lyxose isomerase catalyzes L-ribulose and D-fructose to L-ribose and D-mannose, respectively. In this paper, a putative D-LI from Bacillus velezensis (BvLI) was identified, characterized and used to produce D-mannose and L-ribose from D-fructose and L-arabinose, respectively. The recombinant BvLI exhibited a maximum activity at 55 °C and pH 6.5, in the presence of 0.1 mM Co2+. Approximately 110.75 g/L D-mannose was obtained from 500 g/L D-fructose in 6 h by the recombinant BvLI, and approximately 105 g/L L-ribose was obtained from 500 g/L L-arabinose in 8 h by the successive biocatalysis of L-arabinose isomerase from Bacillus licheniformis (BlAI) and BvLI.
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Characterization of a novel d-lyxose isomerase from Thermoflavimicrobium dichotomicum and its application for D-mannose production. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.05.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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12
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Li B, Li Z, Sun X, Wang Q, Xiao E, Sun W. DNA-SIP Reveals the Diversity of Chemolithoautotrophic Bacteria Inhabiting Three Different Soil Types in Typical Karst Rocky Desertification Ecosystems in Southwest China. MICROBIAL ECOLOGY 2018; 76:976-990. [PMID: 29728707 DOI: 10.1007/s00248-018-1196-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 04/16/2018] [Indexed: 06/08/2023]
Abstract
Autotrophs that inhabit soils receive less attention than their counterparts in other ecosystems, such as deep-sea and subsurface sediments, due to the low abundance of autotrophs in soils with high organic contents. However, the karst rocky desertification region is a unique ecosystem that may have a low level of organic compounds. Therefore, we propose that karst rocky desertification ecosystems may harbor diverse autotrophic microbial communities. In this study, DNA-SIP was employed to identify the chemolithoautotrophic bacteria inhabiting three soil types (i.e., grass, forest, and agriculture) of the karst rocky desertification ecosystems. The results indicated that potential chemolithoautotrophic population was observed in each soil type, even at different time points after amending 13C-NaHCO3, confirming our hypothesis that diverse autotrophs contribute to the carbon cycle in karst soils. Bacteria, such as Ralstonia, Ochrobactrum, Brevibacterium, Acinetobacter, and Corynebacterium, demonstrated their potential to assimilate inorganic carbon and reduce nitrate or thiosulfate as electron acceptors. Putative mixotrophs were identified by DNA-SIP as well, suggesting the metabolic versatility of soil microbiota. A co-occurrence network further indicated that autotrophs and heterotrophs may form associated communities to sustain the ecosystem function. Our current study revealed the metabolic diversity of autotrophic bacteria in soil habitats and demonstrated the potentially important role of chemoautotrophs in karst rocky desertification ecosystems.
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Affiliation(s)
- Baoqin Li
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Zhe Li
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Xiaoxu Sun
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Qi Wang
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Enzong Xiao
- Innovation Center and Key Laboratory of Waters Safety & Protection in the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China.
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Huang J, Yu L, Zhang W, Zhang T, Guang C, Mu W. Production of d-mannose from d-glucose by co-expression of d-glucose isomerase and d-lyxose isomerase in Escherichia coli. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2018; 98:4895-4902. [PMID: 29569257 DOI: 10.1002/jsfa.9021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 03/15/2018] [Accepted: 03/18/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND d-Mannose is not only the epimer of d-glucose at the C-2 position, but also the aldose isomer of d-fructose. Because of its physiological properties and health benefits, d-mannose has attracted public interest. It has been confirmed that d-mannose has broad applications in food, cosmetics, and pharmaceutical industries. According to the Izumoring strategy, d-glucose isomerase (d-GI) and d-lyxose isomerase (d-LI) play important roles in the conversions of d-fructose from d-glucose and of d-mannose from d-fructose respectively. In this study, a one-step enzyme process of d-mannose production from d-glucose has been constructed by co-expression of the d-GI from Acidothermus cellulolyticus and d-LI from Thermosediminibacter oceani in Escherichia coli BL21(DE3) cells. RESULTS The co-expression system exhibits maximum activity at pH 6.5 and 65 °C with Co2+ supplement. It is relatively thermostable at less than 65 °C. When the reaction reaches equilibrium, the ratio of d-glucose, d-fructose, and d-mannose is approximately 34 : 49.6 : 16.4. By using this co-expression system, about 60.0 g L-1 d-mannose is obtained from 400 g L-1 d-glucose in 8 h. CONCLUSION This co-expression of d-GI and d-LI system provides a novel and efficient approach for d-mannose production. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Jiawei Huang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Lina Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Tao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Cuie Guang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
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Isomerases and epimerases for biotransformation of pentoses. Appl Microbiol Biotechnol 2018; 102:7283-7292. [PMID: 29968034 DOI: 10.1007/s00253-018-9150-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 05/23/2018] [Accepted: 05/24/2018] [Indexed: 01/08/2023]
Abstract
Pentoses represent monosaccharides with five carbon atoms. They are organized into two main groups, aldopentoses and ketopentoses. There are eight aldopentoses and four ketopentoses and each ketopentose corresponds to two aldopentoses. Only D-xylose, D-ribose, and L-arabinose are natural sugars, but others belong to rare sugars that occur in very small quantities in nature. Recently, rare pentoses attract much attention because of their great potentials for commercial applications, especially as precursors of many important medical drugs. Pentoses Izumoring strategy provides a complete enzymatic approach to link all pentoses using four types of enzymes, including ketose 3-epimerases, aldose-ketose isomerases, polyol dehydrogenases, and aldose reductases. At least 10 types of epimerases and isomerases have been used for biotransformation of all aldopentoses and ketopentoses, and these enzymes are reviewed in detail in this article.
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McAuliffe O. Symposium review: Lactococcus lactis from nondairy sources: Their genetic and metabolic diversity and potential applications in cheese. J Dairy Sci 2018; 101:3597-3610. [PMID: 29395148 DOI: 10.3168/jds.2017-13331] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/22/2017] [Indexed: 12/21/2022]
Abstract
The widespread dissemination of species of the lactic acid bacteria (LAB) group in different environments testifies to their extraordinary niche adaptability. Members of the LAB are present on grass and other plant material, in dairy products, on human skin, and in the gastrointestinal and reproductive tracts. The selective pressure imparted by these specific environments is a key driver in the genomic diversity observed between strains of the same species deriving from distinct habitats. Strains that are exploited in the dairy industry for the production of fermented dairy products are often referred to as "domesticated" strains. These strains, which initially may have occupied a nondairy niche, have become specialized for growth in the milk environment. In fact, comparative genome analysis of multiple LAB species and strains has revealed a central trend in LAB evolution: the loss of ancestral genes and metabolic simplification toward adaptation to nutritionally rich environments. In contrast, "environmental" strains, or those from raw milk, plants, and animals, exhibit diverse metabolic capabilities and lifestyle characteristics compared with their domesticated counterparts. Because of the limited number of established dairy strains used in fermented food production today, demand is increasing for novel strains, with concerted efforts to mine the microbiota of natural environments for strains of technological interest. Many studies have concentrated on uncovering the genomic and metabolic potential of these organisms, facilitating comparative genome analysis of strains from diverse environments and providing insight into the natural diversity of the LAB, a group of organisms that is at the core of the dairy industry. The natural biodiversity that exists in these environments may be exploited in dairy fermentations to expand flavor profiles, to produce natural "clean label" ingredients, or to develop safer products.
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Affiliation(s)
- Olivia McAuliffe
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland P61 C996.
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16
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d-lyxose isomerase and its application for functional sugar production. Appl Microbiol Biotechnol 2018; 102:2051-2062. [DOI: 10.1007/s00253-018-8746-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/26/2017] [Accepted: 12/27/2017] [Indexed: 12/31/2022]
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17
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A single and two step isomerization process for d-tagatose and l-ribose bioproduction using l-arabinose isomerase and d-lyxose isomerase. Enzyme Microb Technol 2017; 97:27-33. [DOI: 10.1016/j.enzmictec.2016.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/10/2016] [Accepted: 11/03/2016] [Indexed: 11/22/2022]
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18
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Efficient biotransformation of d-fructose to d-mannose by a thermostable d-lyxose isomerase from Thermosediminibacter oceani. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.08.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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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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Hu X, Shi Y, Zhang P, Miao M, Zhang T, Jiang B. d-Mannose: Properties, Production, and Applications: An Overview. Compr Rev Food Sci Food Saf 2016; 15:773-785. [DOI: 10.1111/1541-4337.12211] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 04/09/2016] [Accepted: 04/13/2016] [Indexed: 12/24/2022]
Affiliation(s)
- Xing Hu
- State Key Laboratory of Food Science and Technology; Jiangnan Univ; 1800 Lihu Ave Wuxi Jiangsu 214122 P.R. China
- Synergetic Innovation Center of Food Safety and Nutrition; Jiangnan Univ; 1800 Lihu Avenue Wuxi Jiangsu 214122 P.R. China
| | - Yaning Shi
- State Key Laboratory of Food Science and Technology; Jiangnan Univ; 1800 Lihu Ave Wuxi Jiangsu 214122 P.R. China
- College of Food Science and Technology; Nanjing Agricultural Univ; 1 Weigang Nanjing Jiangsu 210095 P.R. China
| | - Peng Zhang
- State Key Laboratory of Food Science and Technology; Jiangnan Univ; 1800 Lihu Ave Wuxi Jiangsu 214122 P.R. China
- Synergetic Innovation Center of Food Safety and Nutrition; Jiangnan Univ; 1800 Lihu Avenue Wuxi Jiangsu 214122 P.R. China
| | - Ming Miao
- State Key Laboratory of Food Science and Technology; Jiangnan Univ; 1800 Lihu Ave Wuxi Jiangsu 214122 P.R. China
| | - Tao Zhang
- State Key Laboratory of Food Science and Technology; Jiangnan Univ; 1800 Lihu Ave Wuxi Jiangsu 214122 P.R. China
- Synergetic Innovation Center of Food Safety and Nutrition; Jiangnan Univ; 1800 Lihu Avenue Wuxi Jiangsu 214122 P.R. China
| | - Bo Jiang
- State Key Laboratory of Food Science and Technology; Jiangnan Univ; 1800 Lihu Ave Wuxi Jiangsu 214122 P.R. China
- Synergetic Innovation Center of Food Safety and Nutrition; Jiangnan Univ; 1800 Lihu Avenue Wuxi Jiangsu 214122 P.R. China
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Mu W, Yu L, Zhang W, Zhang T, Jiang B. Isomerases for biotransformation of D-hexoses. Appl Microbiol Biotechnol 2015; 99:6571-84. [DOI: 10.1007/s00253-015-6788-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 06/18/2015] [Accepted: 06/19/2015] [Indexed: 10/23/2022]
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22
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Terami Y, Yoshida H, Uechi K, Morimoto K, Takata G, Kamitori S. Essentiality of tetramer formation of Cellulomonas parahominis L-ribose isomerase involved in novel L-ribose metabolic pathway. Appl Microbiol Biotechnol 2015; 99:6303-13. [DOI: 10.1007/s00253-015-6417-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 01/15/2015] [Accepted: 01/18/2015] [Indexed: 11/30/2022]
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23
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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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Beerens K, Desmet T, Soetaert W. Enzymes for the biocatalytic production of rare sugars. ACTA ACUST UNITED AC 2012; 39:823-34. [DOI: 10.1007/s10295-012-1089-x] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 01/13/2012] [Indexed: 11/24/2022]
Abstract
Abstract
Carbohydrates are much more than just a source of energy as they also mediate a variety of recognition processes that are central to human health. As such, saccharides can be applied in the food and pharmaceutical industries to stimulate our immune system (e.g., prebiotics), to control diabetes (e.g., low-calorie sweeteners), or as building blocks for anticancer and antiviral drugs (e.g., l-nucleosides). Unfortunately, only a small number of all possible monosaccharides are found in nature in sufficient amounts to allow their commercial exploitation. Consequently, so-called rare sugars have to be produced by (bio)chemical processes starting from cheap and widely available substrates. Three enzyme classes that can be used for rare sugar production are keto–aldol isomerases, epimerases, and oxidoreductases. In this review, the recent developments in rare sugar production with these biocatalysts are discussed.
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Affiliation(s)
- Koen Beerens
- grid.5342.0 0000000120697798 Centre for Industrial Biotechnology and Biocatalysis, Faculty of Bioscience Engineering Ghent University Coupure links 653 9000 Gent Belgium
| | - Tom Desmet
- grid.5342.0 0000000120697798 Centre for Industrial Biotechnology and Biocatalysis, Faculty of Bioscience Engineering Ghent University Coupure links 653 9000 Gent Belgium
| | - Wim Soetaert
- grid.5342.0 0000000120697798 Centre for Industrial Biotechnology and Biocatalysis, Faculty of Bioscience Engineering Ghent University Coupure links 653 9000 Gent Belgium
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Production of L-ribose from L-ribulose by a triple-site variant of mannose-6-phosphate isomerase from Geobacillus thermodenitrificans. Appl Environ Microbiol 2012; 78:3880-4. [PMID: 22447612 DOI: 10.1128/aem.07012-11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A triple-site variant (W17Q N90A L129F) of mannose-6-phosphate isomerase from Geobacillus thermodenitrificans was obtained by combining variants with residue substitutions at different positions after random and site-directed mutagenesis. The specific activity and catalytic efficiency (k(cat)/K(m)) for L-ribulose isomerization of this variant were 3.1- and 7.1-fold higher, respectively, than those of the wild-type enzyme at pH 7.0 and 70°C in the presence of 1 mM Co(2+). The triple-site variant produced 213 g/liter l-ribose from 300 g/liter L-ribulose for 60 min, with a volumetric productivity of 213 g liter(-1) h(-1), which was 4.5-fold higher than that of the wild-type enzyme. The k(cat)/K(m) and productivity of the triple-site variant were approximately 2-fold higher than those of the Thermus thermophilus R142N variant of mannose-6-phosphate isomerase, which exhibited the highest values previously reported.
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Xiang DF, Kolb P, Fedorov AA, Xu C, Fedorov EV, Narindoshivili T, Williams HJ, Shoichet BK, Almo SC, Raushel FM. Structure-based function discovery of an enzyme for the hydrolysis of phosphorylated sugar lactones. Biochemistry 2012; 51:1762-73. [PMID: 22313111 PMCID: PMC3298459 DOI: 10.1021/bi201838b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Two enzymes of unknown function from the cog1735 subset of the amidohydrolase superfamily (AHS), LMOf2365_2620 (Lmo2620) from Listeria monocytogenes str. 4b F2365 and Bh0225 from Bacillus halodurans C-125, were cloned, expressed, and purified to homogeneity. The catalytic functions of these two enzymes were interrogated by an integrated strategy encompassing bioinformatics, computational docking to three-dimensional crystal structures, and library screening. The three-dimensional structure of Lmo2620 was determined at a resolution of 1.6 Å with two phosphates and a binuclear zinc center in the active site. The proximal phosphate bridges the binuclear metal center and is 7.1 Å from the distal phosphate. The distal phosphate hydrogen bonds with Lys-242, Lys-244, Arg-275, and Tyr-278. Enzymes within cog1735 of the AHS have previously been shown to catalyze the hydrolysis of substituted lactones. Computational docking of the high-energy intermediate form of the KEGG database to the three-dimensional structure of Lmo2620 highly enriched anionic lactones versus other candidate substrates. The active site structure and the computational docking results suggested that probable substrates would likely include phosphorylated sugar lactones. A small library of diacid sugar lactones and phosphorylated sugar lactones was synthesized and tested for substrate activity with Lmo2620 and Bh0225. Two substrates were identified for these enzymes, D-lyxono-1,4-lactone-5-phosphate and l-ribono-1,4-lactone-5-phosphate. The k(cat)/K(m) values for the cobalt-substituted enzymes with these substrates are ~10(5) M(-1) s(-1).
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Affiliation(s)
- Dao Feng Xiang
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - Peter Kolb
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th Street, San Francisco, California 94158-2330
| | - Alexander A. Fedorov
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Chengfu Xu
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - Elena V. Fedorov
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Tamari Narindoshivili
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - Howard J. Williams
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th Street, San Francisco, California 94158-2330,To whom correspondence may be addressed: (FMR) telephone: (979) 845-3373; fax: (979)-845-9452; , (SCA) telephone: (718) 430-2746; fax: (718)-430-8565; , (BKS) telephone: (415)-514-4126; fax: (415)-514-4260;
| | - Steven C. Almo
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461,To whom correspondence may be addressed: (FMR) telephone: (979) 845-3373; fax: (979)-845-9452; , (SCA) telephone: (718) 430-2746; fax: (718)-430-8565; , (BKS) telephone: (415)-514-4126; fax: (415)-514-4260;
| | - Frank M. Raushel
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012,To whom correspondence may be addressed: (FMR) telephone: (979) 845-3373; fax: (979)-845-9452; , (SCA) telephone: (718) 430-2746; fax: (718)-430-8565; , (BKS) telephone: (415)-514-4126; fax: (415)-514-4260;
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Choi JG, Hong SH, Kim YS, Kim KR, Oh DK. Characterization of a recombinant thermostable d-lyxose isomerase from Dictyoglomus turgidum that produces d-lyxose from d-xylulose. Biotechnol Lett 2012; 34:1079-85. [DOI: 10.1007/s10529-012-0874-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 02/02/2012] [Indexed: 11/25/2022]
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28
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Hong YH, Lee DW, Pyun YR, Lee SH. Creation of metal-independent hyperthermophilic L-arabinose isomerase by homologous recombination. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:12939-12947. [PMID: 22103589 DOI: 10.1021/jf203897a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Hyperthermophilic L-arabinose isomerases (AIs) are useful in the commercial production of D-tagatose as a low-calorie bulk sweetener. Their catalysis and thermostability are highly dependent on metals, which is a major drawback in food applications. To study the role of metal ions in the thermostability and catalysis of hyperthermophilic AI, four enzyme chimeras were generated by PCR-based hybridization to replace the variable N- and C-terminal regions of hyperthermophilic Thermotoga maritima AI (TMAI) and thermophilic Geobacillus stearothermophilus AI (GSAI) with those of the homologous mesophilic Bacillus halodurans AI (BHAI). Unlike Mn(2+)-dependent TMAI, the GSAI- and TMAI-based hybrids with the 72 C-terminal residues of BHAI were not metal-dependent for catalytic activity. By contrast, the catalytic activities of the TMAI- and GSAI-based hybrids containing the N-terminus (residues 1-89) of BHAI were significantly enhanced by metals, but their thermostabilities were poor even in the presence of Mn(2+), indicating that the effects of metals on catalysis and thermostability involve different structural regions. Moreover, in contrast to the C-terminal truncate (Δ20 residues) of GSAI, the N-terminal truncate (Δ7 residues) exhibited no activity due to loss of its native structure. The data thus strongly suggest that the metal dependence of the catalysis and thermostability of hyperthermophilic AIs evolved separately to optimize their activity and thermostability at elevated temperatures. This may provide effective target regions for engineering, thereby meeting industrial demands for the production of d-tagatose.
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Affiliation(s)
- Young-Ho Hong
- CJ Foods R & D, CJ Cheiljedang Corporation, Seoul 100-749, Korea
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29
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Hu C, Li L, Zheng Y, Rui L, Hu C. Perspectives of biotechnological production of l-ribose and its purification. Appl Microbiol Biotechnol 2011; 92:449-55. [DOI: 10.1007/s00253-011-3552-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 08/08/2011] [Accepted: 08/13/2011] [Indexed: 12/28/2022]
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30
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Characterization of a recombinant cellobiose 2-epimerase from Caldicellulosiruptor saccharolyticus and its application in the production of mannose from glucose. Appl Microbiol Biotechnol 2011; 92:1187-96. [DOI: 10.1007/s00253-011-3403-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 05/03/2011] [Accepted: 05/19/2011] [Indexed: 10/18/2022]
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31
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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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Park CS, Yeom SJ, Lim YR, Kim YS, Oh DK. Substrate specificity of a recombinant d-lyxose isomerase from Serratia proteamaculans that produces d-lyxose and d-mannose. Lett Appl Microbiol 2010; 51:343-50. [DOI: 10.1111/j.1472-765x.2010.02903.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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33
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Substrate specificity of a recombinant ribose-5-phosphate isomerase from Streptococcus pneumoniae and its application in the production of l-lyxose and l-tagatose. World J Microbiol Biotechnol 2010. [DOI: 10.1007/s11274-010-0511-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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van Staalduinen LM, Park CS, Yeom SJ, Adams-Cioaba MA, Oh DK, Jia Z. Structure-based annotation of a novel sugar isomerase from the pathogenic E. coli O157:H7. J Mol Biol 2010; 401:866-81. [PMID: 20615418 DOI: 10.1016/j.jmb.2010.06.063] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 06/24/2010] [Accepted: 06/28/2010] [Indexed: 11/16/2022]
Abstract
Prokaryotes can use a variety of sugars as carbon sources in order to provide a selective survival advantage. The gene z5688 found in the pathogenic Escherichia coli O157:H7 encodes a "hypothetical" protein of unknown function. Sequence analysis identified the gene product as a putative member of the cupin superfamily of proteins, but no other functional information was known. We have determined the crystal structure of the Z5688 protein at 1.6 A resolution and identified the protein as a novel E. coli sugar isomerase (EcSI) through overall fold analysis and secondary-structure matching. Extensive substrate screening revealed that EcSI is capable of acting on d-lyxose and d-mannose. The complex structure of EcSI with fructose allowed the identification of key active-site residues, and mutagenesis confirmed their importance. The structure of EcSI also suggested a novel mechanism for substrate binding and product release in a cupin sugar isomerase. Supplementation of a nonpathogenic E. coli strain with EcSI enabled cell growth on the rare pentose d-lyxose.
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Kwon HJ, Yeom SJ, Park CS, Oh DK. Substrate specificity of a recombinant d-lyxose isomerase from Providencia stuartii for monosaccharides. J Biosci Bioeng 2010; 110:26-31. [DOI: 10.1016/j.jbiosc.2009.12.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Revised: 12/26/2009] [Accepted: 12/29/2009] [Indexed: 10/19/2022]
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36
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Park CS, Kwon HJ, Yeom SJ, Oh DK. Mannose production from fructose by free and immobilized D-lyxose isomerases from Providencia stuartii. Biotechnol Lett 2010; 32:1305-9. [PMID: 20480207 DOI: 10.1007/s10529-010-0300-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Accepted: 05/06/2010] [Indexed: 11/25/2022]
Abstract
A recombinant D-lyxose isomerase from Providencia stuartii was immobilized on Duolite A568 beads which gave the highest conversion of D-fructose to D-mannose among the various immobilization beads evaluated. Maximum activities of both the free and immobilized enzymes for fructose isomerization were at pH 7.5 and 45 degrees C in the presence of 1 mM Mn(2+). Enzyme half-lives were 14 and 30 h at 35 degrees C and 3.4 and 5.1 h at 45 degrees C, respectively. The immobilized enzyme in 300 g fructose/l (replaced hourly), produced 75 g mannose/l at 35 degrees C = 25% (w/w) yield with a productivity of 75 g mannose l(-1) h(-1) after 23 cycles.
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Affiliation(s)
- Chang-Su Park
- Department of Bioscience and Biotechnology, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 143-701, South Korea
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37
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Ju YH, Oh DK. Characterization of a recombinant l-fucose isomerase from Caldicellulosiruptor saccharolyticus that isomerizes l-fucose, d-arabinose, d-altrose, and l-galactose. Biotechnol Lett 2009; 32:299-304. [DOI: 10.1007/s10529-009-0154-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Revised: 10/04/2009] [Accepted: 10/07/2009] [Indexed: 10/20/2022]
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38
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Substrate specificity of a mannose-6-phosphate isomerase from Bacillus subtilis and its application in the production of L-ribose. Appl Environ Microbiol 2009; 75:4705-10. [PMID: 19447949 DOI: 10.1128/aem.00310-09] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The uncharacterized gene previously proposed as a mannose-6-phosphate isomerase from Bacillus subtilis was cloned and expressed in Escherichia coli. The maximal activity of the recombinant enzyme was observed at pH 7.5 and 40 degrees C in the presence of 0.5 mM Co(2+). The isomerization activity was specific for aldose substrates possessing hydroxyl groups oriented in the same direction at the C-2 and C-3 positions, such as the d and l forms of ribose, lyxose, talose, mannose, and allose. The enzyme exhibited the highest activity for l-ribulose among all pentoses and hexoses. Thus, L-ribose, as a potential starting material for many L-nucleoside-based pharmaceutical compounds, was produced at 213 g/liter from 300-g/liter L-ribulose by mannose-6-phosphate isomerase at 40 degrees C for 3 h, with a conversion yield of 71% and a volumetric productivity of 71 g liter(-1) h(-1).
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Helanto M, Kiviharju K, Granström T, Leisola M, Nyyssölä A. Biotechnological production of l-ribose from l-arabinose. Appl Microbiol Biotechnol 2009; 83:77-83. [DOI: 10.1007/s00253-008-1855-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Revised: 12/30/2008] [Accepted: 12/30/2008] [Indexed: 12/01/2022]
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40
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Characterization of a mannose-6-phosphate isomerase from Geobacillus thermodenitrificans that converts monosaccharides. Biotechnol Lett 2009; 31:1273-8. [DOI: 10.1007/s10529-009-0003-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Revised: 03/31/2009] [Accepted: 03/31/2009] [Indexed: 10/20/2022]
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41
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Yoon RY, Yeom SJ, Park CS, Oh DK. Substrate specificity of a glucose-6-phosphate isomerase from Pyrococcus furiosus for monosaccharides. Appl Microbiol Biotechnol 2009; 83:295-303. [PMID: 19159927 DOI: 10.1007/s00253-009-1859-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Revised: 01/03/2009] [Accepted: 01/05/2009] [Indexed: 11/25/2022]
Abstract
We purified recombinant glucose-6-phosphate isomerase from Pyrococcus furiosus using heat treatment and Hi-Trap anion-exchange chromatography with a final specific activity of 0.39 U mg(-1). The activity of the glucose-6-phosphate isomerase for L: -talose isomerization was optimal at pH 7.0, 95 degrees C, and 1.5 mM Co(2+). The half-lives of the enzyme at 65 degrees C, 75 degrees C, 85 degrees C, and 95 degrees C were 170, 41, 19, and 7.9 h, respectively. Glucose-6-phosphate isomerase catalyzed the interconversion between two different aldoses and ketose for all pentoses and hexoses via two isomerization reactions. This enzyme has a unique activity order as follows: aldose substrates with hydroxyl groups oriented in the same direction at C2, C3, and C4 > C2 and C4 > C2 and C3 > C3 and C4. L: -Talose and D: -ribulose exhibited the most preferred substrates among the aldoses and ketoses, respectively. L: -Talose was converted to L: -tagatose and L: -galactose by glucose-6-phosphate isomerase with 80% and 5% conversion yields after about 420 min, respectively, whereas D: -ribulose was converted to D: -ribose and D: -arabinose with 53% and 8% conversion yields after about 240 min, respectively.
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Affiliation(s)
- Ran-Young Yoon
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 143-701, South Korea
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Cho EA, Lee JS, Lee KC, Jung HC, Pan JG, Pyun YR. Cohnella laeviribosi sp. nov., isolated from a volcanic pond. Int J Syst Evol Microbiol 2007; 57:2902-2907. [DOI: 10.1099/ijs.0.64844-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel thermophilic and endospore-forming Gram-positive bacterium capable of assimilating and isomerizingl-ribose was isolated from a volcanic area in Likupang, Indonesia. The isolate, RI-39T, was able to grow at high temperatures (37–60 °C); optimum growth was observed at pH 6.5 and 45 °C. The strain contained MK-7 (87 %) as the main respiratory quinone and had a DNA G+C content of 51 mol%. The major cellular fatty acids of the isolate were iso-C16 : 0and anteiso-C15 : 0and the predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and lysyl-phosphatidylglycerol. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate represents an evolutionary lineage that is distinct from those of otherCohnellaspecies. Based on morphological, physiological and chemotaxonomic characteristics and 16S rRNA gene sequence comparisons, it is proposed that strain RI-39Trepresents a novel species,Cohnella laeviribosisp. nov. The type strain is RI-39T(=KCTC 3987T=KCCM 10653PT=CCUG 52217T).
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Affiliation(s)
- Eun-Ah Cho
- Department of Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 52 Eoeun-dong, Yusong-gu, Daejeon 305-806, Republic of Korea
| | - Keun Chul Lee
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 52 Eoeun-dong, Yusong-gu, Daejeon 305-806, Republic of Korea
| | - Heung-Chae Jung
- Systems Microbiology Research Center, Korea Research Institute of Bioscience and Biotechnology, 52 Eoeun-dong, Yusong-gu, Daejeon 305-806, Republic of Korea
- GenoFocus Inc., Yusong, Daejeon 305-811, Republic of Korea
| | - Jae-Gu Pan
- Systems Microbiology Research Center, Korea Research Institute of Bioscience and Biotechnology, 52 Eoeun-dong, Yusong-gu, Daejeon 305-806, Republic of Korea
- GenoFocus Inc., Yusong, Daejeon 305-811, Republic of Korea
| | - Yu-Ryang Pyun
- Department of Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
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