Crystallographic study reveals an unexpected substrate for S1‑P1 nuclease

B. Husáková1, 2, K. Adámková1, 2, M. Trundová1, T. Kovaž1, J. Dohnálek1

1 Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Průmyslová 595, 25250 Vestec, Czech Republic

2 University of Chemistry and Technology, Technická 5, 166 28 Prague 6 – Dejvice, Czech Republic

Blanka.Hustakova@ibt.cas.cz

 

S1-P1 nucleases are metal-dependent nucleases cleaving both DNA and RNA. While the S1-P1 nucleases are produced by fungi, plants, trypanosomatids or bacteria, including human pathogens, they are not present in mammals. They found usage in biotechnological application, predominantly nuclease S1 from Aspergillus oryzae [1]. Their activity can also lead to a decrease of tumor growth thus they represent potential tools for antitumor therapy [2]. Recently, it was reported that S1-P1 nucleases from Leishmania can be a part of the pathogen defence against the host immune system as they are able to degrade neutrophil extracellular traps (NETs) [3].

Human opportunistic bacterium Stenotrophomonas maltophilia can induce serious complications to immunocompromised patients and to patients with cystic fibrosis [4]. The growing numbers of multi‑drug resistant isolates lead to the search for the new therapeutic approaches in treatment of S. maltophilia infections. One of the potential targets is the S1-P1 nuclease from S. maltophilia SmNuc1 which was produced in E. coli, characterized and crystallized.

The crystals of SmNuc1 diffracting to high resolution enable fragment screening and ligand binding studies in search for SmNuc1 specific inhibitors or new binding sites. Soaking of cyclic diguanylate (c‑di‑GMP) led to the discovery of its cleavage as only GMP was identified in the difference maps of electron density. To the best of our knowledge it is the first time the hydrolysis of cyclic dinucleotides was reported in the S1-P1 nuclease family. These results suggest a possible role of the nuclease SmNuc1 in the host-pathogen interaction.

1.         Koval, T. and J. Dohnálek, Biotechnology Advances, 2018, 36, pp. 603-612.

2.         Matousek, J., et al., Neoplasma, 2010, 57, pp. 339-48.

3.         Freitas-Mesquita, A.L., et al., Molecular and Biochemical Parasitology, 2019, 229, pp. 6-14.

4.         Brooke, J.S., Clinical Microbiology Reviews, 2012, 25, pp. 2-41.

 This project was supported by the ERDF fund (CZ.02.1.01/0.0/0.0/16_013/0001776 and CZ.02.1.01/0.0/0.0/15_003/0000447), Czech Science Foundation, project 20-12109S, and financial support from specific university research (MSMT‑No‑21‑SVV/2020), by the Ministry of Education, Youth and Sports of the Czech Republic (LM2018127, support of BiocevCMS – core facilities Biophysical Methods, Crystallization of Proteins and Nucleic Acids and Structural Mass Spectrometry of CIISB, part of Instruct-ERIC).