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Cavalheiro GF, Costa ACDA, Garbin ADEP, Silva GADA, Garcia NFL, Paz MFDA, Fonseca GG, Leite RSR. Catalytic properties of amylases produced by Cunninghamella echinulata and Rhizopus microsporus. AN ACAD BRAS CIENC 2023; 95:e20230187. [PMID: 37909570 DOI: 10.1590/0001-3765202320230187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/02/2023] [Indexed: 11/03/2023] Open
Abstract
The present work aimed to characterize and compare the catalytic properties of amylases from Cunninghamella echinulata and Rhizopus microsporus. The highest production of amylase by C. echinulata, 234.94 U g-1 of dry substrate (or 23.49 U mL-1), was obtained using wheat bran as a substrate, with 50-55% initial moisture and kept at 28 °C for 48 h. The highest production of amylases by R. microsporus, 224.85 U g-1 of dry substrate (or 22.48 U mL-1), was obtained cultivating wheat bran with 65% initial moisture at 45 °C for 24 h. The optimal activity of the amylases was observed at pH 5.0 at 60 °C for C. echinulata enzymes and at pH 4.5 at 65 °C for R. microsporus. The amylases produced by C. echinulata were stable at pH 4.0-8.0, while the R. microsporus enzymes were stable at pH 4.0-10.0. The amylases produced by C. echinulata remained stable for 1 h at 50 °C and the R. microsporus amylases maintained catalytic activity for 1 h at 55 °C. The enzymatic extracts of both fungi hydrolyzed starches from different plant sources and showed potential for liquefaction of starch, however the amylolytic complex of C. echinulata exhibited greater saccharifying potential.
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Affiliation(s)
- Gabriela F Cavalheiro
- Universidade Federal da Grande Dourados (UFGD), Faculdade de Ciências Biológicas e Ambientais (FCBA), Laboratório de Enzimologia e Processos Fermentativos (FEPFER), Rodovia Dourados/Itahum, Km 12, 79804-970 Dourados, MS, Brazil
| | - Ana Carolina DA Costa
- Universidade Federal da Grande Dourados (UFGD), Faculdade de Ciências Biológicas e Ambientais (FCBA), Laboratório de Enzimologia e Processos Fermentativos (FEPFER), Rodovia Dourados/Itahum, Km 12, 79804-970 Dourados, MS, Brazil
| | - Andreza DE Paula Garbin
- Universidade Federal da Grande Dourados (UFGD), Faculdade de Ciências Biológicas e Ambientais (FCBA), Laboratório de Enzimologia e Processos Fermentativos (FEPFER), Rodovia Dourados/Itahum, Km 12, 79804-970 Dourados, MS, Brazil
| | - Geisa A DA Silva
- Universidade Federal da Grande Dourados (UFGD), Faculdade de Ciências Biológicas e Ambientais (FCBA), Laboratório de Enzimologia e Processos Fermentativos (FEPFER), Rodovia Dourados/Itahum, Km 12, 79804-970 Dourados, MS, Brazil
| | - Nayara Fernanda L Garcia
- Universidade Federal da Grande Dourados (UFGD), Faculdade de Ciências Biológicas e Ambientais (FCBA), Laboratório de Enzimologia e Processos Fermentativos (FEPFER), Rodovia Dourados/Itahum, Km 12, 79804-970 Dourados, MS, Brazil
| | - Marcelo F DA Paz
- Universidade Federal da Grande Dourados (UFGD), Faculdade de Ciências Biológicas e Ambientais (FCBA), Laboratório de Enzimologia e Processos Fermentativos (FEPFER), Rodovia Dourados/Itahum, Km 12, 79804-970 Dourados, MS, Brazil
| | - Gustavo G Fonseca
- University of Akureyri, Faculty of Natural Resource Sciences, School of Business and Science, Borgir v. Norðurslóð, 600 Akureyri, Iceland
| | - Rodrigo S R Leite
- Universidade Federal da Grande Dourados (UFGD), Faculdade de Ciências Biológicas e Ambientais (FCBA), Laboratório de Enzimologia e Processos Fermentativos (FEPFER), Rodovia Dourados/Itahum, Km 12, 79804-970 Dourados, MS, Brazil
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2
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López-Romero JC, García-Dávila J, Peña-Ramos EA, González-Ríos H, Valenzuela-Melendres M, Osoria M, Juneja VK. Effect of Citral on the Thermal Inactivation of Escherichia coli O104:H4 in Ground Beef. J Food Prot 2022; 85:1635-1639. [PMID: 35776056 DOI: 10.4315/jfp-22-086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/24/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT The objective of the present study was to analyze the combined effect of heat treatment (55 to 62.5°C) and citral (0 to 3%) on the heat resistance of Escherichia coli O104:H4 inoculated into ground beef. Inoculated meat packages were immersed in a circulating water bath stabilized at 55, 57.5, 60, or 62.5°C for various times. The surviving microbial cells were counted after culture on tryptic soy agar. A factorial design (4 × 4) was used to analyze the effects and interaction of heat treatment and citral. Heat and citral promoted E. coli O104:H4 thermal inactivation, suggesting a synergistic effect. At 55°C, the incorporation of citral at 1, 2, and 3% decreased D-values (control = 42.75 min) by 85, 89, and 91%, respectively (P < 0.05). A citral concentration-dependent effect (P < 0.05) also was noted at other evaluated temperatures. These findings could be of value to the food industry for designing a safe thermal process for inactivating E. coli O104:H4 in ground beef under similar thermal inactivation conditions. HIGHLIGHTS
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Affiliation(s)
| | - Jimena García-Dávila
- LIPMAN Family Farms, Boulevard Antonio Quiroga 107i, 83174 Hermosillo, Sonora, México
| | - Etna Aida Peña-Ramos
- Coordinación de Tecnología de Alimentos de Origen Animal, Centro de Investigación en Alimentación y Desarrollo, A.C. Carretera Gustavo Enrique Astiazarán Rosas No. 46, 83304 Hermosillo, Sonora, México
| | - Humberto González-Ríos
- Coordinación de Tecnología de Alimentos de Origen Animal, Centro de Investigación en Alimentación y Desarrollo, A.C. Carretera Gustavo Enrique Astiazarán Rosas No. 46, 83304 Hermosillo, Sonora, México
| | - Martín Valenzuela-Melendres
- Coordinación de Tecnología de Alimentos de Origen Animal, Centro de Investigación en Alimentación y Desarrollo, A.C. Carretera Gustavo Enrique Astiazarán Rosas No. 46, 83304 Hermosillo, Sonora, México
| | - Marangeli Osoria
- U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, Pennsylvania 19308, USA
| | - Vijay K Juneja
- U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, Pennsylvania 19308, USA
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Ahmad A, Rahamtullah, Mishra R. Structural and functional adaptation in extremophilic microbial α-amylases. Biophys Rev 2022; 14:499-515. [PMID: 35528036 PMCID: PMC9043155 DOI: 10.1007/s12551-022-00931-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 01/12/2022] [Indexed: 01/26/2023] Open
Abstract
Maintaining stable native conformation of a protein under a given ecological condition is the prerequisite for survival of organisms. Extremophilic bacteria and archaea have evolved to adapt under extreme conditions of temperature, pH, salt, and pressure. Molecular adaptations of proteins under these conditions are essential for their survival. These organisms have the capability to maintain stable, native conformations of proteins under extreme conditions. The enzymes produced by the extremophiles are also known as extremozyme, which are used in several industries. Stability and functionality of extremozymes under varying temperature, pH, and solvent conditions are the most desirable requirement of industry. α-Amylase is one of the most important enzymes used in food, pharmaceutical, textile, and detergent industries. This enzyme is produced by diverse microorganisms including various extremophiles. Therefore, understanding its stability is important from fundamental as well as an applied point of view. Each class of extremophiles has a distinctive set of dominant non-covalent interactions which are important for their stability. Static information obtained by comparative analysis of amino acid sequence and atomic resolution structure provides information on the prevalence of particular amino acids or a group of non-covalent interactions. Protein folding studies give the information about thermodynamic and kinetic stability in order to understand dynamic aspect of molecular adaptations. In this review, we have summarized information on amino acid sequence, structure, stability, and adaptability of α-amylases from different classes of extremophiles.
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Affiliation(s)
- Aziz Ahmad
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110,067 India
| | - Rahamtullah
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110,067 India
| | - Rajesh Mishra
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110,067 India
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Sorokina I, Mushegian AR, Koonin EV. Is Protein Folding a Thermodynamically Unfavorable, Active, Energy-Dependent Process? Int J Mol Sci 2022; 23:521. [PMID: 35008947 PMCID: PMC8745595 DOI: 10.3390/ijms23010521] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 02/04/2023] Open
Abstract
The prevailing current view of protein folding is the thermodynamic hypothesis, under which the native folded conformation of a protein corresponds to the global minimum of Gibbs free energy G. We question this concept and show that the empirical evidence behind the thermodynamic hypothesis of folding is far from strong. Furthermore, physical theory-based approaches to the prediction of protein folds and their folding pathways so far have invariably failed except for some very small proteins, despite decades of intensive theory development and the enormous increase of computer power. The recent spectacular successes in protein structure prediction owe to evolutionary modeling of amino acid sequence substitutions enhanced by deep learning methods, but even these breakthroughs provide no information on the protein folding mechanisms and pathways. We discuss an alternative view of protein folding, under which the native state of most proteins does not occupy the global free energy minimum, but rather, a local minimum on a fluctuating free energy landscape. We further argue that ΔG of folding is likely to be positive for the majority of proteins, which therefore fold into their native conformations only through interactions with the energy-dependent molecular machinery of living cells, in particular, the translation system and chaperones. Accordingly, protein folding should be modeled as it occurs in vivo, that is, as a non-equilibrium, active, energy-dependent process.
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Affiliation(s)
| | - Arcady R. Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, VA 22314, USA;
- Clare Hall College, University of Cambridge, Cambridge CB3 9AL, UK
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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Modulating Glycoside Hydrolase Activity between Hydrolysis and Transfer Reactions Using an Evolutionary Approach. Molecules 2021; 26:molecules26216586. [PMID: 34770995 PMCID: PMC8587830 DOI: 10.3390/molecules26216586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 01/02/2023] Open
Abstract
The proteins within the CAZy glycoside hydrolase family GH13 catalyze the hydrolysis of polysaccharides such as glycogen and starch. Many of these enzymes also perform transglycosylation in various degrees, ranging from secondary to predominant reactions. Identifying structural determinants associated with GH13 family reaction specificity is key to modifying and designing enzymes with increased specificity towards individual reactions for further applications in industrial, chemical, or biomedical fields. This work proposes a computational approach for decoding the determinant structural composition defining the reaction specificity. This method is based on the conservation of coevolving residues in spatial contacts associated with reaction specificity. To evaluate the algorithm, mutants of α-amylase (TmAmyA) and glucanotransferase (TmGTase) from Thermotoga maritima were constructed to modify the reaction specificity. The K98P/D99A/H222Q variant from TmAmyA doubled the transglycosydation/hydrolysis (T/H) ratio while the M279N variant from TmGTase increased the hydrolysis/transglycosidation ratio five-fold. Molecular dynamic simulations of the variants indicated changes in flexibility that can account for the modified T/H ratio. An essential contribution of the presented computational approach is its capacity to identify residues outside of the active center that affect the reaction specificity.
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Lecocq M, Groussin M, Gouy M, Brochier-Armanet C. The Molecular Determinants of Thermoadaptation: Methanococcales as a Case Study. Mol Biol Evol 2021; 38:1761-1776. [PMID: 33450027 PMCID: PMC8097290 DOI: 10.1093/molbev/msaa312] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Previous reports have shown that environmental temperature impacts proteome evolution in Bacteria and Archaea. However, it is unknown whether thermoadaptation mainly occurs via the sequential accumulation of substitutions, massive horizontal gene transfers, or both. Measuring the real contribution of amino acid substitution to thermoadaptation is challenging, because of confounding environmental and genetic factors (e.g., pH, salinity, genomic G + C content) that also affect proteome evolution. Here, using Methanococcales, a major archaeal lineage, as a study model, we show that optimal growth temperature is the major factor affecting variations in amino acid frequencies of proteomes. By combining phylogenomic and ancestral sequence reconstruction approaches, we disclose a sequential substitutional scheme in which lysine plays a central role by fine tuning the pool of arginine, serine, threonine, glutamine, and asparagine, whose frequencies are strongly correlated with optimal growth temperature. Finally, we show that colonization to new thermal niches is not associated with high amounts of horizontal gene transfers. Altogether, although the acquisition of a few key proteins through horizontal gene transfer may have favored thermoadaptation in Methanococcales, our findings support sequential amino acid substitutions as the main factor driving thermoadaptation.
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Affiliation(s)
- Michel Lecocq
- Laboratoire de Biométrie et Biologie Évolutive, Université de Lyon, Université Lyon 1, CNRS, UMR5558, Villeurbanne, France
| | - Mathieu Groussin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Manolo Gouy
- Laboratoire de Biométrie et Biologie Évolutive, Université de Lyon, Université Lyon 1, CNRS, UMR5558, Villeurbanne, France
| | - Céline Brochier-Armanet
- Laboratoire de Biométrie et Biologie Évolutive, Université de Lyon, Université Lyon 1, CNRS, UMR5558, Villeurbanne, France
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7
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Evolution of Protein Structure and Stability in Global Warming. Int J Mol Sci 2020; 21:ijms21249662. [PMID: 33352933 PMCID: PMC7767258 DOI: 10.3390/ijms21249662] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
This review focuses on the molecular signatures of protein structures in relation to evolution and survival in global warming. It is based on the premise that the power of evolutionary selection may lead to thermotolerant organisms that will repopulate the planet and continue life in general, but perhaps with different kinds of flora and fauna. Our focus is on molecular mechanisms, whereby known examples of thermoresistance and their physicochemical characteristics were noted. A comparison of interactions of diverse residues in proteins from thermophilic and mesophilic organisms, as well as reverse genetic studies, revealed a set of imprecise molecular signatures that pointed to major roles of hydrophobicity, solvent accessibility, disulfide bonds, hydrogen bonds, ionic and π-electron interactions, and an overall condensed packing of the higher-order structure, especially in the hydrophobic regions. Regardless of mutations, specialized protein chaperones may play a cardinal role. In evolutionary terms, thermoresistance to global warming will likely occur in stepwise mutational changes, conforming to the molecular signatures, such that each "intermediate" fits a temporary niche through punctuated equilibrium, while maintaining protein functionality. Finally, the population response of different species to global warming may vary substantially, and, as such, some may evolve while others will undergo catastrophic mass extinction.
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Becker HF, L'Hermitte-Stead C, Myllykallio H. Diversity of circular RNAs and RNA ligases in archaeal cells. Biochimie 2019; 164:37-44. [PMID: 31212038 DOI: 10.1016/j.biochi.2019.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/13/2019] [Indexed: 01/16/2023]
Abstract
Circular RNAs (circRNAs) differ structurally from other types of RNAs and are resistant against exoribonucleases. Although they have been detected in all domains of life, it remains unclear how circularization affects or changes functions of these ubiquitous nucleic acid circles. The biogenesis of circRNAs has been mostly described as a backsplicing event, but in archaea, where RNA splicing is a rare phenomenon, a second pathway for circRNA formation was described in the cases of rRNAs processing, tRNA intron excision, and Box C/D RNAs formation. At least in some archaeal species, circRNAs are formed by a ligation step catalyzed by an atypic homodimeric RNA ligase belonging to Rnl3 family. In this review, we describe archaeal circRNA transcriptomes obtained using high throughput sequencing technologies on Sulfolobus solfataricus, Pyrococcus abyssi and Nanoarchaeum equitans cells. We will discuss the distribution of circular RNAs among the different RNA categories and present the Rnl3 ligase family implicated in the circularization activity. Special focus is given for the description of phylogenetic distributions, protein structures, and substrate specificities of archaeal RNA ligases.
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Affiliation(s)
- Hubert F Becker
- LOB, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128, Palaiseau, France; Sorbonne Université, Faculté des Sciences et Ingénierie, 75005, Paris, France.
| | | | - Hannu Myllykallio
- LOB, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128, Palaiseau, France
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Ikeda M, Ishima Y, Chuang VTG, Sakai M, Osafune H, Ando H, Shimizu T, Okuhira K, Watanabe H, Maruyama T, Otagiri M, Akaike T, Ishida T. Distribution of Polysulfide in Human Biological Fluids and Their Association with Amylase and Sperm Activities. Molecules 2019; 24:molecules24091689. [PMID: 31052207 PMCID: PMC6539915 DOI: 10.3390/molecules24091689] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 04/20/2019] [Accepted: 04/25/2019] [Indexed: 02/02/2023] Open
Abstract
Intracellular polysulfide could regulate the redox balance via its anti-oxidant activity. However, the existence of polysulfide in biological fluids still remains unknown. Recently, we developed a quantitative analytical method for polysulfide and discovered that polysulfide exists in plasma and responds to oxidative stress. In this study, we confirmed the presence of polysulfide in other biological fluids, such as semen and nasal discharge. The levels of polysulfide in these biological fluids from healthy volunteers (n = 9) with identical characteristics were compared. Additionally, the circadian rhythm of plasma polysulfide was also investigated. The polysulfide levels detected from nasal discharge and seminal fluid were approximately 400 and 600 μM, respectively. No correlation could be found between plasma polysulfide and the polysulfide levels of tear, saliva, and nasal discharge. On the other hand, seminal polysulfide was positively correlated with plasma polysulfide, and almost all polysulfide contained in semen was found in seminal fluid. Intriguingly, saliva and seminal polysulfide strongly correlated with salivary amylase and sperm activities, respectively. These results provide a foundation for scientific breakthroughs in various research areas like infertility and the digestive system process.
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Affiliation(s)
- Mayumi Ikeda
- Department of Pharmacokinetics and Biopharmaceutics, Institute of Biomedical Sciences, Tokushima University, 1-78-1, Sho-machi, Tokushima 770-8505, Japan.
| | - Yu Ishima
- Department of Pharmacokinetics and Biopharmaceutics, Institute of Biomedical Sciences, Tokushima University, 1-78-1, Sho-machi, Tokushima 770-8505, Japan.
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya Selangor 47500, Malaysia.
| | - Victor T G Chuang
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya Selangor 47500, Malaysia.
| | - Maki Sakai
- Department of Pharmacokinetics and Biopharmaceutics, Institute of Biomedical Sciences, Tokushima University, 1-78-1, Sho-machi, Tokushima 770-8505, Japan.
| | - Hiroki Osafune
- Department of Pharmacokinetics and Biopharmaceutics, Institute of Biomedical Sciences, Tokushima University, 1-78-1, Sho-machi, Tokushima 770-8505, Japan.
| | - Hidenori Ando
- Department of Pharmacokinetics and Biopharmaceutics, Institute of Biomedical Sciences, Tokushima University, 1-78-1, Sho-machi, Tokushima 770-8505, Japan.
| | - Taro Shimizu
- Department of Pharmacokinetics and Biopharmaceutics, Institute of Biomedical Sciences, Tokushima University, 1-78-1, Sho-machi, Tokushima 770-8505, Japan.
| | - Keiichiro Okuhira
- Department of Pharmacokinetics and Biopharmaceutics, Institute of Biomedical Sciences, Tokushima University, 1-78-1, Sho-machi, Tokushima 770-8505, Japan.
| | - Hiroshi Watanabe
- Department of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Kumamoto 862-0973, Japan.
| | - Toru Maruyama
- Department of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Kumamoto 862-0973, Japan.
| | - Masaki Otagiri
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan.
| | - Takaaki Akaike
- Department of Environmental Health Sciences and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan.
| | - Tatsuhiro Ishida
- Department of Pharmacokinetics and Biopharmaceutics, Institute of Biomedical Sciences, Tokushima University, 1-78-1, Sho-machi, Tokushima 770-8505, Japan.
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Liao SM, Liang G, Zhu J, Lu B, Peng LX, Wang QY, Wei YT, Zhou GP, Huang RB. Influence of Calcium Ions on the Thermal Characteristics of α-amylase from Thermophilic Anoxybacillus sp. GXS-BL. Protein Pept Lett 2019; 26:148-157. [PMID: 30652633 PMCID: PMC6416487 DOI: 10.2174/0929866526666190116162958] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/07/2019] [Accepted: 01/08/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND α-Amylases are starch-degrading enzymes and used widely, the study on thermostability of α-amylase is a central requirement for its application in life science and biotechnology. OBJECTIVE In this article, our motivation is to study how the effect of Ca2+ ions on the structure and thermal characterization of α-amylase (AGXA) from thermophilic Anoxybacillus sp.GXS-BL. METHODS α-Amylase activity was assayed with soluble starch as the substrate, and the amount of sugar released was determined by DNS method. For AGXA with calcium ions and without calcium ions, optimum temperature (Topt), half-inactivation temperature (T50) and thermal inactivation (halflife, t1/2) was evaluated. The thermal denaturation of the enzymes was determined by DSC and CD methods. 3D structure of AGXA was homology modeled with α-amylase (5A2A) as the template. RESULTS With calcium ions, the values of Topt, T50, t1/2, Tm and ΔH in AGXA were significantly higher than those of AGXA without calcium ions, showing calcium ions had stabilizing effects on α-amylase structure with the increased temperature. Based on DSC measurements AGXA underwent thermal denaturation by adopting two-state irreversible unfolding processes. Based on the CD spectra, AGXA without calcium ions exhibited two transition states upon unfolding, including α- helical contents increasing, and the transition from α-helices to β-sheet structures, which was obviously different in AGXA with Ca2+ ions, and up to 4 Ca2+ ions were located on the inter-domain or intra-domain regions according to the modeling structure. CONCLUSION These results reveal that Ca2+ ions have pronounced influences on the thermostability of AGXA structure.
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Affiliation(s)
| | | | | | | | | | | | | | - Guo-Ping Zhou
- Address correspondence to these authors at the Department of Bioengineering, College of Life Science and Technology, Guangxi University, Nanning, 530004, China; E-mail: , Gordon Life Science Institute, 53 South Cottage Road Belmont, MA, 02478, USA; Tel/Fax: +1-9199875774/ +1-9195215550; E-mail:
| | - Ri-Bo Huang
- Address correspondence to these authors at the Department of Bioengineering, College of Life Science and Technology, Guangxi University, Nanning, 530004, China; E-mail: , Gordon Life Science Institute, 53 South Cottage Road Belmont, MA, 02478, USA; Tel/Fax: +1-9199875774/ +1-9195215550; E-mail:
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11
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Morais TPD, Barbosa PMG, Garcia NFL, Rosa-Garzon NGD, Fonseca GG, Paz MFD, Cabral H, Leite RSR. Catalytic and thermodynamic properties of β-glucosidases produced by Lichtheimia corymbifera and Byssochlamys spectabilis. Prep Biochem Biotechnol 2018; 48:777-786. [DOI: 10.1080/10826068.2018.1509083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Tobias Pereira de Morais
- Laboratory of Enzymology and Fermentation Processes, Faculty of Biological and Environmental Sciences, Federal University of Grande Dourados (FCBA/UFGD), Dourados, MS, Brazil
| | - Paula Mirella Gomes Barbosa
- Laboratory of Enzymology and Fermentation Processes, Faculty of Biological and Environmental Sciences, Federal University of Grande Dourados (FCBA/UFGD), Dourados, MS, Brazil
| | - Nayara Fernanda Lisboa Garcia
- Laboratory of Enzymology and Fermentation Processes, Faculty of Biological and Environmental Sciences, Federal University of Grande Dourados (FCBA/UFGD), Dourados, MS, Brazil
| | - Nathália Gonsales da Rosa-Garzon
- Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP Brazil
| | - Gustavo Graciano Fonseca
- Laboratory of Bioengineering, Faculty of Biological and Environmental Sciences, Federal University of Grande Dourados (FCBA/UFGD), Dourados, MS, Brazil
| | - Marcelo Fossa da Paz
- Laboratory of Enzymology and Fermentation Processes, Faculty of Biological and Environmental Sciences, Federal University of Grande Dourados (FCBA/UFGD), Dourados, MS, Brazil
| | - Hamilton Cabral
- Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP Brazil
| | - Rodrigo Simões Ribeiro Leite
- Laboratory of Enzymology and Fermentation Processes, Faculty of Biological and Environmental Sciences, Federal University of Grande Dourados (FCBA/UFGD), Dourados, MS, Brazil
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Sammond DW, Kastelowitz N, Donohoe BS, Alahuhta M, Lunin VV, Chung D, Sarai NS, Yin H, Mittal A, Himmel ME, Guss AM, Bomble YJ. An iterative computational design approach to increase the thermal endurance of a mesophilic enzyme. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:189. [PMID: 30002729 PMCID: PMC6036693 DOI: 10.1186/s13068-018-1178-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 06/18/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND Strategies for maximizing the microbial production of bio-based chemicals and fuels include eliminating branched points to streamline metabolic pathways. While this is often achieved by removing key enzymes, the introduction of nonnative enzymes can provide metabolic shortcuts, bypassing branched points to decrease the production of undesired side-products. Pyruvate decarboxylase (PDC) can provide such a shortcut in industrially promising thermophilic organisms; yet to date, this enzyme has not been found in any thermophilic organism. Incorporating nonnative enzymes into host organisms can be challenging in cases such as this, where the enzyme has evolved in a very different environment from that of the host. RESULTS In this study, we use computational protein design to engineer the Zymomonas mobilis PDC to resist thermal denaturation at the growth temperature of a thermophilic host. We generate thirteen PDC variants using the Rosetta protein design software. We measure thermal stability of the wild-type PDC and PDC variants using circular dichroism. We then measure and compare enzyme endurance for wild-type PDC with the PDC variants at an elevated temperature of 60 °C (thermal endurance) using differential interference contrast imaging. CONCLUSIONS We find that increases in melting temperature (Tm) do not directly correlate with increases in thermal endurance at 60 °C. We also do not find evidence that any individual mutation or design approach is the major contributor to the most thermostable PDC variant. Rather, remarkable cooperativity among sixteen thermostabilizing mutations is key to rationally designing a PDC with significantly enhanced thermal endurance. These results suggest a generalizable iterative computational protein design approach to improve thermal stability and endurance of target enzymes.
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Affiliation(s)
- Deanne W. Sammond
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Noah Kastelowitz
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, CO 80309 USA
| | - Bryon S. Donohoe
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Vladimir V. Lunin
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Daehwan Chung
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Nicholas S. Sarai
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Hang Yin
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, CO 80309 USA
| | - Ashutosh Mittal
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Adam M. Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
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13
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Abstract
A half century of studying protein folding in vitro and modeling it in silico has not provided us with a reliable computational method to predict the native conformations of proteins de novo, let alone identify the intermediates on their folding pathways. In this Opinion article, we suggest that the reason for this impasse is the over-reliance on current physical models of protein folding that are based on the assumption that proteins are able to fold spontaneously without assistance. These models arose from studies conducted in vitro on a biased sample of smaller, easier-to-isolate proteins, whose native structures appear to be thermodynamically stable. Meanwhile, the vast empirical data on the majority of larger proteins suggests that once these proteins are completely denatured in vitro, they cannot fold into native conformations without assistance. Moreover, they tend to lose their native conformations spontaneously and irreversibly in vitro, and therefore such conformations must be metastable. We propose a model of protein folding that is based on the notion that the folding of all proteins in the cell is mediated by the actions of the "protein folding machine" that includes the ribosome, various chaperones, and other components involved in co-translational or post-translational formation, maintenance and repair of protein native conformations in vivo. The most important and universal component of the protein folding machine consists of the ribosome in complex with the welcoming committee chaperones. The concerted actions of molecular machinery in the ribosome peptidyl transferase center, in the exit tunnel, and at the surface of the ribosome result in the application of mechanical and other forces to the nascent peptide, reducing its conformational entropy and possibly creating strain in the peptide backbone. The resulting high-energy conformation of the nascent peptide allows it to fold very fast and to overcome high kinetic barriers along the folding pathway. The early folding intermediates in vivo are stabilized by interactions with the ribosome and welcoming committee chaperones and would not be able to exist in vitro in the absence of such cellular components. In vitro experiments that unfold proteins by heat or chemical treatment produce denaturation ensembles that are very different from folding intermediates in vivo and therefore have very limited use in reconstructing the in vivo folding pathways. We conclude that computational modeling of protein folding should deemphasize the notion of unassisted thermodynamically controlled folding, and should focus instead on the step-by-step reverse engineering of the folding process as it actually occurs in vivo. REVIEWERS This article was reviewed by Eugene Koonin and Frank Eisenhaber.
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14
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Establishment of Aromatic Pairs at the Surface of Chondroitinase ABC I: the Effect on Activity and Stability. Appl Biochem Biotechnol 2018; 186:358-370. [DOI: 10.1007/s12010-018-2741-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 03/18/2018] [Indexed: 10/17/2022]
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15
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He L, Park SH, Hai Dang ND, Duong HX, Duong TPC, Tran PL, Park JT, Ni L, Park KH. Characterization and thermal inactivation kinetics of highly thermostable ramie leaf β-amylase. Enzyme Microb Technol 2017; 101:17-23. [DOI: 10.1016/j.enzmictec.2017.02.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 02/19/2017] [Accepted: 02/24/2017] [Indexed: 11/29/2022]
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16
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Gao Y, Huang M, Sun X, Zhang X, Zhang Y, Zhou X, Cai M. Single-site mutation of C363G or N463T strengthens thermostability improvement of IG181–182 deleted acidic α-amylase from deep-sea thermophile Geobacillus sp. FOOD BIOTECHNOL 2017. [DOI: 10.1080/08905436.2016.1276462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Yanyun Gao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Mengmeng Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xiaoyue Sun
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xiaoxu Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, China
| | - Xiangshan Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Menghao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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17
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Biundo A, Steinkellner G, Gruber K, Spreitzhofer T, Ribitsch D, Guebitz GM. Engineering of the zinc-binding domain of an esterase from Clostridium botulinum towards increased activity on polyesters. Catal Sci Technol 2017. [DOI: 10.1039/c7cy00168a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Variants of the zinc-binding domain of Clostridium botulinum EstA (Cbotu_EstA) release more building blocks (Ta and BTa) from the aromatic/aliphatic copolyester poly(butylene adipate-co-terephthalate) (PBAT).
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Affiliation(s)
- Antonino Biundo
- Austrian Centre for Industrial Biotechnology (ACIB)
- Tulln an der Donau
- Austria
| | - Georg Steinkellner
- Austrian Centre for Industrial Biotechnology (ACIB)
- Tulln an der Donau
- Austria
| | - Karl Gruber
- Austrian Centre for Industrial Biotechnology (ACIB)
- Tulln an der Donau
- Austria
- Institute of Molecular Bioscience
- University of Graz
| | | | - Doris Ribitsch
- Austrian Centre for Industrial Biotechnology (ACIB)
- Tulln an der Donau
- Austria
- Institute of Environmental Biotechnology
- University of Natural Resources and Life Sciences (BOKU)
| | - Georg M. Guebitz
- Institute of Environmental Biotechnology
- University of Natural Resources and Life Sciences (BOKU)
- Tulln an der Donau
- Austria
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18
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Empirical manipulation of the thermoinactivation kinetics of Bacillus amyloliquefaciens and Bacillus licheniformis α-amylases for thermal process evaluations. INNOV FOOD SCI EMERG 2016. [DOI: 10.1016/j.ifset.2016.10.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Unfolding of chondroitinase ABC Ι is dependent on thermodynamic driving force by kinetically rate constant-amplitude compensation: A stopped-flow fluorescence study. Enzyme Microb Technol 2016; 93-94:200-206. [DOI: 10.1016/j.enzmictec.2016.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 08/24/2016] [Accepted: 09/02/2016] [Indexed: 11/18/2022]
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20
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Marine Microbiological Enzymes: Studies with Multiple Strategies and Prospects. Mar Drugs 2016; 14:md14100171. [PMID: 27669268 PMCID: PMC5082319 DOI: 10.3390/md14100171] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/04/2016] [Accepted: 09/14/2016] [Indexed: 11/16/2022] Open
Abstract
Marine microorganisms produce a series of promising enzymes that have been widely used or are potentially valuable for our daily life. Both classic and newly developed biochemistry technologies have been broadly used to study marine and terrestrial microbiological enzymes. In this brief review, we provide a research update and prospects regarding regulatory mechanisms and related strategies of acyl-homoserine lactones (AHL) lactonase, which is an important but largely unexplored enzyme. We also detail the status and catalytic mechanism of the main types of polysaccharide-degrading enzymes that broadly exist among marine microorganisms but have been poorly explored. In order to facilitate understanding, the regulatory and synthetic biology strategies of terrestrial microorganisms are also mentioned in comparison. We anticipate that this review will provide an outline of multiple strategies for promising marine microbial enzymes and open new avenues for the exploration, engineering and application of various enzymes.
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21
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Crystal Structures of Two Isozymes of Citrate Synthase from Sulfolobus tokodaii Strain 7. Biochem Res Int 2016; 2016:7560919. [PMID: 27656296 PMCID: PMC5021468 DOI: 10.1155/2016/7560919] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/17/2016] [Indexed: 11/17/2022] Open
Abstract
Thermoacidophilic archaeon Sulfolobus tokodaii strain 7 has two citrate synthase genes (ST1805-CS and ST0587-CS) in the genome with 45% sequence identity. Because they exhibit similar optimal temperatures of catalytic activity and thermal inactivation profiles, we performed structural comparisons between these isozymes to elucidate adaptation mechanisms to high temperatures in thermophilic CSs. The crystal structures of ST1805-CS and ST0587-CS were determined at 2.0 Å and 2.7 Å resolutions, respectively. Structural comparison reveals that both of them are dimeric enzymes composed of two identical subunits, and these dimeric structures are quite similar to those of citrate synthases from archaea and eubacteria. ST0587-CS has, however, 55 ion pairs within whole dimer structure, while having only 36 in ST1805-CS. Although the number and distributions of ion pairs are distinct from each other, intersubunit ion pairs between two domains of each isozyme are identical especially in interterminal region. Because the location and number of ion pairs are in a trend with other CSs from thermophilic microorganisms, the factors responsible for thermal adaptation of ST-CS isozymes are characterized by ion pairs in interterminal region.
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22
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Mehta D, Satyanarayana T. Bacterial and Archaeal α-Amylases: Diversity and Amelioration of the Desirable Characteristics for Industrial Applications. Front Microbiol 2016; 7:1129. [PMID: 27516755 PMCID: PMC4963412 DOI: 10.3389/fmicb.2016.01129] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/06/2016] [Indexed: 11/13/2022] Open
Abstract
Industrial enzyme market has been projected to reach US$ 6.2 billion by 2020. Major reasons for continuous rise in the global sales of microbial enzymes are because of increase in the demand for consumer goods and biofuels. Among major industrial enzymes that find applications in baking, alcohol, detergent, and textile industries are α-amylases. These are produced by a variety of microbes, which randomly cleave α-1,4-glycosidic linkages in starch leading to the formation of limit dextrins. α-Amylases from different microbial sources vary in their properties, thus, suit specific applications. This review focuses on the native and recombinant α-amylases from bacteria and archaea, their production and the advancements in the molecular biology, protein engineering and structural studies, which aid in ameliorating their properties to suit the targeted industrial applications.
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Affiliation(s)
- Deepika Mehta
- Department of Microbiology, University of Delhi New Delhi, India
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23
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Inactivation Kinetics of the Most Baro-Resistant Enzyme in High Pressure Processed Litchi-Based Mixed Fruit Beverage. FOOD BIOPROCESS TECH 2016. [DOI: 10.1007/s11947-016-1702-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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24
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Li Z, Duan X, Wu J. Improving the thermostability and enhancing the Ca(2+) binding of the maltohexaose-forming α-amylase from Bacillus stearothermophilus. J Biotechnol 2016; 222:65-72. [PMID: 26869314 DOI: 10.1016/j.jbiotec.2016.02.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 02/05/2016] [Indexed: 11/26/2022]
Abstract
The thermostability of the maltohexaose-forming α-amylase from Bacillus stearothermophilus (AmyMH) without added Ca(2+) was improved through structure-based rational design in this study. Through comparison of a homologous model structure of AmyMH with the crystal structure of the thermostable α-amylase from Bacillus licheniformis, Ser242, which located at the beginning of fourth α-helix of the central (β/α)8 barrel was selected for mutation to improve thermostability. In addition, an amide-containing side chain (Asn193) and a loop in domain B (ΔIG mutation), which have been proven to be important for thermostability in corresponding position of other α-amylases, were also investigated. Five mutants carrying the mutations ΔIG, N193F, S242A, ΔIG/N193F, and ΔIG/N193F/S242A were generated and their proteins characterized. The most thermostable mutant protein, ΔIG/N193F/S242A, exhibited a 26-fold improvement in half-life at 95°C compared to the wild-type enzyme without added Ca(2+). Mutant ΔIG/N193F/S242A also exhibited substantially better activity and stability in the presence of the chelator EDTA, demonstrating enhanced Ca(2+) binding. These results suggest that mutant ΔIG/N193F/S242A has potential for use in the industrial liquefaction of starch.
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Affiliation(s)
- Zhu Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Xuguo Duan
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China.
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25
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Asad S, Dastgheib SMM, Khajeh K. Construction of a horseradish peroxidase resistant toward hydrogen peroxide by saturation mutagenesis. Biotechnol Appl Biochem 2015; 63:789-794. [DOI: 10.1002/bab.1437] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 08/18/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Sedigheh Asad
- Department of Biotechnology; College of Science; University of Tehran; Tehran Iran
| | | | - Khosro Khajeh
- Department of Biochemistry; Faculty of Biological Science; Tarbiat Modares University; Tehran Iran
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26
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Critical Role of a Loop at C-Terminal Domain on the Conformational Stability and Catalytic Efficiency of Chondroitinase ABC I. Mol Biotechnol 2015; 57:727-34. [DOI: 10.1007/s12033-015-9864-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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27
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Minten IJ, Abello N, Schooneveld-Bergmans MEF, van den Berg MA. Post-production modification of industrial enzymes. Appl Microbiol Biotechnol 2014; 98:6215-31. [PMID: 24903809 DOI: 10.1007/s00253-014-5799-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 04/23/2014] [Accepted: 04/27/2014] [Indexed: 12/24/2022]
Abstract
Industry has an increasing interest in the use of enzymes as environmentally friendly, highly efficient, and specific bio-catalysts. Enzymes have primarily evolved to function in aqueous environments at ambient temperature and pressure. These conditions however do not always correspond with industrial processes or applications, and only a small portion of all known enzymes are therefore suitable for industrial use. Protein engineering can sometimes be applied to convey more desirable properties to enzymes, such as increased stability, but is limited to the 20 naturally occurring amino acids or homologs thereof. Using post-production modification, which has the potential to combine desirable properties from the enzyme and the conjugated compounds, enzymes can be modified with both natural and synthetic molecules. This offers access to a myriad of possibilities for tuning the properties of enzymes. At this moment, however, the effects of post-production modification cannot yet be reliably predicted. The increasing number of applications will improve this so that the potential of this technology can be fully exploited. This review will focus on post-production modification of enzymes and its use and opportunities in industry.
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Affiliation(s)
- Inge J Minten
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands,
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28
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Park JT, Suwanto A, Tan I, Nuryanto T, Lukman R, Wang K, Jane JL. Molecular cloning and characterization of a thermostable α-amylase exhibiting an unusually high activity. Food Sci Biotechnol 2013. [DOI: 10.1007/s10068-014-0017-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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29
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Sharma A, Satyanarayana T. Structural and biochemical features of acidic α-amylase of Bacillus acidicola. Int J Biol Macromol 2013; 61:416-23. [DOI: 10.1016/j.ijbiomac.2013.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 08/03/2013] [Accepted: 08/06/2013] [Indexed: 11/28/2022]
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30
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Mohammadi M, Kashi MA, Zareian S, Mirshahi M, Khajeh K. Remarkable Improvement of Methylglyoxal Synthase Thermostability by His–His Interaction. Appl Biochem Biotechnol 2013; 172:157-67. [DOI: 10.1007/s12010-013-0404-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 07/17/2013] [Indexed: 12/01/2022]
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31
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Protein adaptations in archaeal extremophiles. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2013; 2013:373275. [PMID: 24151449 PMCID: PMC3787623 DOI: 10.1155/2013/373275] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 07/26/2013] [Accepted: 08/14/2013] [Indexed: 12/25/2022]
Abstract
Extremophiles, especially those in Archaea, have a myriad of adaptations that keep their cellular proteins stable and active under the extreme conditions in which they live. Rather than having one basic set of adaptations that works for all environments, Archaea have evolved separate protein features that are customized for each environment. We categorized the Archaea into three general groups to describe what is known about their protein adaptations: thermophilic, psychrophilic, and halophilic. Thermophilic proteins tend to have a prominent hydrophobic core and increased electrostatic interactions to maintain activity at high temperatures. Psychrophilic proteins have a reduced hydrophobic core and a less charged protein surface to maintain flexibility and activity under cold temperatures. Halophilic proteins are characterized by increased negative surface charge due to increased acidic amino acid content and peptide insertions, which compensates for the extreme ionic conditions. While acidophiles, alkaliphiles, and piezophiles are their own class of Archaea, their protein adaptations toward pH and pressure are less discernible. By understanding the protein adaptations used by archaeal extremophiles, we hope to be able to engineer and utilize proteins for industrial, environmental, and biotechnological applications where function in extreme conditions is required for activity.
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32
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Say R, Şenay RH, Biçen Ö, Ersöz A, Şişman Yılmaz F, Akgöl S, Denizli A. Polymeric amylase nanoparticles as a new semi-synthetic enzyme system for hydrolysis of starch. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2013; 33:1900-6. [DOI: 10.1016/j.msec.2012.12.053] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 10/06/2012] [Accepted: 12/16/2012] [Indexed: 01/28/2023]
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33
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Silva AM, Marçal SL, Vitorino R, Domingues MR, Domingues P. Characterization of in vitro protein oxidation using mass spectrometry: A time course study of oxidized alpha-amylase. Arch Biochem Biophys 2013; 530:23-31. [DOI: 10.1016/j.abb.2012.12.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 12/04/2012] [Accepted: 12/06/2012] [Indexed: 12/19/2022]
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34
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Nazari-Robati M, Khajeh K, Aminian M, Mollania N, Golestani A. Enhancement of thermal stability of chondroitinase ABC I by site-directed mutagenesis: An insight from Ramachandran plot. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:479-86. [DOI: 10.1016/j.bbapap.2012.11.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Revised: 11/05/2012] [Accepted: 11/09/2012] [Indexed: 10/27/2022]
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35
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Sabbaghian M, Ebrahim-Habibi A, Hosseinkhani S, Ghasemi A, Nemat-Gorgani M. Prevention of thermal aggregation of an allosteric protein by small molecules: Some mechanistic insights. Int J Biol Macromol 2011; 49:806-13. [DOI: 10.1016/j.ijbiomac.2011.07.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 07/21/2011] [Accepted: 07/21/2011] [Indexed: 12/18/2022]
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36
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Onaga S, Chinen K, Ito S, Taira T. Highly thermostable chitinase from pineapple: Cloning, expression, and enzymatic properties. Process Biochem 2011. [DOI: 10.1016/j.procbio.2010.11.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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37
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Investigating the structural and functional effects of mutating Asn glycosylation sites of horseradish peroxidase to Asp. Appl Biochem Biotechnol 2010; 164:454-63. [PMID: 21193964 DOI: 10.1007/s12010-010-9147-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 12/07/2010] [Indexed: 10/18/2022]
Abstract
Horseradish peroxidase (HRP) has long attracted intense research interest and is used in many biotechnological fields, including diagnostics, biosensors, and biocatalysis. Enhancement of HRP catalytic activity and/or stability would further increase its applications. One of the problems with heterologus expression of HRP especially in prokaryotic host is lack of glycosylation that affects it's stability toward H(2)O(2) and thermal inactivation. In this study, two asparagine residues which constitute two of the eight glycosylation sites in native HRP (Asn 13 and 268) with respectively 83% and 65% surface accessibility were substituted with aspartic acid in recombinant HRP. Both mutant proteins expressed in Escherichia coli showed increased stabilities against heat (increase in t (1/2) from 20 min in native rHRP to 32 and 67 min in N13D and N268D) and H(2)O(2) (up to threefold). Unexpectedly, despite the distance of the mutated positions from the active site, notable alterations in steady-state k (cat) and K (m) values occurred with phenol/4-aminoantipyrine as reducing substrate which might be due to conformational changes. No significant alteration in flexibility was detected by acrylamide quenching analyses, but ANS binding experiments purposed lesser binding of ANS to hydrophobic patches in mutated HRPs. Double mutation was non-additive and non-synergistic.
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Biophysical Characterization of a Recombinant α-Amylase from Thermophilic Bacillus sp. strain TS-23. Protein J 2010; 29:572-82. [DOI: 10.1007/s10930-010-9287-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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39
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Cloning and characterization of a rhamnose isomerase from Bacillus halodurans. Appl Microbiol Biotechnol 2010; 89:635-44. [DOI: 10.1007/s00253-010-2844-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 08/07/2010] [Accepted: 08/14/2010] [Indexed: 10/19/2022]
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Kumari A, Rosenkranz T, Kayastha AM, Fitter J. The effect of calcium binding on the unfolding barrier: A kinetic study on homologous α-amylases. Biophys Chem 2010; 151:54-60. [DOI: 10.1016/j.bpc.2010.05.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 05/11/2010] [Accepted: 05/12/2010] [Indexed: 11/15/2022]
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41
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Lu T. Seeking new mutation clues from Bacillus licheniformis amylase by molecular dynamics simulations. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.06.066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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42
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Tucker G, Hanby E, Brown H. Development and application of a new time–temperature integrator for the measurement of P-values in mild pasteurisation processes. FOOD AND BIOPRODUCTS PROCESSING 2009. [DOI: 10.1016/j.fbp.2008.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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43
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Production and characteristics comparison of crude β-glucosidases produced by microorganisms Thermoascus aurantiacus e Aureobasidium pullulans in agricultural wastes. Enzyme Microb Technol 2008. [DOI: 10.1016/j.enzmictec.2008.07.006] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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44
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Conformational stability and integrity of α-amylase from mung beans: Evidence of kinetic intermediate in GdmCl-induced unfolding. Biophys Chem 2008; 137:95-9. [DOI: 10.1016/j.bpc.2008.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2008] [Revised: 07/16/2008] [Accepted: 07/24/2008] [Indexed: 11/20/2022]
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Thermotoga maritima TM0298 is a highly thermostable mannitol dehydrogenase. Appl Microbiol Biotechnol 2008; 81:485-95. [PMID: 18719905 DOI: 10.1007/s00253-008-1633-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Revised: 07/21/2008] [Accepted: 07/28/2008] [Indexed: 10/21/2022]
Abstract
Thermotoga maritima TM0298 is annotated as an alcohol dehydrogenase, yet it shows high identity and similarity to mesophilic mannitol dehydrogenases. To investigate this enzyme further, its gene was cloned and expressed in Escherichia coli. The purified recombinant enzyme was most active on fructose and mannitol, making it the first known hyperthermophilic mannitol dehydrogenase. T. maritima mannitol dehydrogenase (TmMtDH) is optimally active between 90 and 100 degrees C and retains 63% of its activity at 120 degrees C but shows no detectable activity at room temperature. Its kinetic inactivation follows a first-order mechanism, with half-lives of 57 min at 80 degrees C and 6 min at 95 degrees C. Although TmMtDH has a higher V (max) with NADPH than with NADH, its catalytic efficiency is 2.2 times higher with NADH than with NADPH and 33 times higher with NAD(+) than with NADP(+). This cofactor specificity can be explained by the high density of negatively charged residues (Glu193, Asp195, and Glu196) downstream of the NAD(P) interaction site, the glycine motif. We demonstrate that TmMtDH contains a single catalytic zinc per subunit. Finally, we provide the first proof of concept that mannitol can be produced directly from glucose in a two-step enzymatic process, using a Thermotoga neapolitana xylose isomerase mutant and TmMtDH at 60 degrees C.
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Thermally induced changes in the structure and activity of yeast hexokinase B. Biophys Chem 2008; 137:88-94. [PMID: 18715685 DOI: 10.1016/j.bpc.2008.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2008] [Revised: 07/14/2008] [Accepted: 07/14/2008] [Indexed: 11/23/2022]
Abstract
Yeast hexokinase has been poorly characterized in regard with its stability. In the present study, various spectroscopic techniques were employed to investigate thermal stability of the monomeric form of yeast hexokinase B (YHB). The enzyme underwent a conformational transition with a T(m) of about 41.9 degrees C. The structural transition proved to be significantly reversible below 55 degrees C and irreversible at higher temperatures. Thermoinactivation studies revealed that enzymatic activity diminished significantly at high temperatures, with greater loss of activity observed above 55 degrees C. Release of ammonia upon deamidation of YHB obeyed a similar temperature-dependence pattern. Dynamic light scattering and size exclusion-HPLC indicated formation of stable aggregates. Taking various findings on the influence of osmolytes and chaperone-like agents on YHB thermal denaturation together, it is proposed that the purely conformational transition of YHB is reversible, and irreversibility is due to aggregation, as a major cause. Deamidation of a critical Asn or Gln residue(s) may also play an important role.
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Kadkhodaee R, Povey MJW. Ultrasonic inactivation of Bacillus alpha-amylase. I. effect of gas content and emitting face of probe. ULTRASONICS SONOCHEMISTRY 2008; 15:133-42. [PMID: 17434783 DOI: 10.1016/j.ultsonch.2007.02.005] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Revised: 02/13/2007] [Accepted: 02/20/2007] [Indexed: 05/14/2023]
Abstract
Sonoinactivation of alpha-amylase from Bacillus amyloliquefacience was studied at a constant frequency of 30 kHz. The effect of sonotrode emitting face and gas content of medium on the efficiency of enzyme inactivation were investigated at different time-temperature combinations and generation of OH free radicals was also monitored. The results showed that ultrasound effectively inactivated alpha-amylase with a minimum overall inactivation rate at 50 degrees C. The tip diameter of the sonotrode and the gas content of the medium both significantly affected the rate of enzyme inactivation. The increase of tip diameter increased the effect of ultrasound on the enzyme, while the removal of dissolved gas adversely influenced the cavitational events and reduced the rate of enzyme inactivation. Calculation of the kinetic and activation parameters revealed that ultrasound decreased the activation energy, E(a), activation enthalpy, DeltaH(#), and the activation Gibbs free energy, DeltaG(#), and strongly reduced the activation entropy, DeltaS(#), down to negative values. This huge reduction in activation entropy was attributed to the different mechanisms of inactivation induced by heat and ultrasound. It is proved in this study that ultrasonically generated OH free radicals and shear forces, which arise from pulsation- or collapse of bubbles, both can destabilize the enzyme, although their contribution to the overall inactivation varies depending on the temperature and the tip diameter of the sonotrode.
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Affiliation(s)
- Rassoul Kadkhodaee
- Department of Food Technology, Khorasan Institute of Food Research, Mashad, Iran.
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Ye T, Zhang X. Characterization of a lysin from deep-sea thermophilic bacteriophage GVE2. Appl Microbiol Biotechnol 2008; 78:635-41. [PMID: 18224315 DOI: 10.1007/s00253-008-1353-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Revised: 01/04/2008] [Accepted: 01/06/2008] [Indexed: 10/22/2022]
Abstract
Thermostable enzymes from thermophiles have attracted extensive studies. However, little is known about thermophilic lysin of bacteriophage obtained from deep-sea hydrothermal vent. In this study, a lysin from deep-sea thermophilic bacteriophage Geobacillus virus E2 (GVE2) was characterized for the first time. It was found that the GVE2 lysin was highly homologous with N-acetylmuramoyl-L-alanine amidases. After expression in Escherichia coli, the recombinant GVE2 lysin was purified. The recombinant lysin was active over a range of temperature from 40 degrees C to 80 degrees C, with an optimum at 60 degrees C. Its optimal pH was 6.0, and it was stable over a wide range of pH from 4.0 to 10.0. The lysin was highly active when some enzyme inhibitors or detergents (phenylmethylsulfonyl fluoride, Tween 20, Triton X-100, and chaps) were used. However, it was strongly inhibited by sodium dodecyl sulfate and ethylene diamine tetraacetic acid. Its enzymatic activity could be slightly stimulated in the presence of Na(+) and Li(+). But the metal ions Mg(2+), Ba(2+), Zn(2+), Fe(3+), Ca(2+), and Mn(2+) at concentrations of 1 or 10 mM showed inhibitions to the lysin activity. Our study demonstrated the first characterization of lysin from deep-sea thermophilic bacteriophage.
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Affiliation(s)
- Ting Ye
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, People's Republic of China
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Strucksberg K, Rosenkranz T, Fitter J. Reversible and irreversible unfolding of multi-domain proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:1591-603. [DOI: 10.1016/j.bbapap.2007.09.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Revised: 09/06/2007] [Accepted: 09/10/2007] [Indexed: 10/22/2022]
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