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Dai T, Ban S, Han L, Li L, Zhang Y, Zhang Y, Zhu W. Effects of exogenous glycine betaine on growth and development of tomato seedlings under cold stress. FRONTIERS IN PLANT SCIENCE 2024; 15:1332583. [PMID: 38584954 PMCID: PMC10995342 DOI: 10.3389/fpls.2024.1332583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/11/2024] [Indexed: 04/09/2024]
Abstract
Low temperature is a type of abiotic stress affecting the tomato (Solanum lycopersicum) growth. Understanding the mechanisms and utilization of exogenous substances underlying plant tolerance to cold stress would lay the foundation for improving temperature resilience in this important crop. Our study is aiming to investigate the effect of exogenous glycine betaine (GB) on tomato seedlings to increase tolerance to low temperatures. By treating tomato seedlings with exogenous GB under low temperature stress, we found that 30 mmol/L exogenous GB can significantly improve the cold tolerance of tomato seedlings. Exogenous GB can influence the enzyme activity of antioxidant defense system and ROS levels in tomato leaves. The seedlings with GB treatment presented higher Fv/Fm value and photochemical activity under cold stress compared with the control. Moreover, analysis of high-throughput plant phenotyping of tomato seedlings also supported that exogenous GB can protect the photosynthetic system of tomato seedlings under cold stress. In addition, we proved that exogenous GB significantly increased the content of endogenous abscisic acid (ABA) and decreased endogenous gibberellin (GA) levels, which protected tomatoes from low temperatures. Meanwhile, transcriptional analysis showed that GB regulated the expression of genes involved in antioxidant capacity, calcium signaling, photosynthesis activity, energy metabolism-related and low temperature pathway-related genes in tomato plants. In conclusion, our findings indicated that exogenous GB, as a cryoprotectant, can enhance plant tolerance to low temperature by improving the antioxidant system, photosynthetic system, hormone signaling, and cold response pathway and so on.
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Affiliation(s)
- Taoyu Dai
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Songtao Ban
- Key Laboratory of Intelligent Agricultural Technology (Yangtze River Delta), Ministry of Agriculture and Rural Affairs, Agricultural Information Institute of Science and Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Liyuan Han
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Linyi Li
- Key Laboratory of Intelligent Agricultural Technology (Yangtze River Delta), Ministry of Agriculture and Rural Affairs, Agricultural Information Institute of Science and Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yingying Zhang
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yuechen Zhang
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Weimin Zhu
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Key Laboratory of Intelligent Agricultural Technology (Yangtze River Delta), Ministry of Agriculture and Rural Affairs, Agricultural Information Institute of Science and Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
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Krela R, Poreba E, Lesniewicz K. Variations in the enzymatic activity of S1-type nucleases results from differences in their active site structures. Biochim Biophys Acta Gen Subj 2023; 1867:130424. [PMID: 37463618 DOI: 10.1016/j.bbagen.2023.130424] [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: 02/13/2023] [Revised: 05/27/2023] [Accepted: 07/02/2023] [Indexed: 07/20/2023]
Abstract
BACKGROUND S1-like nucleases are widespread enzymes commonly used in biotechnology and molecular biology. Although it is commonly believed that they are mainly Zn2+-dependent acidic enzymes, we have found that numerous members of this family deviate from this rule. Therefore, in this work, we decided to check how broad is the range of non‑zinc-dependent S1-like nucleases and what is the molecular basis of their activities. METHODS S1-like nucleases chosen for analysis were achieved through heterologous expression in appropriate eukaryotic hosts. To characterize nucleases' active-site properties, point mutations were introduced in selected positions. The enzymatic activities of wild-type and mutant nucleases were tested by in-gel nuclease activity assay. RESULTS We discovered that S1-like nucleases encoded by non-vascular plants and single-celled protozoa, like their higher plant homologues, exhibit a large variety of catalytic properties. We have shown that these individual properties are determined by specific non-conserved active site residues. CONCLUSIONS Our findings demonstrate that mutations that occur during evolution can significantly alter the catalytic properties of S1-like nucleases. As a result, different ions can compete for particular S1-type nucleases' active sites. This phenomenon undermines the existing classification of S1-like nucleases. GENERAL SIGNIFICANCE Our findings have numerous implications for applications and understanding the S1-like nucleases' biological functions. For example, new biotechnological applications should take into account their unexpected catalytic properties. Moreover, these results demonstrate that the trinuclear zinc-based model commonly used to characterize the catalytic activities of S1-like nucleases is insufficient to explain the actions of non‑zinc-dependent members of this family.
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Affiliation(s)
- Rafal Krela
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, Umultowska St. 89, 61-614 Poznan, Poland; Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice 370 05, Czech Republic.
| | - Elzbieta Poreba
- Department of Genetics, Institute of Experimental Biology, Adam Mickiewicz University in Poznan, Umultowska St. 89, 61-614 Poznan, Poland.
| | - Krzysztof Lesniewicz
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, Umultowska St. 89, 61-614 Poznan, Poland.
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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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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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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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Singla P, Bhardwaj RD. Enzyme promiscuity – A light on the “darker” side of enzyme specificity. BIOCATAL BIOTRANSFOR 2019. [DOI: 10.1080/10242422.2019.1696779] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Prabhjot Singla
- Department of Biochemistry, Punjab Agricultural University, Ludhiana, India
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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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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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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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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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Chou TL, Ko TP, Ko CY, Lin TY, Guo RT, Yu TF, Chan HC, Shaw JF, Wang AHJ. Mechanistic insights to catalysis by a zinc-dependent bi-functional nuclease from Arabidopsis thaliana. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2013. [DOI: 10.1016/j.bcab.2013.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Koval' T, Lipovová P, Podzimek T, Matoušek J, Dušková J, Skálová T, Štěpánková A, Hašek J, Dohnálek J. Plant multifunctional nuclease TBN1 with unexpected phospholipase activity: structural study and reaction-mechanism analysis. Corrigendum. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013. [DOI: 10.1107/s0907444913003284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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