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Imanparast S, Azin M, Mirdamadi S, Zare D. Keratin-reinforced encapsulation of whole cells expressing glucose isomerase: Development of robust and reusable biocatalyst microbeads. Int J Biol Macromol 2024; 282:137052. [PMID: 39481710 DOI: 10.1016/j.ijbiomac.2024.137052] [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: 09/08/2024] [Revised: 10/24/2024] [Accepted: 10/28/2024] [Indexed: 11/02/2024]
Abstract
Glucose isomerase (GI) is crucial in high-fructose corn syrup production. This study introduces a novel approach to enhance GI stability and reusability through whole-cell encapsulation of Streptomyces olivochromogenes PTCC 1457 in hybrid microbeads, utilizing keratin as a multifunctional stabilizer and cross-linker. Optimal bead formation was achieved using 2 % alginate, 2-3 % CaCl2, and 2.5 % keratin at pH 7.0 and 37-40 °C. Keratin played a vital role in forming a robust and flexible matrix. Immobilization in keratin-alginate-biomass beads maintained GI activity (655 GIU·g-1) comparable to free enzyme (650 GIU·g-1), while silicate incorporation reduced activity to 234 GIU·g-1. The immobilized enzyme exhibited enhanced stability over a wider pH (6-9) and temperature (4-60 °C) range compared to the free enzyme. Importantly, the immobilized GI maintained 80 % of its initial activity after 20 reaction cycles. Thermogravimetric analysis, scanning electron microscopy, energy dispersive X-ray spectroscopy, and tensile testing confirmed the formation of hybrid beads with improved thermal and mechanical stability. This novel immobilization strategy, leveraging keratin's unique properties, offers a promising approach for enhancing GI stability, reusability, and storage longevity, potentially improving its industrial applicability in high-fructose corn syrup production.
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Affiliation(s)
- Somaye Imanparast
- Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), P. O. Box 3353-5111, Tehran 3353136846, Iran.
| | - Mehrdad Azin
- Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), P. O. Box 3353-5111, Tehran 3353136846, Iran
| | - Saeed Mirdamadi
- Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), P. O. Box 3353-5111, Tehran 3353136846, Iran
| | - Davood Zare
- Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), P. O. Box 3353-5111, Tehran 3353136846, Iran
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2
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Brouwer B, Della-Felice F, Illies JH, Iglesias-Moncayo E, Roelfes G, Drienovská I. Noncanonical Amino Acids: Bringing New-to-Nature Functionalities to Biocatalysis. Chem Rev 2024; 124:10877-10923. [PMID: 39329413 PMCID: PMC11467907 DOI: 10.1021/acs.chemrev.4c00136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 08/21/2024] [Accepted: 08/26/2024] [Indexed: 09/28/2024]
Abstract
Biocatalysis has become an important component of modern organic chemistry, presenting an efficient and environmentally friendly approach to synthetic transformations. Advances in molecular biology, computational modeling, and protein engineering have unlocked the full potential of enzymes in various industrial applications. However, the inherent limitations of the natural building blocks have sparked a revolutionary shift. In vivo genetic incorporation of noncanonical amino acids exceeds the conventional 20 amino acids, opening new avenues for innovation. This review provides a comprehensive overview of applications of noncanonical amino acids in biocatalysis. We aim to examine the field from multiple perspectives, ranging from their impact on enzymatic reactions to the creation of novel active sites, and subsequent catalysis of new-to-nature reactions. Finally, we discuss the challenges, limitations, and promising opportunities within this dynamic research domain.
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Affiliation(s)
- Bart Brouwer
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Franco Della-Felice
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Jan Hendrik Illies
- Department
of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands
| | - Emilia Iglesias-Moncayo
- Department
of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands
| | - Gerard Roelfes
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Ivana Drienovská
- Department
of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands
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3
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Tabakmakher KM, Makarieva TN, Sabutski YE, Kokoulin MS, Menshov AS, Popov RS, Guzii AG, Shubina LK, Chingizova EA, Chingizov AR, Yurchenko EA, Fedorov SN, Grebnev BB, von Amsberg G, Dyshlovoy SA, Ivanchina NV, Dmitrenok PS. Stonikacidin A, an Antimicrobial 4-Bromopyrrole Alkaloid Containing L-Idonic Acid Core from the Northwestern Pacific Marine Sponge Lissodendoryx papillosa. Mar Drugs 2024; 22:396. [PMID: 39330277 PMCID: PMC11432817 DOI: 10.3390/md22090396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 08/27/2024] [Accepted: 08/28/2024] [Indexed: 09/28/2024] Open
Abstract
Stonikacidin A (1), the first representative of a new class of 4-bromopyrrole alkaloids containing an aldonic acid core, was isolated from the marine sponge Lissodendoryx papillosa. The compound is named in honor of Prof. Valentin A. Stonik, who is one of the outstanding investigators in the field of marine natural chemistry. The structure of 1 was determined using NMR, MS analysis, and chemical correlations. The L-idonic acid core was established by the comparison of GC, NMR, MS, and optical rotation data of methyl-pentaacetyl-aldonates obtained from the hydrolysis products of 1 and standard hexoses. The L-form of the idonic acid residue in 1 was confirmed by GC analysis of pentaacetate of (S)-2-butyl ester of the hydrolysis product from 1 and compared with corresponding derivatives of L- and D-idonic acids. The biosynthetic pathway for stonikacidin A (1) was proposed. The alkaloid 1 inhibited the growth of Staphylococcus aureus and Escherichia coli test strains, as well as affected the formation of S. aureus and E. coli biofilms. Compound 1 inhibited the activity of sortase A. Molecular docking data showed that stonikacidin A (1) can bind with sortase A due to the interactions between its bromine atoms and some amino acid residues of the enzyme.
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Affiliation(s)
- Kseniya M. Tabakmakher
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Tatyana N. Makarieva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Yuri E. Sabutski
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Maxim S. Kokoulin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Alexander S. Menshov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Roman S. Popov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Alla G. Guzii
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Larisa K. Shubina
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Ekaterina A. Chingizova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Artur R. Chingizov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Ekaterina A. Yurchenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Sergey N. Fedorov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Boris B. Grebnev
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Gunhild von Amsberg
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum–University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany; (G.v.A.); (S.A.D.)
- Martini-Klinik, Prostate Cancer Center, University Hospital Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Sergey A. Dyshlovoy
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum–University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany; (G.v.A.); (S.A.D.)
| | - Natalia V. Ivanchina
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Pavel S. Dmitrenok
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
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4
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Hagedoorn PL, Pabst M, Hanefeld U. The metal cofactor: stationary or mobile? Appl Microbiol Biotechnol 2024; 108:391. [PMID: 38910188 PMCID: PMC11194214 DOI: 10.1007/s00253-024-13206-2] [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: 03/11/2024] [Revised: 05/22/2024] [Accepted: 05/27/2024] [Indexed: 06/25/2024]
Abstract
Metal cofactors are essential for catalysis and enable countless conversions in nature. Interestingly, the metal cofactor is not always static but mobile with movements of more than 4 Å. These movements of the metal can have different functions. In the case of the xylose isomerase and medium-chain dehydrogenases, it clearly serves a catalytic purpose. The metal cofactor moves during substrate activation and even during the catalytic turnover. On the other hand, in class II aldolases, the enzymes display resting states and active states depending on the movement of the catalytic metal cofactor. This movement is caused by substrate docking, causing the metal cofactor to take the position essential for catalysis. As these metal movements are found in structurally and mechanistically unrelated enzymes, it has to be expected that this metal movement is more common than currently perceived. KEY POINTS: • Metal ions are essential cofactors that can move during catalysis. • In class II aldolases, the metal cofactors can reside in a resting state and an active state. • In MDR, the movement of the metal cofactor is essential for substrate docking.
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Affiliation(s)
- Peter-Leon Hagedoorn
- Afdeling Biotechnologie, Technische Universiteit Delft, Van der Maasweg 9, Delft, 2629 HZ, The Netherlands
| | - Martin Pabst
- Afdeling Biotechnologie, Technische Universiteit Delft, Van der Maasweg 9, Delft, 2629 HZ, The Netherlands
| | - Ulf Hanefeld
- Afdeling Biotechnologie, Technische Universiteit Delft, Van der Maasweg 9, Delft, 2629 HZ, The Netherlands.
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5
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Yang W, Sha Y, Chen X, Liu X, Wang F, Wang J, Shao P, Chen Q, Gao M, Huang W. Effects of the Interaction between Rumen Microbiota Density-VFAs-Hepatic Gluconeogenesis on the Adaptability of Tibetan Sheep to Plateau. Int J Mol Sci 2024; 25:6726. [PMID: 38928432 PMCID: PMC11203870 DOI: 10.3390/ijms25126726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/13/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024] Open
Abstract
During the adaptive evolution of animals, the host and its gut microbiota co-adapt to different elevations. Currently, there are few reports on the rumen microbiota-hepato-intestinal axis of Tibetan sheep at different altitudes. Therefore, the purpose of this study was to explore the regulatory effect of rumen microorganism-volatile fatty acids (VFAs)-VFAs transporter gene interactions on the key enzymes and genes related to gluconeogenesis in Tibetan sheep. The rumen fermentation parameters, rumen microbial densities, liver gluconeogenesis activity and related genes were determined and analyzed using gas chromatography, RT-qPCR and other research methods. Correlation analysis revealed a reciprocal relationship among rumen microflora-VFAs-hepatic gluconeogenesis in Tibetan sheep at different altitudes. Among the microbiota, Ruminococcus flavefaciens (R. flavefaciens), Ruminococcus albus (R. albus), Fibrobactersuccinogenes and Ruminobacter amylophilus (R. amylophilus) were significantly correlated with propionic acid (p < 0.05), while propionic acid was significantly correlated with the transport genes monocarboxylate transporter 4 (MCT4) and anion exchanger 2 (AE2) (p < 0.05). Propionic acid was significantly correlated with key enzymes such as pyruvate carboxylase, phosphoenolpyruvic acid carboxylase and glucose (Glu) in the gluconeogenesis pathway (p < 0.05). Additionally, the expressions of these genes were significantly correlated with those of the related genes, namely, forkhead box protein O1 (FOXO1) and mitochondrial phosphoenolpyruvate carboxykinase 2 (PCK2) (p < 0.05). The results showed that rumen microbiota densities differed at different altitudes, and the metabolically produced VFA contents differed, which led to adaptive changes in the key enzyme activities of gluconeogenesis and the expressions of related genes.
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Affiliation(s)
| | | | | | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (W.Y.); (Y.S.); (X.C.); (F.W.); (J.W.); (P.S.); (Q.C.); (M.G.); (W.H.)
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6
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Song Y, Maskey S, Lee YG, Lee DS, Nguyen DT, Bae HJ. Optimizing bioconversion processes of rice husk into value-added products: D-psicose, bioethanol, and lactic acid. BIORESOURCE TECHNOLOGY 2024; 395:130363. [PMID: 38253244 DOI: 10.1016/j.biortech.2024.130363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 01/24/2024]
Abstract
Rice husk, rich carbon content, is an agricultural waste produced globally at an amount of 120 million tons annually, and it has high potential as a biorefinery feedstock. Herein, we investigated the feasibility of producing various products as D-psicose, bioethanol and lactic acid from rice husk (RH) through a biorefinery process. Alkali-hydrogen peroxide-acetic acid pretreatment of RH effectively removed lignin and silica, resulting in enzymatic hydrolysis yield of approximately 86.3% under optimal hydrolysis conditions. By using xylose isomerase as well as D-psicose-3-epimerase with borate, glucose present in the RH hydrolysate was converted into D-psicose with a 40.6% conversion yield in the presence of borate. Furthermore, bioethanol (85.4%) and lactic acid (92.5%) were successfully produced from the RH hydrolysate. This study confirmed the high potential of RH as a biorefinery feedstock, and it is expected that various platform chemicals and value-added products can be produced using RH.
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Affiliation(s)
- Younho Song
- Bio-energy Research Center, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Shila Maskey
- Bio-energy Research Center, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Yoon Gyo Lee
- Bio-energy Research Center, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Dae-Seok Lee
- Bio-energy Research Center, Chonnam National University, Gwangju 61186, Republic of Korea
| | | | - Hyeun-Jong Bae
- Bio-energy Research Center, Chonnam National University, Gwangju 61186, Republic of Korea; Department of Bioenergy Science and Technology, Chonnam National University, Gwangju 61186, Republic of Korea.
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7
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Xie X, Huang D, Li Z. Bioproduction of Rare d-Allulose from d-Glucose via Borate-Assisted Isomerization. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3036-3044. [PMID: 38299460 DOI: 10.1021/acs.jafc.3c07100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
d-Allulose is a low-calorie functional rare sugar with excellent processing suitability and unique physiological efficacy. d-Allulose is primarily produced from d-fructose through enzymatic epimerization, facing the constraints of a low conversion yield and high production cost. In this study, a double-enzyme cascade system with tetraborate-assisted isomerization was constructed for the efficient production of d-allulose from inexpensive d-glucose. With the introduction of sodium tetraborate (STB), capable of forming complexes with diol-bearing sugars, the conversion yield of d-allulose from d-glucose substantially escalated from the initial 17.37% to 44.97%. Furthermore, d-allulose was found to exhibit the most pronounced binding affinity for STB with an association constant of 1980.51 M-1, notably surpassing that of d-fructose (183.31 M-1) and d-glucose (35.37 M-1). Additionally, the structural analysis of the sugar-STB complexes demonstrated that d-allulose reacted with STB via the cis 2,3-hydroxyl groups in the α-furanose form. Finally, the mechanism underlying STB-assisted isomerization was proposed, emphasizing the preferential formation of an allulose-STB complex that effectively shifts the isomerization equilibrium to the allulose side, thereby resulting in high yield of d-allulose. Such an STB-facilitated isomerization system would also provide a guidance for the cost-effective synthesis of other rare sugars.
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Affiliation(s)
- Xiaofang Xie
- Department of Food Science and Technology, National University of Singapore, 117542, Singapore
- National University of Singapore (Suzhou) Research Institute, 377 Lin Quan Street, Suzhou, Jiangsu 215123, China
| | - Dejian Huang
- Department of Food Science and Technology, National University of Singapore, 117542, Singapore
- National University of Singapore (Suzhou) Research Institute, 377 Lin Quan Street, Suzhou, Jiangsu 215123, China
| | - Zhaofeng Li
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, Jiangsu 214200, China
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Juretić D, Bonačić Lošić Ž. Theoretical Improvements in Enzyme Efficiency Associated with Noisy Rate Constants and Increased Dissipation. ENTROPY (BASEL, SWITZERLAND) 2024; 26:151. [PMID: 38392406 PMCID: PMC10888251 DOI: 10.3390/e26020151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/18/2024] [Accepted: 02/05/2024] [Indexed: 02/24/2024]
Abstract
Previous studies have revealed the extraordinarily large catalytic efficiency of some enzymes. High catalytic proficiency is an essential accomplishment of biological evolution. Natural selection led to the increased turnover number, kcat, and enzyme efficiency, kcat/KM, of uni-uni enzymes, which convert a single substrate into a single product. We added or multiplied random noise with chosen rate constants to explore the correlation between dissipation and catalytic efficiency for ten enzymes: beta-galactosidase, glucose isomerase, β-lactamases from three bacterial strains, ketosteroid isomerase, triosephosphate isomerase, and carbonic anhydrase I, II, and T200H. Our results highlight the role of biological evolution in accelerating thermodynamic evolution. The catalytic performance of these enzymes is proportional to overall entropy production-the main parameter from irreversible thermodynamics. That parameter is also proportional to the evolutionary distance of β-lactamases PC1, RTEM, and Lac-1 when natural or artificial evolution produces the optimal or maximal possible catalytic efficiency. De novo enzyme design and attempts to speed up the rate-limiting catalytic steps may profit from the described connection between kinetics and thermodynamics.
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Affiliation(s)
- Davor Juretić
- Mediterranean Institute for Life Sciences, Šetalište Ivana Meštrovića 45, 21000 Split, Croatia
- Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia
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9
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Geng X, Li Y, Wang R, Jiang S, Liang Y, Li T, Li C, Tao J, Li Z. Enhanced High-Fructose Corn Syrup Production: Immobilizing Serratia marcescens Glucose Isomerase on MOF (Co)-525 Reduces Co 2+ Dependency in Glucose Isomerization to Fructose. Foods 2024; 13:527. [PMID: 38397503 PMCID: PMC10888103 DOI: 10.3390/foods13040527] [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: 01/12/2024] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
The escalating demand for processed foods has led to the widespread industrial use of glucose isomerase (GI) for high-fructose corn syrup (HFCS) production. This reliance on GIs necessitates continual Co2+ supplementation to sustain high catalytic activity across multiple reaction cycles. In this study, Serratia marcescens GI (SmGI) was immobilized onto surfaces of the metal-organic framework (MOF) material MOF (Co)-525 to generate MOF (Co)-525-GI for use in catalyzing glucose isomerization to generate fructose. Examination of MOF (Co)-525-GI structural features using scanning electron microscopy-energy dispersive spectroscopy, Fourier-transform infrared spectroscopy, and ultraviolet spectroscopy revealed no structural changes after SmGI immobilization and the addition of Co2+. Notably, MOF (Co)-525-GI exhibited optimal catalytic activity at pH 7.5 and 70 °C, with a maximum reaction rate (Vmax) of 37.24 ± 1.91 μM/min and Km value of 46.25 ± 3.03 mM observed. Remarkably, immobilized SmGI exhibited sustained high catalytic activity over multiple cycles without continuous Co2+ infusion, retaining its molecular structure and 96.38% of its initial activity after six reaction cycles. These results underscore the potential of MOF (Co)-525-GI to serve as a safer and more efficient immobilized enzyme technology compared to traditional GI-based food-processing technologies.
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Affiliation(s)
- Xu Geng
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Sciences, Jilin University, Changchun 130012, China; (X.G.); (S.J.); (T.L.)
| | - Yi Li
- National Engineering Research Center for Corn Deep Processing, Jilin COFCO Biochemical Co., Ltd., Changchun 130033, China; (Y.L.); (Y.L.)
| | - Ruizhe Wang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (R.W.); (C.L.)
| | - Song Jiang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Sciences, Jilin University, Changchun 130012, China; (X.G.); (S.J.); (T.L.)
| | - Yingchao Liang
- National Engineering Research Center for Corn Deep Processing, Jilin COFCO Biochemical Co., Ltd., Changchun 130033, China; (Y.L.); (Y.L.)
| | - Tao Li
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Sciences, Jilin University, Changchun 130012, China; (X.G.); (S.J.); (T.L.)
| | - Chen Li
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (R.W.); (C.L.)
| | - Jin Tao
- National Engineering Research Center for Corn Deep Processing, Jilin COFCO Biochemical Co., Ltd., Changchun 130033, China; (Y.L.); (Y.L.)
| | - Zhengqiang Li
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Sciences, Jilin University, Changchun 130012, China; (X.G.); (S.J.); (T.L.)
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10
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Xu Y, Nam KH. Xylitol binding to the M1 site of glucose isomerase induces a conformational change in the substrate binding channel. Biochem Biophys Res Commun 2023; 682:21-26. [PMID: 37793321 DOI: 10.1016/j.bbrc.2023.09.087] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/06/2023]
Abstract
Glucose isomerase (GI) is extensively used in the food industry for production of high-fructose corn syrup and for the production of biofuels and other renewable chemicals. Structure-based studies on GI inhibitors are important for improving its efficiency in industrial applications. Here, we report the subatomic crystal structure of Streptomyces rubiginosus GI (SruGI) complexed with its inhibitor, xylitol, at 0.99 Å resolution. Electron density map and temperature factor analysis showed partial binding of xylitol to the M1 metal binding site of SruGI, providing two different conformations of the metal binding site and the substrate binding channel. The xylitol molecule induced a conformational change in the M2 metal ion-interacting Asp255 residue, which subsequently led to a conformational change in the side chain of Asp181 residue. This led to the positional shift of Pro25 by 1.71 Å and side chain rotation of Phe26 by 21°, where located on the neighboring protomer in tetrameric SruGI. The conformation change of these two residues affect the size of the substrate-binding channel of GI. Therefore, xylitol binding to M1 site of SruGI induces not only a conformational changes of the metal-binding site, but also conformational change of substrate-binding channel of the tetrameric SruGI. These results expand our knowledge about the mechanism underlying the inhibitory effect of xylitol on GI.
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Affiliation(s)
- Yongbin Xu
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, China; Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian, 116600, China
| | - Ki Hyun Nam
- College of General Education, Kookmin University, Seoul, 02707, South Korea.
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11
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Borgonovi SM, Chiarello E, Pasini F, Picone G, Marzocchi S, Capozzi F, Bordoni A, Barbiroli A, Marti A, Iametti S, Di Nunzio M. Effect of Sprouting on Biomolecular and Antioxidant Features of Common Buckwheat ( Fagopyrum esculentum). Foods 2023; 12:foods12102047. [PMID: 37238865 DOI: 10.3390/foods12102047] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/14/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Buckwheat is a pseudo-cereal widely grown and consumed throughout the world. Buckwheat is recognized as a good source of nutrients and, in combination with other health-promoting components, is receiving increasing attention as a potential functional food. Despite the high nutritional value of buckwheat, a variety of anti-nutritional features makes it difficult to exploit its full potential. In this framework, sprouting (or germination) may represent a process capable of improving the macromolecular profile, including reducing anti-nutritional factors and/or synthesizing or releasing bioactives. This study addressed changes in the biomolecular profile and composition of buckwheat that was sprouted for 48 and 72 h. Sprouting increased the content of peptides and free-phenolic compounds and the antioxidant activity, caused a marked decline in the concentration of several anti-nutritional components, and affected the metabolomic profile with an overall improvement in the nutritional characteristics. These results further confirm sprouting as a process suitable for improving the compositional traits of cereals and pseudo-cereals, and are further steps towards the exploitation of sprouted buckwheat as a high-quality ingredient in innovative products of industrial interest.
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Affiliation(s)
- Sara Margherita Borgonovi
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - Elena Chiarello
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Piazza Goidanich 60, 47521 Cesena, Italy
| | - Federica Pasini
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Piazza Goidanich 60, 47521 Cesena, Italy
- Interdepartmental Centre for Industrial Agri-Food Research (CIRI), University of Bologna, Piazza Goidanich 60, 47521 Cesena, Italy
| | - Gianfranco Picone
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Piazza Goidanich 60, 47521 Cesena, Italy
| | - Silvia Marzocchi
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Piazza Goidanich 60, 47521 Cesena, Italy
| | - Francesco Capozzi
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Piazza Goidanich 60, 47521 Cesena, Italy
- Interdepartmental Centre for Industrial Agri-Food Research (CIRI), University of Bologna, Piazza Goidanich 60, 47521 Cesena, Italy
| | - Alessandra Bordoni
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Piazza Goidanich 60, 47521 Cesena, Italy
- Interdepartmental Centre for Industrial Agri-Food Research (CIRI), University of Bologna, Piazza Goidanich 60, 47521 Cesena, Italy
| | - Alberto Barbiroli
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - Alessandra Marti
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - Stefania Iametti
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - Mattia Di Nunzio
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy
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12
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Ethica SN, Zilda DS, Oedjijono O, Muhtadi M, Patantis G, Darmawati S, Dewi SS, Sabdono A, Uria AR. Biotechnologically potential genes in a polysaccharide-degrading epibiont of the Indonesian brown algae Hydroclathrus sp. J Genet Eng Biotechnol 2023; 21:18. [PMID: 36786886 PMCID: PMC9928984 DOI: 10.1186/s43141-023-00461-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/06/2023] [Indexed: 02/15/2023]
Abstract
BACKGROUND Marine bacteria have recently attracted increasing attention to be harnessed for the production of valuable enzymes, vitamins, and bioactive compounds. Bacteria associated with the surfaces of marine macroalgae, called epibionts, are particularly interesting from ecological and biotechnological points of view, as they often exhibit antimicrobial activities to compete with pathogenic bacteria for nutrients and spaces. In search for biotechnologically potential genes from marine bacteria, we sequenced and analysed the genome of the epibiont HI03-3b, a polysaccharide-degrading bacterium associated with the surface of the Indonesian brown algae Hydroclathrus sp. RESULTS The algal epibiont HI03-3b has a genome of approximately 4,860,704 bp in size with 42.02 mol% G + C content, consisting of 5655 open reading frames (ORFs), 4409 genes coding for proteins (CDSs), 94 genes for tRNAs, and 32 genes for rRNAs. The genome sequence of HI03-3b was most closely related to that of Cytobacillus firmus NCTC10335 with the average amino acid identity (AAI) of 95.0 %, average nucleotide identity (ANI) of 94.1 %, and a recommended DNA-DNA hybridization (DDH) of 57.60 %. These scores are lower than the most frequently used standard for species demarcation (95% ANI cutoff) and the new species threshold (DDH > 70.0% for the same bacterial species). Some differences in genome features and gene composition were observed between HI03-3b and NCTC10335, such as genes encoding carbohydrate active enzymes. These suggest that HI03-3b is unique and likely a novel species within Cytobacillus genus, and we therefore proposed its name as Cytobacillus wakatobiense HI03-3b. Genome sequence analyses indicated the presence of genes involved not only in polysaccharide and protein degradation but also in vitamin and secondary metabolite biosynthesis. Some of them encode enzymes and compounds with biotechnological interest, such as protease, chitinase, subtilisin, pullulanase, and bacillolysin, which are often associated with antimicrobial or antibiofilm activities. This antimicrobial potential is supported by our finding that the extracellular protein fraction of this epibiont inhibited the growth of the bacterial pathogen Staphylococcus aureus. CONCLUSION The epibiont Cytobacillus HI03-3b harbours genes for polysaccharide and protein degradation as well as for natural product biosynthesis, suggesting its potential ecological roles in outcompeting other bacteria during biofilm formation as well as in protecting its algal host from predation. Due to the presence of genes for vitamin biosynthesis, it might also provide the algal host with vitamins for growth and development. Some of these metabolic genes are biotechnologically important, as they could become a platform for bioengineering to generate various seaweed-derived substances sustainably, such as antibiofilm agents and vitamins, which are beneficial for human health.
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Affiliation(s)
- Stalis Norma Ethica
- grid.444265.50000 0004 0386 6520Magister Program of Clinical Laboratory Science, Universitas Muhammadiyah Semarang (UNIMUS), Jalan Kedungmundu Raya, Semarang, 50273 Indonesia
| | - Dewi Seswita Zilda
- Research Center for Deep Sea, Earth Sciences and Maritime Research Organization, National Research and Innovation Agency (BRIN), Jl. Pasir Putih Raya, Pademangan, North Jakarta City, Jakarta 14430 Indonesia
| | - Oedjijono Oedjijono
- grid.444191.d0000 0000 9134 0078Faculty of Biology, Universitas Jenderal Soedirman, Purwokerto, 53122 Indonesia
| | - Muhtadi Muhtadi
- grid.444490.90000 0000 8731 0765Faculty of Pharmacy, Universitas Muhammadiyah Surakarta (UMS), Sukoharjo, 57162 Indonesia
| | - Gintung Patantis
- Research Center for Marine and Land Bioindustry, Earth Sciences and Maritime Research Organization, National Research and Innovation Agency (BRIN), Kodek Bay, North Lombok, West Nusa Tenggara 83352 Indonesia
| | - Sri Darmawati
- grid.444265.50000 0004 0386 6520Magister Program of Clinical Laboratory Science, Universitas Muhammadiyah Semarang (UNIMUS), Jalan Kedungmundu Raya, Semarang, 50273 Indonesia
| | - Sri Sinto Dewi
- grid.444265.50000 0004 0386 6520Diploma Study Program of Medical Laboratory Technology, Faculty of Nursing and Health Sciences, Universitas Muhammadiyah Semarang, Semarang, 50273 Indonesia
| | - Agus Sabdono
- grid.412032.60000 0001 0744 0787Department of Marine Science, Faculty of Fisheries and Marine Science, Diponegoro University, Semarang, 50272 Indonesia
| | - Agustinus Robert Uria
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12 Nishi 6 Kita-ku, Sapporo, 060-0812, Japan. .,Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita 12 Nishi 6, Sapporo, 060-0812, Japan.
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13
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Delidovich I. Toward Understanding Base-Catalyzed Isomerization of Saccharides. ACS Catal 2023. [DOI: 10.1021/acscatal.2c04786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Irina Delidovich
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Getreidemarkt 9, A-1060 Vienna, Austria
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14
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Kadriye İnan Bektas. Isolation and Molecular Identification of Xylanase and Glucose-Isomerase Producer Geobacillus and Brevibacillus Strains from Hot Springs in Turkey. BIOL BULL+ 2022. [DOI: 10.1134/s1062359021150085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Mokale Kognou AL, Shrestha S, Jiang ZH, Xu C, Sun F, Qin W. High-fructose corn syrup production and its new applications for 5-hydroxymethylfurfural and value-added furan derivatives: Promises and challenges. JOURNAL OF BIORESOURCES AND BIOPRODUCTS 2022. [DOI: 10.1016/j.jobab.2022.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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