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Husťáková B, Trundová M, Adámková K, Kovaľ T, Dušková J, Dohnálek J. A highly active S1-P1 nuclease from the opportunistic pathogen Stenotrophomonas maltophilia cleaves c-di-GMP. FEBS Lett 2023; 597:2103-2118. [PMID: 37309731 DOI: 10.1002/1873-3468.14683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/14/2023]
Abstract
A number of multidrug-resistant bacterial pathogens code for S1-P1 nucleases with a poorly understood role. We have characterized a recombinant form of S1-P1 nuclease from Stenotrophomonas maltophilia, an opportunistic pathogen. S. maltophilia nuclease 1 (SmNuc1) acts predominantly as an RNase and is active in a wide range of temperatures and pH. It retains a notable level of activity towards RNA and ssDNA at pH 5 and 9 and about 10% of activity towards RNA at 10 °C. SmNuc1 with very high catalytic rates outperforms S1 nuclease from Aspergillus oryzae and other similar nucleases on all types of substrates. SmNuc1 degrades second messenger c-di-GMP, which has potential implications for its role in the pathogenicity of S. maltophilia.
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Affiliation(s)
- Blanka Husťáková
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Vestec, Czech Republic
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Mária Trundová
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Vestec, Czech Republic
| | - Kristýna Adámková
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Vestec, Czech Republic
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Tomáš Kovaľ
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Vestec, Czech Republic
| | - Jarmila Dušková
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Vestec, Czech Republic
| | - Jan Dohnálek
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Vestec, Czech Republic
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2
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Yu M, Arai N, Ochiai T, Ohyama T. Expression and function of an S1-type nuclease in the digestive fluid of a sundew, Drosera adelae. ANNALS OF BOTANY 2023; 131:335-346. [PMID: 36546767 PMCID: PMC9992940 DOI: 10.1093/aob/mcac150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND AND AIMS Carnivorous plants trap and digest insects and similar-sized animals. Many studies have examined enzymes in the digestive fluids of these plants and have gradually unveiled the origins and gene expression of these enzymes. However, only a few attempts have been made at characterization of nucleases. This study aimed to reveal gene expression and the structural, functional and evolutionary characteristics of an S1-type nuclease (DAN1) in the digestive fluid of an Australian sundew, Drosera adelae, whose trap organ shows unique gene expression and related epigenetic regulation. METHODS Organ-specificity in Dan1 expression was examined using glandular tentacles, laminas, roots and inflorescences, and real-time PCR. The methylation status of the Dan1 promoter in each organ was clarified by bisulphite sequencing. The structural characteristics of DAN1 were studied by a comparison of primary structures of S1-type nucleases of three carnivorous and seven non-carnivorous plants. DAN1 was prepared using a cell-free protein synthesis system. Requirements for metal ions, optimum pH and temperature, and substrate preference were examined using conventional methods. KEY RESULTS Dan1 is exclusively expressed in the glandular tentacles and its promoter is almost completely unmethylated in all organs. This is in contrast to the S-like RNase gene da-I of Dr. adelae, which shows similar organ-specific expression, but is controlled by a promoter that is specifically unmethylated in the glandular tentacles. Comparison of amino acid sequences of S1-type nucleases identifies seven and three positions where amino acid residues are conserved only among the carnivorous plants and only among the non-carnivorous plants, respectively. DAN1 prefers a substrate RNA over DNA in the presence of Zn2+, Mn2+ or Ca2+ at an optimum pH of 4.0. CONCLUSIONS Uptake of phosphates from prey is suggested to be the main function of DAN1, which is very different from the known functions of S1-type nucleases. Evolution has modified the structure and expression of Dan1 to specifically function in the digestive fluid.
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Affiliation(s)
- Meng Yu
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Naoki Arai
- Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama-shi, Kanagawa 221-8686, Japan
| | - Tadahiro Ochiai
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Takashi Ohyama
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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Matoušek J, Steger G. The Splicing Variant TFIIIA-7ZF of Viroid-Modulated Transcription Factor IIIA Causes Physiological Irregularities in Transgenic Tobacco and Transient Somatic Depression of "Degradome" Characteristic for Developing Pollen. Cells 2022; 11:784. [PMID: 35269406 PMCID: PMC8909551 DOI: 10.3390/cells11050784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/20/2022] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Viroids are small, non-coding, pathogenic RNAs with a significant ability of adaptation to several basic cellular processes in plants. TFIIIA-7ZF, a splicing variant of transcription factor IIIA, is involved in replication of nuclear-replicating viroids by DNA-dependent polymerase II. We overexpressed NbTFIIIA-7ZF from Nicotiana benthamiana in tobacco (Nicotiana tabacum) where it caused morphological and physiological deviations like plant stunting, splitting of leaf petioles, pistils or apexes, irregular branching of shoots, formation of double-blade leaves, deformation of main stems, and modification of glandular trichomes. Plant aging and senescence was dramatically delayed in transgenic lines. Factors potentially involved in viroid degradation and elimination in pollen were transiently depressed in transgenic leaves. This depressed "degradome" in young plants involved NtTudor S-like nuclease, dicers, argonoute 5, and pollen extracellular nuclease I showing expression in tobacco anthers and leaves. Analysis of the "degradome" in tobacco leaves transformed with either of two hop viroids confirmed modifications of the "degradome" and TFIIIA expression. Thus, the regulatory network connected to TFIIIA-7ZF could be involved in plant pathogenesis as well as in viroid adaptation to avoid its degradation. These results support the hypothesis on a significant impact of limited TFIIIA-7ZF on viroid elimination in pollen.
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Affiliation(s)
- Jaroslav Matoušek
- Biology Centre of the Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic;
| | - Gerhard Steger
- Institutfür Pysikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
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Zhu W, McQuarrie S, Grüschow S, McMahon SA, Graham S, Gloster TM, White MF. The CRISPR ancillary effector Can2 is a dual-specificity nuclease potentiating type III CRISPR defence. Nucleic Acids Res 2021; 49:2777-2789. [PMID: 33590098 PMCID: PMC7969007 DOI: 10.1093/nar/gkab073] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/22/2021] [Accepted: 01/27/2021] [Indexed: 12/26/2022] Open
Abstract
Cells and organisms have a wide range of mechanisms to defend against infection by viruses and other mobile genetic elements (MGE). Type III CRISPR systems detect foreign RNA and typically generate cyclic oligoadenylate (cOA) second messengers that bind to ancillary proteins with CARF (CRISPR associated Rossman fold) domains. This results in the activation of fused effector domains for antiviral defence. The best characterised CARF family effectors are the Csm6/Csx1 ribonucleases and DNA nickase Can1. Here we investigate a widely distributed CARF family effector with a nuclease domain, which we name Can2 (CRISPR ancillary nuclease 2). Can2 is activated by cyclic tetra-adenylate (cA4) and displays both DNase and RNase activity, providing effective immunity against plasmid transformation and bacteriophage infection in Escherichia coli. The structure of Can2 in complex with cA4 suggests a mechanism for the cA4-mediated activation of the enzyme, whereby an active site cleft is exposed on binding the activator. These findings extend our understanding of type III CRISPR cOA signalling and effector function.
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Affiliation(s)
- Wenlong Zhu
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Stuart McQuarrie
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Sabine Grüschow
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Stephen A McMahon
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Shirley Graham
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Tracey M Gloster
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
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Phylogenetic Analysis and In Vitro Bifunctional Nuclease Assay of Arabidopsis BBD1 and BBD2. Molecules 2020; 25:molecules25092169. [PMID: 32384799 PMCID: PMC7249048 DOI: 10.3390/molecules25092169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/01/2020] [Accepted: 05/04/2020] [Indexed: 01/08/2023] Open
Abstract
Nucleases are a very diverse group of enzymes that play important roles in many crucial physiological processes in plants. We previously reported that the highly conserved region (HCR), domain of unknown function 151 (DUF151) and UV responsive (UVR) domain-containing OmBBD is a novel nuclease that does not share homology with other well-studied plant nucleases. Here, we report that DUF151 domain-containing proteins are present in bacteria, archaea and only Viridiplantae kingdom of eukarya, but not in any other eukaryotes. Two Arabidopsis homologs of OmBBD, AtBBD1 and AtBBD2, shared 43.69% and 44.38% sequence identity and contained all three distinct domains of OmBBD. We confirmed that the recombinant MBP-AtBBD1 and MBP-AtBBD2 exhibited non-substrate-specific DNase and RNase activity, like OmBBD. We also found that a metal cofactor is not necessarily required for DNase activity of AtBBD1 and AtBBD2, but their activities were much enhanced in the presence of Mg2+ or Mn2+. Using a yeast two-hybrid assay, we found that AtBBD1 and AtBBD2 each form a homodimer but not a heterodimer and that the HCR domain is possibly crucial for dimerization.
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Podzimek T, Přerovská T, Šantrůček J, Kovaľ T, Dohnálek J, Matoušek J, Lipovová P. N-glycosylation of tomato nuclease TBN1 produced in N. benthamiana and its effect on the enzyme activity. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 276:152-161. [PMID: 30348313 DOI: 10.1016/j.plantsci.2018.08.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 06/08/2023]
Abstract
A unique analysis of an enzyme activity versus structure modification of the tomato nuclease R-TBN1 is presented. R-TBN1, the non-specific nuclease belonging to the S1-P1 nuclease family, was recombinantly produced in N. benthamiana. The native structure is posttranslationally modified by N-glycosylation at three sites. In this work, it was found that this nuclease is modified by high-mannose type N-glycosylation with a certain degree of macro- and microheterogeneity. To monitor the role of N-glycosylation in its activity, hypo- and hyperglycosylated nuclease mutants, R-TBN1 digested by α-mannosidase, and R-TBN1 deglycosylated by PNGase F were prepared. Deglycosylated R-TBN1 and mutant N94D/N112D were virtually inactive. Compared to R-TBN1 wt, both N94D and N112D mutants showed about 60% and 10% of the activity, respectively, while the N186D, D36S, and D36S/E104 N mutants were equally or even more active than R-TBN1 wt. The partial demannosylation of R-TBN1 did not affect the nuclease activity; moreover, a little shift in substrate specificity was observed. The results show two facts: 1) which sites must be occupied by a glycan for the proper folding and stability and 2) how N. benthamiana glycosylates the foreign nuclease. At the same time, the modifications can be interesting in designing the nuclease activity or specificity through its glycosylation.
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Affiliation(s)
- Tomáš Podzimek
- University of Chemical Technology Prague, Technická 3, Prague 6, 166 28, Czech Republic.
| | - Tereza Přerovská
- University of Chemical Technology Prague, Technická 3, Prague 6, 166 28, Czech Republic
| | - Jiří Šantrůček
- University of Chemical Technology Prague, Technická 3, Prague 6, 166 28, Czech Republic
| | - Tomáš Kovaľ
- Institute of Biotechnology of the Czech Academy of Sciences, v. v. i., Biocev, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Jan Dohnálek
- Institute of Biotechnology of the Czech Academy of Sciences, v. v. i., Biocev, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Jaroslav Matoušek
- Biology Centre, ASCR v.v.i., Institute of Plant Molecular Biology, Branišovská 32, 370 05, České Budějovice, Czech Republic
| | - Petra Lipovová
- University of Chemical Technology Prague, Technická 3, Prague 6, 166 28, Czech Republic
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Koval T, Dohnálek J. Characteristics and application of S1–P1 nucleases in biotechnology and medicine. Biotechnol Adv 2018; 36:603-612. [DOI: 10.1016/j.biotechadv.2017.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/08/2017] [Accepted: 12/13/2017] [Indexed: 12/18/2022]
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8
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Trundová M, Kovaľ T, Owens RJ, Fejfarová K, Dušková J, Kolenko P, Dohnálek J. Highly stable single-strand-specific 3'-nuclease/nucleotidase from Legionella pneumophila. Int J Biol Macromol 2018; 114:776-787. [PMID: 29580999 DOI: 10.1016/j.ijbiomac.2018.03.113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/19/2018] [Accepted: 03/21/2018] [Indexed: 12/20/2022]
Abstract
The Gram-negative bacterium Legionella pneumophila is one of the known opportunistic human pathogens with a gene coding for a zinc-dependent S1-P1 type nuclease. Bacterial zinc-dependent 3'-nucleases/nucleotidases are little characterized and not fully understood, including L. pneumophila nuclease 1 (Lpn1), in contrast to many eukaryotic representatives with in-depth studies available. To help explain the principle properties and role of these enzymes in intracellular prokaryotic pathogens we have designed and optimized a heterologous expression protocol utilizing E. coli together with an efficient purification procedure, and performed detailed characterization of the enzyme. Replacement of Ni2+ ions by Zn2+ ions in affinity purification proved to be a crucial step in the production of pure and stable protein. The production protocol provides protein with high yield, purity, stability, and solubility for structure-function studies. We show that highly thermostable Lpn1 is active mainly towards RNA and ssDNA, with pH optima 7.0 and 6.0, respectively, with low activity towards dsDNA; the enzyme features pronounced substrate inhibition. Bioinformatic and experimental analysis, together with computer modeling and electrostatics calculations point to an unusually high positive charge on the enzyme surface under optimal conditions for catalysis. The results help explain the catalytic properties of Lpn1 and its substrate inhibition.
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Affiliation(s)
- Mária Trundová
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Průmyslová 595, 25250 Vestec, Czech Republic.
| | - Tomáš Kovaľ
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Průmyslová 595, 25250 Vestec, Czech Republic.
| | - Raymond J Owens
- OPPF-UK, The Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, UK.
| | - Karla Fejfarová
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Průmyslová 595, 25250 Vestec, Czech Republic.
| | - Jarmila Dušková
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Průmyslová 595, 25250 Vestec, Czech Republic.
| | - Petr Kolenko
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Průmyslová 595, 25250 Vestec, Czech Republic.
| | - Jan Dohnálek
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Průmyslová 595, 25250 Vestec, Czech Republic.
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Wang Y, Jia P, Sharif R, Li Z, Li Y, Chen P. High-Level Production of DNA-Specific Endonuclease AsEndI with Synonymous Codon and its Potential Utilization for Removing DNA Contamination. Appl Biochem Biotechnol 2017; 185:641-654. [PMID: 29250754 DOI: 10.1007/s12010-017-2672-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/30/2017] [Indexed: 12/19/2022]
Abstract
Endonuclease I is a widely distributed periplasmic or extracellular enzyme. A method for the high-level production of recombinant AsEndI (endonuclease I from Aliivibrio salmonicida) in Escherichia coli with secretion expression is investigated. The coding sequence of AsEndI gene was assembled according to the E. coli codon usage bias, and AsEndI was expressed in the periplasm of E. coli TOP10 with a C-terminal 6× His-tagged fusion. The recombinant AsEndI (His-AsEndI) was purified by Ni-NTA resin with a yield of 1.29 × 107 U from 1-L LB medium. His-AsEndI could be classified into Ca2+/Mg2+-dependent nucleases and showed highest nuclease activity to dsDNA at pH 8.0 and 37 °C. His-AsEndI is highly active in a broad range of salt concentration range up to 1.0 M with optimal NaCl concentration at 0.4 M. His-AsEndI can effectively remove DNA contamination in RNA sample or in PCR reagents to the level that cannot be detected by highly sensitive nested PCR and without adverse effects on the subsequent PCR reaction. His-AsEndI can remove DNA contamination at high salt conditions, especially for the DNA that may be shielded by DNA-binding protein at low salt conditions.
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Affiliation(s)
- Yuan Wang
- College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China
| | - Peng Jia
- College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China
| | - Rahat Sharif
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China
| | - Zhengchen Li
- College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China
| | - Yuhong Li
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China.
| | - Peng Chen
- College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China.
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Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition. PLoS One 2016; 11:e0168832. [PMID: 28036383 PMCID: PMC5201275 DOI: 10.1371/journal.pone.0168832] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 12/07/2016] [Indexed: 01/08/2023] Open
Abstract
The single-strand-specific S1 nuclease from Aspergillus oryzae is an archetypal enzyme of the S1-P1 family of nucleases with a widespread use for biochemical analyses of nucleic acids. We present the first X-ray structure of this nuclease along with a thorough analysis of the reaction and inhibition mechanisms and of its properties responsible for identification and binding of ligands. Seven structures of S1 nuclease, six of which are complexes with products and inhibitors, and characterization of catalytic properties of a wild type and mutants reveal unknown attributes of the S1-P1 family. The active site can bind phosphate, nucleosides, and nucleotides in several distinguished ways. The nucleoside binding site accepts bases in two binding modes-shallow and deep. It can also undergo remodeling and so adapt to different ligands. The amino acid residue Asp65 is critical for activity while Asn154 secures interaction with the sugar moiety, and Lys68 is involved in interactions with the phosphate and sugar moieties of ligands. An additional nucleobase binding site was identified on the surface, which explains the absence of the Tyr site known from P1 nuclease. For the first time ternary complexes with ligands enable modeling of ssDNA binding in the active site cleft. Interpretation of the results in the context of the whole S1-P1 nuclease family significantly broadens our knowledge regarding ligand interaction modes and the strategies of adjustment of the enzyme surface and binding sites to achieve particular specificity.
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11
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Dan X, Liu W, Wong JH, Ng TB. A Ribonuclease Isolated from Wild Ganoderma Lucidum Suppressed Autophagy and Triggered Apoptosis in Colorectal Cancer Cells. Front Pharmacol 2016; 7:217. [PMID: 27504094 PMCID: PMC4958627 DOI: 10.3389/fphar.2016.00217] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 07/05/2016] [Indexed: 11/13/2022] Open
Abstract
The mushroom Ganoderma lucidum (G. lucidum) has been consumed in China as a medicine for promoting health and longevity for thousands of years. Due to its paramount and multiple pharmaceutical effects, G. lucidum has received considerable attention from researchers and its chemical constituents as well as their respective functions were gradually unveiled by using modern research methods. Herein, we reported the isolation of a protein (Ganoderma lucidum ribonuclease, GLR) with anti-colorectal cancer activities from G. lucidum. This protein is a 17.4-kDa RNA degrading enzyme (ribonuclease) and was purified by using liquid chromatography procedures. GLR manifested potent anti-proliferative and anti-colony formation activities on HT29 and HCT116 colorectal cancer cells by inducing cell cycle arrest in G1 phase through the regulation of cyclin D1 and P53 expression. GLR was demonstrated to induce cell apoptosis in HCT116 cells by activating unfolded protein response and caspase-9 regulated pathways. Besides, the ability to undergo autophagy which is a stress adaption mechanism to cope with metabolic crisis was significantly suppressed by GLR treatment in HCT116 cells. The activation of apoptosis in GLR-treated HT29 cells was, however, independent of caspase-9 and the suppression of autophagy was also relatively minor. Thus the apoptosis of HT29 cells triggered by GLR was much milder than that in HCT116 cells. Our findings show that the RNase from G. lucidum may be one of the bioactive components that contribute to the anti-colorectal cancer activity of G. lucidum.
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Affiliation(s)
- Xiuli Dan
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong Hong Kong, China
| | - Wenlong Liu
- Shenzhen Key Laboratory of Marine Biomedical Materials, Shenzhen Institutes of Advanced Technology, The Chinese Academy of Sciences Shenzhen, China
| | - Jack H Wong
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong Hong Kong, China
| | - Tzi B Ng
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong Hong Kong, China
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Stránský J, Koval’ T, Podzimek T, Týcová A, Lipovová P, Matoušek J, Kolenko P, Fejfarová K, Dušková J, Skálová T, Hašek J, Dohnálek J. Phosphate binding in the active centre of tomato multifunctional nuclease TBN1 and analysis of superhelix formation by the enzyme. Acta Crystallogr F Struct Biol Commun 2015; 71:1408-15. [PMID: 26527269 PMCID: PMC4631591 DOI: 10.1107/s2053230x15018324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 09/30/2015] [Indexed: 11/10/2022] Open
Abstract
Tomato multifunctional nuclease TBN1 belongs to the type I nuclease family, which plays an important role in apoptotic processes and cell senescence in plants. The newly solved structure of the N211D mutant is reported. Although the main crystal-packing motif (the formation of superhelices) is conserved, the details differ among the known structures. A phosphate ion was localized in the active site of the enzyme. The binding of the surface loop to the active centre is stabilized by the phosphate ion, which correlates with the observed aggregation of TBN1 in phosphate buffer. The conserved binding of the surface loop to the active centre suggests biological relevance of the contact in a regulatory function or in the formation of oligomers.
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Affiliation(s)
- Jan Stránský
- Institute of Biotechnology CAS, v.v.i., Vídeňská 1083, 142 20 Praha 4, Czech Republic
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University, Břehová 7, 115 19 Praha 1, Czech Republic
| | - Tomáš Koval’
- Institute of Biotechnology CAS, v.v.i., Vídeňská 1083, 142 20 Praha 4, Czech Republic
- Institute of Macromolecular Chemistry CAS, v.v.i., Heyrovského nám. 2, 162 06 Praha 6, Czech Republic
| | - Tomáš Podzimek
- University of Chemistry and Technology, Technická 5, 166 28 Praha 6, Czech Republic
| | - Anna Týcová
- Institute of Plant Molecular Biology, Biology Centre, CAS, v.v.i., Branišovská 31, 370 05 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Petra Lipovová
- University of Chemistry and Technology, Technická 5, 166 28 Praha 6, Czech Republic
| | - Jaroslav Matoušek
- Institute of Plant Molecular Biology, Biology Centre, CAS, v.v.i., Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Petr Kolenko
- Institute of Biotechnology CAS, v.v.i., Vídeňská 1083, 142 20 Praha 4, Czech Republic
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University, Břehová 7, 115 19 Praha 1, Czech Republic
- Institute of Macromolecular Chemistry CAS, v.v.i., Heyrovského nám. 2, 162 06 Praha 6, Czech Republic
| | - Karla Fejfarová
- Institute of Biotechnology CAS, v.v.i., Vídeňská 1083, 142 20 Praha 4, Czech Republic
- Institute of Macromolecular Chemistry CAS, v.v.i., Heyrovského nám. 2, 162 06 Praha 6, Czech Republic
| | - Jarmila Dušková
- Institute of Biotechnology CAS, v.v.i., Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Tereza Skálová
- Institute of Biotechnology CAS, v.v.i., Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Jindřich Hašek
- Institute of Biotechnology CAS, v.v.i., Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Jan Dohnálek
- Institute of Biotechnology CAS, v.v.i., Vídeňská 1083, 142 20 Praha 4, Czech Republic
- Institute of Macromolecular Chemistry CAS, v.v.i., Heyrovského nám. 2, 162 06 Praha 6, Czech Republic
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Isolation of a Ribonuclease with Antiproliferative and HIV-1 Reverse Transcriptase Inhibitory Activities from Japanese Large Brown Buckwheat Seeds. Appl Biochem Biotechnol 2014; 175:2456-67. [DOI: 10.1007/s12010-014-1438-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 11/28/2014] [Indexed: 01/03/2023]
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14
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Structural insights of the ssDNA binding site in the multifunctional endonuclease AtBFN2 from Arabidopsis thaliana. PLoS One 2014; 9:e105821. [PMID: 25157844 PMCID: PMC4144908 DOI: 10.1371/journal.pone.0105821] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 07/14/2014] [Indexed: 12/02/2022] Open
Abstract
The multi S1/P1 nuclease AtBFN2 (EC 3.1.30.1) encoded by the Arabidopsis thaliana At1g68290 gene is a glycoprotein that digests RNA, ssDNA, and dsDNA. AtBFN2 depends on three zinc ions for cleaving DNA and RNA at 3′-OH to yield 5′-nucleotides. In addition, AtBFN2′s enzymatic activity is strongly glycan dependent. Plant Zn2+-dependent endonucleases present a unique fold, and belong to the Phospholipase C (PLC)/P1 nuclease superfamily. In this work, we present the first complete, ligand-free, AtBFN2 crystal structure, along with sulfate, phosphate and ssDNA co-crystal structures. With these, we were able to provide better insight into the glycan structure and possible enzymatic mechanism. In comparison with other nucleases, the AtBFN2/ligand-free and AtBFN2/PO4 models suggest a similar, previously proposed, catalytic mechanism. Our data also confirm that the phosphate and vanadate can inhibit the enzyme activity by occupying the active site. More importantly, the AtBFN2/A5T structure reveals a novel and conserved secondary binding site, which seems to be important for plant Zn2+-dependent endonucleases. Based on these findings, we propose a rational ssDNA binding model, in which the ssDNA wraps itself around the protein and the attached surface glycan, in turn, reinforces the binding complex.
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Sánchez-Pons N, Vicient CM. Identification of a type I Ca2+/Mg2+-dependent endonuclease induced in maize cells exposed to camptothecin. BMC PLANT BIOLOGY 2013; 13:186. [PMID: 24256432 PMCID: PMC4225560 DOI: 10.1186/1471-2229-13-186] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 11/16/2013] [Indexed: 05/24/2023]
Abstract
BACKGROUND Camptothecin is a plant alkaloid that specifically binds topoisomerase I, inhibiting its activity and inducing double stranded breaks in DNA and activating the cell responses to DNA damage. RESULTS Maize cultured cells were incubated in the presence of different concentrations of camptothecin. Camptothecin inhibits cultured cell growth, induces genomic DNA degradation, and induces a 32 kDa Ca2+/Mg2+-dependent nuclease activity. This nuclease, we called CaMNUC32, is inhibited by Zn2+ and by acid pH, it is mainly localized in the nucleus and it cleaves single- and double-stranded DNA, with a higher activity against single-stranded DNA. Two-dimensional electrophoresis combined with mass spectrometry suggests that CaMNUC32 is a member of the type I S1/P1 nuclease family. This type of nucleases are usually Zn2+-dependent but our results support previous indications that S1-type nucleases have a wide variety of enzyme activities, including Ca2+/Mg2+-dependent. CONCLUSIONS We have identified and characterized CaMNUC32, a 32 kDa Ca2+/Mg2+-dependent nuclease of the S1/P1 family induced by the topoisomerase I inhibitor camptothecin in maize cultured cells.
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Affiliation(s)
- Núria Sánchez-Pons
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - Carlos M Vicient
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
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16
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Lesniewicz K, Karlowski WM, Pienkowska JR, Krzywkowski P, Poreba E. The plant s1-like nuclease family has evolved a highly diverse range of catalytic capabilities. PLANT & CELL PHYSIOLOGY 2013; 54:1064-78. [PMID: 23620482 DOI: 10.1093/pcp/pct061] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Plant S1-like nucleases, often referred to as nuclease I enzymes, are the main class of enzymes involved in nucleic acid degradation during plant programmed cell death. The catalytically active site of these enzymes shows a significant similarity to the well-described P1 nuclease from Penicillium citrinum. Previously published studies reported that plant S1-like nucleases possess catalytic activities similar to their fungal orthologs, i.e. they hydrolyze single-stranded DNA and RNA, and less efficiently double-stranded DNA, in the presence of zinc ions. Here we describe a comprehensive study of the nucleolytic activities of all Arabidopsis S1-like paralogs. Our results revealed that different members of this family are characterized by a surprisingly large variety of catalytic properties. We found that, in addition to Zn(2+)-dependent enzymes, this family also comprises nucleases activated by Ca(2+) and Mn(2+), which implies that the apparently well-known S1 nuclease active site in plant nucleases is able to cooperate with different activatory ions. Moreover, particular members of this class differ in their optimum pH value and substrate specificity. These results shed new light on the widely accepted classification of plant nucleases which is based on the assumption that the catalytic requirements of plant nucleases reflect their phylogenetic origin. Our results imply the need to redefine the understanding of the term 'nuclease I'. Analysis of the phylogenetic relationships between S1-like enzymes shows that plant representatives of this family evolve toward an increase in catalytic diversity. The importance of this process for the biological functions of plant S1-type enzymes is discussed.
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Affiliation(s)
- Krzysztof Lesniewicz
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, 89 Umultowska St., 61-614 Poznan, Poland.
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Koval' T, Lipovová P, Podzimek T, Matoušek J, Dušková J, Skálová T, Stěpánková A, Hašek J, Dohnálek J. Plant multifunctional nuclease TBN1 with unexpected phospholipase activity: structural study and reaction-mechanism analysis. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:213-26. [PMID: 23385457 DOI: 10.1107/s0907444912043697] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 10/22/2012] [Indexed: 11/11/2022]
Abstract
Type I plant nucleases play an important role in apoptotic processes and cell senescence. Recently, they have also been indicated to be potent anticancer agents in in vivo studies. The first structure of tomato nuclease I (TBN1) has been determined, its oligomerization and activity profiles have been analyzed and its unexpected activity towards phospholipids has been discovered, and conclusions are drawn regarding its catalytic mechanism. The structure-solution process required X-ray diffraction data from two crystal forms. The first form was used for phase determination; the second form was used for model building and refinement. TBN1 is mainly α-helical and is stabilized by four disulfide bridges. Three observed oligosaccharides are crucial for its stability and solubility. The active site is localized at the bottom of the positively charged groove and contains a zinc cluster that is essential for enzymatic activity. An equilibrium between monomers, dimers and higher oligomers of TBN1 was observed in solution. Principles of the reaction mechanism of the phosphodiesterase activity are suggested, with central roles for the zinc cluster, the nucleobase-binding pocket (Phe-site) and Asp70, Arg73 and Asn167. Based on the distribution of surface residues, possible binding sites for dsDNA and other nucleic acids with secondary structure were identified. The phospholipase activity of TBN1, which is reported for the first time for a nuclease, significantly broadens the substrate promiscuity of the enzyme, and the resulting release of diacylglycerol, which is an important second messenger, can be related to the role of TBN1 in apoptosis.
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Affiliation(s)
- Tomáš Koval'
- Institute of Macromolecular Chemistry, AS CR, v.v.i., Heyrovskeho nam. 2, 162 06 Praha 6, Czech Republic.
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