1
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Gourlay LJ, Mangiagalli M, Moroni E, Lotti M, Nardini M. Structural determinants of cold activity and glucose tolerance of a family 1 glycoside hydrolase (GH1) from Antarctic Marinomonas sp. ef1. FEBS J 2024; 291:2897-2917. [PMID: 38400529 DOI: 10.1111/febs.17096] [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: 07/24/2023] [Revised: 01/19/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024]
Abstract
Cold-active enzymes support life at low temperatures due to their ability to maintain high activity in the cold and can be useful in several biotechnological applications. Although information on the mechanisms of enzyme cold adaptation is still too limited to devise general rules, it appears that very diverse structural and functional changes are exploited in different protein families and within the same family. In this context, we studied the cold adaptation mechanism and the functional properties of a member of the glycoside hydrolase family 1 (GH1) from the Antarctic bacterium Marinomonas sp. ef1. This enzyme exhibits all typical functional hallmarks of cold adaptation, including high catalytic activity at 5 °C, broad substrate specificity, low thermal stability, and higher lability of the active site compared to the overall structure. Analysis of the here-reported crystal structure (1.8 Å resolution) and molecular dynamics simulations suggest that cold activity and thermolability may be due to a flexible region around the active site (residues 298-331), whereas the dynamic behavior of loops flanking the active site (residues 47-61 and 407-413) may favor enzyme-substrate interactions at the optimal temperature of catalysis (Topt) by tethering together protein regions lining the active site. Stapling of the N-terminus onto the surface of the β-barrel is suggested to partly counterbalance protein flexibility, thus providing a stabilizing effect. The tolerance of the enzyme to glucose and galactose is accounted for by the presence of a "gatekeeping" hydrophobic residue (Leu178), located at the entrance of the active site.
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Affiliation(s)
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Elisabetta Moroni
- Institute of Chemical Sciences and Technologies, National Research Council of Italy, SCITE-CNR, Milan, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Italy
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2
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Liu P, Chen Y, Ma C, Ouyang J, Zheng Z. β-Galactosidase: a traditional enzyme given multiple roles through protein engineering. Crit Rev Food Sci Nutr 2023:1-20. [PMID: 38108277 DOI: 10.1080/10408398.2023.2292282] [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: 12/19/2023]
Abstract
β-Galactosidases are crucial carbohydrate-active enzymes that naturally catalyze the hydrolysis of galactoside bonds in oligo- and disaccharides. These enzymes are commonly used to degrade lactose and produce low-lactose and lactose-free dairy products that are beneficial for lactose-intolerant people. β-galactosidases exhibit transgalactosylation activity, and they have been employed in the synthesis of galactose-containing compounds such as galactooligosaccharides. However, most β-galactosidases have intrinsic limitations, such as low transglycosylation efficiency, significant product inhibition effects, weak thermal stability, and a narrow substrate spectrum, which greatly hinder their applications. Enzyme engineering offers a solution for optimizing their catalytic performance. The study of the enzyme's structure paves the way toward explaining catalytic mechanisms and increasing the efficiency of enzyme engineering. In this review, the structure features of β-galactosidases from different glycosyl hydrolase families and the catalytic mechanisms are summarized in detail to offer guidance for protein engineering. The properties and applications of β-galactosidases are discussed. Additionally, the latest progress in β-galactosidase engineering and the strategies employed are highlighted. Based on the combined analysis of structure information and catalytic mechanisms, the ultimate goal of this review is to furnish a thorough direction for β-galactosidases engineering and promote their application in the food and dairy industries.
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Affiliation(s)
- Peng Liu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, People's Republic of China
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Yuehua Chen
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Cuiqing Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Jia Ouyang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Zhaojuan Zheng
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, People's Republic of China
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3
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Nowak JS, Otzen DE. Helping proteins come in from the cold: 5 burning questions about cold-active enzymes. BBA ADVANCES 2023; 5:100104. [PMID: 38162634 PMCID: PMC10755280 DOI: 10.1016/j.bbadva.2023.100104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/21/2023] [Accepted: 09/05/2023] [Indexed: 01/03/2024] Open
Abstract
Enzymes from psychrophilic (cold-loving) organisms have attracted considerable interest over the past decades for their potential in various low-temperature industrial processes. However, we still lack large-scale commercialization of their activities. Here, we review their properties, limitations and potential. Our review is structured around answers to 5 central questions: 1. How do cold-active enzymes achieve high catalytic rates at low temperatures? 2. How is protein flexibility connected to cold-activity? 3. What are the sequence-based and structural determinants for cold-activity? 4. How does the thermodynamic stability of psychrophilic enzymes reflect their cold-active capabilities? 5. How do we effectively identify novel cold-active enzymes, and can we apply them in an industrial context? We conclude that emerging screening technologies combined with big-data handling and analysis make it reasonable to expect a bright future for our understanding and exploitation of cold-active enzymes.
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Affiliation(s)
- Jan Stanislaw Nowak
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK – 8000 Aarhus C, Denmark
| | - Daniel E. Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK – 8000 Aarhus C, Denmark
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4
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Sun J, Wang W, Hao J. GH2 family β-galactosidases evolution using degenerate oligonucleotide gene shuffling. Biotechnol Lett 2023; 45:655-665. [PMID: 37071382 DOI: 10.1007/s10529-023-03368-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 03/20/2023] [Accepted: 03/31/2023] [Indexed: 04/19/2023]
Abstract
OBJECTIVES To improve the biochemical characteristics of the GH2 family β-galactosidases using a family shuffling method based on degenerate oligonucleotide gene shuffling. RESULTS Four β-galactosidase genes from the genus Alteromonas were divided into 14 gene segments, and each included the homologous sequence in the adjacent segments. The gene segments were regenerated into complete β-galactosidase genes and amplified by PCR. The obtained chimeric genes were cloned into a plasmid and screened for β-galactosidase activity. Approximately 320 positive clones were observed on the screening plate, of which nine sequenced genes were chimera. Additionally, the M22 and M250 mutants were expressed, purified, and characterized. The optimal temperature and substrate specificity of the recombinant M22 and M250 were consistent with those of the wild-type enzymes. The catalytic efficiency of recombinant M22 enzyme was higher than that of the wild-type enzymes, and the recombinant M250 displayed weak transglycosylation activity. CONCLUSIONS The chimeric genes of GH2 β-galactosidase were obtained using a controlled family shuffling that will provide an enzyme evolutionary method to obtain the β-galactosidases with excellent characteristics for laboratory and industrial purposes.
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Affiliation(s)
- Jingjing Sun
- Key Laboratory of Sustainable Development of Polar Fishery, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Laboratory for Marine Drugs and Bioproducts, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Wei Wang
- Key Laboratory of Sustainable Development of Polar Fishery, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Laboratory for Marine Drugs and Bioproducts, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Jianhua Hao
- Key Laboratory of Sustainable Development of Polar Fishery, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
- Laboratory for Marine Drugs and Bioproducts, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
- Jiangsu Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resource, Lianyungang, 222005, China.
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5
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Marchetti A, Orlando M, Mangiagalli M, Lotti M. A cold‐active esterase enhances mesophilic properties through Mn
2+
binding. FEBS J 2022; 290:2394-2411. [PMID: 36266734 DOI: 10.1111/febs.16661] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/20/2022] [Accepted: 10/19/2022] [Indexed: 12/12/2022]
Abstract
A key aspect of adaptation to cold environments is the production of cold-active enzymes by psychrophilic organisms. These enzymes not only have high activity at low temperatures, but also exhibit remarkable structural flexibility and thermolability. In this context, the role of metal ions has been little explored, and the few available studies seem to suggest that metal binding counteracts structural flexibility. This article reports an investigation into the role of the binding of manganese ion (Mn2+ ) in the thermal adaptation of an esterase (M-Est) of the GDSx family, identified in the genome of the Antarctic bacterium Marinomonas sp. ef1. M-Est is specific for esters containing acetate groups and turned out to be a highly thermolabile cold-active enzyme, with a catalysis optimum temperature of 5 °C and a melting temperature of 31.7 °C. A combination of biochemical and computational analyses, including molecular dynamics simulations, revealed that M-Est binds Mn2+ ions via a single binding site located on the surface of the enzyme, close to the active site. Although the interaction between M-Est and Mn2+ induces only local conformational changes involving the active site, quite surprisingly they trigger an improvement in both thermal stability and catalytic efficiency under mild temperature conditions. These results, together with the conservation of the Mn2+ binding site among psychrophilic and psychrotolerant homologues, suggest that Mn2+ binding may be a useful, albeit atypical, strategy to mitigate the detrimental effects of temperature on true cold-active enzymes.
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Affiliation(s)
| | - Marco Orlando
- Department of Biotechnology and Biosciences University of Milano‐Bicocca Italy
- Department of Biotechnology and Life Sciences University of Insubria Varese Italy
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences University of Milano‐Bicocca Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences University of Milano‐Bicocca Italy
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6
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Long C, Qi XL, Venema K. Chemical and nutritional characteristics, and microbial degradation of rapeseed meal recalcitrant carbohydrates: A review. Front Nutr 2022; 9:948302. [PMID: 36245487 PMCID: PMC9554435 DOI: 10.3389/fnut.2022.948302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Approximately 35% of rapeseed meal (RSM) dry matter (DM) are carbohydrates, half of which are water-soluble carbohydrates. The cell wall of rapeseed meal contains arabinan, galactomannan, homogalacturonan, rhamnogalacturonan I, type II arabinogalactan, glucuronoxylan, XXGG-type and XXXG-type xyloglucan, and cellulose. Glycoside hydrolases including in the degradation of RSM carbohydrates are α-L-Arabinofuranosidases (EC 3.2.1.55), endo-α-1,5-L-arabinanases (EC 3.2.1.99), Endo-1,4-β-mannanase (EC 3.2.1.78), β-mannosidase (EC 3.2.1.25), α-galactosidase (EC 3.2.1.22), reducing-end-disaccharide-lyase (pectate disaccharide-lyase) (EC 4.2.2.9), (1 → 4)-6-O-methyl-α-D-galacturonan lyase (pectin lyase) (EC 4.2.2.10), (1 → 4)-α-D-galacturonan reducing-end-trisaccharide-lyase (pectate trisaccharide-lyase) (EC 4.2.2.22), α-1,4-D-galacturonan lyase (pectate lyase) (EC 4.2.2.2), (1 → 4)-α-D-galacturonan glycanohydrolase (endo-polygalacturonase) (EC 3.2.1.15), Rhamnogalacturonan hydrolase, Rhamnogalacturonan lyase (EC 4.2.2.23), Exo-β-1,3-galactanase (EC 3.2.1.145), endo-β-1,6-galactanase (EC 3.2.1.164), Endo-β-1,4-glucanase (EC 3.2.1.4), α-xylosidase (EC 3.2.1.177), β-glucosidase (EC 3.2.1.21) endo-β-1,4-glucanase (EC 3.2.1.4), exo-β-1,4-glucanase (EC 3.2.1.91), and β-glucosidase (EC 3.2.1.21). In conclusion, this review summarizes the chemical and nutritional compositions of RSM, and the microbial degradation of RSM cell wall carbohydrates which are important to allow to develop strategies to improve recalcitrant RSM carbohydrate degradation by the gut microbiota, and eventually to improve animal feed digestibility, feed efficiency, and animal performance.
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Affiliation(s)
- Cheng Long
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
- Faculty of Science and Engineering, Centre for Healthy Eating and Food Innovation, Maastricht University - Campus Venlo, Venlo, Netherlands
| | - Xiao-Long Qi
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Koen Venema
- Faculty of Science and Engineering, Centre for Healthy Eating and Food Innovation, Maastricht University - Campus Venlo, Venlo, Netherlands
- *Correspondence: Koen Venema
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7
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Koval'ová T, Kovaľ T, Stránský J, Kolenko P, Dušková J, Švecová L, Vodičková P, Spiwok V, Benešová E, Lipovová P, Dohnálek J. The first structure–function study of GH151 α‐
l
‐fucosidase uncovers new oligomerization pattern, active site complementation, and selective substrate specificity. FEBS J 2022; 289:4998-5020. [DOI: 10.1111/febs.16387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 11/21/2021] [Accepted: 02/02/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Terézia Koval'ová
- Laboratory of Structure and Function of Biomolecules Institute of Biotechnology of the Czech Academy of Sciences Vestec Czech Republic
- Department of Biochemistry and Microbiology University of Chemistry and Technology Prague Czech Republic
| | - Tomáš Kovaľ
- Laboratory of Structure and Function of Biomolecules Institute of Biotechnology of the Czech Academy of Sciences Vestec Czech Republic
| | - Jan Stránský
- Laboratory of Structure and Function of Biomolecules Institute of Biotechnology of the Czech Academy of Sciences Vestec Czech Republic
| | - Petr Kolenko
- Laboratory of Structure and Function of Biomolecules Institute of Biotechnology of the Czech Academy of Sciences Vestec Czech Republic
| | - Jarmila Dušková
- Laboratory of Structure and Function of Biomolecules Institute of Biotechnology of the Czech Academy of Sciences Vestec Czech Republic
| | - Leona Švecová
- Laboratory of Structure and Function of Biomolecules Institute of Biotechnology of the Czech Academy of Sciences Vestec Czech Republic
| | - Patricie Vodičková
- Department of Biochemistry and Microbiology University of Chemistry and Technology Prague Czech Republic
| | - Vojtěch Spiwok
- Department of Biochemistry and Microbiology University of Chemistry and Technology Prague Czech Republic
| | - Eva Benešová
- Department of Biochemistry and Microbiology University of Chemistry and Technology Prague Czech Republic
| | - Petra Lipovová
- Department of Biochemistry and Microbiology University of Chemistry and Technology Prague Czech Republic
| | - Jan Dohnálek
- Laboratory of Structure and Function of Biomolecules Institute of Biotechnology of the Czech Academy of Sciences Vestec Czech Republic
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8
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Ghosh U, Yau WM, Collinge J, Tycko R. Structural differences in amyloid-β fibrils from brains of nondemented elderly individuals and Alzheimer's disease patients. Proc Natl Acad Sci U S A 2021; 118:e2111863118. [PMID: 34725161 PMCID: PMC8609303 DOI: 10.1073/pnas.2111863118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 09/20/2021] [Indexed: 02/05/2023] Open
Abstract
Although amyloid plaques composed of fibrillar amyloid-β (Aβ) assemblies are a diagnostic hallmark of Alzheimer's disease (AD), quantities of amyloid similar to those in AD patients are observed in brain tissue of some nondemented elderly individuals. The relationship between amyloid deposition and neurodegeneration in AD has, therefore, been unclear. Here, we use solid-state NMR to investigate whether molecular structures of Aβ fibrils from brain tissue of nondemented elderly individuals with high amyloid loads differ from structures of Aβ fibrils from AD tissue. Two-dimensional solid-state NMR spectra of isotopically labeled Aβ fibrils, prepared by seeded growth from frontal lobe tissue extracts, are similar in the two cases but with statistically significant differences in intensity distributions of cross-peak signals. Differences in solid-state NMR data are greater for 42-residue amyloid-β (Aβ42) fibrils than for 40-residue amyloid-β (Aβ40) fibrils. These data suggest that similar sets of fibril polymorphs develop in nondemented elderly individuals and AD patients but with different relative populations on average.
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Affiliation(s)
- Ujjayini Ghosh
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892-0520
- Department of Chemistry, Michigan State University, East Lansing, MI 48824
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892-0520
| | - John Collinge
- Medical Research Council Prion Unit, University College London, London W1W 7FF, United Kingdom
- Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892-0520;
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9
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Benešová E, Šućur Z, Těšínský M, Spiwok V, Lipovová P. Transglycosylation abilities of β-d-galactosidases from GH family 2. 3 Biotech 2021; 11:168. [PMID: 33816045 DOI: 10.1007/s13205-021-02715-w] [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: 10/06/2020] [Accepted: 03/03/2021] [Indexed: 12/11/2022] Open
Abstract
The ability to predict the transglycosylation activity of glycosidases by in silico analysis was investigated. The transglycosylation abilities of 7 different β-d-galactosidases from GH family 2 were tested experimentally using 7 different acceptors and p-nitrophenyl-β-d-galactopyranoside as a donor of galactosyl moiety. Similar transglycosylation abilities were confirmed for all enzymes originating from bacteria belonging to Enterobacteriaceae, which were able to use all tested acceptor molecules. Higher acceptor selectivity was observed for all others used bacterial strains. Structure models of all enzymes were constructed using homology modeling. Ligand-docking method was used for enzymes-transglycosylation products models construction and evaluation. Results obtained by in silico analysis were compared with results arisen out of experimental testing. The experiments confirmed that significant differences in transglycosylation abilities are caused by small differences in active sites composition of analyzed enzymes. According to obtained result, it is possible to conclude that homology modeling may serve as a quick starting point for detection or exclusion of enzymes with defined transglycosylation abilities, which can be used for subsequent synthesis of e.g., pharmaceutically interesting glycosides. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02715-w.
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Affiliation(s)
- Eva Benešová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 5, Prague 6, 166 28 Czech Republic
| | - Zoran Šućur
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 5, Prague 6, 166 28 Czech Republic
| | - Miroslav Těšínský
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 5, Prague 6, 166 28 Czech Republic
| | - Vojtěch Spiwok
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 5, Prague 6, 166 28 Czech Republic
| | - Petra Lipovová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 5, Prague 6, 166 28 Czech Republic
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10
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Mangiagalli M, Barbiroli A, Santambrogio C, Ferrari C, Nardini M, Lotti M, Brocca S. The activity and stability of a cold-active acylaminoacyl peptidase rely on its dimerization by domain swapping. Int J Biol Macromol 2021; 181:263-274. [PMID: 33775759 DOI: 10.1016/j.ijbiomac.2021.03.150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/15/2021] [Accepted: 03/23/2021] [Indexed: 01/07/2023]
Abstract
The study of enzymes from extremophiles arouses interest in Protein Science because of the amazing solutions these proteins adopt to cope with extreme conditions. Recently solved, the structure of the psychrophilic acyl aminoacyl peptidase from Sporosarcina psychrophila (SpAAP) pinpoints a mechanism of dimerization unusual for this class of enzymes. The quaternary structure of SpAAP relies on a domain-swapping mechanism involving the N-terminal A1 helix. The A1 helix is conserved among homologous mesophilic and psychrophilic proteins and its deletion causes the formation of a monomeric enzyme, which is inactive and prone to aggregate. Here, we investigate the dimerization mechanism of SpAAP through the analysis of chimeric heterodimers where a protomer lacking the A1 helix combines with a protomer carrying the inactivated catalytic site. Our results indicate that the two active sites are independent, and that a single A1 helix is sufficient to partially recover the quaternary structure and the activity of chimeric heterodimers. Since catalytically competent protomers are unstable and inactive unless they dimerize, SpAAP reveals as an "obligomer" for both structural and functional reasons.
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Affiliation(s)
- Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
| | - Alberto Barbiroli
- Department of Food, Environmental and Nutritional Sciences, University of Milano, Via Celoria 2, 20133 Milano, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Cristian Ferrari
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
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11
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Glycoside hydrolase family 2 exo-β-1,6-galactosidase LpGal2 from Lactobacillus plantarum: Cloning, expression, and enzymatic characterization. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Liu M, Yu J, Lv B, Hou Y, Liu X, Feng X, Li C. Improving the activity and thermostability of GH2 β-glucuronidases via domain reassembly. Biotechnol Bioeng 2021; 118:1962-1972. [PMID: 33559890 DOI: 10.1002/bit.27710] [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: 01/05/2021] [Accepted: 01/31/2021] [Indexed: 11/07/2022]
Abstract
Glycoside hydrolase family 2 (GH2) enzymes are generally composed of three domains: TIM-barrel domain (TIM), immunoglobulin-like β-sandwich domain (ISD), and sugar-binding domain (SBD). The combination of these three domains yields multiple structural combinations with different properties. Theoretically, the drawbacks of a given GH2 fold may be circumvented by efficiently reassembling the three domains. However, very few successful cases have been reported. In this study, we used six GH2 β-glucuronidases (GUSs) from bacteria, fungi, or humans as model enzymes and constructed a series of mutants by reassembling the domains from different GUSs. The mutants PGUS-At, GUS-PAA, and GUS-PAP, with reassembled domains from fungal GUSs, showed improved expression levels, activity, and thermostability, respectively. Specifically, compared to the parental enzyme, the mutant PGUS-At displayed 3.8 times higher expression, the mutant GUS-PAA displayed 1.0 time higher catalytic efficiency (kcat /Km ), and the mutant GUS-PAP displayed 7.5 times higher thermostability at 65°C. Furthermore, two-hybrid mutants, GUS-AEA and GUS-PEP, were constructed with the ISD from a bacterial GUS and SBD and TIM domain from fungal GUSs. GUS-AEA and GUS-PEP showed 30.4% and 23.0% higher thermostability than GUS-PAP, respectively. Finally, molecular dynamics simulations were conducted to uncover the molecular reasons for the increased thermostability of the mutant.
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Affiliation(s)
- Mingzhu Liu
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, PR China
| | - Jing Yu
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, PR China
| | - Bo Lv
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, PR China
| | - Yuhui Hou
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, PR China
| | - Xinhe Liu
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, PR China
| | - Xudong Feng
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, PR China
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, PR China.,Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, PR China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, PR China
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13
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Mangiagalli M, Lotti M. Cold-Active β-Galactosidases: Insight into Cold Adaption Mechanisms and Biotechnological Exploitation. Mar Drugs 2021; 19:md19010043. [PMID: 33477853 PMCID: PMC7832830 DOI: 10.3390/md19010043] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 01/22/2023] Open
Abstract
β-galactosidases (EC 3.2.1.23) catalyze the hydrolysis of β-galactosidic bonds in oligosaccharides and, under certain conditions, transfer a sugar moiety from a glycosyl donor to an acceptor. Cold-active β-galactosidases are identified in microorganisms endemic to permanently low-temperature environments. While mesophilic β-galactosidases are broadly studied and employed for biotechnological purposes, the cold-active enzymes are still scarcely explored, although they may prove very useful in biotechnological processes at low temperature. This review covers several issues related to cold-active β-galactosidases, including their classification, structure and molecular mechanisms of cold adaptation. Moreover, their applications are discussed, focusing on the production of lactose-free dairy products as well as on the valorization of cheese whey and the synthesis of glycosyl building blocks for the food, cosmetic and pharmaceutical industries.
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14
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Rutkiewicz M, Wanarska M, Bujacz A. Mapping the Transglycosylation Relevant Sites of Cold-Adapted β-d-Galactosidase from Arthrobacter sp. 32cB. Int J Mol Sci 2020; 21:E5354. [PMID: 32731412 PMCID: PMC7432029 DOI: 10.3390/ijms21155354] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 11/16/2022] Open
Abstract
β-Galactosidase from Arthrobacter sp. 32cB (ArthβDG) is a cold-adapted enzyme able to catalyze hydrolysis of β-d-galactosides and transglycosylation reaction, where galactosyl moiety is being transferred onto an acceptor larger than a water molecule. Mutants of ArthβDG: D207A and E517Q were designed to determine the significance of specific residues and to enable formation of complexes with lactulose and sucrose and to shed light onto the structural basis of the transglycosylation reaction. The catalytic assays proved loss of function mutation E517 into glutamine and a significant drop of activity for mutation of D207 into alanine. Solving crystal structures of two new mutants, and new complex structures of previously presented mutant E441Q enables description of introduced changes within active site of enzyme and determining the importance of mutated residues for active site size and character. Furthermore, usage of mutants with diminished and abolished enzymatic activity enabled solving six complex structures with galactose, lactulose or sucrose bounds. As a result, not only the galactose binding sites were mapped on the enzyme's surface but also the mode of lactulose, product of transglycosylation reaction, and binding within the enzyme's active site were determined and the glucopyranose binding site in the distal of active site was discovered. The latter two especially show structural details of transglycosylation, providing valuable information that may be used for engineering of ArthβDG or other analogous galactosidases belonging to GH2 family.
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Affiliation(s)
- Maria Rutkiewicz
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland;
- Macromolecular Structure and Interaction, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Marta Wanarska
- Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland;
| | - Anna Bujacz
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland;
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15
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Li D, Li S, Wu Y, Jin M, Zhou Y, Wang Y, Chen X, Han Y. Cloning and Characterization of a New β-Galactosidase from Alteromonas sp. QD01 and Its Potential in Synthesis of Galacto-Oligosaccharides. Mar Drugs 2020; 18:md18060312. [PMID: 32545859 PMCID: PMC7344425 DOI: 10.3390/md18060312] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/10/2020] [Accepted: 06/10/2020] [Indexed: 12/11/2022] Open
Abstract
As prebiotics, galacto-oligosaccharides (GOSs) can improve the intestinal flora and have important applications in medicine. β-galactosidases could promote the synthesis of GOSs in lactose and catalyze the hydrolysis of lactose. In this study, a new β-galactosidase gene (gal2A), which belongs to the glycoside hydrolase family 2, was cloned from marine bacterium Alteromonas sp. QD01 and expressed in Escherichia coli. The molecular weight of Gal2A was 117.07 kDa. The optimal pH and temperature of Gal2A were 8.0 and 40 °C, respectively. At the same time, Gal2A showed wide pH stability in the pH range of 6.0–9.5, which is suitable for lactose hydrolysis in milk. Most metal ions promoted the activity of Gal2A, especially Mn2+ and Mg2+. Importantly, Gal2A exhibited high transglycosylation activity, which can catalyze the formation of GOS from milk and lactose. These characteristics indicated that Gal2A may be ideal for producing GOSs and lactose-reducing dairy products.
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16
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Mangiagalli M, Lapi M, Maione S, Orlando M, Brocca S, Pesce A, Barbiroli A, Camilloni C, Pucciarelli S, Lotti M, Nardini M. The co-existence of cold activity and thermal stability in an Antarctic GH42 β-galactosidase relies on its hexameric quaternary arrangement. FEBS J 2020; 288:546-565. [PMID: 32363751 DOI: 10.1111/febs.15354] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/25/2020] [Accepted: 04/29/2020] [Indexed: 11/28/2022]
Abstract
To survive in cold environments, psychrophilic organisms produce enzymes endowed with high specific activity at low temperature. The structure of these enzymes is usually flexible and mostly thermolabile. In this work, we investigate the structural basis of cold adaptation of a GH42 β-galactosidase from the psychrophilic Marinomonas ef1. This enzyme couples cold activity with astonishing robustness for a psychrophilic protein, for it retains 23% of its highest activity at 5 °C and it is stable for several days at 37 °C and even 50 °C. Phylogenetic analyses indicate a close relationship with thermophilic β-galactosidases, suggesting that the present-day enzyme evolved from a thermostable scaffold modeled by environmental selective pressure. The crystallographic structure reveals the overall similarity with GH42 enzymes, along with a hexameric arrangement (dimer of trimers) not found in psychrophilic, mesophilic, and thermophilic homologues. In the quaternary structure, protomers form a large central cavity, whose accessibility to the substrate is promoted by the dynamic behavior of surface loops, even at low temperature. A peculiar cooperative behavior of the enzyme is likely related to the increase of the internal cavity permeability triggered by heating. Overall, our results highlight a novel strategy of enzyme cold adaptation, based on the oligomerization state of the enzyme, which effectively challenges the paradigm of cold activity coupled with intrinsic thermolability. DATABASE: Structural data are available in the Protein Data Bank database under the accession number 6Y2K.
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Affiliation(s)
- Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Michela Lapi
- Department of Biosciences, University of Milano, Italy
| | - Serena Maione
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Marco Orlando
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | | | - Alberto Barbiroli
- Department of Food, Environmental and Nutritional Sciences, University of Milano, Italy
| | | | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Italy
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17
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β-Galactosidases: A great tool for synthesizing galactose-containing carbohydrates. Biotechnol Adv 2020; 39:107465. [DOI: 10.1016/j.biotechadv.2019.107465] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/26/2019] [Accepted: 10/31/2019] [Indexed: 12/17/2022]
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18
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Míguez Amil S, Jiménez-Ortega E, Ramírez-Escudero M, Talens-Perales D, Marín-Navarro J, Polaina J, Sanz-Aparicio J, Fernandez-Leiro R. The cryo-EM Structure of Thermotoga maritima β-Galactosidase: Quaternary Structure Guides Protein Engineering. ACS Chem Biol 2020; 15:179-188. [PMID: 31874027 DOI: 10.1021/acschembio.9b00752] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Lactose intolerance is a common digestive disorder that affects a large proportion of the adult human population. The severity of the symptoms is highly variable, depending on the susceptibility to the sugar and the amount digested. For that reason, enzymes that can be used for the production of lactose-free milk and milk derivatives have acquired singular biotechnological importance. One such case is Thermotoga maritima β-galactosidase (TmLac). Here, we report the cryo-EM structure of TmLac at 2.0 Å resolution. The protein features a newly solved domain at its C-terminus, characteristic of the genus Thermotoga, which promotes a peculiar octameric arrangement. We have assessed the constraints imposed by the quaternary protein structure on the construction of hybrid versions of this GH2 enzyme. Carbohydrate binding modules (CBM) from the CBM2 and CBM9 families have been added at either the amino or carboxy terminus, and the structural and functional effects of such modifications have been analyzed. The results provide a basis for the rational design of hybrid enzymes that can be efficiently attached to different solid supports.
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Affiliation(s)
- Samuel Míguez Amil
- Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Elena Jiménez-Ortega
- Institute of Physical-Chemistry Rocasolano, Spanish National Research Council (CSIC), Serrano 119, 28006, Madrid, Spain
| | - Mercedes Ramírez-Escudero
- Institute of Physical-Chemistry Rocasolano, Spanish National Research Council (CSIC), Serrano 119, 28006, Madrid, Spain
| | - David Talens-Perales
- Institute of Agrochemical and Food Technology, Spanish National Research Council (CSIC), 46980-Paterna, Valencia, Spain
| | - Julia Marín-Navarro
- Institute of Agrochemical and Food Technology, Spanish National Research Council (CSIC), 46980-Paterna, Valencia, Spain
| | - Julio Polaina
- Institute of Agrochemical and Food Technology, Spanish National Research Council (CSIC), 46980-Paterna, Valencia, Spain
| | - Julia Sanz-Aparicio
- Institute of Physical-Chemistry Rocasolano, Spanish National Research Council (CSIC), Serrano 119, 28006, Madrid, Spain
| | - Rafael Fernandez-Leiro
- Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
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19
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Structural features of cold-adapted dimeric GH2 β-D-galactosidase from Arthrobacter sp. 32cB. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:776-786. [PMID: 31195142 DOI: 10.1016/j.bbapap.2019.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 05/12/2019] [Accepted: 06/06/2019] [Indexed: 12/21/2022]
Abstract
Crystal structures of cold-adapted β-d-galactosidase (EC 3.2.1.23) from the Antarctic bacterium Arthrobacter sp. 32cB (ArthβDG) have been determined in an unliganded form resulting from diffraction experiments conducted at 100 K (at resolution 1.8 Å) and at room temperature (at resolution 3.0 Å). A detailed comparison of those two structures of the same enzyme was performed in order to estimate differences in their molecular flexibility and rigidity and to study structural rationalization for the cold-adaptation of the investigated enzyme. Furthermore, a comparative analysis with structures of homologous enzymes from psychrophilic, mesophilic, and thermophilic sources has been discussed to elucidate the relationship between structure and cold-adaptation in a wider context. The performed studies confirm that the structure of cold-adapted ArthβDG maintains balance between molecular stability and structural flexibility, which can be observed independently on the temperature of conducted X-ray diffraction experiments. Obtained information about proper protein function under given conditions provide a guideline for rational engineering of proteins in terms of their temperature optimum and thermal stability.
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20
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Abd Latip MA, Abdul Hamid AA, Nordin NFH. Microbial hydrolytic enzymes: In silico studies between polar and tropical regions. POLAR SCIENCE 2019; 20:9-18. [DOI: 10.1016/j.polar.2019.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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21
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Kovalová T, Koval T, Benešová E, Vodicková P, Spiwok V, Lipovová P, Dohnálek J. Active site complementation and hexameric arrangement in the GH family 29; a structure-function study of α-l-fucosidase isoenzyme 1 from Paenibacillus thiaminolyticus. Glycobiology 2019; 29:59-73. [PMID: 30544181 DOI: 10.1093/glycob/cwy078] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/22/2018] [Indexed: 12/12/2022] Open
Abstract
α-l-Fucosidase isoenzyme 1 from bacterium Paenibacillus thiaminolyticus is a member of the glycoside hydrolase family GH29 capable of cleaving l-fucose from nonreducing termini of oligosaccharides and glycoconjugates. Here we present the first crystal structure of this protein revealing a novel quaternary state within this family. The protein is in a unique hexameric assembly revealing the first observed case of active site complementation by a residue from an adjacent monomer in this family. Mutation of the complementing tryptophan residue caused changes in the catalytic properties including a shift of the pH optimum, a change of affinity to an artificial chromogenic substrate and a decreased reaction rate for a natural substrate. The wild-type enzyme was active on most of the tested naturally occurring oligosaccharides and capable of transglycosylation on a variety of acceptor molecules, including saccharides, alcohols or chromogenic substrates. Mutation of the complementing residue changed neither substrate specificity nor the preference for the type of transglycosylation acceptor molecule; however, the yields of the reactions were lower in both cases. Maltose molecules bound to the enzyme in the crystal structure identified surface carbohydrate-binding sites, possibly participating in binding of larger oligosaccharides.
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Affiliation(s)
- Terézia Kovalová
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Biocev, Vestec, Czech Republic.,Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Tomáš Koval
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Biocev, Vestec, Czech Republic
| | - Eva Benešová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Patricie Vodicková
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Vojtech Spiwok
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Petra Lipovová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Jan Dohnálek
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Biocev, Vestec, Czech Republic
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22
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Cloning, Expression and Characterization of a Novel Cold-adapted β-galactosidase from the Deep-sea Bacterium Alteromonas sp. ML52. Mar Drugs 2018; 16:md16120469. [PMID: 30486362 PMCID: PMC6315854 DOI: 10.3390/md16120469] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/22/2018] [Accepted: 11/23/2018] [Indexed: 01/13/2023] Open
Abstract
The bacterium Alteromonas sp. ML52, isolated from deep-sea water, was found to synthesize an intracellular cold-adapted β-galactosidase. A novel β-galactosidase gene from strain ML52, encoding 1058 amino acids residues, was cloned and expressed in Escherichia coli. The enzyme belongs to glycoside hydrolase family 2 and is active as a homotetrameric protein. The recombinant enzyme had maximum activity at 35 °C and pH 8 with a low thermal stability over 30 °C. The enzyme also exhibited a Km of 0.14 mM, a Vmax of 464.7 U/mg and a kcat of 3688.1 S-1 at 35 °C with 2-nitrophenyl-β-d-galactopyranoside as a substrate. Hydrolysis of lactose assay, performed using milk, indicated that over 90% lactose in milk was hydrolyzed after incubation for 5 h at 25 °C or 24 h at 4 °C and 10 °C, respectively. These properties suggest that recombinant Alteromonas sp. ML52 β-galactosidase is a potential biocatalyst for the lactose-reduced dairy industry.
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23
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Domingues MN, Souza FHM, Vieira PS, de Morais MAB, Zanphorlin LM, Dos Santos CR, Pirolla RAS, Honorato RV, de Oliveira PSL, Gozzo FC, Murakami MT. Structural basis of exo-β-mannanase activity in the GH2 family. J Biol Chem 2018; 293:13636-13649. [PMID: 29997257 PMCID: PMC6120203 DOI: 10.1074/jbc.ra118.002374] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 06/23/2018] [Indexed: 11/06/2022] Open
Abstract
The classical microbial strategy for depolymerization of β-mannan polysaccharides involves the synergistic action of at least two enzymes, endo-1,4-β-mannanases and β-mannosidases. In this work, we describe the first exo-β-mannanase from the GH2 family, isolated from Xanthomonas axonopodis pv. citri (XacMan2A), which can efficiently hydrolyze both manno-oligosaccharides and β-mannan into mannose. It represents a valuable process simplification in the microbial carbon uptake that could be of potential industrial interest. Biochemical assays revealed a progressive increase in the hydrolysis rates from mannobiose to mannohexaose, which distinguishes XacMan2A from the known GH2 β-mannosidases. Crystallographic analysis indicates that the active-site topology of XacMan2A underwent profound structural changes at the positive-subsite region, by the removal of the physical barrier canonically observed in GH2 β-mannosidases, generating a more open and accessible active site with additional productive positive subsites. Besides that, XacMan2A contains two residue substitutions in relation to typical GH2 β-mannosidases, Gly439 and Gly556, which alter the active site volume and are essential to its mode of action. Interestingly, the only other mechanistically characterized mannose-releasing exo-β-mannanase so far is from the GH5 family, and its mode of action was attributed to the emergence of a blocking loop at the negative-subsite region of a cleft-like active site, whereas in XacMan2A, the same activity can be explained by the removal of steric barriers at the positive-subsite region in an originally pocket-like active site. Therefore, the GH2 exo-β-mannanase represents a distinct molecular route to this rare activity, expanding our knowledge about functional convergence mechanisms in carbohydrate-active enzymes.
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Affiliation(s)
| | | | | | | | | | | | | | - Rodrigo Vargas Honorato
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo 13083-970, Brazil and
| | - Paulo Sergio Lopes de Oliveira
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo 13083-970, Brazil and
| | - Fabio Cesar Gozzo
- the Dalton Mass Spectrometry Laboratory, University of Campinas, Campinas, São Paulo 13083-970, Brazil
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24
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Brininger C, Spradlin S, Cobani L, Evilia C. The more adaptive to change, the more likely you are to survive: Protein adaptation in extremophiles. Semin Cell Dev Biol 2018; 84:158-169. [PMID: 29288800 DOI: 10.1016/j.semcdb.2017.12.016] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 12/25/2017] [Accepted: 12/25/2017] [Indexed: 12/22/2022]
Abstract
Discovering how organisms and their proteins adapt to extreme conditions is a complicated process. Every condition has its own set of adaptations that make it uniquely stable in its environment. The purpose of our review is to discuss what is known in the extremophilic community about protein adaptations. To simplify our mission, we broke the extremophiles into three broad categories: thermophiles, halophiles and psychrophiles. While there are crossover organisms- organisms that exist in two or more extremes, like heat plus acid or cold plus pressure, most of them have a primary adaptation that is within one of these categories which tends to be the most easily identifiable one. While the generally known adaptations are still accepted, like thermophilic proteins have increased ionic interactions and a hardier hydrophobic core, halophilic proteins have a large increase in acidic amino acids and amino acid/peptide insertions and psychrophiles have a much more open structure and reduced ionic interactions, some new information has come to light. Thermophilic stability can be improved by increased subunit-subunit or subunit-cofactor interactions. Halophilic proteins have reversible folding when in the presence of salt. Psychrophilic proteins have an increase in cavities that not only decrease the formation of ice, but also increase flexibility under low temperature conditions. In a proof of concept experiment, we applied what is currently known about adaptations to a well characterized protein, malate dehydrogenase (MDH). While this protein has been profiled in the literature, we are applying our adaptation predictions to its sequence and structure to see if the described adaptations apply. Our analysis demonstrates that thermophilic and halophilic adaptations fit the corresponding MDHs very well. However, because the number of psychrophiles MDH sequences and structures is low, our analysis on psychrophiles is inconclusive and needs more information. By discussing known extremophilic adaptations and applying them to a random, conserved protein, we have found that general adaptations are conserved and can be predicted in proposed extremophilic proteins. The present field of extremophile adaptations is discovering more and more ways organisms and their proteins have adapted. The more that is learned about protein adaptation, the closer we get to custom proteins, designed to fit any extreme and solve some of the world's most pressing environmental problems.
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Affiliation(s)
- C Brininger
- Department of Chemistry, Idaho State University, Pocatello, ID 83209, USA
| | - S Spradlin
- Department of Chemistry, Idaho State University, Pocatello, ID 83209, USA
| | - L Cobani
- Department of Chemistry, Idaho State University, Pocatello, ID 83209, USA
| | - C Evilia
- Department of Chemistry, Idaho State University, Pocatello, ID 83209, USA.
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25
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In Situ Random Microseeding and Streak Seeding Used for Growth of Crystals of Cold-Adapted β-d-Galactosidases: Crystal Structure of βDG from Arthrobacter sp. 32cB. CRYSTALS 2018. [DOI: 10.3390/cryst8010013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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26
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Stranava M, Man P, Skálová T, Kolenko P, Blaha J, Fojtikova V, Martínek V, Dohnálek J, Lengalova A, Rosůlek M, Shimizu T, Martínková M. Coordination and redox state-dependent structural changes of the heme-based oxygen sensor AfGcHK associated with intraprotein signal transduction. J Biol Chem 2017; 292:20921-20935. [PMID: 29092908 DOI: 10.1074/jbc.m117.817023] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/18/2017] [Indexed: 11/06/2022] Open
Abstract
The heme-based oxygen sensor histidine kinase AfGcHK is part of a two-component signal transduction system in bacteria. O2 binding to the Fe(II) heme complex of its N-terminal globin domain strongly stimulates autophosphorylation at His183 in its C-terminal kinase domain. The 6-coordinate heme Fe(III)-OH- and -CN- complexes of AfGcHK are also active, but the 5-coordinate heme Fe(II) complex and the heme-free apo-form are inactive. Here, we determined the crystal structures of the isolated dimeric globin domains of the active Fe(III)-CN- and inactive 5-coordinate Fe(II) forms, revealing striking structural differences on the heme-proximal side of the globin domain. Using hydrogen/deuterium exchange coupled with mass spectrometry to characterize the conformations of the active and inactive forms of full-length AfGcHK in solution, we investigated the intramolecular signal transduction mechanisms. Major differences between the active and inactive forms were observed on the heme-proximal side (helix H5), at the dimerization interface (helices H6 and H7 and loop L7) of the globin domain and in the ATP-binding site (helices H9 and H11) of the kinase domain. Moreover, separation of the sensor and kinase domains, which deactivates catalysis, increased the solvent exposure of the globin domain-dimerization interface (helix H6) as well as the flexibility and solvent exposure of helix H11. Together, these results suggest that structural changes at the heme-proximal side, the globin domain-dimerization interface, and the ATP-binding site are important in the signal transduction mechanism of AfGcHK. We conclude that AfGcHK functions as an ensemble of molecules sampling at least two conformational states.
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Affiliation(s)
- Martin Stranava
- From the Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, 128 43 Czech Republic
| | - Petr Man
- From the Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, 128 43 Czech Republic.,the Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Biocev, 252 50 Vestec, Czech Republic
| | - Tereza Skálová
- the Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Biocev, 252 50 Vestec, Czech Republic, and
| | - Petr Kolenko
- the Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Biocev, 252 50 Vestec, Czech Republic, and.,the Department of Solid State Engineering, Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Brehova 7, 115 19 Praha 1, Czech Republic
| | - Jan Blaha
- From the Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, 128 43 Czech Republic
| | - Veronika Fojtikova
- From the Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, 128 43 Czech Republic
| | - Václav Martínek
- From the Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, 128 43 Czech Republic
| | - Jan Dohnálek
- the Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Biocev, 252 50 Vestec, Czech Republic, and
| | - Alzbeta Lengalova
- From the Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, 128 43 Czech Republic
| | - Michal Rosůlek
- From the Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, 128 43 Czech Republic.,the Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Biocev, 252 50 Vestec, Czech Republic
| | - Toru Shimizu
- From the Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, 128 43 Czech Republic
| | - Markéta Martínková
- From the Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, 128 43 Czech Republic,
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27
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Abstract
Many carbohydrate-binding proteins contain aromatic amino acid residues in their binding sites. These residues interact with carbohydrates in a stacking geometry via CH/π interactions. These interactions can be found in carbohydrate-binding proteins, including lectins, enzymes and carbohydrate transporters. Besides this, many non-protein aromatic molecules (natural as well as artificial) can bind saccharides using these interactions. Recent computational and experimental studies have shown that carbohydrate–aromatic CH/π interactions are dispersion interactions, tuned by electrostatics and partially stabilized by a hydrophobic effect in solvated systems.
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Yin H, Pijning T, Meng X, Dijkhuizen L, van Leeuwen SS. Biochemical Characterization of the Functional Roles of Residues in the Active Site of the β-Galactosidase from Bacillus circulans ATCC 31382. Biochemistry 2017; 56:3109-3118. [PMID: 28538097 PMCID: PMC5481816 DOI: 10.1021/acs.biochem.7b00207] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/14/2017] [Indexed: 12/29/2022]
Abstract
The β-galactosidase enzyme from Bacillus circulans ATCC 31382 BgaD is widely used in the food industry to produce prebiotic galactooligosaccharides (GOS). Recently, the crystal structure of a C-terminally truncated version of the enzyme (BgaD-D) has been elucidated. The roles of active site amino acid residues in β-galactosidase enzyme reaction and product specificity have remained unknown. On the basis of a structural alignment of the β-galactosidase enzymes BgaD-D from B. circulans and BgaA from Streptococcus pneumoniae, and the complex of BgaA with LacNAc, we identified eight active site amino acid residues (Arg185, Asp481, Lys487, Tyr511, Trp570, Trp593, Glu601, and Phe616) in BgaD-D. This study reports an investigation of the functional roles of these residues, using site-directed mutagenesis, and a detailed biochemical characterization and product profile analysis of the mutants obtained. The data show that these residues are involved in binding and positioning of the substrate and thus determine the BgaD-D activity and product linkage specificity. This study provides detailed insights into the structure-function relationships of the B. circulans BgaD-D enzyme, especially regarding GOS product linkage specificity, allowing the rational mutation of β-galactosidase enzymes to produce specific mixtures of GOS structures.
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Affiliation(s)
- Huifang Yin
- Microbial
Physiology, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Tjaard Pijning
- Biophysical
Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Xiangfeng Meng
- Microbial
Physiology, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Lubbert Dijkhuizen
- Microbial
Physiology, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Sander S. van Leeuwen
- Microbial
Physiology, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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29
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Talens-Perales D, Górska A, Huson DH, Polaina J, Marín-Navarro J. Analysis of Domain Architecture and Phylogenetics of Family 2 Glycoside Hydrolases (GH2). PLoS One 2016; 11:e0168035. [PMID: 27930742 PMCID: PMC5145203 DOI: 10.1371/journal.pone.0168035] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 11/23/2016] [Indexed: 11/23/2022] Open
Abstract
In this work we report a detailed analysis of the topology and phylogenetics of family 2 glycoside hydrolases (GH2). We distinguish five topologies or domain architectures based on the presence and distribution of protein domains defined in Pfam and Interpro databases. All of them share a central TIM barrel (catalytic module) with two β-sandwich domains (non-catalytic) at the N-terminal end, but differ in the occurrence and nature of additional non-catalytic modules at the C-terminal region. Phylogenetic analysis was based on the sequence of the Pfam Glyco_hydro_2_C catalytic module present in most GH2 proteins. Our results led us to propose a model in which evolutionary diversity of GH2 enzymes is driven by the addition of different non-catalytic domains at the C-terminal region. This model accounts for the divergence of β-galactosidases from β-glucuronidases, the diversification of β-galactosidases with different transglycosylation specificities, and the emergence of bicistronic β-galactosidases. This study also allows the identification of groups of functionally uncharacterized protein sequences with potential biotechnological interest.
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Affiliation(s)
- David Talens-Perales
- Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Paterna, Valencia, Spain
| | - Anna Górska
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany
| | - Daniel H. Huson
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany
| | - Julio Polaina
- Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Paterna, Valencia, Spain
| | - Julia Marín-Navarro
- Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Paterna, Valencia, Spain
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30
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Afzal M, Shafeeq S, Ahmed H, Kuipers OP. N-acetylgalatosamine-Mediated Regulation of the aga Operon by AgaR in Streptococcus pneumoniae. Front Cell Infect Microbiol 2016; 6:101. [PMID: 27672623 PMCID: PMC5018945 DOI: 10.3389/fcimb.2016.00101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/29/2016] [Indexed: 11/14/2022] Open
Abstract
Here, we analyze the transcriptomic response of Streptococcus pneumoniae D39 to N-acetylgalactosamine (NAGa). Transcriptome comparison of S. pneumoniae D39 grown in NAGaM17 (0.5% NAGa + M17) to that grown in GM17 (0.5% Glucose + M17) revealed the elevated expression of various carbon metabolic genes/operons, including a PTS operon (denoted here as the aga operon), which is putatively involved in NAGa transport and utilization, in the presence of NAGa. We further studied the role of a GntR-family transcriptional regulator (denoted here as AgaR) in the regulation of aga operon. Our transcriptome and RT-PCR data suggest the role of AgaR as a transcriptional repressor of the aga operon. We predicted a 20-bp operator site of AagR (5′-ATAATTAATATAACAACAAA-3′) in the promoter region of the aga operon (PbgaC), which was further verified by mutating the AgaR operator site in the respective promoter. The role of CcpA in the additional regulation of the aga operon was elucidated by further transcriptome analyses and confirmed by quantitative RT-PCR.
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Affiliation(s)
- Muhammad Afzal
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningen, Netherlands; Department of Bioinformatics and Biotechnology, Government College University FaisalabadFaisalabad, Pakistan
| | - Sulman Shafeeq
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Stockholm, Sweden
| | - Hifza Ahmed
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Groningen, Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Groningen, Netherlands
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Santiago M, Ramírez-Sarmiento CA, Zamora RA, Parra LP. Discovery, Molecular Mechanisms, and Industrial Applications of Cold-Active Enzymes. Front Microbiol 2016; 7:1408. [PMID: 27667987 PMCID: PMC5016527 DOI: 10.3389/fmicb.2016.01408] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 08/25/2016] [Indexed: 11/17/2022] Open
Abstract
Cold-active enzymes constitute an attractive resource for biotechnological applications. Their high catalytic activity at temperatures below 25°C makes them excellent biocatalysts that eliminate the need of heating processes hampering the quality, sustainability, and cost-effectiveness of industrial production. Here we provide a review of the isolation and characterization of novel cold-active enzymes from microorganisms inhabiting different environments, including a revision of the latest techniques that have been used for accomplishing these paramount tasks. We address the progress made in the overexpression and purification of cold-adapted enzymes, the evolutionary and molecular basis of their high activity at low temperatures and the experimental and computational techniques used for their identification, along with protein engineering endeavors based on these observations to improve some of the properties of cold-adapted enzymes to better suit specific applications. We finally focus on examples of the evaluation of their potential use as biocatalysts under conditions that reproduce the challenges imposed by the use of solvents and additives in industrial processes and of the successful use of cold-adapted enzymes in biotechnological and industrial applications.
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Affiliation(s)
- Margarita Santiago
- Department of Chemical Engineering and Biotechnology, Centre for Biochemical Engineering and Biotechnology, Universidad de ChileSantiago, Chile
| | - César A. Ramírez-Sarmiento
- Schools of Engineering, Medicine and Biological Sciences, Institute for Biological and Medical Engineering, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Ricardo A. Zamora
- Departamento de Biología, Facultad de Ciencias, Universidad de ChileSantiago, Chile
| | - Loreto P. Parra
- Schools of Engineering, Medicine and Biological Sciences, Institute for Biological and Medical Engineering, Pontificia Universidad Católica de ChileSantiago, Chile
- Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de ChileSantiago, Chile
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Rutkiewicz-Krotewicz M, Pietrzyk-Brzezinska AJ, Sekula B, Cieśliński H, Wierzbicka-Woś A, Kur J, Bujacz A. Structural studies of a cold-adapted dimeric β-D-galactosidase fromParacoccussp. 32d. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:1049-61. [DOI: 10.1107/s2059798316012535] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 08/03/2016] [Indexed: 12/20/2022]
Abstract
The crystal structure of a novel dimeric β-D-galactosidase fromParacoccussp. 32d (ParβDG) was solved in space groupP212121at a resolution of 2.4 Å by molecular replacement with multiple models using theBALBESsoftware. This enzyme belongs to glycoside hydrolase family 2 (GH2), similar to the tetrameric and hexameric β-D-galactosidases fromEscherichia coliandArthrobactersp. C2-2, respectively. It is the second known structure of a cold-active GH2 β-galactosidase, and the first in the form of a functional dimer, which is also present in the asymmetric unit. Cold-adapted β-D-galactosidases have been the focus of extensive research owing to their utility in a variety of industrial technologies. One of their most appealing applications is in the hydrolysis of lactose, which not only results in the production of lactose-free dairy, but also eliminates the `sandy effect' and increases the sweetness of the product, thus enhancing its quality. The determined crystal structure represents the five-domain architecture of the enzyme, with its active site located in close vicinity to the dimer interface. To identify the amino-acid residues involved in the catalytic reaction and to obtain a better understanding of the mechanism of action of this atypical β-D-galactosidase, the crystal structure in complex with galactose (ParβDG–Gal) was also determined. The catalytic site of the enzyme is created by amino-acid residues from the central domain 3 and from domain 4 of an adjacent monomer. The crystal structure of this dimeric β-D-galactosidase reveals significant differences in comparison to other β-galactosidases. The largest difference is in the fifth domain, named Bgal_windup domain 5 inParβDG, which contributes to stabilization of the functional dimer. The location of this domain 5, which is unique in size and structure, may be one of the factors responsible for the creation of a functional dimer and cold-adaptation of this enzyme.
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33
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Morrison JM, Elshahed MS, Youssef N. A multifunctional GH39 glycoside hydrolase from the anaerobic gut fungus Orpinomyces sp. strain C1A. PeerJ 2016; 4:e2289. [PMID: 27547582 PMCID: PMC4975031 DOI: 10.7717/peerj.2289] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/05/2016] [Indexed: 01/05/2023] Open
Abstract
Background. The anaerobic gut fungi (phylum Neocallimastigomycota) represent a promising source of novel lignocellulolytic enzymes. Here, we report on the cloning, expression, and characterization of a glycoside hydrolase family 39 (GH39) enzyme (Bgxg1) that is highly transcribed by the anaerobic fungus Orpinomycessp. strain C1A under different growth conditions. This represents the first study of a GH39-family enzyme from the anaerobic fungi. Methods. Using enzyme activity assays, we performed a biochemical characterization of Bgxg1 on a variety of substrates over a wide range of pH and temperature values to identify the optimal enzyme conditions and the specificity of the enzyme. In addition, substrate competition studies and comparative modeling efforts were completed. Results. Contrary to the narrow range of activities (β-xylosidase or α-L-iduronidase) observed in previously characterized GH39 enzymes, Bgxg1 is unique in that it is multifunctional, exhibiting strong β-xylosidase, β-glucosidase, β-galactosidase activities (11.5 ± 1.2, 73.4 ± 7.15, and 54.6 ± 2.26 U/mg, respectively) and a weak xylanase activity (10.8 ± 1.25 U/mg), as compared to previously characterized enzymes. Further, Bgxg1 possesses extremely high affinity (as evident by the lowest K m values), compared to all previously characterized β-glucosidases, β-galactosidases, and xylanases. Physiological characterization revealed that Bgxg1 is active over a wide range of pH (3-8, optimum 6) and temperatures (25-60 °C, optimum 39 °C), and possesses excellent temperature and thermal stability. Substrate competition assays suggest that all observed activities occur at a single active site. Using comparative modeling and bioinformatics approaches, we putatively identified ten amino acid differences between Bgxg1 and previously biochemically characterized GH39 β-xylosidases that we speculate could impact active site architecture, size, charge, and/or polarity. Discussion. Collectively, the unique capabilities and multi-functionality of Bgxg1 render it an excellent candidate for inclusion in enzyme cocktails mediating cellulose and hemicellulose saccharification from lignocellulosic biomass.
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Affiliation(s)
- Jessica M Morrison
- Department of Microbiology and Molecular Genetics, Oklahoma State University , Stillwater , OK , USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University , Stillwater , OK , USA
| | - Noha Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University , Stillwater , OK , USA
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34
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Tycko R. Molecular Structure of Aggregated Amyloid-β: Insights from Solid-State Nuclear Magnetic Resonance. Cold Spring Harb Perspect Med 2016; 6:a024083. [PMID: 27481836 PMCID: PMC4968170 DOI: 10.1101/cshperspect.a024083] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Amyloid-β (Aβ) peptides aggregate to form polymorphic amyloid fibrils and a variety of intermediate assemblies, including oligomers and protofibrils, both in vitro and in human brain tissue. Since the beginning of the 21st century, considerable progress has been made to characterize the molecular structures of Aβ aggregates. Full molecular structural models based primarily on data from measurements using solid-state nuclear magnetic resonance (ssNMR) have been developed for several in vitro Aβ fibrils and one metastable protofibril. Partial structural characterization of other aggregation intermediates has been achieved. One full structural model for fibrils derived from brain tissue has also been reported. Future work is likely to focus on additional structures from brain tissue and on further clarification of nonfibrillar Aβ aggregates.
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Affiliation(s)
- Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520
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35
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Affiliation(s)
- Prakram Singh Chauhan
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, SAS Nagar, Mohali, India and
| | - Naveen Gupta
- Department of Microbiology, Panjab University, Chandigarh, India
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36
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Fan Y, Yi J, Hua X, Feng Y, Yang R, Zhang Y. Structure analysis of a glycosides hydrolase family 42 cold-adapted β-galactosidase from Rahnella sp. R3. RSC Adv 2016. [DOI: 10.1039/c6ra04529d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The β-galactosidase isolated from a psychrotrophic bacterium, Rahnella sp. R3 (R-β-Gal), exhibits high activity at low temperature and has potential in the dairy industry.
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Affiliation(s)
- Yuting Fan
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- 214122 Wuxi
- China
| | - Jiang Yi
- College of Chemistry and Environmental Engineering
- Shenzhen University
- 518060 Shenzhen
- China
| | - Xiao Hua
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- 214122 Wuxi
- China
| | - Yinghui Feng
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- 214122 Wuxi
- China
| | - Ruijin Yang
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- 214122 Wuxi
- China
| | - Yuzhu Zhang
- US Department of Agriculture
- Agriculture Research Service
- Western Regional Research Center
- Albany
- USA
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37
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Razavi BS, Blagodatskaya E, Kuzyakov Y. Nonlinear temperature sensitivity of enzyme kinetics explains canceling effect-a case study on loamy haplic Luvisol. Front Microbiol 2015; 6:1126. [PMID: 26528272 PMCID: PMC4604301 DOI: 10.3389/fmicb.2015.01126] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 09/28/2015] [Indexed: 11/13/2022] Open
Abstract
The temperature sensitivity of enzymes responsible for organic matter decomposition in soil is crucial for predicting the effects of global warming on the carbon cycle and sequestration. We tested the hypothesis that differences in temperature sensitivity of enzyme kinetic parameters V max and K m will lead to a canceling effect: strong reduction of temperature response of catalytic reactions. Short-term temperature response of V max and K m of three hydrolytic enzymes responsible for decomposition of cellulose (β-glucosidase, cellobiohydrolase) and hemicelluloses (xylanase) were analyzed in situ from 0 to 40°C. The apparent activation energy varied between enzymes from 20.7 to 35.2 kJ mol(-1) corresponding to the Q 10 values of the enzyme activities of 1.4-1.9 (with V max - Q 10 1.0-2.5 and K m - Q 10 0.94-2.3). Temperature response of all tested enzymes fitted well to the Arrhenius equation. Despite that, the fitting of Arrhenius model revealed the non-linear increase of two cellulolytic enzymes activities with two distinct thresholds at 10-15°C and 25-30°C, which were less pronounced for xylanase. The nonlinearity between 10 and 15°C was explained by 30-80% increase in V max . At 25-30°C, however, the abrupt decrease of enzyme-substrate affinity was responsible for non-linear increase of enzyme activities. Our study is the first demonstrating nonlinear response of V max and K m to temperature causing canceling effect, which was most strongly pronounced at low substrate concentrations and at temperatures above 15°C. Under cold climate, however, the regulation of hydrolytic activity by canceling in response to warming is negligible because canceling was never observed below 10°C. The canceling, therefore, can be considered as natural mechanism reducing the effects of global warming on decomposition of soil organics at moderate temperatures. The non-linearity of enzyme responses to warming and the respective thresholds should therefore be investigated for other enzymes, and incorporated into Earth system models to improve the predictions at regional and global levels.
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Affiliation(s)
- Bahar S. Razavi
- Department of Agricultural Soil Science, University of GöttingenGöttingen, Germany
| | - Evgenia Blagodatskaya
- Department of Soil Science of Temperate Ecosystems, University of GöttingenGöttingen, Germany
- Institute of Physicochemical and Biological Problem in Soil Science, Russian Academy of SciencePushchino, Russia
| | - Yakov Kuzyakov
- Department of Agricultural Soil Science, University of GöttingenGöttingen, Germany
- Department of Soil Science of Temperate Ecosystems, University of GöttingenGöttingen, Germany
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38
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Li J, Flick F, Verheugd P, Carloni P, Lüscher B, Rossetti G. Insight into the Mechanism of Intramolecular Inhibition of the Catalytic Activity of Sirtuin 2 (SIRT2). PLoS One 2015; 10:e0139095. [PMID: 26407304 PMCID: PMC4583397 DOI: 10.1371/journal.pone.0139095] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/09/2015] [Indexed: 12/26/2022] Open
Abstract
Sirtuin 2 (SIRT2) is a NAD+-dependent deacetylase that has been associated with neurodegeneration and cancer. SIRT2 is composed of a central catalytic domain, the structure of which has been solved, and N- and C-terminal extensions that are thought to control SIRT2 function. However structural information of these N- and C-terminal regions is missing. Here, we provide the first full-length molecular models of SIRT2 in the absence and presence of NAD+. We also predict the structural alterations associated with phosphorylation of SIRT2 at S331, a modification that inhibits catalytic activity. Bioinformatics tools and molecular dynamics simulations, complemented by in vitro deacetylation assays, provide a consistent picture based on which the C-terminal region of SIRT2 is suggested to function as an autoinhibitory region. This has the capacity to partially occlude the NAD+ binding pocket or stabilize the NAD+ in a non-productive state. Furthermore, our simulations suggest that the phosphorylation at S331 causes large conformational changes in the C-terminal region that enhance the autoinhibitory activity, consistent with our previous findings that phosphorylation of S331 by cyclin-dependent kinases inhibits SIRT2 catalytic activity. The molecular insight into the role of the C-terminal region in controlling SIRT2 function described in this study may be useful for future design of selective inhibitors targeting SIRT2 for therapeutic applications.
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Affiliation(s)
- Jinyu Li
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425, Jülich, Germany
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, 52057, Aachen, Germany
| | - Franziska Flick
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, 52057, Aachen, Germany
| | - Patricia Verheugd
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, 52057, Aachen, Germany
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425, Jülich, Germany
- Computational Biophysics, German Research School for Simulation Sciences, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, 52057, Aachen, Germany
| | - Giulia Rossetti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425, Jülich, Germany
- Jülich Supercomputing Centre, Forschungszentrum Jülich, 52425, Jülich, Germany
- Department of Oncology, Hematology and Stem Cell Transplantation, RWTH Aachen University, Aachen, Germany
- * E-mail:
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39
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Vukić V, Hrnjez D, Milanović S, Iličić M, Kanurić K, Petri E. Comparative Molecular Modeling and Docking Analysis of β-galactosidase Enzymes from Commercially Important Starter Cultures Used in the Dairy Industry. FOOD BIOTECHNOL 2015. [DOI: 10.1080/08905436.2015.1059766] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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40
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Tajiri T, Matsumoto S, Imato T, Okamoto T, Haraguchi M. Optical characterization of the antigen-antibody thin layer using the whispering gallery mode. ANAL SCI 2015; 30:799-804. [PMID: 25109641 DOI: 10.2116/analsci.30.799] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We immobilized an antibody (anti-β-Galactosidase) on a polystyrene microsphere by using a covalent bond, and observed the resonance peaks in the scattered light intensity spectra related to the whispering gallery mode (WGM) excitation of the microsphere. The amount and the optical parameters, i.e., thickness and refractive index, of anti-β-Galactosidase on the sphere surface were evaluated based on an absorbance measurement and a resonance peak shift measurement, respectively. Moreover, we measured the variation of the WGM spectra depending on the concentration of the enzyme solution (β-Galactosidase), which allowed us to optically evaluate the thickness and the refractive index of the antigen-antibody layer from the shift of the WGM spectra peak.
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41
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Pawlak-Szukalska A, Wanarska M, Popinigis AT, Kur J. A novel cold-active β-d-galactosidase with transglycosylation activity from the Antarctic Arthrobacter sp. 32cB – Gene cloning, purification and characterization. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.09.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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42
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Immobilization of thermostable β-galactosidase on epoxy support and its use for lactose hydrolysis and galactooligosaccharides biosynthesis. World J Microbiol Biotechnol 2014; 30:989-98. [PMID: 24122101 DOI: 10.1007/s11274-013-1517-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 10/07/2013] [Indexed: 01/20/2023]
Abstract
Thermoresistant, recombinant β-galactosidase from Thermotoga maritima was purified and immobilized on the surface of epoxy-coated magnetic beads. The enzyme, which has hexameric quaternary structure as shown by gel filtration chromatography, attaches to the resin through multiple covalent linkages that involve different subunits. The bound enzyme shows higher stability than the free form. The immobilized enzyme showed to be efficient for the hydrolysis of lactose and the biosynthesis of galactooligosaccharides (GOS). The chemical structure of synthesized GOS has been determined by NMR revealing that the main product was β-3′-galactosyl lactose. Although β-galactosidases from different sources have been used for the same purposes, the distinct advantage of the methodology described in this communication is that the enzyme can be easily produced, purified and immobilized in large quantities.
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43
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Nascimento AS, Muniz JRC, Aparício R, Golubev AM, Polikarpov I. Insights into the structure and function of fungal β-mannosidases from glycoside hydrolase family 2 based on multiple crystal structures of the Trichoderma harzianum enzyme. FEBS J 2014; 281:4165-78. [PMID: 24975648 DOI: 10.1111/febs.12894] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/15/2014] [Accepted: 06/24/2014] [Indexed: 11/28/2022]
Abstract
UNLABELLED Hemicellulose is an important part of the plant cell wall biomass, and is relevant to cellulosic ethanol technologies. β-Mannosidases are enzymes capable of cleaving nonreducing residues of β-d-mannose from β-d-mannosides and hemicellulose mannose-containing polysaccharides, such as mannans and galactomannans. β-Mannosidases are distributed between glycoside hydrolase (GH) families 1, 2, and 5, and only a handful of the enzymes have been structurally characterized to date. The only published X-ray structure of a GH family 2 mannosidase is that of the bacterial Bacteroides thetaiotaomicron enzyme. No structures of eukaryotic mannosidases of this family are currently available. To fill this gap, we set out to solve the structure of Trichoderma harzianum GH family 2 β-mannosidase and to refine it to 1.9-Å resolution. Structural comparisons of the T. harzianum GH2 β-mannosidase highlight similarities in its structural architecture with other members of GH family 2, reveal the molecular mechanism of β-mannoside binding and recognition, and shed light on its putative galactomannan-binding site. DATABASE Coordinates and observed structure factor amplitudes have been deposited with the Protein Data Bank (4CVU and 4UOJ). The T. harzianum β-mannosidase 2A nucleotide sequence has GenBank accession number BankIt1712036 GeneMark.hmm KJ624918.
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Díez-Municio M, Herrero M, Olano A, Moreno FJ. Synthesis of novel bioactive lactose-derived oligosaccharides by microbial glycoside hydrolases. Microb Biotechnol 2014; 7:315-31. [PMID: 24690139 PMCID: PMC4241725 DOI: 10.1111/1751-7915.12124] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/21/2014] [Accepted: 02/23/2014] [Indexed: 12/17/2022] Open
Abstract
Prebiotic oligosaccharides are increasingly demanded within the Food Science domain because of the interesting healthy properties that these compounds may induce to the organism, thanks to their beneficial intestinal microbiota growth promotion ability. In this regard, the development of new efficient, convenient and affordable methods to obtain this class of compounds might expand even further their use as functional ingredients. This review presents an overview on the most recent interesting approaches to synthesize lactose-derived oligosaccharides with potential prebiotic activity paying special focus on the microbial glycoside hydrolases that can be effectively employed to obtain these prebiotic compounds. The most notable advantages of using lactose-derived carbohydrates such as lactosucrose, galactooligosaccharides from lactulose, lactulosucrose and 2-α-glucosyl-lactose are also described and commented.
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Affiliation(s)
- Marina Díez-Municio
- Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM), CEI (UAM+CSIC)C/ Nicolás Cabrera 9, Madrid, 28049, Spain
| | - Miguel Herrero
- Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM), CEI (UAM+CSIC)C/ Nicolás Cabrera 9, Madrid, 28049, Spain
| | - Agustín Olano
- Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM), CEI (UAM+CSIC)C/ Nicolás Cabrera 9, Madrid, 28049, Spain
| | - F Javier Moreno
- Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM), CEI (UAM+CSIC)C/ Nicolás Cabrera 9, Madrid, 28049, Spain
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In Silico Analysis of β-Galactosidases Primary and Secondary Structure in relation to Temperature Adaptation. JOURNAL OF AMINO ACIDS 2014; 2014:475839. [PMID: 24790757 PMCID: PMC3982409 DOI: 10.1155/2014/475839] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 02/06/2014] [Indexed: 11/18/2022]
Abstract
β -D-Galactosidases (EC 3.2.1.23) hydrolyze the terminal nonreducing β -D-galactose residues in β -D-galactosides and are ubiquitously present in all life forms including extremophiles. Eighteen microbial β -galactosidase protein sequences, six each from psychrophilic, mesophilic, and thermophilic microbes, were analyzed. Primary structure reveals alanine, glycine, serine, and arginine to be higher in psychrophilic β -galactosidases whereas valine, glutamine, glutamic acid, phenylalanine, threonine, and tyrosine are found to be statistically preferred by thermophilic β -galactosidases. Cold active β -galactosidase has a strong preference towards tiny and small amino acids, whereas high temperature inhabitants had higher content of basic and aromatic amino acids. Thermophilic β -galactosidases have higher percentage of α -helix region responsible for temperature tolerance while cold loving β -galactosidases had higher percentage of sheet and coil region. Secondary structure analysis revealed that charged and aromatic amino acids were significant for sheet region of thermophiles. Alanine was found to be significant and high in the helix region of psychrophiles and valine counters in thermophilic β -galactosidase. Coil region of cold active β -galactosidase has higher content of tiny amino acids which explains their high catalytic efficiency over their counterparts from thermal habitat. The present study has revealed the preference or prevalence of certain amino acids in primary and secondary structure of psychrophilic, mesophilic, and thermophilic β -galactosidase.
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Mojallali L, Shahbani Zahiri H, Rajaei S, Akbari Noghabi K, Haghbeen K. A novel ∼34-kDa α-amylase from psychrotroph Exiguobacterium sp. SH3: production, purification, and characterization. Biotechnol Appl Biochem 2013; 61:118-25. [PMID: 23826950 DOI: 10.1002/bab.1140] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 06/21/2013] [Indexed: 11/06/2022]
Abstract
An amylase-producing psychrotroph bacterium was isolated from soil and identified as belonging to the genus Exiguobacterium. A novel cold-adapted α-amylase, Amy SH3, was purified from culture medium of this bacterium using acetone precipitation and DEAE-Sepharose anion-exchange chromatography. The molecular mass of the enzyme was estimated about 34 kDa using SDS-PAGE. Biochemical characterization of Amy SH3 revealed that the optimum temperature for maximum activity of Amy SH3 was 37°C. However, Amy SH3 was also active at cold temperatures, showing 13% and 39% activity at 0 and 10°C, respectively. The optimum pH for maximum activity of Amy SH3 was pH 7, whereas the amylase was active over a pH range of 5 to 10. The activity of Amy SH3 was enhanced by Co²⁺ but decreased by Mg²⁺, Mn²⁺, Zn²⁺, Fe²⁺, and Ca²⁺. Amy SH3 was able to retain 76% of its activity in the presence of 0.5% SDS. The K(m) and V(max) of the enzyme were calculated to be 0.06 mg/mL and 4,010 U/mL, respectively. The cold-adapted Amy SH3 seems very promising for applications at ambient temperature.
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Affiliation(s)
- Leila Mojallali
- Department of Molecular Genetics, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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Psychrophily and catalysis. BIOLOGY 2013; 2:719-41. [PMID: 24832805 PMCID: PMC3960892 DOI: 10.3390/biology2020719] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 03/18/2013] [Accepted: 03/18/2013] [Indexed: 11/24/2022]
Abstract
Polar and other low temperature environments are characterized by a low content in energy and this factor has a strong incidence on living organisms which populate these rather common habitats. Indeed, low temperatures have a negative effect on ectothermic populations since they can affect their growth, reaction rates of biochemical reactions, membrane permeability, diffusion rates, action potentials, protein folding, nucleic acids dynamics and other temperature-dependent biochemical processes. Since the discovery that these ecosystems, contrary to what was initially expected, sustain a rather high density and broad diversity of living organisms, increasing efforts have been dedicated to the understanding of the molecular mechanisms involved in their successful adaptation to apparently unfavorable physical conditions. The first question that comes to mind is: How do these organisms compensate for the exponential decrease of reaction rate when temperature is lowered? As most of the chemical reactions that occur in living organisms are catalyzed by enzymes, the kinetic and thermodynamic properties of cold-adapted enzymes have been investigated. Presently, many crystallographic structures of these enzymes have been elucidated and allowed for a rather clear view of their adaptation to cold. They are characterized by a high specific activity at low and moderate temperatures and a rather low thermal stability, which induces a high flexibility that prevents the freezing effect of low temperatures on structure dynamics. These enzymes also display a low activation enthalpy that renders them less dependent on temperature fluctuations. This is accompanied by a larger negative value of the activation entropy, thus giving evidence of a more disordered ground state. Appropriate folding kinetics is apparently secured through a large expression of trigger factors and peptidyl–prolyl cis/trans-isomerases.
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Wheatley RW, Lo S, Jancewicz LJ, Dugdale ML, Huber RE. Structural explanation for allolactose (lac operon inducer) synthesis by lacZ β-galactosidase and the evolutionary relationship between allolactose synthesis and the lac repressor. J Biol Chem 2013; 288:12993-3005. [PMID: 23486479 DOI: 10.1074/jbc.m113.455436] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
β-Galactosidase (lacZ) has bifunctional activity. It hydrolyzes lactose to galactose and glucose and catalyzes the intramolecular isomerization of lactose to allolactose, the lac operon inducer. β-Galactosidase promotes the isomerization by means of an acceptor site that binds glucose after its cleavage from lactose and thus delays its exit from the site. However, because of its relatively low affinity for glucose, details of this site have remained elusive. We present structural data mapping the glucose site based on a substituted enzyme (G794A-β-galactosidase) that traps allolactose. Various lines of evidence indicate that the glucose of the trapped allolactose is in the acceptor position. The evidence includes structures with Bis-Tris (2,2-bis(hydroxymethyl)-2,2',2″-nitrilotriethanol) and L-ribose in the site and kinetic binding studies with substituted β-galactosidases. The site is composed of Asn-102, His-418, Lys-517, Ser-796, Glu-797, and Trp-999. Ser-796 and Glu-797 are part of a loop (residues 795-803) that closes over the active site. This loop appears essential for the bifunctional nature of the enzyme because it helps form the glucose binding site. In addition, because the loop is mobile, glucose binding is transient, allowing the release of some glucose. Bioinformatics studies showed that the residues important for interacting with glucose are only conserved in a subset of related enzymes. Thus, intramolecular isomerization is not a universal feature of β-galactosidases. Genomic analyses indicated that lac repressors were co-selected only within the conserved subset. This shows that the glucose binding site of β-galactosidase played an important role in lac operon evolution.
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Affiliation(s)
- Robert W Wheatley
- Division of Biochemistry, Faculty of Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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Demo G, Fliedrová B, Weignerová L, Wimmerová M. Crystallization and preliminary X-ray crystallographic analysis of recombinant β-mannosidase from Aspergillus niger. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:288-91. [PMID: 23519806 PMCID: PMC3606576 DOI: 10.1107/s1744309113002522] [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: 01/07/2013] [Accepted: 01/24/2013] [Indexed: 11/10/2022]
Abstract
β-Mannosidase (EC 3.2.1.25) is an important exoglycosidase specific for the hydrolysis of terminal β-linked mannoside in various oligomeric saccharide structures. β-Mannosidase from Aspergillus niger was expressed in Pichia pastoris and purified to clear homogeneity. β-Mannosidase was crystallized in the presence of D-mannose and the crystal diffracted to 2.41 Å resolution. The crystal belonged to space group P1, with unit-cell parameters a=62.37, b=69.73, c=69.90 Å, α=108.20, β=101.51, γ=103.20°. The parameters derived from the data collection indicate the presence of one molecule in the asymmetric unit.
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Affiliation(s)
- Gabriel Demo
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Barbora Fliedrová
- Laboratory of Biotransformation, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Prague, Czech Republic
| | - Lenka Weignerová
- Laboratory of Biotransformation, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Michaela Wimmerová
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
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Feller G. Psychrophilic enzymes: from folding to function and biotechnology. SCIENTIFICA 2013; 2013:512840. [PMID: 24278781 PMCID: PMC3820357 DOI: 10.1155/2013/512840] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 11/06/2012] [Indexed: 05/10/2023]
Abstract
Psychrophiles thriving permanently at near-zero temperatures synthesize cold-active enzymes to sustain their cell cycle. Genome sequences, proteomic, and transcriptomic studies suggest various adaptive features to maintain adequate translation and proper protein folding under cold conditions. Most psychrophilic enzymes optimize a high activity at low temperature at the expense of substrate affinity, therefore reducing the free energy barrier of the transition state. Furthermore, a weak temperature dependence of activity ensures moderate reduction of the catalytic activity in the cold. In these naturally evolved enzymes, the optimization to low temperature activity is reached via destabilization of the structures bearing the active site or by destabilization of the whole molecule. This involves a reduction in the number and strength of all types of weak interactions or the disappearance of stability factors, resulting in improved dynamics of active site residues in the cold. These enzymes are already used in many biotechnological applications requiring high activity at mild temperatures or fast heat-inactivation rate. Several open questions in the field are also highlighted.
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Affiliation(s)
- Georges Feller
- Laboratory of Biochemistry, Centre for Protein Engineering, Institute of Chemistry, University of Liège, B6a, 4000 Liège, Belgium
- *Georges Feller:
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