Abstract
Restriction–modification (R-M) systems form a large superfamily constituting bacterial innate immunity mechanism. The restriction endonucleases (REases) are very diverse in subunit structure, DNA recognition, co-factor requirement, and mechanism of action. Among the different catalytic motifs, HNH active sites containing REases are the second largest group distinguished by the presence of the ββα-metal finger fold. KpnI is the first member of the HNH-family REases whose homologs are present in many bacteria of Enterobacteriaceae having varied degrees of sequence similarity between them. Considering that the homologs with a high similarity may have retained KpnI-like properties, while those with a low similarity could be different, we have characterized a distant KpnI homolog present in a pathogenic Klebsiella pneumoniae NTUH K2044. A comparison of the properties of KpnI and KpnK revealed that despite their similarity and the HNH motif, these two enzymes have different properties viz oligomerization, cleavage pattern, metal ion requirement, recognition sequence, and sequence specificity. Unlike KpnI, KpnK is a monomer in solution, nicks double-stranded DNA, recognizes degenerate sequence, and catalyses the degradation of DNA into smaller products after the initial cleavage at preferred sites. Due to several distinctive properties, it can be classified as a variant of the Type IIS enzyme having nicking endonuclease activity.
Key points
• KpnK is a distant homolog of KpnI and belongs to the ββα-metal finger superfamily.
• Both KpnI and KpnK have widespread occurrence in K. pneumoniae strains.
• KpnK is a Type IIS restriction endonuclease with a single-strand nicking property.
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Most data generated or analysed during this study are included in this manuscript (and its ‘Supplementary information’ files).
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Acknowledgements
We thank Dr. Vijaya Srinivasan from CSIR-IMTECH for providing the K. pneumoniae NTUH strain. Debarghya Ghose is acknowledged for the initial cloning of KpnK, and Iqball Faheem is acknowledged for his help in size exclusion chromatography. We acknowledge the central facility of phosphor imaging at the Indian Institute of Science, supported by the Department of Biotechnology, Government of India, and VN laboratory members for their valuable suggestions and critical inputs. MS acknowledges the University Grants Commission, Government of India, for financial assistance through Junior Research Fellowship (JRF) and Senior Research Fellowship (SRF).
Funding
This research was supported by grants to V.N. from the Science and Engineering Research Board, Department of Science and Technology (CRG/2019/000077), and Department of Biotechnology (BT/PR41348/MED/29/1536/2020), Government of India.
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MS, BE and SME: performed the experiments. EN, SME, and BE: prepared constructs used in the study. ISR: performed bioinformatic analyses. MS and VN: analysed the data and wrote the manuscript. VN: designed the experiments, supervision, and resources. All authors read and approved the final manuscript.
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Santoshi, M., Engleng, B., Eligar, S.M. et al. Identification and characterization of a new HNH restriction endonuclease with unusual properties. Appl Microbiol Biotechnol 107, 6263–6275 (2023). https://doi.org/10.1007/s00253-023-12717-8
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DOI: https://doi.org/10.1007/s00253-023-12717-8