1
|
Oztug M, Kilinc E, Akgoz M, Karaguler NG. Thermal Proteome Profiling and Meltome Analysis of a Thermophilic Bacterial Strain, Geobacillus thermoleovorans ARTRW1: Toward Industrial Applications. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 24:756-765. [PMID: 33085568 DOI: 10.1089/omi.2020.0115] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Thermophilic microorganisms that thrive in extreme environments are of great importance because they express heat-resistant enzymes with the potential to serve as biocatalysts in industrial applications. Thermal proteome profiling (TPP) is a multiplexed quantitative mass spectrometry method for analyses of structural information and melting behavior of thousands of proteins, simultaneously determining the thermal denaturation profiles of each protein. We report, in this study, TPP applied to a thermophilic bacterial proteome, a recently isolated strain of Geobacillus thermoleovorans named as ARTRW1. The proteome was investigated in terms of thermostable enzymes that are relevant to industrial applications. In this study, we present the thermostability profiles of its 868 proteins. The majority of G. thermoleovorans proteome was observed to melt between 62.5°C and 72°C, with melting point (Tm) mean value of 68.1°C ± 6.6°C. Unfolding characteristics of several enzymes, including amylase, protease, and lipase, were demonstrated which are highly informative in terms of their applicability to specific industrial processes. A significant correlation was observed between protein melting temperature and the structural features such as molecular weight and abundance, whereas correlations were modest or weak in relation to the α-helix structure percentages. Taken together, we demonstrated a system-wide melting profile analysis of a thermal proteome and listed proteins with elevated Tm values that are highly promising for applications in medicine, food engineering, and cosmetics in particular. The extracted Tm values were found similar to those obtained by biophysical methods applied to purified proteins. TPP analysis has significant industrial and biomedical potentials to accelerate thermophilic enzyme research and innovation.
Collapse
Affiliation(s)
- Merve Oztug
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology-Biotechnology and Genetics Research Center, Istanbul Technical University, Istanbul, Turkey.,National Metrology Institute, TUBITAK UME, Gebze, Turkey
| | - Evren Kilinc
- Department of Biophysics, School of Medicine, Acıbadem Mehmet Ali Aydınlar University, İstanbul, Turkey
| | - Muslum Akgoz
- National Metrology Institute, TUBITAK UME, Gebze, Turkey
| | - Nevin Gul Karaguler
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology-Biotechnology and Genetics Research Center, Istanbul Technical University, Istanbul, Turkey
| |
Collapse
|
2
|
Huang P, Chu SKS, Frizzo HN, Connolly MP, Caster RW, Siegel JB. Evaluating Protein Engineering Thermostability Prediction Tools Using an Independently Generated Dataset. ACS OMEGA 2020; 5:6487-6493. [PMID: 32258884 PMCID: PMC7114132 DOI: 10.1021/acsomega.9b04105] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/06/2020] [Indexed: 05/04/2023]
Abstract
Engineering proteins to enhance thermal stability is a widely utilized approach for creating industrially relevant biocatalysts. The development of new experimental datasets and computational tools to guide these engineering efforts remains an active area of research. Thus, to complement the previously reported measures of T 50 and kinetic constants, we are reporting an expansion of our previously published dataset of mutants for β-glucosidase to include both measures of T M and ΔΔG. For a set of 51 mutants, we found that T 50 and T M are moderately correlated, with a Pearson correlation coefficient and Spearman's rank coefficient of 0.58 and 0.47, respectively, indicating that the two methods capture different physical features. The performance of predicted stability using nine computational tools was also evaluated on the dataset of 51 mutants, none of which are found to be strong predictors of the observed changes in T 50, T M, or ΔΔG. Furthermore, the ability of the nine algorithms to predict the production of isolatable soluble protein was examined, which revealed that Rosetta ΔΔG, FoldX, DeepDDG, PoPMuSiC, and SDM were capable of predicting if a mutant could be produced and isolated as a soluble protein. These results further highlight the need for new algorithms for predicting modest, yet important, changes in thermal stability as well as a new utility for current algorithms for prescreening designs for the production of mutants that maintain fold and soluble production properties.
Collapse
Affiliation(s)
- Peishan Huang
- Biophysics
Graduate Group, University of California, Davis 95616, California, United States
| | - Simon K. S. Chu
- Biophysics
Graduate Group, University of California, Davis 95616, California, United States
| | - Henrique N. Frizzo
- Genome
Center, University of California, Davis 95616, California, United States
| | - Morgan P. Connolly
- Microbiology
Graduate Group, University of California, Davis 95616, California, United States
| | - Ryan W. Caster
- Genome
Center, University of California, Davis 95616, California, United States
| | - Justin B. Siegel
- Genome
Center, University of California, Davis 95616, California, United States
- Department
of Biochemistry & Molecular Medicine, University of California, Davis 95616, California, United States
- Department
of Chemistry, University of California, Davis 95616, California, United States
| |
Collapse
|
3
|
Wang Y, Kim E, Lin Y, Kim N, Kit-Anan W, Gopal S, Agarwal S, Howes PD, Stevens MM. Rolling Circle Transcription-Amplified Hierarchically Structured Organic-Inorganic Hybrid RNA Flowers for Enzyme Immobilization. ACS APPLIED MATERIALS & INTERFACES 2019; 11:22932-22940. [PMID: 31252470 PMCID: PMC6613047 DOI: 10.1021/acsami.9b04663] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/03/2019] [Indexed: 05/07/2023]
Abstract
Programmable nucleic acids have emerged as powerful building blocks for the bottom-up fabrication of two- or three-dimensional nano- and microsized constructs. Here we describe the construction of organic-inorganic hybrid RNA flowers (hRNFs) via rolling circle transcription (RCT), an enzyme-catalyzed nucleic acid amplification reaction. These hRNFs are highly adaptive structures with controlled sizes, specific nucleic acid sequences, and a highly porous nature. We demonstrated that hRNFs are applicable as potential biological platforms, where the hRNF scaffold can be engineered for versatile surface functionalization and the inorganic component (magnesium ions) can serve as an enzyme cofactor. For surface functionalization, we proposed robust and straightforward approaches including in situ synthesis of functional hRNFs and postfunctionalization of hRNFs that enable facile conjugation with various biomolecules and nanomaterials (i.e., proteins, enzymes, organic dyes, inorganic nanoparticles) using selective chemistries (i.e., avidin-biotin interaction, copper-free click reaction). In particular, we showed that hRNFs can serve as soft scaffolds for β-galactosidase immobilization and greatly enhance enzymatic activity and stability. Therefore, the proposed concepts and methodologies are not only fundamentally interesting when designing RNA scaffolds or RNA bionanomaterials assembled with enzymes but also have significant implications on their future utilization in biomedical applications ranging from enzyme cascades to biosensing and drug delivery.
Collapse
Affiliation(s)
| | | | - Yiyang Lin
- Department of Materials, Department of Bioengineering,
and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Nayoung Kim
- Department of Materials, Department of Bioengineering,
and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Worrapong Kit-Anan
- Department of Materials, Department of Bioengineering,
and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Sahana Gopal
- Department of Materials, Department of Bioengineering,
and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Shweta Agarwal
- Department of Materials, Department of Bioengineering,
and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Molly M. Stevens
- Department of Materials, Department of Bioengineering,
and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| |
Collapse
|
4
|
Ritchie ME. Reaction and diffusion thermodynamics explain optimal temperatures of biochemical reactions. Sci Rep 2018; 8:11105. [PMID: 30038415 PMCID: PMC6056565 DOI: 10.1038/s41598-018-28833-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 06/28/2018] [Indexed: 01/18/2023] Open
Abstract
Ubiquitous declines in biochemical reaction rates above optimal temperatures (Topt) are normally attributed to enzyme state changes, but such mechanisms appear inadequate to explain pervasive Topt well below enzyme deactivation temperatures (Tden). Here, a meta-analysis of 92 experimental studies shows that product formation responds twice as strongly to increased temperature than diffusion or transport. This response difference has multiple consequences for biochemical reactions, such as potential shifts in the factors limiting reactions as temperature increases and reaction-diffusion dynamics that predict potential product inhibition and limitation of the reaction by entropy production at temperatures below Tden. Maximizing entropy production by the reaction predicts Topt that depend on enzyme concentration and efficiency as well as reaction favorability, which are patterns not predicted by mechanisms of enzyme state change. However, these predictions are strongly supported by patterns in a meta-analysis of 121 enzyme kinetic studies. Consequently, reaction-diffusion thermodynamics and entropy production may constrain organism performance at higher temperatures, yielding temperature optima of life that may depend on reaction characteristics and environmental features rather than just enzyme state changes.
Collapse
Affiliation(s)
- Mark E Ritchie
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA.
| |
Collapse
|
5
|
Saqib AAN, Siddiqui KS. How to calculate thermostability of enzymes using a simple approach. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 46:398-402. [PMID: 29717551 DOI: 10.1002/bmb.21127] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 02/08/2018] [Accepted: 04/08/2018] [Indexed: 06/08/2023]
Abstract
Determination of thermostability of enzymes is of prime importance for their successful industrial applications and, yet, the published data has often been incompletely analyzed to assess the suitability of enzymes. It is possible to determine meaningful thermostability parameters from the routinely acquired data through a straightforward method that is not only more informative but also provides a means to compare thermostability of enzymes from different sources. Here, we describe a simple, effective, and economical way to determine enzyme thermostability. In our opinion, including this method in Biochemistry and Molecular Biology curricula will encourage students to include thermostability analysis in their future work, leading to a more meaningful approach to evaluate and compare enzymes. Furthermore, as the method requires minimum specialized equipment, the analysis will be particularly suitable for labs that cannot afford expensive setup. © 2018 by The International Union of Biochemistry and Molecular Biology, 46:398-402, 2018.
Collapse
Affiliation(s)
- Abdul A N Saqib
- Green Biologics Ltd, Milton Park, Abingdon, Oxfordshire, OX14 4SD, United Kingdom
| | - Khawar S Siddiqui
- Life Sciences Department, King Fahd University of Petroleum & Minerals, Dhahran, Saudi Arabia
| |
Collapse
|
6
|
Rachinskiy K, Kunze M, Graf C, Schultze H, Boy M, Büchs J. Extension and application of the "enzyme test bench" for oxygen consuming enzyme reactions. Biotechnol Bioeng 2013; 111:244-53. [PMID: 23928872 DOI: 10.1002/bit.25020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 07/18/2013] [Accepted: 07/29/2013] [Indexed: 11/08/2022]
Abstract
Within industrial process development, powerful screening techniques are required to select the optimal biocatalyst regarding such process characteristics as cost effectiveness, turnover number or space time yield. Conventional measurement of the initial enzyme activity, which is the established high throughput screening technique, disregards the long-term stability of an enzyme. A new model based technique called "enzyme test bench" was recently presented before by our group which addresses this issue. It combines the high throughput screening approach with an extensive enzyme characterization, focusing especially on the long-term stability. The technique is based on modeling enzyme activation and deactivation as temperature dependent reactions in accordance with the Arrhenius law. Controlling these reactions by tailor made temperature profiles, the slow long-term deactivation effects are accelerated and characterizing models are parameterized. Thus, the process properties of an enzyme can be predicted and included into the screening procedure. Moreover, the optimum process temperature as function of the envisaged operation time can be found by these means. In this work, the technique is extended to the important class of oxygen consuming reactions. For this aim, a suitable assay and a defined oxygen supply were established. This extended technique was applied to characterize and to optimize a complex, multi-stage laccase-mediator system (LMS). For the variation and optimization of the enzyme to mediator to substrate ratio, experiments in microtiter plates were performed. Predictions from this high throughput characterization were compared to long-term experiments in a RAMOS device (Respiration Activity Monitoring System), a technique for on-line monitoring of the oxygen transfer rate in shake flasks. Within the limits of the model validity, the enzyme test bench predictions are in good agreement with the long-term experiments.
Collapse
|
7
|
Machado MF, Queirós RP, Santos MD, Fidalgo LG, Delgadillo I, Saraiva JA. Effect of ionic liquids alkyl chain length on horseradish peroxidase thermal inactivation kinetics and activity recovery after inactivation. World J Microbiol Biotechnol 2013; 30:487-94. [DOI: 10.1007/s11274-013-1466-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Accepted: 08/16/2013] [Indexed: 10/26/2022]
|
8
|
Rachinskiy K, Schultze H, Boy M, Bornscheuer U, Büchs J. “Enzyme Test Bench,” a high-throughput enzyme characterization technique including the long-term stability. Biotechnol Bioeng 2009; 103:305-22. [DOI: 10.1002/bit.22242] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
9
|
Roy S, Fortin M, Gagnon J, Ghinet MG, Lehoux JG, Dupuis G, Brzezinski R. Quantitative fluorometric analysis of the protective effect of chitosan on thermal unfolding of catalytically active native and genetically-engineered chitosanases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:975-84. [PMID: 17644457 DOI: 10.1016/j.bbapap.2007.05.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Revised: 05/17/2007] [Accepted: 05/29/2007] [Indexed: 10/23/2022]
Abstract
We have taken advantage of the intrinsic fluorescence properties of chitosanases to rapidly and quantitatively evaluate the protective effect of chitosan against thermal denaturation of chitosanases. The studies were done using wild type chitosanases N174 produced by Streptomyces sp. N174 and SCO produced by Streptomyces coelicolor A3(2). In addition, two mutants of N174 genetically engineered by single amino acid substitutions (A104L and K164R) and one "consensus" (N174-CONS) chitosanase designed by multiple amino acid substitutions of N174 were analyzed. Chitosan used had a weight average molecular weight (Mw) of 220 kDa and was 85% deacetylated. Results showed a pH and concentration-dependent protective effect of chitosan in all the cases. However, the extent of thermal protection varied depending on chitosanases, suggesting that key amino acid residues contributed to resistance to heat denaturation. The transition temperatures (T(m)) of N174 were 54 degrees C and 69.5 degrees C in the absence and presence (6 g/l) of chitosan, respectively. T(m) were increased by 11.6 degrees C (N174-CONS), 13.8 degrees C (CSN-A104L), 15.6 degrees C (N174-K164R) and 25.2 degrees C (SCO) in the presence of chitosan (6 g/l). The thermal protective effect was attributed to an enzyme-ligand thermostabilization mechanism since it was not mimicked by the presence of anionic (carboxymethyl cellulose, heparin) or cationic (polyethylene imine) polymers, polyhydroxylated (glycerol, sorbitol) compounds or inorganic salts. Furthermore, the data from fluorometry experiments were in agreement with those obtained by analysis of reaction time-courses performed at 61 degrees C in which case CSN-A104L was rapidly inactivated whereas N174, N174-CONS and N174-K164R remained active over a reaction time of 90 min. This study presents evidence that (1) the fluorometric determination of T(m) in the presence of chitosan is a reliable technique for a rapid assessment of the thermal behavior of chitosanases, (2) it is applicable to structure-function studies of mutant chitosanases and, (3) it can be useful to provide an insight into the mechanism by which mutations can influence chitosanase stability.
Collapse
Affiliation(s)
- Sébastien Roy
- Diversified Natural Products Research Laboratory, Institut de Pharmacologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1H 5N4.
| | | | | | | | | | | | | |
Collapse
|
10
|
|
11
|
Analysis of mechanism and kinetics of thermal inactivation of enzymes: Evaluation of multitemperature data applied to inactivation of yeast invertase. Enzyme Microb Technol 1997. [DOI: 10.1016/s0141-0229(96)00150-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
12
|
Polakovic̆ M, Vrábel P. Analysis of the mechanism and kinetics of thermal inactivation of enzymes: Critical assessment of isothermal inactivation experiments. Process Biochem 1996. [DOI: 10.1016/s0032-9592(96)00026-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
13
|
Hamon V, Dallet S, Legoy MD. The pressure-dependence of two beta-glucosidases with respect to their thermostability. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1294:195-203. [PMID: 8645739 DOI: 10.1016/0167-4838(96)00022-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A comparative study of temperature and pressure effects were carried out by using two homologous enzymes exhibiting different thermostability and oligomery: almond beta-glucosidase and Sulfolobus solfataricus beta-glucosidase. Both the activity and stability were studied using an in-house built bioreactor allowing injection, stirring, sampling and on-line spectrophometric monitoring with retention of pressure up to 2.5 kbar and temperature control possible up to 150 degrees C. Almond beta-glucosidase, the most pressure sensitive enzyme of the two was continuously affected by pressure up to 1.5 kbar. Activation volume changes revealed that the inactivation of almond beta-glucosidase was due to both catalytic step inactivation and enzyme-substrate binding inactivation. Structural modifications generated by pressure, related to a loss of activity did not affect the global conformation of almond beta-glucosidase, after depressurization. In contrast, Sulfolobus solfataricus beta-glucosidase was a highly barostable enzyme. It maintained a half-life of 91 h at 60 degrees C and 2.5 kbar. Moreover, this enzyme appeared to be activated by pressure between atmospheric pressure and 2.5 kbar with a maximal activity at 1.25 kbar. However, this enzyme still displayed the best catalytic efficiency at atmospheric pressure because of a Km value drastically increased by pressure. Activation volume changes indicated that the hydrolysis reaction catalysed by Sulfolobus solfataricus beta-glucosidase, was alternatively favoured and disfavoured by pressure due to the catalytic step activation or inactivation associated with the enzyme-substrate binding step being continuously inactivated by pressure.
Collapse
Affiliation(s)
- V Hamon
- Laboratoire de Technologie Enzymatique, URA 1442 CNRS, Université de Technologie de Compiègne, France
| | | | | |
Collapse
|
14
|
Michels PC, Hei D, Clark DS. Pressure effects on enzyme activity and stability at high temperatures. ADVANCES IN PROTEIN CHEMISTRY 1996; 48:341-76. [PMID: 8791629 DOI: 10.1016/s0065-3233(08)60366-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- P C Michels
- Department of Chemical Engineering, University of California, Berkeley 94720, USA
| | | | | |
Collapse
|