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Skowron PM, Łubkowska B, Sobolewski I, Zylicz-Stachula A, Šimoliūnienė M, Šimoliūnas E. Bacteriophages of Thermophilic ' Bacillus Group' Bacteria-A Systematic Review, 2023 Update. Int J Mol Sci 2024; 25:3125. [PMID: 38542099 PMCID: PMC10969951 DOI: 10.3390/ijms25063125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 04/05/2024] Open
Abstract
Bacteriophages associated with thermophiles are gaining increased attention due to their pivotal roles in various biogeochemical and ecological processes, as well as their applications in biotechnology and bionanotechnology. Although thermophages are not suitable for controlling bacterial infections in humans or animals, their individual components, such as enzymes and capsid proteins, can be employed in molecular biology and significantly contribute to the enhancement of human and animal health. Despite their significance, thermophages still remain underrepresented in the known prokaryotic virosphere, primarily due to limited in-depth investigations. However, due to their unique properties, thermophages are currently attracting increasing interest, as evidenced by several newly discovered phages belonging to this group. This review offers an updated compilation of thermophages characterized to date, focusing on species infecting the thermophilic bacilli. Moreover, it presents experimental findings, including novel proteomic data (39 proteins) concerning the model TP-84 bacteriophage, along with the first announcement of 6 recently discovered thermophages infecting Geobacillus thermodenitrificans: PK5.2, PK2.1, NIIg10.1, NIIg2.1, NIIg2.2, and NIIg2.3. This review serves as an update to our previous publication in 2021.
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Affiliation(s)
- Piotr M. Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.S.); (A.Z.-S.)
| | - Beata Łubkowska
- Faculty of Health and Life Sciences, Gdansk University of Physical Education and Sport, K. Gorskiego 1, 80-336 Gdansk, Poland;
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy
| | - Ireneusz Sobolewski
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.S.); (A.Z.-S.)
| | - Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.S.); (A.Z.-S.)
| | - Monika Šimoliūnienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio Av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Š.)
| | - Eugenijus Šimoliūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio Av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Š.)
- Department of Microbiology and Biotechnology, Institute of Bioscience, Life Sciences Center, Vilnius University, Sauletekio Av. 7, LT-10257 Vilnius, Lithuania
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Łubkowska B, Sobolewski I, Adamowicz K, Zylicz-Stachula A, Skowron PM. Recombinant TP-84 Bacteriophage Glycosylase-Depolymerase Confers Activity against Thermostable Geobacillus stearothermophilus via Capsule Degradation. Int J Mol Sci 2024; 25:722. [PMID: 38255796 PMCID: PMC10815759 DOI: 10.3390/ijms25020722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
The TP-84 bacteriophage, which infects Geobacillus stearothermophilus strain 10 (G. stearothermophilus), has a genome size of 47.7 kilobase pairs (kbps) and contains 81 predicted protein-coding ORFs. One of these, TP84_26 encodes a putative tail fiber protein possessing capsule depolymerase activity. In this study, we cloned the TP84_26 gene into a high-expression Escherichia coli (E. coli) system, modified its N-terminus with His-tag, expressed both the wild type gene and His-tagged variant, purified the recombinant depolymerase variants, and further evaluated their properties. We developed a direct enzymatic assay for the depolymerase activity toward G. stearothermophilus capsules. The recombinant TP84_26 protein variants effectively degraded the existing bacterial capsules and inhibited the formation of new ones. Our results provide insights into the novel TP84_26 depolymerase with specific activity against thermostable G. stearothermophilus and its role in the TP-84 life cycle. The identification and characterization of novel depolymerases, such as TP84_26, hold promise for innovative strategies to combat bacterial infections and improve various industrial processes.
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Affiliation(s)
- Beata Łubkowska
- Faculty of Health and Life Sciences, Gdansk University of Physical Education and Sport, K. Gorskiego 1, 80-336 Gdansk, Poland
| | - Ireneusz Sobolewski
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.S.); (K.A.); (A.Z.-S.); (P.M.S.)
| | - Katarzyna Adamowicz
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.S.); (K.A.); (A.Z.-S.); (P.M.S.)
| | - Agnieszka Zylicz-Stachula
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.S.); (K.A.); (A.Z.-S.); (P.M.S.)
| | - Piotr M. Skowron
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.S.); (K.A.); (A.Z.-S.); (P.M.S.)
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Brankiewicz W, Kalathiya U, Padariya M, Węgrzyn K, Prusinowski M, Zebrowska J, Zylicz-Stachula A, Skowron P, Drab M, Szajewski M, Ciesielski M, Gawrońska M, Kallingal A, Makowski M, Bagiński M. Modified Peptide Molecules As Potential Modulators of Shelterin Protein Functions; TRF1. Chemistry 2023; 29:e202300970. [PMID: 37332024 DOI: 10.1002/chem.202300970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 06/20/2023]
Abstract
In this work, we present studies on relatively new and still not well-explored potential anticancer targets which are shelterin proteins, in particular the TRF1 protein can be blocked by in silico designed "peptidomimetic" molecules. TRF1 interacts directly with the TIN2 protein, and this protein-protein interaction is crucial for the proper functioning of telomere, which could be blocked by our novel modified peptide molecules. Our chemotherapeutic approach is based on assumption that modulation of TRF1-TIN2 interaction may be more harmful for cancer cells as cancer telomeres are more fragile than in normal cells. We have shown in vitro within SPR experiments that our modified peptide PEP1 molecule interacts with TRF1, presumably at the site originally occupied by the TIN2 protein. Disturbance of the shelterin complex by studied molecule may not in short term lead to cytotoxic effects, however blocking TRF1-TIN2 resulted in cellular senescence in cellular breast cancer lines used as a cancer model. Thus, our compounds appeared useful as starting model compounds for precise blockage of TRF proteins.
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Affiliation(s)
- Wioletta Brankiewicz
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St 11/12, 80-233, Gdansk, Poland
| | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822, Gdańsk, Poland
| | - Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822, Gdańsk, Poland
| | - Katarzyna Węgrzyn
- Intercollegiate Faculty of Biotechnology, University of Gdansk, Abrahama 58, 80-307, Gdansk, Poland
| | - Maciej Prusinowski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Joanna Zebrowska
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | | | - Piotr Skowron
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Marek Drab
- Unit of Nanostructural Bio-Interactions, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 12 Weigla-Street, 53-114, Wrocław, Poland
| | - Mariusz Szajewski
- Department of Oncological Surgery, Gdynia Oncology Centre, Gdynia, Poland
- Division of Propaedeutics of Oncology, Medical University of Gdańsk, Gdańsk, Poland
| | - Maciej Ciesielski
- Department of Oncological Surgery, Gdynia Oncology Centre, Gdynia, Poland
- Division of Propaedeutics of Oncology, Medical University of Gdańsk, Gdańsk, Poland
| | - Małgorzata Gawrońska
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Anoop Kallingal
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St 11/12, 80-233, Gdansk, Poland
| | - Mariusz Makowski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Maciej Bagiński
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St 11/12, 80-233, Gdansk, Poland
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Łubkowska B, Czajkowska E, Stodolna A, Sroczyński M, Zylicz-Stachula A, Sobolewski I, Skowron PM. Correction: A novel thermostable TP-84 capsule depolymerase: a method for rapid polyethyleneimine processing of a bacteriophage-expressed proteins. Microb Cell Fact 2023; 22:146. [PMID: 37537640 PMCID: PMC10398908 DOI: 10.1186/s12934-023-02157-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023] Open
Affiliation(s)
- Beata Łubkowska
- Faculty of Health and Life Sciences, Division of Biochemistry, Gdansk University of Physical Education and Sport, Gorskiego 1, Gdansk, 80-336, Poland.
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland.
| | - Edyta Czajkowska
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
| | - Aleksandra Stodolna
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
| | - Michał Sroczyński
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
| | - Agnieszka Zylicz-Stachula
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
| | - Ireneusz Sobolewski
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
- BioGel Sp. z o.o. (Ltd.), ul. Promienista 83, Poznań, 60-141, Poland
| | - Piotr M Skowron
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
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Witkowska M, Jedrzejczak RP, Joachimiak A, Cavdar O, Malankowska A, Skowron PM, Zylicz-Stachula A. Promising approaches for the assembly of the catalytically active, recombinant Desulfomicrobium baculatum hydrogenase with substitutions at the active site. Microb Cell Fact 2023; 22:134. [PMID: 37479997 PMCID: PMC10362691 DOI: 10.1186/s12934-023-02127-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/17/2023] [Indexed: 07/23/2023] Open
Abstract
BACKGROUND Hydrogenases (H2ases) are metalloenzymes capable of the reversible conversion of protons and electrons to molecular hydrogen. Exploiting the unique enzymatic activity of H2ases can lead to advancements in the process of biohydrogen evolution and green energy production. RESULTS Here we created of a functional, optimized operon for rapid and robust production of recombinant [NiFe] Desulfomicrobium baculatum hydrogenase (Dmb H2ase). The conversion of the [NiFeSe] Dmb H2ase to [NiFe] type was performed on genetic level by site-directed mutagenesis. The native dmb operon includes two structural H2ase genes, coding for large and small subunits, and an additional gene, encoding a specific maturase (protease) that is essential for the proper maturation of the enzyme. Dmb, like all H2ases, needs intricate bio-production machinery to incorporate its crucial inorganic ligands and cofactors. Strictly anaerobic, sulfate reducer D. baculatum bacteria are distinct, in terms of their biology, from E. coli. Thus, we introduced a series of alterations within the native dmb genes. As a result, more than 100 elements, further compiled into 32 operon variants, were constructed. The initial requirement for a specific maturase was omitted by the artificial truncation of the large Dmb subunit. The assembly of the produced H2ase subunit variants was investigated both, in vitro and in vivo. This approach resulted in 4 recombinant [NiFe] Dmb enzyme variants, capable of H2 evolution. The aim of this study was to overcome the gene expression, protein biosynthesis, maturation and ligand loading bottlenecks for the easy, fast, and cost-effective delivery of recombinant [NiFe] H2ase, using a commonly available E. coli strains. CONCLUSION The optimized genetic constructs together with the developed growth and purification procedures appear to be a promising platform for further studies toward fully-active and O2 tolerant, recombinant [NiFeSe] Dmb H2ase, resembling the native Dmb enzyme. It could likely be achieved by selective cysteine to selenocysteine substitution within the active site of the [NiFe] Dmb variant.
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Affiliation(s)
- Malgorzata Witkowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
| | - Robert P Jedrzejczak
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Andrzej Joachimiak
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Onur Cavdar
- Department of Environmental Technology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
| | - Anna Malankowska
- Department of Environmental Technology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
| | - Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
| | - Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland.
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Łubkowska B, Czajkowska E, Stodolna A, Sroczyński M, Zylicz-Stachula A, Sobolewski I, Skowron PM. A novel thermostable TP-84 capsule depolymerase: a method for rapid polyethyleneimine processing of a bacteriophage-expressed proteins. Microb Cell Fact 2023; 22:80. [PMID: 37098567 PMCID: PMC10131341 DOI: 10.1186/s12934-023-02086-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/09/2023] [Indexed: 04/27/2023] Open
Abstract
BACKGROUND In spite of the fact that recombinant enzymes are preferably biotechnologically obtained using recombinant clones, the purification of proteins from native microorganisms, including those encoded by bacteriophages, continues. The native bacteriophage protein isolation is often troubled by large volumes of the infected bacterial cell lysates needed to be processed, which is highly undesired in scaled-up industrial processing. A well-known ammonium sulphate fractionation is often a method of choice during purification of the native bacteriophage protein. However, this method is time-consuming and cumbersome, and requires large amounts of the relatively expensive reagent. Thus, other effective and inexpensive methods of reversible protein precipitation are highly desirable. We have previously characterized thermophilic TP-84 bacteriophage, defined a new genus TP84virus within Siphoviridae family, conducted the TP-84 genome annotation and proteomic analysis. The longest Open Reading Frame (ORF) identified in the genome is TP84_26. We have previously annotated this ORF as a hydrolytic enzyme depolymerizing the thick polysaccharides host's capsule. RESULTS The TP84_26 'capsule depolymerase' (depolymerase) is a large, 112 kDa protein, biosynthesized by the infected Geobacillus stearothermophilus 10 (G. stearothermophilus 10) cells. The TP84_26 protein biosynthesis was confirmed by three approaches: (i) purification of the protein of the expected size; (ii) mass spectrometry (LC-MS) analysis and (iii) detection of the enzymatic activity toward G. stearothermophilus polysaccharide capsules. Streptomycin-resistant mutant of the host was generated and microbiological aspects of both the TP-84 and G. stearothermophilus 10 were determined. A new variant of polyethyleneimine (PEI)-mediated purification method was developed, using the novel TP-84 depolymerase as a model. The enzyme was characterized. Three depolymerase forms were detected: soluble, unbound proteins in the bacteriophage/cells lysate and another integrated into the TP-84 virion. CONCLUSIONS The novel TP-84 depolymerase was purified and characterized. The enzyme exists in three forms. The soluble, unbound forms are probably responsible for the weakening of the capsules of the uninfected bacterial cells. The form integrated into virion particles may generate a local passage for the invading TP-84. The developed PEI purification method appears well suited for the scaled-up or industrial production of bacteriophage proteins.
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Affiliation(s)
- Beata Łubkowska
- Faculty of Health and Life Sciences, Division of Biochemistry, Gdansk University of Physical Education and Sport, Gorskiego 1, 80-336, Gdansk, Poland.
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland.
| | - Edyta Czajkowska
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Aleksandra Stodolna
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Michał Sroczyński
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Agnieszka Zylicz-Stachula
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Ireneusz Sobolewski
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
- BioGel Sp. z o.o. (Ltd.), ul. Promienista 83, 60-141, Poznań, Poland
| | - Piotr M Skowron
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
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Krawczun N, Bielawa M, Szemiako K, Łubkowska B, Sobolewski I, Zylicz-Stachula A, Skowron PM. A method for the transient inhibition of toxicity of secretory recombinant proteins, exemplified by bacterial alkaline phosphatase. Novel protocol for problematic DNA termini dephosphorylation. MethodsX 2021; 8:101340. [PMID: 34430244 PMCID: PMC8374387 DOI: 10.1016/j.mex.2021.101340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 04/01/2021] [Indexed: 11/28/2022] Open
Abstract
Genes encoding proteins ‘toxic' to recombinant host are difficult for cloning/expression and recombinant clones are unstable. Even tightly controlled inducible T7-lac, PBAD, PL, PR promoters are not totally silent in an uninduced state and thus not adequate for highly toxic proteins. An innovative approach to engineering and expression of the gene, encoding bacterial alkaline phosphatase (BAP) is proposed. The native precursor enzyme contains a signal peptide at the N-terminus and is secreted to the Escherichia coli (E. coli) periplasm. The signal peptide is then removed that allows oxidation and formation of active dimers. To decrease toxicity of the bap gene, its secretion leader coding section was replaced with a N-terminal His6-tag. The gene was expressed in E. coli in a PBAD vector, resulting in the accumulation of soluble His6-BAP in the cytoplasm. The His6-BAP was neutral to the cells, as no maturation was possible in the reducing cytoplasm. The purified homogenous protein was further reactivated in a redox buffer containing the protein structure stabilizing cofactors. The His6-BAP exhibited high activity. A dephosphorylation protocol for all types of DNA termini was developed.The method appears well suited for the industrial production of BAP and can be applied to other problematic proteins.Efficient toxic gene expression Novel approach to toxic gene cloning, engineering, expression, purification and reactivation of the transiently inactivated enzyme Scaled-up production of ultrapure BAP Improved protocol for all types of DNA termini dephosphorylation
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Affiliation(s)
- Natalia Krawczun
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland
| | - Marta Bielawa
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland
| | - Kasjan Szemiako
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland
| | - Beata Łubkowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland
| | - Ireneusz Sobolewski
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland
| | - Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland
| | - Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland
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Krawczun N, Bielawa M, Szemiako K, Łubkowska B, Sobolewski I, Zylicz-Stachula A, Skowron PM. Boosting toxic protein biosynthesis: transient in vivo inactivation of engineered bacterial alkaline phosphatase. Microb Cell Fact 2020; 19:166. [PMID: 32811518 PMCID: PMC7437050 DOI: 10.1186/s12934-020-01424-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/11/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The biotechnology production of enzymes is often troubled by the toxicity of the recombinant products of cloned and expressed genes, which interferes with the recombinant hosts' metabolism. Various approaches have been taken to overcome these limitations, exemplified by tight control of recombinant genes or secretion of recombinant proteins. An industrial approach to protein production demands maximum possible yields of biosynthesized proteins, balanced with the recombinant host's viability. Bacterial alkaline phosphatase (BAP) from Escherichia coli (E. coli) is a key enzyme used in protein/antibody detection and molecular cloning. As it removes terminal phosphate from DNA, RNA and deoxyribonucleoside triphosphates, it is used to lower self-ligated vectors' background. The precursor enzyme contains a signal peptide at the N-terminus and is secreted to the E. coli periplasm. Then, the leader is clipped off and dimers are formed upon oxidation. RESULTS We present a novel approach to phoA gene cloning, engineering, expression, purification and reactivation of the transiently inactivated enzyme. The recombinant bap gene was modified by replacing a secretion leader coding section with a N-terminal His6-tag, cloned and expressed in E. coli in a PBAD promoter expression vector. The gene expression was robust, resulting in accumulation of His6-BAP in the cytoplasm, exceeding 50% of total cellular proteins. The His6-BAP protein was harmless to the cells, as its natural toxicity was inhibited by the reducing environment within the E. coli cytoplasm, preventing formation of the active enzyme. A simple protocol based on precipitation and immobilized metal affinity chromatography (IMAC) purification yielded homogeneous protein, which was reactivated by dialysis into a redox buffer containing reduced and oxidized sulfhydryl group compounds, as well as the protein structure stabilizing cofactors Zn2+, Mg2+ and phosphate. The reconstituted His6-BAP exhibited high activity and was used to develop an efficient protocol for all types of DNA termini, including problematic ones (blunt, 3'-protruding). CONCLUSIONS The developed method appears well suited for the industrial production of ultrapure BAP. Further, the method of transient inactivation of secreted toxic enzymes by conducting their biosynthesis in an inactive state in the cytoplasm, followed by in vitro reactivation, can be generally applied to other problematic proteins.
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Affiliation(s)
- Natalia Krawczun
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Marta Bielawa
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Kasjan Szemiako
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Beata Łubkowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Ireneusz Sobolewski
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland.
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Skowron PM, Krawczun N, Żebrowska J, Krefft D, Żołnierkiewicz O, Bielawa M, Jeżewska-Frąckowiak J, Janus Ł, Witkowska M, Palczewska M, Schumacher A, Wardowska A, Deptuła M, Czupryn A, Mucha P, Piotrowski A, Sachadyn P, Rodziewicz-Motowidło S, Pikuła M, Zylicz-Stachula A. Data regarding a new, vector-enzymatic DNA fragment amplification-expression technology for the construction of artificial, concatemeric DNA, RNA and proteins, as well as biological effects of selected polypeptides obtained using this method. Data Brief 2020; 28:105069. [PMID: 31956674 PMCID: PMC6956754 DOI: 10.1016/j.dib.2019.105069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 10/25/2022] Open
Abstract
Applications of bioactive peptides and polypeptides are emerging in areas such as drug development and drug delivery systems. These compounds are bioactive, biocompatible and represent a wide range of chemical properties, enabling further adjustments of obtained biomaterials. However, delivering large quantities of peptide derivatives is still challenging. Several methods have been developed for the production of concatemers - multiple copies of the desired protein segments. We have presented an efficient method for the production of peptides of desired length, expressed from concatemeric Open Reading Frame. The method employs specific amplification-expression DNA vectors. The main methodological approaches are described by Skowron et al., 2020 [1]. As an illustration of the demonstrated method's utility, an epitope from the S protein of Hepatitis B virus (HBV) was amplified. Additionally, peptides, showing potentially pro-regenerative properties, derived from the angiopoietin-related growth factor (AGF) were designed and amplified. Here we present a dataset including: (i) detailed protocols for the purification of HBV and AGF - derived polyepitopic protein concatemers, (ii) sequences of the designed primers, vectors and recombinant constructs, (iii) data on cytotoxicity, immunogenicity and stability of AGF-derived polypeptides.
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Affiliation(s)
- Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland.,BioVentures Institute Ltd., Poznan, 60-141, Poland
| | - Natalia Krawczun
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland.,BioVentures Institute Ltd., Poznan, 60-141, Poland
| | - Joanna Żebrowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland.,BioVentures Institute Ltd., Poznan, 60-141, Poland
| | - Daria Krefft
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland.,BioVentures Institute Ltd., Poznan, 60-141, Poland
| | - Olga Żołnierkiewicz
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland
| | | | - Joanna Jeżewska-Frąckowiak
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland.,BioVentures Institute Ltd., Poznan, 60-141, Poland
| | - Łukasz Janus
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland.,BioVentures Institute Ltd., Poznan, 60-141, Poland
| | - Małgorzata Witkowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland
| | - Małgorzata Palczewska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland
| | - Adriana Schumacher
- Department of Embryology, Faculty of Medicine, Medical University of Gdansk, Gdansk, 80-211, Poland.,Department of Clinical Immunology and Transplantology, Faculty of Medicine, Medical University of Gdansk, 80-210, Poland
| | - Anna Wardowska
- Department of Clinical Immunology and Transplantology, Faculty of Medicine, Medical University of Gdansk, 80-210, Poland.,Laboratory of Tissue Engineering and Regenerative Medicine, Department of Embryology, Faculty of Medicine, Medical University of Gdansk, Gdansk, 80-211, Poland
| | - Milena Deptuła
- Laboratory of Tissue Engineering and Regenerative Medicine, Department of Embryology, Faculty of Medicine, Medical University of Gdansk, Gdansk, 80-211, Poland
| | - Artur Czupryn
- Nencki Institute of Experimental Biology, Warsaw, 02-093, Poland
| | - Piotr Mucha
- Department of Molecular Biochemistry, Faculty of Chemistry, University of Gdansk, 80-308, Poland
| | - Arkadiusz Piotrowski
- Department of Biology and Pharmaceutical Botany, Faculty of Pharmacy, Medical University of Gdansk, 80-416, Poland.,International Research Agenda - 3P Medicine Lab, Medical University of Gdansk, 80-416, Poland
| | - Paweł Sachadyn
- Laboratory for Regenerative Biotechnology, Faculty of Chemistry, Gdansk University of Technology, Gdansk, 80-233, Poland
| | | | - Michał Pikuła
- Department of Clinical Immunology and Transplantology, Faculty of Medicine, Medical University of Gdansk, 80-210, Poland.,Laboratory of Tissue Engineering and Regenerative Medicine, Department of Embryology, Faculty of Medicine, Medical University of Gdansk, Gdansk, 80-211, Poland
| | - Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland.,BioVentures Institute Ltd., Poznan, 60-141, Poland
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Skowron PM, Krawczun N, Żebrowska J, Krefft D, Żołnierkiewicz O, Bielawa M, Jeżewska-Frąckowiak J, Janus Ł, Witkowska M, Palczewska M, Zylicz-Stachula A. An efficient method for the construction of artificial, concatemeric DNA, RNA and proteins with genetically programmed functions, using a novel, vector-enzymatic DNA fragment amplification-expression technology. MethodsX 2020; 7:101070. [PMID: 33083239 PMCID: PMC7551362 DOI: 10.1016/j.mex.2020.101070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 08/25/2020] [Accepted: 09/17/2020] [Indexed: 11/18/2022] Open
Affiliation(s)
- Piotr M. Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland
- BioVentures Institute Ltd., Poznan 60-141, Poland
- Corresponding author at: Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland.
| | - Natalia Krawczun
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland
- BioVentures Institute Ltd., Poznan 60-141, Poland
| | - Joanna Żebrowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland
- BioVentures Institute Ltd., Poznan 60-141, Poland
| | - Daria Krefft
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland
- BioVentures Institute Ltd., Poznan 60-141, Poland
| | - Olga Żołnierkiewicz
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland
| | | | - Joanna Jeżewska-Frąckowiak
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland
- BioVentures Institute Ltd., Poznan 60-141, Poland
| | - Łukasz Janus
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland
- BioVentures Institute Ltd., Poznan 60-141, Poland
| | - Małgorzata Witkowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland
| | - Małgorzata Palczewska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland
| | - Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland
- BioVentures Institute Ltd., Poznan 60-141, Poland
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Skowron PM, Krawczun N, Zebrowska J, Krefft D, Zołnierkiewicz O, Bielawa M, Jezewska-Frackowiak J, Janus L, Witkowska M, Palczewska M, Schumacher A, Wardowska A, Deptula M, Czupryn A, Mucha P, Piotrowski A, Sachadyn P, Rodziewicz-Motowidlo S, Pikula M, Zylicz-Stachula A. A vector-enzymatic DNA fragment amplification-expression technology for construction of artificial, concatemeric DNA, RNA and proteins for novel biomaterials, biomedical and industrial applications. Mater Sci Eng C Mater Biol Appl 2019; 108:110426. [PMID: 31923928 DOI: 10.1016/j.msec.2019.110426] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 10/17/2019] [Accepted: 11/11/2019] [Indexed: 12/12/2022]
Abstract
A DNA fragment amplification/expression technology for the production of new generation biomaterials for scientific, industrial and biomedical applications is described. The technology enables the formation of artificial Open Reading Frames (ORFs) encoding concatemeric RNAs and proteins. It recruits the Type IIS SapI restriction endonuclease (REase) for an assembling of DNA fragments in an ordered head-to-tail-orientation. The technology employs a vector-enzymatic system, dedicated to the expression of newly formed, concatemeric ORFs from strong promoters. Four vector series were constructed to suit specialised needs. As a proof of concept, a model amplification of a 7-amino acid (aa) epitope from the S protein of HBV virus was performed, resulting in 500 copies of the epitope-coding DNA segment, consecutively linked and expressed in Escherichia coli (E. coli). Furthermore, a peptide with potential pro-regenerative properties (derived from an angiopoietin-related growth factor) was designed. Its aa sequence was back-translated, codon usage optimized and synthesized as a continuous ORF 10-mer. The 10-mer was cloned into the amplification vector, enabling the N-terminal fusion and multiplication of the encoded protein with MalE signal sequence. The obtained genes were expressed, and the proteins were purified. Conclusively, we show that the proteins are neither cytotoxic nor immunogenic and they have a very low allergic potential.
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Affiliation(s)
- Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland; BioVentures Institute Ltd., Poznan 60-141, Poland.
| | - Natalia Krawczun
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland; BioVentures Institute Ltd., Poznan 60-141, Poland
| | - Joanna Zebrowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland; BioVentures Institute Ltd., Poznan 60-141, Poland
| | - Daria Krefft
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland; BioVentures Institute Ltd., Poznan 60-141, Poland
| | - Olga Zołnierkiewicz
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland
| | | | - Joanna Jezewska-Frackowiak
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland; BioVentures Institute Ltd., Poznan 60-141, Poland
| | - Lukasz Janus
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland; BioVentures Institute Ltd., Poznan 60-141, Poland
| | - Malgorzata Witkowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland
| | - Malgorzata Palczewska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland
| | - Adriana Schumacher
- Department of Embryology, Faculty of Medicine, Medical University of Gdansk, Gdansk 80-211, Poland; Department of Clinical Immunology and Transplantology, Faculty of Medicine, Medical University of Gdansk, 80-210, Poland
| | - Anna Wardowska
- Department of Clinical Immunology and Transplantology, Faculty of Medicine, Medical University of Gdansk, 80-210, Poland; Laboratory of Tissue Engineering and Regenerative Medicine, Department of Embryology, Faculty of Medicine, Medical University of Gdansk, Gdansk 80-211, Poland
| | - Milena Deptula
- Laboratory of Tissue Engineering and Regenerative Medicine, Department of Embryology, Faculty of Medicine, Medical University of Gdansk, Gdansk 80-211, Poland
| | - Artur Czupryn
- Nencki Institute of Experimental Biology, Warsaw 02-093, Poland
| | - Piotr Mucha
- Department of Molecular Biochemistry, Faculty of Chemistry, University of Gdansk, 80-308, Poland
| | - Arkadiusz Piotrowski
- Department of Biology and Pharmaceutical Botany, Faculty of Pharmacy, Medical University of Gdansk, 80-416, Poland; International Research Agenda - 3P Medicine Lab, Medical University of Gdansk, 80-416, Poland
| | - Pawel Sachadyn
- Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdansk University of Technology, Gdansk 80-233, Poland
| | | | - Michal Pikula
- Department of Clinical Immunology and Transplantology, Faculty of Medicine, Medical University of Gdansk, 80-210, Poland; Laboratory of Tissue Engineering and Regenerative Medicine, Department of Embryology, Faculty of Medicine, Medical University of Gdansk, Gdansk 80-211, Poland
| | - Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk 80-308, Poland; BioVentures Institute Ltd., Poznan 60-141, Poland
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Zebrowska J, Jezewska-Frackowiak J, Wieczerzak E, Kasprzykowski F, Zylicz-Stachula A, Skowron PM. Novel parameter describing restriction endonucleases: Secondary-Cognate-Specificity and chemical stimulation of TsoI leading to substrate specificity change. Appl Microbiol Biotechnol 2019; 103:3439-3451. [PMID: 30879089 PMCID: PMC6449304 DOI: 10.1007/s00253-019-09731-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/22/2019] [Accepted: 02/27/2019] [Indexed: 11/30/2022]
Abstract
Over 470 prototype Type II restriction endonucleases (REases) are currently known. Most recognise specific DNA sequences 4–8 bp long, with very few exceptions cleaving DNA more frequently. TsoI is a thermostable Type IIC enzyme that recognises the DNA sequence TARCCA (R = A or G) and cleaves downstream at N11/N9. The enzyme exhibits extensive top-strand nicking of the supercoiled single-site DNA substrate. The second DNA strand of such substrate is specifically cleaved only in the presence of duplex oligonucleotides containing a cognate site. We have previously shown that some Type IIC/IIG/IIS enzymes from the Thermus-family exhibit ‘affinity star’ activity, which can be induced by the S-adenosyl-L-methionine (SAM) cofactor analogue—sinefungin (SIN). Here, we define a novel type of inherently built-in ‘star’ activity, exemplified by TsoI. The TsoI ‘star’ activity cannot be described under the definition of the classic ‘star’ activity as it is independent of the reaction conditions used and cannot be separated from the cognate specificity. Therefore, we define this phenomenon as Secondary-Cognate-Specificity (SCS). The TsoI SCS comprises several degenerated variants of the cognate site. Although the efficiency of TsoI SCS cleavage is lower in comparison to the cognate TsoI recognition sequence, it can be stimulated by S-adenosyl-L-cysteine (SAC). We present a new route for the chemical synthesis of SAC. The TsoI/SAC REase may serve as a novel tool for DNA manipulation.
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Affiliation(s)
- Joanna Zebrowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, 63 Wita Stwosza Street, 80-308, Gdansk, Poland
| | - Joanna Jezewska-Frackowiak
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, 63 Wita Stwosza Street, 80-308, Gdansk, Poland
| | - Ewa Wieczerzak
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, 63 Wita Stwosza Street, 80-308, Gdansk, Poland
| | - Franciszek Kasprzykowski
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, 63 Wita Stwosza Street, 80-308, Gdansk, Poland
| | - Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, 63 Wita Stwosza Street, 80-308, Gdansk, Poland.
| | - Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, 63 Wita Stwosza Street, 80-308, Gdansk, Poland.
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Krefft D, Papkov A, Prusinowski M, Zylicz-Stachula A, Skowron PM. Randomized DNA libraries construction tool: a new 3-bp 'frequent cutter' TthHB27I/sinefungin endonuclease with chemically-induced specificity. BMC Genomics 2018; 19:361. [PMID: 29751745 PMCID: PMC5948728 DOI: 10.1186/s12864-018-4748-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 04/30/2018] [Indexed: 12/14/2022] Open
Abstract
Background Acoustic or hydrodynamic shearing, sonication and enzymatic digestion are used to fragment DNA. However, these methods have several disadvantages, such as DNA damage, difficulties in fragmentation control, irreproducibility and under-representation of some DNA segments. The DNA fragmentation tool would be a gentle enzymatic method, offering cleavage frequency high enough to eliminate DNA fragments distribution bias and allow for easy control of partial digests. Only three such frequently cleaving natural restriction endonucleases (REases) were discovered: CviJI, SetI and FaiI. Therefore, we have previously developed two artificial enzymatic specificities, cleaving DNA approximately every ~ 3-bp: TspGWI/sinefungin (SIN) and TaqII/SIN. Results In this paper we present the third developed specificity: TthHB27I/SIN(SAM) - a new genomic tool, based on Type IIS/IIC/IIG Thermus-family REases-methyltransferases (MTases). In the presence of dimethyl sulfoxide (DMSO) and S-adenosyl-L-methionine (SAM) or its analogue SIN, the 6-bp cognate TthHB27I recognition sequence 5’-CAARCA-3′ is converted into a combined 3.2–3.0-bp ‘site’ or its statistical equivalent, while a cleavage distance of 11/9 nt is retained. Protocols for various modes of limited DNA digestions were developed. Conclusions In the presence of DMSO and SAM or SIN, TthHB27I is transformed from rare 6-bp cutter to a very frequent one, approximately 3-bp. Thus, TthHB27I/SIN(SAM) comprises a new tool in the very low-represented segment of such prototype REases specificities. Moreover, this modified TthHB27I enzyme is uniquely suited for controlled DNA fragmentation, due to partial DNA cleavage, which is an inherent feature of the Thermus-family enzymes. Such tool can be used for quasi-random libraries generation as well as for other DNA manipulations, requiring high frequency cleavage and uniform distribution of cuts along DNA. Electronic supplementary material The online version of this article (10.1186/s12864-018-4748-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daria Krefft
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Aliaksei Papkov
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Maciej Prusinowski
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland.
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Skowron PM, Kropinski AM, Zebrowska J, Janus L, Szemiako K, Czajkowska E, Maciejewska N, Skowron M, Łoś J, Łoś M, Zylicz-Stachula A. Correction: Sequence, genome organization, annotation and proteomics of the thermophilic, 47.7-kb Geobacillus stearothermophilus bacteriophage TP-84 and its classification in the new Tp84virus genus. PLoS One 2018; 13:e0196798. [PMID: 29698531 PMCID: PMC5919628 DOI: 10.1371/journal.pone.0196798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Skowron PM, Anton BP, Czajkowska E, Zebrowska J, Sulecka E, Krefft D, Jezewska-Frackowiak J, Zolnierkiewicz O, Witkowska M, Morgan RD, Wilson GG, Fomenkov A, Roberts RJ, Zylicz-Stachula A. The third restriction-modification system from Thermus aquaticus YT-1: solving the riddle of two TaqII specificities. Nucleic Acids Res 2017; 45:9005-9018. [PMID: 28911108 PMCID: PMC5587805 DOI: 10.1093/nar/gkx599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 07/04/2017] [Indexed: 11/12/2022] Open
Abstract
Two restriction-modification systems have been previously discovered in Thermus aquaticus YT-1. TaqI is a 263-amino acid (aa) Type IIP restriction enzyme that recognizes and cleaves within the symmetric sequence 5'-TCGA-3'. TaqII, in contrast, is a 1105-aa Type IIC restriction-and-modification enzyme, one of a family of Thermus homologs. TaqII was originally reported to recognize two different asymmetric sequences: 5'-GACCGA-3' and 5'-CACCCA-3'. We previously cloned the taqIIRM gene, purified the recombinant protein from Escherichia coli, and showed that TaqII recognizes the 5'-GACCGA-3' sequence only. Here, we report the discovery, isolation, and characterization of TaqIII, the third R-M system from T. aquaticus YT-1. TaqIII is a 1101-aa Type IIC/IIL enzyme and recognizes the 5'-CACCCA-3' sequence previously attributed to TaqII. The cleavage site is 11/9 nucleotides downstream of the A residue. The enzyme exhibits striking biochemical similarity to TaqII. The 93% identity between their aa sequences suggests that they have a common evolutionary origin. The genes are located on two separate plasmids, and are probably paralogs or pseudoparalogs. Putative positions and aa that specify DNA recognition were identified and recognition motifs for 6 uncharacterized Thermus-family enzymes were predicted.
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Affiliation(s)
- Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Brian P Anton
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Edyta Czajkowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Joanna Zebrowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Ewa Sulecka
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Daria Krefft
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Joanna Jezewska-Frackowiak
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Olga Zolnierkiewicz
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Malgorzata Witkowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | | | | | - Alexey Fomenkov
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | | | - Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
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Westphal K, Zdrowowicz M, Zylicz-Stachula A, Rak J. Chemically–enzymatic synthesis of photosensitive DNA. Journal of Photochemistry and Photobiology B: Biology 2017; 167:228-235. [DOI: 10.1016/j.jphotobiol.2017.01.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/20/2016] [Accepted: 01/03/2017] [Indexed: 01/24/2023]
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Zebrowska J, Zolnierkiewicz O, Skowron MA, Zylicz-Stachula A, Jezewska-Frackowiak J, Skowron PM. A putative Type IIS restriction endonuclease GeoICI from Geobacillus sp.--A robust, thermostable alternative to mezophilic prototype BbvI. J Biosci 2016; 41:27-38. [PMID: 26949085 DOI: 10.1007/s12038-016-9595-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Screening of extreme environments in search for novel microorganisms may lead to the discovery of robust enzymes with either new substrate specificities or thermostable equivalents of those already found in mesophiles, better suited for biotechnology applications. Isolates from Iceland geysers' biofilms, exposed to a broad range of temperatures, from ambient to close to water boiling point, were analysed for the presence of DNA-interacting proteins, including restriction endonucleases (REases). GeoICI, a member of atypical Type IIS REases, is the most thermostable isoschizomer of the prototype BbvI, recognizing/cleaving 5'-GCAGC(N8/12)-3'DNA sequences. As opposed to the unstable prototype, which cleaves DNA at 30°C, GeoICI is highly active at elevated temperatures, up to 73°C and over a very wide salt concentration range. Recognition/cleavage sites were determined by: (i) digestion of plasmid and bacteriophage lambda DNA (Λ); (ii) cleavage of custom PCR substrates, (iii) run-off sequencing of GeoICI cleavage products and (iv) shotgun cloning and sequencing of Λ DNA fragmented with GeoICI. Geobacillus sp. genomic DNA was PCR-screened for the presence of other specialized REases-MTases and as a result, another putative REase- MTase, GeoICII, related to the Thermus sp. family of bifunctional REases-methyltransferases (MTases) was detected.
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Affiliation(s)
- Joanna Zebrowska
- Department of Molecular Biotechnology, Institute for Environment and Human Health Protection, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
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Zylicz-Stachula A, Zebrowska J, Czajkowska E, Wrese W, Sulecka E, Skowron PM. Engineering TaqII bifunctional endonuclease DNA recognition fidelity: the effect of a single amino acid substitution within the methyltransferase catalytic site. Mol Biol Rep 2016; 43:269-82. [PMID: 26886214 DOI: 10.1007/s11033-016-3949-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 02/08/2016] [Indexed: 01/04/2023]
Abstract
The aim of this study was to improve a useful molecular tool-TaqII restriction endonuclease-methyltransferase-by rational protein engineering, as well as to show an application of our novel method of restriction endonuclease activity modulation through a single amino acid change in the NPPY motif of methyltransferase. An amino acid change was introduced using site-directed mutagenesis into the taqIIRM gene. The mutated gene was expressed in Escherichia coli. The protein variant was purified and characterized. Previously, we described a TspGWI variant with an amino acid change in the methyltransferase motif IV. Here, we investigate a complex, pleiotropic effect of an analogous amino acid change on its homologue-TaqII. The methyltransferase activity is reduced, but not abolished, while TaqII restriction endonuclease can be reactivated by sinefungin, with an increased DNA recognition fidelity. The general method for engineering of the IIS/IIC/IIG restriction endonuclease activity/fidelity is developed along with the generation of an improved TaqII enzyme for biotechnological applications. A successful application of our novel strategy for restriction endonuclease activity/fidelity alteration, based on bioinformatics analyses, mutagenesis and the use of cofactor-analogue activity modulation, is presented.
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Affiliation(s)
- Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Division of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
| | - Joanna Zebrowska
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Division of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
| | - Edyta Czajkowska
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Division of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
| | - Weronika Wrese
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Division of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
| | - Ewa Sulecka
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Division of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
| | - Piotr M Skowron
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Division of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
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Krefft D, Zylicz-Stachula A, Mulkiewicz E, Papkov A, Jezewska-Frackowiak J, Skowron PM. Two-stage gene assembly/cloning of a member of the TspDTI subfamily of bifunctional restriction endonucleases, TthHB27I. J Biotechnol 2014; 194:67-80. [PMID: 25486633 DOI: 10.1016/j.jbiotec.2014.11.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 11/22/2014] [Accepted: 11/27/2014] [Indexed: 10/24/2022]
Abstract
The Thermus sp. family of bifunctional type IIS/IIG/IIC restriction endonucleases (REase)-methyltransferases (MTase) comprises thermo-stable TaqII, TspGWI, TspDTI, TsoI, Tth111II/TthHB27I enzymes as well as a number of putative enzymes/open reading frames (ORFs). All of the family members share properties including a large protein size (ca. 120kDa), amino acid (aa) sequence homologies, enzymatic activity modulation by S-adenosylmethionine (SAM), recognition of similar asymmetric cognate DNA sites and cleavage at a distance of 11/9 nt. Analysis of the enzyme aa sequences and domain/motif organisation led to further Thermus sp. family division into the TspDTI and TspGWI subfamilies. The latter exhibits an unprecedented phenomenon of DNA recognition change upon substitution of SAM by its analogue, sinefungin (SIN), towards a very frequent DNA cleavage. We report cloning in Escherichia coli (E. coli), using a two-stage procedure and a putative tthHB27IRM gene, detected by bioinformatics analysis of the Thermus thermophilus HB27 (T. thermophilus) genome. The functionality of a 3366 base pair (bp)-/1121 aa-long, high GC content ORF was validated experimentally through the expression in E. coli. Protein features corroborated with the reclassification of TthHB27I into the TspDTI subfamily, which manifested in terms of aa-sequence/motif homologies and insensitivity to SIN-induced specificity shift. However, both SAM and SIN stimulated the REase DNA cleavage activity by at least 16-32 times; the highest was observed for the Thermus sp. family. The availability of TthHB27I and the need to include SAM or SIN in the reaction in order to convert the enzyme from "hibernation" status to efficient DNA cleavage is of practical significance in molecular biotechnology, extending the palette of available REase specificities.
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Affiliation(s)
- Daria Krefft
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Division of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
| | - Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Division of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
| | - Ewa Mulkiewicz
- Department of Environment Analysis, Institute for Environmental and Human Health Protection, Division of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
| | - Aliaksei Papkov
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Division of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
| | - Joanna Jezewska-Frackowiak
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Division of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
| | - Piotr M Skowron
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Division of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
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Jezewska-Frackowiak J, Lubys A, Vitkute J, Zakareviciene L, Zebrowska J, Krefft D, Skowron MA, Zylicz-Stachula A, Skowron PM. A new prototype IIS/IIC/IIG endonuclease-methyltransferase TsoI from the thermophile Thermus scotoductus, recognising 5'-TARCCA(N11/9)-3' sequences. J Biotechnol 2014; 194:19-26. [PMID: 25481098 DOI: 10.1016/j.jbiotec.2014.11.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 11/22/2014] [Accepted: 11/26/2014] [Indexed: 11/26/2022]
Abstract
The Thermus sp. family of IIS/IIG/IIC enzymes includes the thermostable, bifunctional, fused restriction endonuclease (REase)-methyltransferases (MTase): TaqII, Tth111II/TthHB27I, TspGWI, TspDTI and TsoI. The enzymes are large proteins (approximately 120kDa), their enzymatic activities are affected by S-adenosylmethionine (SAM), they recognise similar asymmetric cognate sites and cleave at a distance of 11/9 nucleotides (nt). The enzymes exhibit similarities of their amino acid (aa) sequences and DNA catalytic motifs. Thermus sp. enzymes are an example of functional aa sequence homologies among REases recognising different, yet related DNA sequences. The family consists of TspGWI- and TspDTI-subfamilies. TsoI appears to be a non-identical 'triplet', related to TspDTI and Tth111II/TthHB27I. The discovery of TsoI, purified from Thermus scotoductus, is described. This prototype, displaying a novel specificity, which was determined by: (i) cleavage of a reference plasmid and bacteriophage DNA, (ii) cleavage of custom PCR DNA substrates, (iii) run-off sequencing of cleavage products and (iv) shotgun cloning and sequencing of bacteriophage lambda (λ) DNA digested with TsoI. The enzyme recognises a degenerated 5'-TARCCA-3' sequence, whereas DNA strands are cut 11/9 nt downstream. The discovery of the TsoI prototype is of practical importance in biotechnology, as it extends the palette of cleavage specificities for gene cloning.
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Affiliation(s)
- Joanna Jezewska-Frackowiak
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Division of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
| | - Arvydas Lubys
- Thermo Fisher Scientific Baltics UAB, V.A. Graiciuno 8, LT-02241 Vilnius, Lithuania; Department of Botany and Genetics, Vilnius University, M.K. Ciurlionio 21/27, LT-03101 Vilnius, Lithuania.
| | - Jolanta Vitkute
- Thermo Fisher Scientific Baltics UAB, V.A. Graiciuno 8, LT-02241 Vilnius, Lithuania.
| | - Laimute Zakareviciene
- Thermo Fisher Scientific Baltics UAB, V.A. Graiciuno 8, LT-02241 Vilnius, Lithuania.
| | - Joanna Zebrowska
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Division of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
| | - Daria Krefft
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Division of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
| | - Marta A Skowron
- Department of Molecular Biology, Division of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland.
| | - Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Division of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
| | - Piotr M Skowron
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Division of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
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Zylicz-Stachula A, Bujnicki JM, Skowron PM. Erratum to: Cloning and analysis of a bifunctional methyltransferase/restriction endonuclease TspGWI, the prototype of a Thermussp. enzyme family. BMC Mol Biol 2014. [DOI: 10.1186/1471-2199-15-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Zylicz-Stachula A, Polska K, Skowron P, Rak J. Artificial plasmid labeled with 5-bromo-2'-deoxyuridine: a universal molecular system for strand break detection. Chembiochem 2014; 15:1409-12. [PMID: 24850054 DOI: 10.1002/cbic.201402082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Indexed: 01/08/2023]
Abstract
DNA strand breaks (SBs) are among the most cytotoxic forms of DNA damage, and their residual levels correlate directly with cell death. Hence, the type and amount of SBs is directly related to the efficacy of a given anticancer therapy. In this study, we describe a molecular tool that can differentiate between single (SSBs) and double (DSBs) strand breaks and also assess them quantitatively. Our method involves PCR amplification of a linear DNA fragment labeled with a sensitizing nucleotide, circularization of that fragment, and enzymatic introduction of supercoils to transform the circular relaxed form of the synthesized plasmid into a supercoiled one. After exposure of the molecule to a damaging factor, SSB and DSB levels can be easily assayed with gel electrophoresis. We applied this method to prepare an artificial plasmid labeled with 5-bromo-2'-deoxyuridine and to assay SBs photoinduced in the synthesized plasmid.
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Zdrowowicz M, Michalska B, Zylicz-Stachula A, Rak J. Photoinduced single strand breaks and intrastrand cross-links in an oligonucleotide labeled with 5-bromouracil. J Phys Chem B 2014; 118:5009-16. [PMID: 24766391 DOI: 10.1021/jp500192z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
5-Bromouracil (BrU) is photoreactive toward near UVB photons and can be introduced into genomic DNA during its biosynthesis in cells. However, PCR seems to be a simpler approach, which can be used to obtain labeled DNA similar to that synthesized within the cell. In the current work, PCR has been employed and optimized in order to substitute all thymines (besides those present in starters) with BrU in the dsDNA fragment of 80 base pairs (bp) in length. The modified oligonucleotide was irradiated with 300 nm photons in a buffered aqueous solution (pH = 7) and digested with a cocktail of enzymes specific to the phosphodiester bond cleavage. Initially, the extent of damage in the intact photolyte was measured with DHPLC. Then, the digested reaction mixture was subjected to HPLC and MS analyses and, in addition to the formation of 5-bromo-2'-deoxuyridine, which proves the occurrence of single strand breaks (SSBs) due to irradiation, U∧U and U∧C dimers were found, whose molecular structure was confirmed by MS/MS analysis. Although the abundance of such tandem lesions is lower than that of the SSB type, they pose a potent threat to genome integrity. Thus, our findings shed new light on the photosensitizing properties of BrU toward DNA.
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Affiliation(s)
- Magdalena Zdrowowicz
- Faculty of Chemistry, University of Gdańsk , Wita Stwosza 63, 80-308 Gdańsk, Poland
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Zylicz-Stachula A, Jeżewska-Frąckowiak J, Skowron PM. Cofactor analogue-induced chemical reactivation of endonuclease activity in a DNA cleavage/methylation deficient TspGWI N₄₇₃A variant in the NPPY motif. Mol Biol Rep 2014; 41:2313-23. [PMID: 24442320 PMCID: PMC3968444 DOI: 10.1007/s11033-014-3085-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 01/04/2014] [Indexed: 11/26/2022]
Abstract
We reported previously that TspGWI, a prototype enzyme of a new Thermus sp. family of restriction endonucleases-methyltransferases (REases-MTases), undergoes the novel phenomenon of sinefungin (SIN)-caused specificity transition. Here we investigated mutant TspGWI N473A, containing a single amino acid (aa) substitution in the NPPY motif of the MTase. Even though the aa substitution is located within the MTase polypeptide segment, DNA cleavage and modification are almost completely abolished, indicating that the REase and MTase are intertwined. Remarkably, the TspGWI N473A REase functionality can be completely reconstituted by the addition of SIN. We hypothesize that SIN binds specifically to the enzyme and restores the DNA cleavage-competent protein tertiary structure. This indicates the significant role of allosteric effectors in DNA cleavage in Thermus sp. enzymes. This is the first case of REase mutation suppression by an S-adenosylmethionine (SAM) cofactor analogue. Moreover, the TspGWI N473A clone strongly affects E. coli division control, acting as a ‘selfish gene’. The mutant lacks the competing MTase activity and therefore might be useful for applications in DNA manipulation. Here we present a case study of a novel strategy for REase activity/specificity alteration by a single aa substitution, based on the bioinformatic analysis of active motif locations, combining (a) aa sequence engineering (b) the alteration of protein enzymatic properties, and (c) the use of cofactor–analogue cleavage reconstitution and stimulation.
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Affiliation(s)
- Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-952 Gdansk, Poland
| | - Joanna Jeżewska-Frąckowiak
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-952 Gdansk, Poland
| | - Piotr M. Skowron
- Department of Molecular Biotechnology, Institute for Environmental and Human Health Protection, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-952 Gdansk, Poland
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Zylicz-Stachula A, Zolnierkiewicz O, Sliwinska K, Jezewska-Frackowiak J, Skowron PM. Modified 'one amino acid-one codon' engineering of high GC content TaqII-coding gene from thermophilic Thermus aquaticus results in radical expression increase. Microb Cell Fact 2014; 13:7. [PMID: 24410856 PMCID: PMC3893498 DOI: 10.1186/1475-2859-13-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 01/03/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND An industrial approach to protein production demands maximization of cloned gene expression, balanced with the recombinant host's viability. Expression of toxic genes from thermophiles poses particular difficulties due to high GC content, mRNA secondary structures, rare codon usage and impairing the host's coding plasmid replication.TaqII belongs to a family of bifunctional enzymes, which are a fusion of the restriction endonuclease (REase) and methyltransferase (MTase) activities in a single polypeptide. The family contains thermostable REases with distinct specificities: TspGWI, TaqII, Tth111II/TthHB27I, TspDTI and TsoI and a few enzymes found in mesophiles. While not being isoschizomers, the enzymes exhibit amino acid (aa) sequence homologies, having molecular sizes of ~120 kDa share common modular architecture, resemble Type-I enzymes, cleave DNA 11/9 nt from the recognition sites, their activity is affected by S-adenosylmethionine (SAM). RESULTS We describe the taqIIRM gene design, cloning and expression of the prototype TaqII. The enzyme amount in natural hosts is extremely low. To improve expression of the taqIIRM gene in Escherichia coli (E. coli), we designed and cloned a fully synthetic, low GC content, low mRNA secondary structure taqIIRM, codon-optimized gene under a bacteriophage lambda (λ) PR promoter. Codon usage based on a modified 'one amino acid-one codon' strategy, weighted towards low GC content codons, resulted in approximately 10-fold higher expression of the synthetic gene. 718 codons of total 1105 were changed, comprising 65% of the taqIIRM gene. The reason for we choose a less effective strategy rather than a resulting in high expression yields 'codon randomization' strategy, was intentional, sub-optimal TaqII in vivo production, in order to decrease the high 'toxicity' of the REase-MTase protein. CONCLUSIONS Recombinant wt and synthetic taqIIRM gene were cloned and expressed in E. coli. The modified 'one amino acid-one codon' method tuned for thermophile-coded genes was applied to obtain overexpression of the 'toxic' taqIIRM gene. The method appears suited for industrial production of thermostable 'toxic' enzymes in E. coli. This novel variant of the method biased toward increasing a gene's AT content may provide economic benefits for industrial applications.
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Affiliation(s)
| | | | | | | | - Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
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Skowron PM, Vitkute J, Ramanauskaite D, Mitkaite G, Jezewska-Frackowiak J, Zebrowska J, Zylicz-Stachula A, Lubys A. Three-stage biochemical selection: cloning of prototype class IIS/IIC/IIG restriction endonuclease-methyltransferase TsoI from the thermophile Thermus scotoductus. BMC Mol Biol 2013; 14:17. [PMID: 23919831 PMCID: PMC3751577 DOI: 10.1186/1471-2199-14-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 07/24/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In continuing our research into the new family of bifunctional restriction endonucleases (REases), we describe the cloning of the tsoIRM gene. Currently, the family includes six thermostable enzymes: TaqII, Tth111II, TthHB27I, TspGWI, TspDTI, TsoI, isolated from various Thermus sp. and two thermolabile enzymes: RpaI and CchII, isolated from mesophilic bacteria Rhodopseudomonas palustris and Chlorobium chlorochromatii, respectively. The enzymes have several properties in common. They are large proteins (molecular size app. 120 kDa), coded by fused genes, with the REase and methyltransferase (MTase) in a single polypeptide, where both activities are affected by S-adenosylmethionine (SAM). They recognize similar asymmetric cognate sites and cleave at a distance of 11/9 nt from the recognition site. Thus far, we have cloned and characterised TaqII, Tth111II, TthHB27I, TspGWI and TspDTI. RESULTS TsoI REase, which originate from thermophilic Thermus scotoductus RFL4 (T. scotoductus), was cloned in Escherichia coli (E. coli) using two rounds of biochemical selection of the T. scotoductus genomic library for the TsoI methylation phenotype. DNA sequencing of restriction-resistant clones revealed the common open reading frame (ORF) of 3348 bp, coding for a large polypeptide of 1116 aminoacid (aa) residues, which exhibited a high level of similarity to Tth111II (50% identity, 60% similarity). The ORF was PCR-amplified, subcloned into a pET21 derivative under the control of a T7 promoter and was subjected to the third round of biochemical selection in order to isolate error-free clones. Induction experiments resulted in synthesis of an app. 125 kDa protein, exhibiting TsoI-specific DNA cleavage. Also, the wild-type (wt) protein was purified and reaction optima were determined. CONCLUSIONS Previously we identified and cloned the Thermus family RM genes using a specially developed method based on partial proteolysis of thermostable REases. In the case of TsoI the classic biochemical selection method was successful, probably because of the substantially lower optimal reaction temperature of TsoI (app. 10-15°C). That allowed for sufficient MTase activity in vivo in recombinant E. coli. Interestingly, TsoI originates from bacteria with a high optimum growth temperature of 67°C, which indicates that not all bacterial enzymes match an organism's thermophilic nature, and yet remain functional cell components. Besides basic research advances, the cloning and characterisation of the new prototype REase from the Thermus sp. family enzymes is also of practical importance in gene manipulation technology, as it extends the range of available DNA cleavage specificities.
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Affiliation(s)
- Piotr M Skowron
- Division of Molecular Biotechnology, Department of Chemistry, Institute for Environmental and Human Health Protection, University of Gdansk, Gdansk, Poland
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Zylicz-Stachula A, Zolnierkiewicz O, Jasiecki J, Skowron PM. A new genomic tool, ultra-frequently cleaving TaqII/sinefungin endonuclease with a combined 2.9-bp recognition site, applied to the construction of horse DNA libraries. BMC Genomics 2013; 14:370. [PMID: 23724933 PMCID: PMC3681635 DOI: 10.1186/1471-2164-14-370] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Accepted: 05/23/2013] [Indexed: 12/22/2022] Open
Abstract
Background Genomics and metagenomics are currently leading research areas, with DNA sequences accumulating at an exponential rate. Although enormous advances in DNA sequencing technologies are taking place, progress is frequently limited by factors such as genomic contig assembly and generation of representative libraries. A number of DNA fragmentation methods, such as hydrodynamic sharing, sonication or DNase I fragmentation, have various drawbacks, including DNA damage, poor fragmentation control, irreproducibility and non-overlapping DNA segment representation. Improvements in these limited DNA scission methods are consequently needed. An alternative method for obtaining higher quality DNA fragments involves partial digestion with restriction endonucleases (REases). We have shown previously that class-IIS/IIC/IIG TspGWI REase, the prototype member of the Thermus sp. enzyme family, can be chemically relaxed by a cofactor analogue, allowing it to recognize very short DNA sequences of 3-bp combined frequency. Such frequently cleaving REases are extremely rare, with CviJI/CviJI*, SetI and FaiI the only other ones found in nature. Their unusual features make them very useful molecular tools for the development of representative DNA libraries. Results We constructed a horse genomic library and a deletion derivative library of the butyrylcholinesterase cDNA coding region using a novel method, based on TaqII, Thermus sp. family bifunctional enzyme exhibiting cofactor analogue specificity relaxation. We used sinefungin (SIN) – an S-adenosylmethionine (SAM) analogue with reversed charge pattern, and dimethylsulfoxide (DMSO), to convert the 6-bp recognition site TaqII (5′-GACCGA-3′ [11/9]) into a theoretical 2.9-bp REase, with 70 shortened variants of the canonical recognition sequence detected. Because partial DNA cleavage is an inherent feature of the Thermus sp. enzyme family, this modified TaqII is uniquely suited to quasi-random library generation. Conclusions In the presence of SIN/DMSO, TaqII REase is transformed from cleaving every 4096 bp on average to cleaving every 58 bp. TaqII SIN/DMSO thus extends the palette of available REase prototype specificities. This phenomenon, employed under partial digestion conditions, was applied to quasi-random DNA fragmentation. Further applications include high sensitivity probe generation and metagenomic DNA amplification.
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Zylicz-Stachula A, Zolnierkiewicz O, Lubys A, Ramanauskaite D, Mitkaite G, Bujnicki JM, Skowron PM. Related bifunctional restriction endonuclease-methyltransferase triplets: TspDTI, Tth111II/TthHB27I and TsoI with distinct specificities. BMC Mol Biol 2012; 13:13. [PMID: 22489904 PMCID: PMC3384240 DOI: 10.1186/1471-2199-13-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 04/10/2012] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND We previously defined a family of restriction endonucleases (REases) from Thermus sp., which share common biochemical and biophysical features, such as the fusion of both the nuclease and methyltransferase (MTase) activities in a single polypeptide, cleavage at a distance from the recognition site, large molecular size, modulation of activity by S-adenosylmethionine (SAM), and incomplete cleavage of the substrate DNA. Members include related thermophilic REases with five distinct specificities: TspGWI, TaqII, Tth111II/TthHB27I, TspDTI and TsoI. RESULTS TspDTI, TsoI and isoschizomers Tth111II/TthHB27I recognize different, but related sequences: 5'-ATGAA-3', 5'-TARCCA-3' and 5'-CAARCA-3' respectively. Their amino acid sequences are similar, which is unusual among REases of different specificity. To gain insight into this group of REases, TspDTI, the prototype member of the Thermus sp. enzyme family, was cloned and characterized using a recently developed method for partially cleaving REases. CONCLUSIONS TspDTI, TsoI and isoschizomers Tth111II/TthHB27I are closely related bifunctional enzymes. They comprise a tandem arrangement of Type I-like domains, like other Type IIC enzymes (those with a fusion of a REase and MTase domains), e.g. TspGWI, TaqII and MmeI, but their sequences are only remotely similar to these previously characterized enzymes. The characterization of TspDTI, a prototype member of this group, extends our understanding of sequence-function relationships among multifunctional restriction-modification enzymes.
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Zylicz-Stachula A, Zołnierkiewicz O, Sliwińska K, Jeżewska-Frąckowiak J, Skowron PM. Bifunctional TaqII restriction endonuclease: redefining the prototype DNA recognition site and establishing the Fidelity Index for partial cleaving. BMC Biochem 2011; 12:62. [PMID: 22141927 PMCID: PMC3280180 DOI: 10.1186/1471-2091-12-62] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 12/05/2011] [Indexed: 01/06/2023]
Abstract
Background The TaqII enzyme is a member of the Thermus sp. enzyme family that we propounded previously within Type IIS restriction endonucleases, containing related thermophilic bifunctional endonucleases-methyltransferases from various Thermus sp.: TaqII, Tth111II, TthHB27I, TspGWI, TspDTI and TsoI. These enzymes show significant nucleotide and amino acid sequence similarities, a rare phenomenon among restriction endonucleases, along with similarities in biochemical properties, molecular size, DNA recognition sequences and cleavage sites. They also feature some characteristics of Types I and III. Results Barker et al. reported the Type IIS/IIC restriction endonuclease TaqII as recognizing two distinct cognate site variants (5'-GACCGA-3' and 5'-CACCCA-3') while cleaving 11/9 nucleotides downstream. We used four independent methods, namely, shotgun cloning and sequencing, restriction pattern analysis, digestion of particular custom substrates and GeneScan analysis, to demonstrate that the recombinant enzyme recognizes only 5'-GACCGA-3' sites and cleaves 11/9 nucleotides downstream. We did not observe any 5'-CACCCA-3' cleavage under a variety of conditions and site arrangements tested. We also characterized the enzyme biochemically and established new digestion conditions optimal for practical enzyme applications. Finally, we developed and propose a new version of the Fidelity Index - the Fidelity Index for Partial Cleavage (FI-PC). Conclusions The DNA recognition sequence of the bifunctional prototype TaqII endonuclease-methyltransferase from Thermus aquaticus has been redefined as recognizing only 5'-GACCGA-3' cognate sites. The reaction conditions (pH and salt concentrations) were designed either to minimize (pH = 8.0 and 10 mM ammonium sulphate) or to enhance star activity (pH = 6.0 and no salt). Redefinition of the recognition site and reaction conditions makes this prototype endonuclease a useful tool for DNA manipulation; as yet, this enzyme has no practical applications. The extension of the Fidelity Index will be helpful for DNA manipulation with enzymes only partially cleaving DNA.
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Affiliation(s)
- Agnieszka Zylicz-Stachula
- Institute for Environmental and Human Health Protection, Department of Chemistry University of Gdańsk, Gdańsk, Poland
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Michalska B, Sobolewski I, Polska K, Zielonka J, Zylicz-Stachula A, Skowron P, Rak J. PCR synthesis of double stranded DNA labeled with 5-bromouridine. A step towards finding a bromonucleoside for clinical trials. J Pharm Biomed Anal 2011; 56:671-7. [PMID: 21840661 DOI: 10.1016/j.jpba.2011.07.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 07/08/2011] [Accepted: 07/22/2011] [Indexed: 11/24/2022]
Abstract
Incorporation of 5-bromouridine (5BrdU) into DNA makes it sensitive to UV and ionizing radiation, which opens up a prospective route for the clinical usage of 5-bromouridine and other halonucleosides. In the present work the polymerase chain reaction (PCR) protocol, which enables a long DNA fragment (resembling DNA synthesized in the cell in the presence of halonucleosides) to be completely substituted with 5BrdU, was optimized. Using HPLC coupled to enzymatic digestion, it was demonstrated that the actual amounts of native nucleosides and 5BrdU correspond very well to those calculated from the sequence of PCR products. The synthesized DNA is photosensitive to photons of 300nm. HPLC analysis demonstrated that the photolysis of labeled PCR products leads to a significant decrease in the 5BrdU signal and the simultaneous occurrence of a uridine peak. Agarose and polyacrylamide gel electrophoresis suggest that single strand breaks and cross-links are formed as a result of UV irradiation. The PCR protocol described in the current paper may be employed for labeling DNA not only with BrdU but also with other halonucleosides.
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Affiliation(s)
- Barbara Michalska
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland
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Zylicz-Stachula A, Bujnicki JM, Skowron PM. Cloning and analysis of a bifunctional methyltransferase/restriction endonuclease TspGWI, the prototype of a Thermus sp. enzyme family. BMC Mol Biol 2009; 10:52. [PMID: 19480701 PMCID: PMC2700111 DOI: 10.1186/1471-2199-10-52] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2008] [Accepted: 05/29/2009] [Indexed: 01/09/2023] Open
Abstract
Background Restriction-modification systems are a diverse class of enzymes. They are classified into four major types: I, II, III and IV. We have previously proposed the existence of a Thermus sp. enzyme family, which belongs to type II restriction endonucleases (REases), however, it features also some characteristics of types I and III. Members include related thermophilic endonucleases: TspGWI, TaqII, TspDTI, and Tth111II. Results Here we describe cloning, mutagenesis and analysis of the prototype TspGWI enzyme that recognises the 5'-ACGGA-3' site and cleaves 11/9 nt downstream. We cloned, expressed, and mutagenised the tspgwi gene and investigated the properties of its product, the bifunctional TspGWI restriction/modification enzyme. Since TspGWI does not cleave DNA completely, a cloning method was devised, based on amino acid sequencing of internal proteolytic fragments. The deduced amino acid sequence of the enzyme shares significant sequence similarity with another representative of the Thermus sp. family – TaqII. Interestingly, these enzymes recognise similar, yet different sequences in the DNA. Both enzymes cleave DNA at the same distance, but differ in their ability to cleave single sites and in the requirement of S-adenosylmethionine as an allosteric activator for cleavage. Both the restriction endonuclease (REase) and methyltransferase (MTase) activities of wild type (wt) TspGWI (either recombinant or isolated from Thermus sp.) are dependent on the presence of divalent cations. Conclusion TspGWI is a bifunctional protein comprising a tandem arrangement of Type I-like domains; particularly noticeable is the central HsdM-like module comprising a helical domain and a highly conserved S-adenosylmethionine-binding/catalytic MTase domain, containing DPAVGTG and NPPY motifs. TspGWI also possesses an N-terminal PD-(D/E)XK nuclease domain related to the corresponding domains in HsdR subunits, but lacks the ATP-dependent translocase module of the HsdR subunit and the additional domains that are involved in subunit-subunit interactions in Type I systems. The MTase and REase activities of TspGWI are autonomous and can be uncoupled. Structurally and functionally, the TspGWI protomer appears to be a streamlined 'half' of a Type I enzyme.
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Affiliation(s)
- Agnieszka Zylicz-Stachula
- Division of Environmental Molecular Biotechnology, Department of Chemistry, University of Gdansk, Sobieskiego 18, Gdansk 80-952, Poland.
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Skowron PM, Majewski J, Zylicz-Stachula A, Rutkowska SM, Jaworowska I, Harasimowicz-Słowińska RI. A new Thermus sp. class-IIS enzyme sub-family: isolation of a 'twin' endonuclease TspDTI with a novel specificity 5'-ATGAA(N(11/9))-3', related to TspGWI, TaqII and Tth111II. Nucleic Acids Res 2003; 31:e74. [PMID: 12853651 PMCID: PMC167652 DOI: 10.1093/nar/gng074] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2003] [Revised: 05/13/2003] [Accepted: 05/13/2003] [Indexed: 11/14/2022] Open
Abstract
The TspDTI restriction endonuclease, which shows a novel recognition specificity 5'-ATGAA(N(11/9))-3', was isolated from Thermus sp. DT. TspDTI appears to be a 'twin' of restriction endonuclease TspGWI from Thermus sp. GW, as we have previously reported. TspGWI was isolated from the same location as TspDTI, it recognizes a related sequence 5'-ACGGA(N(11/9))-3' and has conserved cleavage positions. Both enzymes resemble two other class-IIS endonucleases from Thermus sp.: TaqII and Tth111II. N-terminal amino acid sequences of TspGWI tryptic peptides exhibit 88.9-100% similarity to the TaqII sequence. All four enzymes were purified to homogeneity; their polypeptide sizes (114.5-122 kDa) make them the largest class-IIS restriction endonucleases known to date. The existence of a Thermus sp. sub-family of class-IIS restriction endonucleases of a common origin is herein proposed.
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Zylicz-Stachula A, Harasimowicz-Slowińska RI, Sobolewski I, Skowron PM. TspGWI, a thermophilic class-IIS restriction endonuclease from Thermus sp., recognizes novel asymmetric sequence 5'-ACGGA(N11/9)-3'. Nucleic Acids Res 2002; 30:e33. [PMID: 11917039 PMCID: PMC101857 DOI: 10.1093/nar/30.7.e33] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A novel prototype class-IIS restriction endonuclease, TspGWI, was isolated from the thermophilic bacterium Thermus sp. GW. The recognition sequence and cleavage positions have been established: TspGWI recognizes the non-palindromic 5-bp sequence 5'-ACGGA-3' and cleaves the DNA 11 and 9 nt downstream in the top and bottom strand, respectively. In addition, an accompanying endonuclease, TspGWII, an isoschizomer of Pst I, was found in Thermus sp. GW cells.
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