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Hu W, Wang J, Li J, Yang M, Li Z, Zhang X, Wu F, Zhang Y, Luo Z, Xu H. Improvement of duplex-specific nuclease salt tolerance by fusing DNA-binding domain of DNase from an extremely halotolerant bacterium Thioalkalivibrio sp. K90mix. Extremophiles 2023; 27:11. [PMID: 37178420 DOI: 10.1007/s00792-023-01296-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/07/2023] [Indexed: 05/15/2023]
Abstract
Salt tolerance is an important property of duplex-specific nuclease (DSN). DSN with high salt tolerance can be more widely used in genetic engineering, especially in the production of nucleic acid drugs. To improve the salt tolerance of DSN, we selected five DNA-binding domains from extremophilic organisms, which have been shown the ability to improve salt tolerance of DNA polymerases and nucleases. The experimental results demonstrated that the fusion protein TK-DSN produced by fusing a N-terminal DNA-binding domain, which comprised two HhH (helix-hairpin-helix) motifs domain from an extremely halotolerant bacterium Thioalkalivibrio sp. K90mix, has a significantly improved salt tolerance. TK-DSN can tolerate the concentration of NaCl up to 800 mM; in addition, the ability of digesting DNA was also enhanced during in vitro transcription and RNA purification. This strategy provides the method for the personalized customization of biological tool enzymes for different applications.
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Affiliation(s)
- Wenhao Hu
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Jin Wang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Juan Li
- Key Laboratory of Edible Oil Quality and Safety for State Market Regulation, Wuhan Institute for Food and Cosmetic Control, Wuhan, 430040, China
| | - Mengxia Yang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Zhixing Li
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Xuning Zhang
- Jiangsu BestEnzymes Biotech Co. Ltd, Lianyungang, 222005, China
| | - Fang Wu
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Yaqi Zhang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Zhidan Luo
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China.
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China.
| | - Henghao Xu
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China.
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China.
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Improving the catalytic efficiency and substrate affinity of a novel esterase from marine Klebsiella aerogenes by random and site-directed mutation. World J Microbiol Biotechnol 2021; 37:106. [PMID: 34037848 DOI: 10.1007/s11274-021-03069-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 05/12/2021] [Indexed: 10/21/2022]
Abstract
A novel esterase (EstKa) from marine Klebsiella aerogenes was characterized with hydrolytic activity against p-nitrophenyl caprylate (pNPC, C8) under optimum conditions (50 °C and pH 8.5). After two rounds of mutagenesis, two highly potential mutants (I6E9 and L7B11) were obtained with prominent activity, substrate affinity and thermostability. I6E9 (L90Q/P96T) and L7B11 (A37S/Q100L/S133G/R138C/Q156R) were 1.56- and 1.65-fold higher than EstKa in relative catalytic efficiency. The influence of each amino acid on enzyme activity was explored by site-directed mutation. The mutants Pro96Thr and Gln156Arg showed 1.29- and 1.48-fold increase in catalytic efficiency (Kcat/Km) and 54.4 and 36.2% decrease in substrate affinity (Km), respectively. The compound mutant Pro96Thr/Gln156Arg exhibited 68.9% decrease in Km and 1.41-fold increase in Kcat/Km relative to EstKa. Homology model structure analysis revealed that the replacement of Gln by hydrophilic Arg on the esterase surface improved the microenvironment stability and the activity. The replacement of Pro by Thr enabled the esterase enzyme to retain 90% relative activity after 3 h incubation at 45 °C. Structural analysis confirmed that the formation of a hydrogen bond leads to a notable increase of catalytic efficiency under high temperature conditions.
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Shaukat A, Anaya-Plaza E, Julin S, Linko V, Torres T, de la Escosura A, Kostiainen MA. Phthalocyanine-DNA origami complexes with enhanced stability and optical properties. Chem Commun (Camb) 2021; 56:7341-7344. [PMID: 32483566 DOI: 10.1039/d0cc01916j] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this communication, electrostatically assembled phthalocyanine (Pc)-DNA origami (DO) complexes are formed and their optical properties are demonstrated. The formation of the complex prevents the Pc aggregation, thus yielding an enhanced optical response and photooxidative resilience towards aggregation in biologically relevant media. Simultaneously, the Pc protects the DO against enzymatic digestion. Both features solve previous drawbacks associated with phthalocyanine photosensitizers and DNA nanocarriers. The studied complexes may find use in technologies related to the photogeneration of singlet oxygen, e.g., photocatalysis, diagnositic arrays and photodynamic therapy.
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Affiliation(s)
- Ahmed Shaukat
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, FI-00076 Aalto, Finland.
| | - Eduardo Anaya-Plaza
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, FI-00076 Aalto, Finland.
| | - Sofia Julin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, FI-00076 Aalto, Finland.
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, FI-00076 Aalto, Finland. and HYBER Centre, Department of Applied Physics, Aalto University, FI-00076 Aalto, Finland
| | - Tomas Torres
- Department of Organic Chemistry, Universidad Autónoma de Madrid (UAM), Calle Francisco Tomás y Valiente, 7, 28049 Madrid, Spain. and Institute for Advanced Research in Chemical Sciences (IAdChem), 28049 Cantoblanco, Madrid, Spain and IMDEA Nanosience, Ciudad Universitaria de Cantoblanco, 28049 Madrid, Spain
| | - Andrés de la Escosura
- Department of Organic Chemistry, Universidad Autónoma de Madrid (UAM), Calle Francisco Tomás y Valiente, 7, 28049 Madrid, Spain. and Institute for Advanced Research in Chemical Sciences (IAdChem), 28049 Cantoblanco, Madrid, Spain
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, FI-00076 Aalto, Finland. and HYBER Centre, Department of Applied Physics, Aalto University, FI-00076 Aalto, Finland
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Liao Y, Williams TJ, Ye J, Charlesworth J, Burns BP, Poljak A, Raftery MJ, Cavicchioli R. Morphological and proteomic analysis of biofilms from the Antarctic archaeon, Halorubrum lacusprofundi. Sci Rep 2016; 6:37454. [PMID: 27874045 PMCID: PMC5118699 DOI: 10.1038/srep37454] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/26/2016] [Indexed: 12/21/2022] Open
Abstract
Biofilms enhance rates of gene exchange, access to specific nutrients, and cell survivability. Haloarchaea in Deep Lake, Antarctica, are characterized by high rates of intergenera gene exchange, metabolic specialization that promotes niche adaptation, and are exposed to high levels of UV-irradiation in summer. Halorubrum lacusprofundi from Deep Lake has previously been reported to form biofilms. Here we defined growth conditions that promoted the formation of biofilms and used microscopy and enzymatic digestion of extracellular material to characterize biofilm structures. Extracellular DNA was found to be critical to biofilms, with cell surface proteins and quorum sensing also implicated in biofilm formation. Quantitative proteomics was used to define pathways and cellular processes involved in forming biofilms; these included enhanced purine synthesis and specific cell surface proteins involved in DNA metabolism; post-translational modification of cell surface proteins; specific pathways of carbon metabolism involving acetyl-CoA; and specific responses to oxidative stress. The study provides a new level of understanding about the molecular mechanisms involved in biofilm formation of this important member of the Deep Lake community.
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Affiliation(s)
- Y Liao
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - T J Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - J Ye
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia.,Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - J Charlesworth
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - B P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - A Poljak
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales, Australia
| | - M J Raftery
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales, Australia
| | - R Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
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