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Yusof NY, Quay DHX, Kamaruddin S, Jonet MA, Md Illias R, Mahadi NM, Firdaus-Raih M, Abu Bakar FD, Abdul Murad AM. Biochemical and in silico structural characterization of a cold-active arginase from the psychrophilic yeast, Glaciozyma antarctica PI12. Extremophiles 2024; 28:15. [PMID: 38300354 DOI: 10.1007/s00792-024-01333-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 12/30/2023] [Indexed: 02/02/2024]
Abstract
Glaciozyma antarctica PI12 is a psychrophilic yeast isolated from Antarctica. In this work, we describe the heterologous production, biochemical properties and in silico structure analysis of an arginase from this yeast (GaArg). GaArg is a metalloenzyme that catalyses the hydrolysis of L-arginine to L-ornithine and urea. The cDNA of GaArg was reversed transcribed, cloned, expressed and purified as a recombinant protein in Escherichia coli. The purified protein was active against L-arginine as its substrate in a reaction at 20 °C, pH 9. At 10-35 °C and pH 7-9, the catalytic activity of the protein was still present around 50%. Mn2+, Ni2+, Co2+ and K+ were able to enhance the enzyme activity more than two-fold, while GaArg is most sensitive to SDS, EDTA and DTT. The predicted structure model of GaArg showed a very similar overall fold with other known arginases. GaArg possesses predominantly smaller and uncharged amino acids, fewer salt bridges, hydrogen bonds and hydrophobic interactions compared to the other counterparts. GaArg is the first reported arginase that is cold-active, facilitated by unique structural characteristics for its adaptation of catalytic functions at low-temperature environments. The structure and function of cold-active GaArg provide insights into the potentiality of new applications in various biotechnology and pharmaceutical industries.
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Affiliation(s)
- Nik Yusnoraini Yusof
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian, 16150, Kelantan, Malaysia.
- Department of Biological Sciences & Biotechnology, Faculty of Sciences and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
| | - Doris Huai Xia Quay
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, 43600, Bangi, Selangor, Malaysia.
| | - Shazilah Kamaruddin
- Department of Biological Sciences & Biotechnology, Faculty of Sciences and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Mohd Anuar Jonet
- Malaysia Genome and Vaccine Institute, Jalan Bangi Lama, 43000, Kajang, Selangor, Malaysia
| | - Rosli Md Illias
- Department of Bioprocess Engineering, Faculty of Chemical Engineering, Universiti Teknologi Malaysia, 81300, Skudai, Johor, Malaysia
| | - Nor Muhammad Mahadi
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Mohd Firdaus-Raih
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, 43600, Bangi, Selangor, Malaysia
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Farah Diba Abu Bakar
- Department of Biological Sciences & Biotechnology, Faculty of Sciences and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Abdul Munir Abdul Murad
- Department of Biological Sciences & Biotechnology, Faculty of Sciences and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
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2
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Liu Z, Cao L, Fu X, Liang Q, Sun H, Mou H. A multi-functional genetic manipulation system and its use in high-level expression of a β-mannanase mutant with high specific activity in Pichia pastoris. Microb Biotechnol 2021; 14:1525-1538. [PMID: 33942496 PMCID: PMC8313266 DOI: 10.1111/1751-7915.13812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/23/2021] [Accepted: 03/29/2021] [Indexed: 11/29/2022] Open
Abstract
To further extend the practical application of a thermostable and acidic resistance β-mannanase (ManAK) in animal feed additives, an effective strategy that combined directed evolution and metabolic engineering was developed. Four positive mutants (P191M, P194E, S199G and S268Q) with enhanced specific activity (25.5%-60.9%) were obtained. The S199G mutant exhibited 56.7% enhancement of specific activity at 37°C and good thermostability, and this was selected for high-level expression in P. pastoris X33. A multi-functional and scarless genetic manipulation system was proposed and functionally verified (gene deletion, substitution/insertion and point mutation). This was then subjected to Rox1p (an oxygen related transcription regulator) deletion and Vitreoscilla haemoglobin (VHb) co-expression for high enzyme productivity in P. pastoris X33VIIManAKS199G . An excellent strain, named X33VIIManAKS199G ∆rox1::VHb, was achieved by combining these two factors, and then the maximum enzymatic activity was further increased to 3753 U ml-1 , which was nearly twice as much as the maximum production of ManAK in P. pastoris. This work provides a systematic and effective method to improve the enzymatic yield of β-mannanase, promotes the application of ManAK in feed additives, and also demonstrated that a scarless genetic manipulation tool is useful in P. pastoris.
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Affiliation(s)
- Zhemin Liu
- College of Food Science and EngineeringOcean University of ChinaQingdao266003China
| | - Linyuan Cao
- College of Food Science and EngineeringOcean University of ChinaQingdao266003China
| | - Xiaodan Fu
- College of Food Science and EngineeringOcean University of ChinaQingdao266003China
| | - Qingping Liang
- College of Food Science and EngineeringOcean University of ChinaQingdao266003China
| | - Han Sun
- College of Food Science and EngineeringOcean University of ChinaQingdao266003China
| | - Haijin Mou
- College of Food Science and EngineeringOcean University of ChinaQingdao266003China
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3
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Characterization of SdGA, a cold-adapted glucoamylase from Saccharophagus degradans. ACTA ACUST UNITED AC 2021; 30:e00625. [PMID: 34041001 PMCID: PMC8141877 DOI: 10.1016/j.btre.2021.e00625] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 04/24/2021] [Accepted: 04/28/2021] [Indexed: 11/24/2022]
Abstract
We investigated the structural and functional properties of SdGA, a glucoamylase (GA) from Saccharophagus degradans, a marine bacterium which degrades different complex polysaccharides at high rate. SdGA is composed mainly by a N-terminal GH15_N domain linked to a C-terminal catalytic domain (CD) found in the GH15 family of glycosylhydrolases with an overall structure similar to other bacterial GAs. The protein was expressed in Escherichia coli cells, purified and its biochemical properties were investigated. Although SdGA has a maximum activity at 39 °C and pH 6.0, it also shows high activity in a wide range, from low to mild temperatures, like cold-adapted enzymes. Furthermore, SdGA has a higher content of flexible residues and a larger CD due to various amino acid insertions compared to other thermostable GAs. We propose that this novel SdGA, is a cold-adapted enzyme that might be suitable for use in different industrial processes that require enzymes which act at low or medium temperatures.
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4
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A meta-analysis of the activity, stability, and mutational characteristics of temperature-adapted enzymes. Biosci Rep 2021; 41:228416. [PMID: 33871022 PMCID: PMC8150157 DOI: 10.1042/bsr20210336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/29/2021] [Accepted: 04/19/2021] [Indexed: 11/17/2022] Open
Abstract
Understanding the characteristics that define temperature-adapted enzymes has been a major goal of extremophile enzymology in recent decades. In the present study, we explore these characteristics by comparing psychrophilic, mesophilic, and thermophilic enzymes. Through a meta-analysis of existing data, we show that psychrophilic enzymes exhibit a significantly larger gap (Tg) between their optimum and melting temperatures compared with mesophilic and thermophilic enzymes. These results suggest that Tg may be a useful indicator as to whether an enzyme is psychrophilic or not and that models of psychrophilic enzyme catalysis need to account for this gap. Additionally, by using predictive protein stability software, HoTMuSiC and PoPMuSiC, we show that the deleterious nature of amino acid substitutions to protein stability increases from psychrophiles to thermophiles. How this ultimately affects the mutational tolerance and evolutionary rate of temperature adapted organisms is currently unknown.
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5
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Pinney MM, Mokhtari DA, Akiva E, Yabukarski F, Sanchez DM, Liang R, Doukov T, Martinez TJ, Babbitt PC, Herschlag D. Parallel molecular mechanisms for enzyme temperature adaptation. Science 2021; 371:371/6533/eaay2784. [PMID: 33674467 DOI: 10.1126/science.aay2784] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/23/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
The mechanisms that underly the adaptation of enzyme activities and stabilities to temperature are fundamental to our understanding of molecular evolution and how enzymes work. Here, we investigate the molecular and evolutionary mechanisms of enzyme temperature adaption, combining deep mechanistic studies with comprehensive sequence analyses of thousands of enzymes. We show that temperature adaptation in ketosteroid isomerase (KSI) arises primarily from one residue change with limited, local epistasis, and we establish the underlying physical mechanisms. This residue change occurs in diverse KSI backgrounds, suggesting parallel adaptation to temperature. We identify residues associated with organismal growth temperature across 1005 diverse bacterial enzyme families, suggesting widespread parallel adaptation to temperature. We assess the residue properties, molecular interactions, and interaction networks that appear to underly temperature adaptation.
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Affiliation(s)
- Margaux M Pinney
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.
| | - Daniel A Mokhtari
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences and Quantitative Biosciences Institute, University of California, San Francisco, CA 94158, USA
| | - Filip Yabukarski
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94110, USA
| | - David M Sanchez
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Department of Photon Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Ruibin Liang
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Department of Photon Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Tzanko Doukov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Todd J Martinez
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Department of Photon Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences and Quantitative Biosciences Institute, University of California, San Francisco, CA 94158, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA. .,Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.,Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
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6
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Zhang ZB, Xia YL, Dong GH, Fu YX, Liu SQ. Exploring the Cold-Adaptation Mechanism of Serine Hydroxymethyltransferase by Comparative Molecular Dynamics Simulations. Int J Mol Sci 2021; 22:1781. [PMID: 33670090 PMCID: PMC7916883 DOI: 10.3390/ijms22041781] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 12/20/2022] Open
Abstract
Cold-adapted enzymes feature a lower thermostability and higher catalytic activity compared to their warm-active homologues, which are considered as a consequence of increased flexibility of their molecular structures. The complexity of the (thermo)stability-flexibility-activity relationship makes it difficult to define the strategies and formulate a general theory for enzyme cold adaptation. Here, the psychrophilic serine hydroxymethyltransferase (pSHMT) from Psychromonas ingrahamii and its mesophilic counterpart, mSHMT from Escherichia coli, were subjected to μs-scale multiple-replica molecular dynamics (MD) simulations to explore the cold-adaptation mechanism of the dimeric SHMT. The comparative analyses of MD trajectories reveal that pSHMT exhibits larger structural fluctuations and inter-monomer positional movements, a higher global flexibility, and considerably enhanced local flexibility involving the surface loops and active sites. The largest-amplitude motion mode of pSHMT describes the trends of inter-monomer dissociation and enlargement of the active-site cavity, whereas that of mSHMT characterizes the opposite trends. Based on the comparison of the calculated structural parameters and constructed free energy landscapes (FELs) between the two enzymes, we discuss in-depth the physicochemical principles underlying the stability-flexibility-activity relationships and conclude that (i) pSHMT adopts the global-flexibility mechanism to adapt to the cold environment and, (ii) optimizing the protein-solvent interactions and loosening the inter-monomer association are the main strategies for pSHMT to enhance its flexibility.
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Affiliation(s)
- Zhi-Bi Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China; (Z.-B.Z.); (Y.-L.X.); (G.-H.D.)
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine & Biomedical Engineering Research Center, Kunming Medical University, Kunming 650500, China
| | - Yuan-Ling Xia
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China; (Z.-B.Z.); (Y.-L.X.); (G.-H.D.)
| | - Guang-Heng Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China; (Z.-B.Z.); (Y.-L.X.); (G.-H.D.)
| | - Yun-Xin Fu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China; (Z.-B.Z.); (Y.-L.X.); (G.-H.D.)
- Human Genetics Center and Division of Biostatistics, School of Public Health, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Shu-Qun Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China; (Z.-B.Z.); (Y.-L.X.); (G.-H.D.)
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7
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Jaafar NR, Mahadi NM, Mackeen MM, Illias RM, Murad AMA, Abu Bakar FD. Structural and functional characterisation of a cold-active yet heat-tolerant dehydroquinase from Glaciozyma antarctica PI12. J Biotechnol 2021; 329:118-127. [PMID: 33539893 DOI: 10.1016/j.jbiotec.2021.01.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 11/25/2022]
Abstract
Dehydroquinase or 3-dehydroquinate dehydratase (DHQD) reversibly cleaves 3-dehydroquinate to form 3-dehydroshikimate. Here, we describe the functional and structural features of a cold active type II 3-dehydroquinate dehydratase from the psychrophilic yeast, Glaciozyma antarctica PI12 (GaDHQD). Functional studies showed that the enzyme was active at low temperatures (10-30 °C), but displayed maximal activity at 40 °C. Yet the enzyme was stable over a wide range of temperatures (10-70 °C) and between pH 6.0-10.0 with an optimum pH of 8.0. Interestingly, the enzyme was highly thermo-tolerant, denaturing only at approximately 84 °C. Three-dimensional structure analyses showed that the G. antarctica dehydroquinase (GaDHQD) possesses psychrophilic features in comparison with its mesophilic and thermophilic counterparts such as higher numbers of non-polar residues on the surface, lower numbers of arginine and higher numbers of glycine-residues with lower numbers of hydrophobic interactions. On the other hand, GaDHQD shares some traits (i.e. total number of hydrogen bonds, number of proline residues and overall folding) with its mesophilic and thermophilic counterparts. Combined, these features contribute synergistically towards the enzyme's ability to function at both low and high temperatures.
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Affiliation(s)
- Nardiah Rizwana Jaafar
- School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81210, Skudai, Johor Darul Takzim, Malaysia; Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Nor Muhammad Mahadi
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Mukram Mohamed Mackeen
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia; Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Rosli Md Illias
- School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81210, Skudai, Johor Darul Takzim, Malaysia
| | - Abdul Munir Abdul Murad
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Farah Diba Abu Bakar
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia.
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8
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Hjörleifsson JG, Helland R, Magnúsdóttir M, Ásgeirsson B. The high catalytic rate of the cold-active Vibrio alkaline phosphatase requires a hydrogen bonding network involving a large interface loop. FEBS Open Bio 2020; 11:173-184. [PMID: 33197282 PMCID: PMC7780099 DOI: 10.1002/2211-5463.13041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 11/24/2022] Open
Abstract
The role of surface loops in mediating communication through residue networks is still a relatively poorly understood part in the study of cold adaptation of enzymes, especially in terms of their quaternary interactions. Alkaline phosphatase (AP) from the psychrophilic marine bacterium Vibrio splendidus (VAP) is characterized by an analogous large surface loop in each monomer, referred to as the large loop, that hovers over the active site of the other monomer. It presumably has a role in the high catalytic efficiency of VAP which accompanies its extremely low thermal stability. Here, we designed several different variants of VAP with the aim of removing intersubunit interactions at the dimer interface. Breaking the intersubunit contacts from one residue in particular (Arg336) reduced the temperature stability of the catalytically potent conformation and caused a 40% drop in catalytic rate. The high catalytic rates of enzymes from cold‐adapted organisms are often associated with increased dynamic flexibility. Comparison of the relative B‐factors of the R336L crystal structure to that of the wild‐type confirmed surface flexibility was increased in a loop on the opposite monomer, but not in the large loop. The increase in flexibility resulted in a reduced catalytic rate. The large loop increases the area of the interface between the subunits through its contacts and may facilitate an alternating structural cycle demanded by a half‐of‐sites reaction mechanism through stronger ties, as the dimer oscillates between high affinity (active) or low phosphoryl group affinity (inactive).
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Affiliation(s)
| | - Ronny Helland
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT, The Arctic University of Tromsø, Norway
| | - Manuela Magnúsdóttir
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavik, Iceland
| | - Bjarni Ásgeirsson
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavik, Iceland
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9
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The Role of Surface Exposed Lysine in Conformational Stability and Functional Properties of Lipase from Staphylococcus Family. Molecules 2020; 25:molecules25173858. [PMID: 32854267 PMCID: PMC7504586 DOI: 10.3390/molecules25173858] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 11/17/2022] Open
Abstract
Surface charge residues have been recognized as one of the stability determinants in protein. In this study, we sought to compare and analyse the stability and conformational dynamics of staphylococcal lipase mutants with surface lysine mutation using computational and experimental methods. Three highly mutable and exposed lysine residues (Lys91, Lys177, Lys325) were targeted to generate six mutant lipases in silico. The model structures were simulated in water environment at 25 °C. Our simulations showed that the stability was compromised when Lys177 was substituted while mutation at position 91 and 325 improved the stability. To illustrate the putative alterations of enzyme stability in the stabilising mutants, we characterized single mutant K325G and double mutant K91A/K325G. Both mutants showed a 5 °C change in optimal temperature compared to their wild type. Single mutant K325G rendered a longer half-life at 25 °C (T1/2 = 21 h) while double mutant K91A/K325G retained only 40% of relative activity after 12 h incubation. The optimal pH for mutant K325G was shifted from 8 to 9 and similar substrate preference was observed for the wild type and two mutants. Our findings indicate that surface lysine mutation alters the enzymatic behaviour and, thus, rationalizes the functional effects of surface exposed lysine in conformational stability and activity of this lipase.
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10
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Chrast L, Tratsiak K, Planas-Iglesias J, Daniel L, Prudnikova T, Brezovsky J, Bednar D, Kuta Smatanova I, Chaloupkova R, Damborsky J. Deciphering the Structural Basis of High Thermostability of Dehalogenase from Psychrophilic Bacterium Marinobacter sp. ELB17. Microorganisms 2019; 7:E498. [PMID: 31661858 PMCID: PMC6920932 DOI: 10.3390/microorganisms7110498] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 10/19/2019] [Accepted: 10/23/2019] [Indexed: 12/17/2022] Open
Abstract
Haloalkane dehalogenases are enzymes with a broad application potential in biocatalysis, bioremediation, biosensing and cell imaging. The new haloalkane dehalogenase DmxA originating from the psychrophilic bacterium Marinobacter sp. ELB17 surprisingly possesses the highest thermal stability (apparent melting temperature Tm,app = 65.9 °C) of all biochemically characterized wild type haloalkane dehalogenases belonging to subfamily II. The enzyme was successfully expressed and its crystal structure was solved at 1.45 Å resolution. DmxA structure contains several features distinct from known members of haloalkane dehalogenase family: (i) a unique composition of catalytic residues; (ii) a dimeric state mediated by a disulfide bridge; and (iii) narrow tunnels connecting the enzyme active site with the surrounding solvent. The importance of narrow tunnels in such paradoxically high stability of DmxA enzyme was confirmed by computational protein design and mutagenesis experiments.
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Affiliation(s)
- Lukas Chrast
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.
| | - Katsiaryna Tratsiak
- Institute of Chemistry and Biochemistry, Faculty of Science, University of South Bohemia Ceske Budejovice and Institute of Microbiology Academy of Sciences of the Czech Republic, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic.
| | - Joan Planas-Iglesias
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.
| | - Lukas Daniel
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.
| | - Tatyana Prudnikova
- Institute of Chemistry and Biochemistry, Faculty of Science, University of South Bohemia Ceske Budejovice and Institute of Microbiology Academy of Sciences of the Czech Republic, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.
| | - Jan Brezovsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic.
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic.
| | - Ivana Kuta Smatanova
- Institute of Chemistry and Biochemistry, Faculty of Science, University of South Bohemia Ceske Budejovice and Institute of Microbiology Academy of Sciences of the Czech Republic, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.
| | - Radka Chaloupkova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.
- Enantis Ltd., Biotechnology Incubator INBIT, Kamenice 771/34, 625 00 Brno, Czech Republic.
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic.
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11
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“Bridge regions” regulate catalysis and protein stability of acylpeptide hydrolase. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.01.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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12
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Michetti D, Brandsdal BO, Bon D, Isaksen GV, Tiberti M, Papaleo E. A comparative study of cold- and warm-adapted Endonucleases A using sequence analyses and molecular dynamics simulations. PLoS One 2017; 12:e0169586. [PMID: 28192428 PMCID: PMC5305256 DOI: 10.1371/journal.pone.0169586] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/19/2016] [Indexed: 01/14/2023] Open
Abstract
The psychrophilic and mesophilic endonucleases A (EndA) from Aliivibrio salmonicida (VsEndA) and Vibrio cholera (VcEndA) have been studied experimentally in terms of the biophysical properties related to thermal adaptation. The analyses of their static X-ray structures was no sufficient to rationalize the determinants of their adaptive traits at the molecular level. Thus, we used Molecular Dynamics (MD) simulations to compare the two proteins and unveil their structural and dynamical differences. Our simulations did not show a substantial increase in flexibility in the cold-adapted variant on the nanosecond time scale. The only exception is a more rigid C-terminal region in VcEndA, which is ascribable to a cluster of electrostatic interactions and hydrogen bonds, as also supported by MD simulations of the VsEndA mutant variant where the cluster of interactions was introduced. Moreover, we identified three additional amino acidic substitutions through multiple sequence alignment and the analyses of MD-based protein structure networks. In particular, T120V occurs in the proximity of the catalytic residue H80 and alters the interaction with the residue Y43, which belongs to the second coordination sphere of the Mg2+ ion. This makes T120V an amenable candidate for future experimental mutagenesis.
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Affiliation(s)
- Davide Michetti
- The Centre for Theoretical and Computational Chemistry, Department of Chemistry, Faculty of Science and Technology, The Arctic University of Norway, Tromsø, Norway
| | - Bjørn Olav Brandsdal
- The Centre for Theoretical and Computational Chemistry, Department of Chemistry, Faculty of Science and Technology, The Arctic University of Norway, Tromsø, Norway
| | - Davide Bon
- The Centre for Theoretical and Computational Chemistry, Department of Chemistry, Faculty of Science and Technology, The Arctic University of Norway, Tromsø, Norway
| | - Geir Villy Isaksen
- The Centre for Theoretical and Computational Chemistry, Department of Chemistry, Faculty of Science and Technology, The Arctic University of Norway, Tromsø, Norway
| | - Matteo Tiberti
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Centre, Strandboulevarden 49, Copenhagen, Denmark
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza 2, Milan, Italy
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13
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Physical and molecular bases of protein thermal stability and cold adaptation. Curr Opin Struct Biol 2016; 42:117-128. [PMID: 28040640 DOI: 10.1016/j.sbi.2016.12.007] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 11/15/2016] [Accepted: 12/11/2016] [Indexed: 11/20/2022]
Abstract
The molecular bases of thermal and cold stability and adaptation, which allow proteins to remain folded and functional in the temperature ranges in which their host organisms live and grow, are still only partially elucidated. Indeed, both experimental and computational studies fail to yield a fully precise and global physical picture, essentially because all effects are context-dependent and thus quite intricate to unravel. We present a snapshot of the current state of knowledge of this highly complex and challenging issue, whose resolution would enable large-scale rational protein design.
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14
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Truongvan N, Jang SH, Lee C. Flexibility and Stability Trade-Off in Active Site of Cold-Adapted Pseudomonas mandelii Esterase EstK. Biochemistry 2016; 55:3542-9. [DOI: 10.1021/acs.biochem.6b00177] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ngoc Truongvan
- Department of Biomedical
Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan 38453, South Korea
| | - Sei-Heon Jang
- Department of Biomedical
Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan 38453, South Korea
| | - ChangWoo Lee
- Department of Biomedical
Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan 38453, South Korea
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15
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Improving the Thermostability and Activity of a Thermophilic Subtilase by Incorporating Structural Elements of Its Psychrophilic Counterpart. Appl Environ Microbiol 2015; 81:6302-13. [PMID: 26150464 DOI: 10.1128/aem.01478-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 06/29/2015] [Indexed: 11/20/2022] Open
Abstract
The incorporation of the structural elements of thermostable enzymes into their less stable counterparts is generally used to improve enzyme thermostability. However, the process of engineering enzymes with both high thermostability and high activity remains an important challenge. Here, we report that the thermostability and activity of a thermophilic subtilase were simultaneously improved by incorporating structural elements of a psychrophilic subtilase. There were 64 variable regions/residues (VRs) in the alignment of the thermophilic WF146 protease, mesophilic sphericase, and psychrophilic S41. The WF146 protease was subjected to systematic mutagenesis, in which each of its VRs was replaced with those from S41 and sphericase. After successive rounds of combination and screening, we constructed the variant PBL5X with eight amino acid residues from S41. The half-life of PBL5X at 85°C (57.1 min) was approximately 9-fold longer than that of the wild-type (WT) WF146 protease (6.3 min). The substitutions also led to an increase in the apparent thermal denaturation midpoint temperature (Tm) of the enzyme by 5.5°C, as determined by differential scanning calorimetry. Compared to the WT, PBL5X exhibited high caseinolytic activity (25 to 95°C) and high values of Km and kcat (25 to 80°C). Our study may provide a rational basis for developing highly stable and active enzymes, which are highly desired in industrial applications.
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16
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Colloc'h N, Prangé T. Functional relevance of the internal hydrophobic cavity of urate oxidase. FEBS Lett 2014; 588:1715-9. [PMID: 24657440 DOI: 10.1016/j.febslet.2014.03.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 03/10/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
Abstract
Urate oxidase from Aspergillus flavus is a 135 kDa homo-tetramer which has a hydrophobic cavity buried within each monomer and located close to its active site. Crystallographic studies under moderate gas pressure and high hydrostatic pressure have shown that both gas presence and high pressure would rigidify the cavity leading to an inhibition of the catalytic activity. Analysis of the cavity volume variations and functional modifications suggest that the flexibility of the cavity would be an essential parameter for the active site efficiency. This cavity would act as a connecting vessel to give flexibility to the neighboring active site, and its expansion under pure oxygen pressure reveals that it might serve as a transient reservoir on its pathway to the active site.
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Affiliation(s)
- Nathalie Colloc'h
- CERVoxy Team, ISTCT UMR 6301, CNRS, Centre Cyceron, Caen, France; ISTCT UMR 6301, CEA, DSV/I2BM, Caen, France; ISTCT UMR 6301, Université de Caen Basse-Normandie, Normandie Université, Caen, France.
| | - Thierry Prangé
- LCRB UMR 8015, CNRS, Université Paris Descartes, Faculté de Pharmacie, 4 Avenue de l'Observatoire, 75006 Paris, France
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17
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Kumar V, Yedavalli P, Gupta V, Rao NM. Engineering lipase A from mesophilic Bacillus subtilis for activity at low temperatures. Protein Eng Des Sel 2014; 27:73-82. [PMID: 24402332 DOI: 10.1093/protein/gzt064] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Loops or unordered regions of a protein are structurally dynamic and are strongly implicated in activity, stability and proteolytic susceptibility of proteins. Diminished activity of proteins at lower temperatures is considered to be due to compromised dynamics of the protein at lower temperatures. To evolve an active mesophilic lipase (Bacillus subtilis) at low temperatures, we subjected all the loop residues (n = 88) to site saturation mutagenesis (SSM). Based on a three-level screening protocol, we identified 14 substitutions, among 16,000 mutant population, which contributed to a substantial increase in activity at 5 °C. Based on the preliminary activity of recombinants at several temperatures, 5 substitutions among the 14 were found to be beneficial. A recombinant of these five mutations, named as 5CR, exhibited 7-fold higher catalytic efficiency than wild-type (WT) lipase at 10 °C. All the mutants, individually and in a recombinant (5CR), were characterized by substrate-binding parameters, melting temperatures and secondary structure. 5CR was similar to WT in substrate preferences and showed a significant improvement in activity at both lower and higher temperatures compared with the WT. To establish the contribution of mutations on the dynamics of the protein, we performed 100-ns molecular dynamics (MD) simulations on the WT and mutant lipase at 10 and 37 °C. The root mean square fluctuations (RMSFs) indeed showed that the mutations enhance the protein dynamics locally in the loop region having a catalytic residue, which may help in improved activities at lower temperatures.
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Affiliation(s)
- Virender Kumar
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, India
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18
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The universality of enzymatic rate-temperature dependency. Trends Biochem Sci 2013; 39:1-7. [PMID: 24315123 DOI: 10.1016/j.tibs.2013.11.001] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 10/31/2013] [Accepted: 11/01/2013] [Indexed: 11/21/2022]
Abstract
Organismal adaptation to extreme temperatures yields enzymes with distinct configurational stabilities, including thermophilic and psychrophilic enzymes, which are adapted to high and low temperatures, respectively. These enzymes are widely assumed to also have unique rate-temperature dependencies. Thermophilic enzymes, for example, are considered optimal at high temperatures and effectively inactive at low temperatures due to excess rigidity. Surveying published data, we find that thermophilic, mesophilic, and psychrophilic enzymes exhibit indistinguishable rate-temperature dependencies. Furthermore, given the nonenzymatic rate-temperature dependency, all enzymes, regardless of their operation temperatures, become >10-fold less powerful catalysts per 25 °C temperature increase. Among other factors, this loss of rate acceleration may be ascribed to thermally induced vibrations compromising the active-site catalytic configuration, suggesting that many enzymes are in fact insufficiently rigid.
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19
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Roman EA, Faraj SE, Cousido-Siah A, Mitschler A, Podjarny A, Santos J. Frataxin from Psychromonas ingrahamii as a model to study stability modulation within the CyaY protein family. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1834:1168-80. [PMID: 23429177 DOI: 10.1016/j.bbapap.2013.02.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 01/26/2013] [Accepted: 02/11/2013] [Indexed: 10/27/2022]
Abstract
Adaptation of life to low temperatures influences both protein stability and flexibility. Thus, proteins from psychrophilic organisms are excellent models to study relations between these properties. Here we focused on frataxin from Psychromonas ingrahamii (pFXN), an extreme psychrophilic sea ice bacterium that can grow at temperatures as low as -12°C. This α/β protein is highly conserved and plays a key role in iron homeostasis as an iron chaperone. In contrast to other frataxin homologs, chemical and temperature unfolding experiments showed that the thermodynamic stability of pFXN is strongly modulated by pHs: ranging from 5.5±0.9 (pH6.0) to 0.9±0.3kcalmol(-1) (pH8.0). This protein was crystallized and its X-ray structure solved at 1.45Å. Comparison of B-factor profiles between Escherichia coli and P. ingrahamii frataxin variants (51% of identity) suggests that, although both proteins share the same structural features, their flexibility distribution is different. Molecular dynamics simulations showed that protonation of His44 or His67 in pFXN lowers the mobility of regions encompassing residues 20-30 and the C-terminal end, probably through favorable electrostatic interactions with residues Asp27, Glu42 and Glu99. Since the C-terminal end of the protein is critical for the stabilization of the frataxin fold, the predictions presented may be reporting on the microscopic origin of the decrease in global stability produced near neutral pH in the psychrophilic variant. We propose that suboptimal electrostatic interactions may have been an evolutionary strategy for the adaptation of frataxin flexibility and function to cold environments.
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Affiliation(s)
- Ernesto A Roman
- Instituto de Química y Fisicoquímica Biológicas, Universidad de Buenos Aires, Buenos Aires, Argentina
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20
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Papaleo E, Renzetti G, Invernizzi G, Ásgeirsson B. Dynamics fingerprint and inherent asymmetric flexibility of a cold-adapted homodimeric enzyme. A case study of the Vibrio alkaline phosphatase. Biochim Biophys Acta Gen Subj 2013; 1830:2970-80. [DOI: 10.1016/j.bbagen.2012.12.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 12/11/2012] [Accepted: 12/13/2012] [Indexed: 01/31/2023]
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21
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Fraccalvieri D, Tiberti M, Pandini A, Bonati L, Papaleo E. Functional annotation of the mesophilic-like character of mutants in a cold-adapted enzyme by self-organising map analysis of their molecular dynamics. MOLECULAR BIOSYSTEMS 2013; 8:2680-91. [PMID: 22802143 DOI: 10.1039/c2mb25192b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multiple comparison of the Molecular Dynamics (MD) trajectories of mutants in a cold-adapted α-amylase (AHA) could be used to elucidate functional features required to restore mesophilic-like activity. Unfortunately it is challenging to identify the different dynamic behaviors and correctly relate them to functional activity by routine analysis. We here employed a previously developed and robust two-stage approach that combines Self-Organising Maps (SOMs) and hierarchical clustering to compare conformational ensembles of proteins. Moreover, we designed a novel strategy to identify the specific mutations that more efficiently convert the dynamic signature of the psychrophilic enzyme (AHA) to that of the mesophilic counterpart (PPA). The SOM trained on AHA and its variants was used to classify a PPA MD ensemble and successfully highlighted the relationships between the flexibilities of the target enzyme and of the different mutants. Moreover the local features of the mutants that mostly influence their global flexibility in a mesophilic-like direction were detected. It turns out that mutations of the cold-adapted enzyme to hydrophobic and aromatic residues are the most effective in restoring the PPA dynamic features and could guide the design of more mesophilic-like mutants. In conclusion, our strategy can efficiently extract specific dynamic signatures related to function from multiple comparisons of MD conformational ensembles. Therefore, it can be a promising tool for protein engineering.
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22
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Feller G. Psychrophilic enzymes: from folding to function and biotechnology. SCIENTIFICA 2013; 2013:512840. [PMID: 24278781 PMCID: PMC3820357 DOI: 10.1155/2013/512840] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 11/06/2012] [Indexed: 05/10/2023]
Abstract
Psychrophiles thriving permanently at near-zero temperatures synthesize cold-active enzymes to sustain their cell cycle. Genome sequences, proteomic, and transcriptomic studies suggest various adaptive features to maintain adequate translation and proper protein folding under cold conditions. Most psychrophilic enzymes optimize a high activity at low temperature at the expense of substrate affinity, therefore reducing the free energy barrier of the transition state. Furthermore, a weak temperature dependence of activity ensures moderate reduction of the catalytic activity in the cold. In these naturally evolved enzymes, the optimization to low temperature activity is reached via destabilization of the structures bearing the active site or by destabilization of the whole molecule. This involves a reduction in the number and strength of all types of weak interactions or the disappearance of stability factors, resulting in improved dynamics of active site residues in the cold. These enzymes are already used in many biotechnological applications requiring high activity at mild temperatures or fast heat-inactivation rate. Several open questions in the field are also highlighted.
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Affiliation(s)
- Georges Feller
- Laboratory of Biochemistry, Centre for Protein Engineering, Institute of Chemistry, University of Liège, B6a, 4000 Liège, Belgium
- *Georges Feller:
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23
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Kuhn E. Toward understanding life under subzero conditions: the significance of exploring psychrophilic "cold-shock" proteins. ASTROBIOLOGY 2012; 12:1078-86. [PMID: 23082745 DOI: 10.1089/ast.2012.0858] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Understanding the behavior of proteins under freezing conditions is vital for detecting and locating extraterrestrial life in cold environments, such as those found on Mars and the icy moons of Jupiter and Saturn. This review highlights the importance of studying psychrophilic "cold-shock" proteins, a topic that has yet to be explored. A strategy for analyzing the psychrophilic RNA helicase protein CsdA (Psyc_1082) from Psychrobacter arcticus 273-4 as a key protein for life under freezing temperatures is proposed. The experimental model presented here was developed based on previous data from investigations of Escherichia coli, P. arcticus 273-4, and RNA helicases. P. arcticus 273-4 is considered a model for life in freezing environments. It is capable of growing in temperatures as cold as -10°C by using physiological strategies to survive not only in freezing temperatures but also under low-water-activity and limited-nutrient-availability conditions. The analyses of its genome, transcriptome, and proteome revealed specific adaptations that allow it to inhabit freezing environments by adopting a slow metabolic strategy rather than a cellular dormancy state. During growth at subzero temperatures, P. arcticus 273-4 genes related to energy metabolism and carbon substrate incorporation are downregulated, and genes for maintenance of membranes, cell walls, and nucleic acid motion are upregulated. At -6°C, P. arcticus 273-4 does not upregulate the expression of either RNA or protein chaperones; however, it upregulates the expression of its cold-shock induced DEAD-box RNA helicase protein A (CsdA - Psyc_1082). CsdA - Psyc_1082 was investigated as a key helper protein for sustaining life in subzero conditions. Proving CsdA - Psyc_1082 to be functional as a key protein for life under freezing temperatures may extend the known minimum growth temperature of a mesophilic cell and provide key information about the mechanisms that underlie cold-induced biological systems in icy worlds.
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Affiliation(s)
- Emanuele Kuhn
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, Nevada 89512, USA.
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24
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Optimization to low temperature activity in psychrophilic enzymes. Int J Mol Sci 2012; 13:11643-11665. [PMID: 23109875 PMCID: PMC3472767 DOI: 10.3390/ijms130911643] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 09/07/2012] [Accepted: 09/10/2012] [Indexed: 01/20/2023] Open
Abstract
Psychrophiles, i.e., organisms thriving permanently at near-zero temperatures, synthesize cold-active enzymes to sustain their cell cycle. These enzymes are already used in many biotechnological applications requiring high activity at mild temperatures or fast heat-inactivation rate. Most psychrophilic enzymes optimize a high activity at low temperature at the expense of substrate affinity, therefore reducing the free energy barrier of the transition state. Furthermore, a weak temperature dependence of activity ensures moderate reduction of the catalytic activity in the cold. In these naturally evolved enzymes, the optimization to low temperature activity is reached via destabilization of the structures bearing the active site or by destabilization of the whole molecule. This involves a reduction in the number and strength of all types of weak interactions or the disappearance of stability factors, resulting in improved dynamics of active site residues in the cold. Considering the subtle structural adjustments required for low temperature activity, directed evolution appears to be the most suitable methodology to engineer cold activity in biological catalysts.
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25
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Santovito G, Marino SM, Sattin G, Cappellini R, Bubacco L, Beltramini M. Cloning and characterization of cytoplasmic carbonic anhydrase from gills of four Antarctic fish: insights into the evolution of fish carbonic anhydrase and cold adaptation. Polar Biol 2012. [DOI: 10.1007/s00300-012-1200-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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26
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Fluorescence Studies on the Stability, Flexibility and Substrate-Induced Conformational Changes of Acetate Kinases from Psychrophilic and Mesophilic Bacteria. Protein J 2012; 31:337-44. [DOI: 10.1007/s10930-012-9408-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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27
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Serine hydroxymethyltransferase from the cold adapted microorganism Psychromonas ingrahamii: a low temperature active enzyme with broad substrate specificity. Int J Mol Sci 2012; 13:1314-1326. [PMID: 22408393 PMCID: PMC3291962 DOI: 10.3390/ijms13021314] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 01/12/2012] [Accepted: 01/12/2012] [Indexed: 11/17/2022] Open
Abstract
Serine hydroxymethyltransferase from the psychrophilic microorganism Psychromonas ingrahamii was expressed in Escherichia coli and purified as a His-tag fusion protein. The enzyme was characterized with respect to its spectroscopic, catalytic, and thermodynamic properties. The properties of the psychrophilic enzyme have been contrasted with the characteristics of the homologous counterpart from E. coli, which has been structurally and functionally characterized in depth and with which it shares 75% sequence identity. Spectroscopic measures confirmed that the psychrophilic enzyme displays structural properties almost identical to those of the mesophilic counterpart. At variance, the P. ingrahamii enzyme showed decreased thermostability and high specific activity at low temperature, both of which are typical features of cold adapted enzymes. Furthermore, it was a more efficient biocatalyst compared to E. coli serine hydroxymethyltransferase (SHMT) particularly for side reactions. Many β-hydroxy-α-amino acids are SHMT substrates and represent important compounds in the synthesis of pharmaceuticals, agrochemicals and food additives. Thanks to these attractive properties, this enzyme could have a significant potential for biotechnological applications.
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Paredes DI, Watters K, Pitman DJ, Bystroff C, Dordick JS. Comparative void-volume analysis of psychrophilic and mesophilic enzymes: Structural bioinformatics of psychrophilic enzymes reveals sources of core flexibility. BMC STRUCTURAL BIOLOGY 2011; 11:42. [PMID: 22013889 PMCID: PMC3224250 DOI: 10.1186/1472-6807-11-42] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2011] [Accepted: 10/20/2011] [Indexed: 11/26/2022]
Abstract
Background Psychrophiles, cold-adapted organisms, have adapted to live at low temperatures by using a variety of mechanisms. Their enzymes are active at cold temperatures by being structurally more flexible than mesophilic enzymes. Even though, there are some indications of the possible structural mechanisms by which psychrophilic enzymes are catalytic active at cold temperatures, there is not a generalized structural property common to all psychrophilic enzymes. Results We examine twenty homologous enzyme pairs from psychrophiles and mesophiles to investigate flexibility as a key characteristic for cold adaptation. B-factors in protein X-ray structures are one way to measure flexibility. Comparing psychrophilic to mesophilic protein B-factors reveals that psychrophilic enzymes are more flexible in 5-turn and strand secondary structures. Enzyme cavities, identified using CASTp at various probe sizes, indicate that psychrophilic enzymes have larger average cavity sizes at probe radii of 1.4-1.5 Å, sufficient for water molecules. Furthermore, amino acid side chains lining these cavities show an increased frequency of acidic groups in psychrophilic enzymes. Conclusions These findings suggest that embedded water molecules may play a significant role in cavity flexibility, and therefore, overall protein flexibility. Thus, our results point to the important role enzyme flexibility plays in adaptation to cold environments.
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Affiliation(s)
- Diana I Paredes
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
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Hayashi S, Akanuma S, Onuki W, Tokunaga C, Yamagishi A. Substitutions of coenzyme-binding, nonpolar residues improve the low-temperature activity of thermophilic dehydrogenases. Biochemistry 2011; 50:8583-93. [PMID: 21894900 DOI: 10.1021/bi200925f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although enzymes of thermophilic organisms are often very resistant to thermal denaturation, they are usually less active than their mesophilic or psychrophilic homologues at moderate or low temperatures. To explore the structural features that would improve the activity of a thermophilic enzyme at less than optimal temperatures, we randomly mutated the DNA of single-site mutants of the thermostable Thermus thermophilus 3-isopropylmalate dehydrogenase that already had improved low-temperature activity and selected for additional improved low-temperature activity. A mutant (Ile279 → Val) with improved low-temperature activity contained a residue that directly interacts with the adenine of the coenzyme NAD(+), suggesting that modulation of the coenzyme-binding pocket's volume can enhance low-temperature activity. This idea was further supported by a saturation mutagenesis study of the two codons of two other residues that interact with the adenine. Furthermore, a similar type of amino acid substitution also improved the catalytic efficiency of another thermophilic dehydrogenase, T. thermophilus lactate dehydrogenase. Steady-state kinetic experiments showed that the mutations all favorably affected the catalytic turnover numbers. Thermal stability measurements demonstrated that the mutants remain very resistant to heat. Calculation of the energetic contributions to catalysis indicated that the increased turnover numbers are the result of destabilized enzyme-substrate-coenzyme complexes. Therefore, small changes in the side chain volumes of coenzyme-binding residues improved the catalytic efficiencies of two thermophilic dehydrogenases while preserving their high thermal stabilities and may be a way to improve low-temperature activities of dehydrogenases in general.
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Affiliation(s)
- Sayaka Hayashi
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
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30
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Zhao W, Zheng J, Zhou HB. A thermotolerant and cold-active mannan endo-1,4-β-mannosidase from Aspergillus niger CBS 513.88: Constitutive overexpression and high-density fermentation in Pichia pastoris. BIORESOURCE TECHNOLOGY 2011; 102:7538-7547. [PMID: 21632240 DOI: 10.1016/j.biortech.2011.04.070] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 04/19/2011] [Accepted: 04/20/2011] [Indexed: 05/30/2023]
Abstract
The mannan endo-1,4-β-mannosidase gene man26A from Aspergillus niger CBS 513.88 was optimized according to the codon usage bias in Pichia pastoris and synthesized by splicing overlap extension PCR. It was successfully expressed in P. pastoris using constitutive expression vector pGAPzαA. The recombinant endo-beta-1,4-mannanase could work in an extremely board temperature range and over 30% relative activity were retained in the temperature range of 5-60°C. The optimal pH value and temperature for activity were 5.0 and 45°C, respectively. It was highly thermotolerant with a half-life time of 15min at 90°C. A novel fed-batch strategy was developed successfully for high cell-density fermentation and mannanase activity reached 5069U/mL after cultivation for 56h in 50L fermenter. The broad working temperature range, high thermotolerance and efficient expression made this enzyme possible to be applied in food, animal feed and the production of biofuels.
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Affiliation(s)
- Wei Zhao
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China.
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31
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Tiberti M, Papaleo E. Dynamic properties of extremophilic subtilisin-like serine-proteases. J Struct Biol 2011; 174:69-83. [DOI: 10.1016/j.jsb.2011.01.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 12/19/2010] [Accepted: 01/20/2011] [Indexed: 10/18/2022]
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32
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Cavicchioli R, Charlton T, Ertan H, Mohd Omar S, Siddiqui KS, Williams TJ. Biotechnological uses of enzymes from psychrophiles. Microb Biotechnol 2011; 4:449-60. [PMID: 21733127 PMCID: PMC3815257 DOI: 10.1111/j.1751-7915.2011.00258.x] [Citation(s) in RCA: 194] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The bulk of the Earth's biosphere is cold (e.g. 90% of the ocean's waters are ≤ 5°C), sustaining a broad diversity of microbial life. The permanently cold environments vary from the deep ocean to alpine reaches and to polar regions. Commensurate with the extent and diversity of the ecosystems that harbour psychrophilic life, the functional capacity of the microorganisms that inhabitat the cold biosphere are equally diverse. As a result, indigenous psychrophilic microorganisms provide an enormous natural resource of enzymes that function effectively in the cold, and these cold‐adapted enzymes have been targeted for their biotechnological potential. In this review we describe the main properties of enzymes from psychrophiles and describe some of their known biotechnological applications and ways to potentially improve their value for biotechnology. The review also covers the use of metagenomics for enzyme screening, the development of psychrophilic gene expression systems and the use of enzymes for cleaning.
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Affiliation(s)
- R Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.
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Extremophiles: from abyssal to terrestrial ecosystems and possibly beyond. Naturwissenschaften 2011; 98:253-79. [DOI: 10.1007/s00114-011-0775-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Revised: 02/17/2011] [Accepted: 02/18/2011] [Indexed: 01/27/2023]
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Siglioccolo A, Gerace R, Pascarella S. “Cold spots” in protein cold adaptation: Insights from normalized atomic displacement parameters (B′-factors). Biophys Chem 2010; 153:104-14. [DOI: 10.1016/j.bpc.2010.10.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Revised: 10/13/2010] [Accepted: 10/13/2010] [Indexed: 11/16/2022]
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Feller G. Protein stability and enzyme activity at extreme biological temperatures. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:323101. [PMID: 21386475 DOI: 10.1088/0953-8984/22/32/323101] [Citation(s) in RCA: 163] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Psychrophilic microorganisms thrive in permanently cold environments, even at subzero temperatures. To maintain metabolic rates compatible with sustained life, they have improved the dynamics of their protein structures, thereby enabling appropriate molecular motions required for biological activity at low temperatures. As a consequence of this structural flexibility, psychrophilic proteins are unstable and heat-labile. In the upper range of biological temperatures, thermophiles and hyperthermophiles grow at temperatures > 100 °C and synthesize ultra-stable proteins. However, thermophilic enzymes are nearly inactive at room temperature as a result of their compactness and rigidity. At the molecular level, both types of extremophilic proteins have adapted the same structural factors, but in opposite directions, to address either activity at low temperatures or stability in hot environments. A model based on folding funnels is proposed accounting for the stability-activity relationships in extremophilic proteins.
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Affiliation(s)
- Georges Feller
- Laboratory of Biochemistry, Centre for Protein Engineering, Institute of Chemistry B6a, University of Liège, B-4000 Liège, Belgium.
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Siglioccolo A, Bossa F, Pascarella S. Structural adaptation of serine hydroxymethyltransferase to low temperatures. Int J Biol Macromol 2009; 46:37-46. [PMID: 19815026 DOI: 10.1016/j.ijbiomac.2009.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Revised: 09/24/2009] [Accepted: 09/28/2009] [Indexed: 11/16/2022]
Abstract
Structural adaptation of serine hydroxymethyltransferase (SHMT), a pyridoxal-5'-phosphate dependent enzyme that catalyzes the reversible conversion of l-serine and tetrahydropteroylglutamate to glycine and 5,10-methylene-tetrahydropteroylglutamate, synthesized by microorganisms adapted to low temperatures has been analyzed using a comparative approach. The variations of amino acid properties and frequencies among three temperature populations (psychrophilic, mesophilic, hyper- and thermophilic) of SHMT sequences have been tested. SHMTs display a general increase of polarity specially in the core, a more negatively charged surface, and enhanced flexibility. Subunit interface is more hydrophilic and less compact. Electrostatic potential of the tetrahydrofolate binding site has been compared. The enzyme from Psychromonas ingrahamii, the organism with the lowest adaptation temperatures, displayed the most positive potential. In general, the property variations show a coherent opposite trend in the hyperthermophilic population: in particular, increase of hydrophobicity, packing and decrease of flexibility was observed.
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Affiliation(s)
- Alessandro Siglioccolo
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Italy
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