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Miyamoto RY, de Melo RR, de Mesquita Sampaio IL, de Sousa AS, Morais ER, Sargo CR, Zanphorlin LM. Paradigm shift in xylose isomerase usage: a novel scenario with distinct applications. Crit Rev Biotechnol 2021; 42:693-712. [PMID: 34641740 DOI: 10.1080/07388551.2021.1962241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Isomerases are enzymes that induce physical changes in a molecule without affecting the original molecular formula. Among this class of enzymes, xylose isomerases (XIs) are the most studied to date, partly due to their extensive application in industrial processes to produce high-fructose corn sirups. In recent years, the need for sustainable initiatives has triggered efforts to improve the biobased economy through the use of renewable raw materials. In this context, D-xylose usage is crucial as it is the second-most abundant sugar in nature. The application of XIs in biotransforming xylose, enabling downstream metabolism in several microorganisms, is a smart strategy for ensuring a low-carbon footprint and producing several value-added biochemicals with broad industrial applications such as in the food, cosmetics, pharmaceutical, and polymer industries. Considering recent advancements that have expanded the range of applications of XIs, this review provides a comprehensive and concise overview of XIs, from their primary sources to the biochemical and structural features that influence their mechanisms of action. This comprehensive review may help address the challenges involved in XI applications in different industries and facilitate the exploitation of xylose bioprocesses.
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Affiliation(s)
- Renan Yuji Miyamoto
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil.,Faculty of Pharmaceutical Sciences (FCF), State University of Campinas (UNICAMP), Campinas, Brazil
| | - Ricardo Rodrigues de Melo
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Isabelle Lobo de Mesquita Sampaio
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil.,Faculty of Food Engineering (FEA), State University of Campinas (UNICAMP), Campinas, Brazil
| | - Amanda Silva de Sousa
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Edvaldo Rodrigo Morais
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil.,Faculty of Food Engineering (FEA), State University of Campinas (UNICAMP), Campinas, Brazil
| | - Cintia Regina Sargo
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Leticia Maria Zanphorlin
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
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Cheng K, Zheng W, Chen H, Zhang YHPJ. Upgrade of wood sugar d-xylose to a value-added nutraceutical by in vitro metabolic engineering. Metab Eng 2018; 52:1-8. [PMID: 30389613 DOI: 10.1016/j.ymben.2018.10.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 10/09/2018] [Accepted: 10/27/2018] [Indexed: 11/30/2022]
Abstract
The upgrade of D-xylose, the most abundant pentose, to value-added biochemicals is economically important to next-generation biorefineries. myo-Inositol, as vitamin B8, has a six-carbon carbon-carbon ring. Here we designed an in vitro artificial NAD(P)-free 12-enzyme pathway that can effectively convert the five-carbon xylose to inositol involving xylose phosphorylation, carbon-carbon (C-C) rearrangement, C-C bond circulation, and dephosphorylation. The reaction conditions catalyzed by all thermostable enzymes from hyperthermophilic microorganisms Thermus thermophiles, Thermotoga maritima, and Archaeoglobus fulgidus were optimized in reaction temperature, buffer type and concentration, enzyme composition, Mg2+ concentration, and fed-batch addition of ATP. The 11-enzyme cocktail, whereas a fructose 1,6-bisphosphatase from T. maritima has another function of inositol monophosphatase, converted 20 mM xylose to 16.1 mM inositol with a conversion efficiency of 96.6% at 70 °C. Polyphosphate was found to replace ATP for xylulose phosphorylation due to broad substrate promiscuity of the T. maritima xylulokinase. The Tris-HCl buffer effectively mitigated the Maillard reaction at 70 °C or higher temperature. The co-production of value-added biochemicals, such as inositol, from wood sugar could greatly improve economics of new biorefineries, similar to oil refineries that make value-added plastic precursors to subsidize gasoline/diesel production.
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Affiliation(s)
- Kun Cheng
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Wenming Zheng
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China; College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China
| | - Hongge Chen
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China; College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China.
| | - Yi-Heng P Job Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China.
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Rhimi M, Bermudez-Humaran LG, Huang Y, Boudebbouze S, Gaci N, Garnier A, Gratadoux JJ, Mkaouar H, Langella P, Maguin E. The secreted L-arabinose isomerase displays anti-hyperglycemic effects in mice. Microb Cell Fact 2015; 14:204. [PMID: 26691177 PMCID: PMC4687139 DOI: 10.1186/s12934-015-0391-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/27/2015] [Indexed: 12/02/2022] Open
Abstract
Background The l-arabinose isomerase is an intracellular enzyme which converts l-arabinose into l-ribulose in living systems and d-galactose into d-tagatose in industrial processes and at industrial scales. d-tagatose is a natural ketohexose with potential uses in pharmaceutical and food industries. The d-galactose isomerization reaction is thermodynamically equilibrated, and leads to secondary subproducts at high pH. Therefore, an attractive l-arabinose isomerase should be thermoactive and acidotolerant with high catalytic efficiency. While many reports focused on the set out of a low cost process for the industrial production of d-tagatose, these procedures remain costly. When compared to intracellular enzymes, the production of extracellular ones constitutes an interesting strategy to increase the suitability of the biocatalysts. Results The l-arabinose isomerase (l-AI) from Lactobacillus sakei was expressed in Lactococcus lactis in fusion with the signal peptide of usp45 (SPUsp45). The l-AI protein and activity were detected only in the supernatant of the induced cultures of the recombinant L. lactis demonstrating the secretion in the medium of the intracellular L. sakeil-AI in an active form. Moreover, we showed an improvement in the enzyme secretion using either (1) L. lactis strains deficient for their two major proteases, ClpP and HtrA, or (2) an enhancer of protein secretion in L. lactis fused to the recombinant l-AI with the SPUsp45. Th l-AI enzyme secreted by the recombinant L. lactis strains or produced intracellularly in E. coli, showed the same functional properties than the native enzyme. Furthermore, when mice are fed with the L. lactis strain secreting the l-AI and galactose, tagatose was produced in vivo and reduced the glycemia index. Conclusions We report for the first time the secretion of the intracellular l-arabinose isomerase in the supernatant of food grade L. lactis cultures with hardly
display other secreted proteins. The secreted l-AI originated from the food grade L. sakei 23 K was active and showed the same catalytic and structural properties as the intracellular enzyme. The L. lactis strains secreting the l-arabinose isomerase has the ability to produce d-tagatose in vivo and conferred an anti-hyperglycemic effect to mice.
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Affiliation(s)
- Moez Rhimi
- INRA, UMR 1319 Micalis, Interactions of Firmicutes With Their Environments, 78352, Jouy-en-Josas Cedex, France. .,AgroParisTech, Micalis, Interactions of Firmicutes With Their Environments, 78352, Jouy-en-Josas Cedex, France.
| | - Luis G Bermudez-Humaran
- INRA, UMR 1319 Micalis, Commensal and Probiotics-Host Interactions Laboratory, 78352, Jouy-en-Josas Cedex, France. .,AgroParisTech, Micalis, Commensal and Probiotics-Host Interactions Laboratory, 78352, Jouy-en-Josas Cedex, France.
| | - Yuan Huang
- INRA, UMR 1319 Micalis, Interactions of Firmicutes With Their Environments, 78352, Jouy-en-Josas Cedex, France. .,AgroParisTech, Micalis, Interactions of Firmicutes With Their Environments, 78352, Jouy-en-Josas Cedex, France.
| | - Samira Boudebbouze
- INRA, UMR 1319 Micalis, Interactions of Firmicutes With Their Environments, 78352, Jouy-en-Josas Cedex, France. .,AgroParisTech, Micalis, Interactions of Firmicutes With Their Environments, 78352, Jouy-en-Josas Cedex, France.
| | - Nadia Gaci
- INRA, UMR 1319 Micalis, Interactions of Firmicutes With Their Environments, 78352, Jouy-en-Josas Cedex, France. .,AgroParisTech, Micalis, Interactions of Firmicutes With Their Environments, 78352, Jouy-en-Josas Cedex, France.
| | - Alexandrine Garnier
- INRA, UMR 1319 Micalis, Interactions of Firmicutes With Their Environments, 78352, Jouy-en-Josas Cedex, France. .,AgroParisTech, Micalis, Interactions of Firmicutes With Their Environments, 78352, Jouy-en-Josas Cedex, France.
| | - Jean-Jacques Gratadoux
- INRA, UMR 1319 Micalis, Commensal and Probiotics-Host Interactions Laboratory, 78352, Jouy-en-Josas Cedex, France. .,AgroParisTech, Micalis, Commensal and Probiotics-Host Interactions Laboratory, 78352, Jouy-en-Josas Cedex, France.
| | - Héla Mkaouar
- INRA, UMR 1319 Micalis, Interactions of Firmicutes With Their Environments, 78352, Jouy-en-Josas Cedex, France. .,AgroParisTech, Micalis, Interactions of Firmicutes With Their Environments, 78352, Jouy-en-Josas Cedex, France.
| | - Philippe Langella
- INRA, UMR 1319 Micalis, Commensal and Probiotics-Host Interactions Laboratory, 78352, Jouy-en-Josas Cedex, France. .,AgroParisTech, Micalis, Commensal and Probiotics-Host Interactions Laboratory, 78352, Jouy-en-Josas Cedex, France.
| | - Emmanuelle Maguin
- INRA, UMR 1319 Micalis, Interactions of Firmicutes With Their Environments, 78352, Jouy-en-Josas Cedex, France. .,AgroParisTech, Micalis, Interactions of Firmicutes With Their Environments, 78352, Jouy-en-Josas Cedex, France.
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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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