Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Crystal Structure of the Metallo-Endoribonuclease YbeY from Staphylococcus aureus

  • Jinwook Lee (Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Department of Agricultural Biotechnology, CALS, Seoul National University) ;
  • Inseong Jo (Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Department of Agricultural Biotechnology, CALS, Seoul National University) ;
  • Ae-Ran Kwon (Department of Beauty Care, College of Medical Science, Daegu Haany University) ;
  • Nam-Chul Ha (Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Department of Agricultural Biotechnology, CALS, Seoul National University)
  • Received : 2022.09.13
  • Accepted : 2022.11.17
  • Published : 2023.01.28
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Abstract

Endoribonuclease YbeY is specific to the single-stranded RNA of ribosomal RNAs and small RNAs. This enzyme is essential for the maturation and quality control of ribosomal RNA in a wide range of bacteria and for virulence in some pathogenic bacteria. In this study, we determined the crystal structure of YbeY from Staphylococcus aureus at a resolution of 1.9 Å in the presence of zinc chloride. The structure showed a zinc ion at the active site and two molecules of tricarboxylic acid citrate, which were also derived from the crystallization conditions. Our structure showed the zinc ionbound local environment at the molecular level for the first time. Molecular comparisons were performed between the carboxylic moieties of citrate and the phosphate moiety of the RNA backbone, and a model of YbeY in complex with a single strand of RNA was subsequently constructed. Our findings provide molecular insights into how the YbeY enzyme recognizes singlestranded RNA in bacteria.

Keywords

Acknowledgement

This study was supported by the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries (iPET), which is funded by the Ministry of Agriculture, Food, and Rural Affairs (MAFRA, 321036052HD020), and the Bio & Medical Technology Development Program of the National Research Foundation (NRF), which is funded by the Ministry of Science & ICT (2019M3E5D606386521). We used the Pohang Accelerator Laboratory 5C beamline (Pohang, Republic of Korea) and MALS and ITC equipment in the Korea Basic Science Institute (KBSI, Ochang, Republic of Korea).

References

  1. Grunberg-Manago M. 1999. Messenger RNA stability and its role in control of gene expression in bacteria and phages. Ann. Rev. Genet. 33: 193-227. https://doi.org/10.1146/annurev.genet.33.1.193
  2. Raines RT. 1998. Ribonuclease A. Chem. Rev. 98: 1045-1066. https://doi.org/10.1021/cr960427h
  3. Itoh T, Tomizawa J. 1979. Presented at the Cold Spring Harbor Symposia on Quantitative Biology.
  4. Jacob AI, Kohrer C, Davies BW, RajBhandary UL, Walker GC. 2013. Conserved bacterial RNase YbeY plays key roles in 70S ribosome quality control and 16S rRNA maturation. Mol. Cell 49: 427-438. https://doi.org/10.1016/j.molcel.2012.11.025
  5. Vercruysse M, Kohrer C, Shen Y, Proulx S, Ghosal A, Davies BW, et al. 2016. Identification of YbeY-protein interactions involved in 16S rRNA maturation and stress regulation in Escherichia coli. mBio 7: e01785-16.
  6. Pandey SP, Winkler JA, Li H, Camacho DM, Collins JJ, Walker GC. 2014. Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria. BMC Genomics 15: 121.
  7. Xia Y, Weng Y, Xu C, Wang D, Pan X, Tian Z, et al. 2020. Endoribonuclease YbeY is essential for RNA processing and virulence in Pseudomonas aeruginosa. mBio 11: e00659-20.
  8. Xia Y, Xu C, Wang D, Weng Y, Jin Y, Bai F, et al. 2021. Ybey controls the type III and type VI secretion systems and biofilm formation through RetS in Pseudomonas aeruginosa. Appl. Environ. Microbiol. 87: e02171-20.
  9. Zhan C, Fedorov EV, Shi W, Ramagopal U, Thirumuruhan R, Manjasetty BA, et al. 2005. The ybeY protein from Escherichia coli is a metalloprotein. Acta Crystallogr. Sec. F Struct. Biol. Cryst. Commun. 61: 959-963. https://doi.org/10.1107/S1744309105031131
  10. Babu VM, Sankari S, Budnick JA, Caswell CC, Walker GC. 2020. Sinorhizobium meliloti YbeY is a zinc-dependent single-strand specific endoribonuclease that plays an important role in 16S ribosomal RNA processing. NucleicAacids Res. 48: 332-348. https://doi.org/10.1093/nar/gkz1095
  11. Davies BW, Kohrer C, Jacob AI, Simmons LA, Zhu J, Aleman LM, et al. 2010. Role of Escherichia coli YbeY, a highly conserved protein, in rRNA processing. Mol. Microbiol. 78: 506-518. https://doi.org/10.1111/j.1365-2958.2010.07351.x
  12. Cox EH, McLendon GL. 2000. Zinc-dependent protein folding. Curr. Opin. Chem. Biol. 4: 162-165. https://doi.org/10.1016/S1367-5931(99)00070-8
  13. Vercruysse M, Kohrer C, Davies BW, Arnold MF, Mekalanos JJ, RajBhandary UL, et al. 2014. The highly conserved bacterial RNase YbeY is essential in Vibrio cholerae, playing a critical role in virulence, stress regulation, and RNA processing. PLoS Pathog. 10: e1004175.
  14. Otwinowski Z, Minor W. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276: 307-326. https://doi.org/10.1016/S0076-6879(97)76066-X
  15. Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N, et al. 2010. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. Sect. D Biol. Crystallogr. 66: 213-221. https://doi.org/10.1107/S0907444909052925
  16. Emsley P, Cowtan K. 2004. Coot: model-building tools for molecular graphics. Acta Crystallographica Section D: Biological Crystallography 60: 2126-2132. https://doi.org/10.1107/S0907444904019158
  17. Afonine PV, Mustyakimov M, Grosse-Kunstleve RW, Moriarty NW, Langan P, Adams PD. 2010. Joint X-ray and neutron refinement with phenix. refine. Acta Crystallogr. Sect. D Biol. Crystallogr. 66: 1153-1163. https://doi.org/10.1107/S0907444910026582
  18. Kang H, Bhardwaj K, Li Y, Palaninathan S, Sacchettini J, Guarino L, et al. 2007. Biochemical and genetic analyses of murine hepatitis virus Nsp15 endoribonuclease. J. Virol. 81: 13587-13597. https://doi.org/10.1128/JVI.00547-07
  19. Tu C, Zhou X, Tarasov SG, Tropea JE, Austin BP, Waugh DS, et al. 2011. The Era GTPase recognizes the GAUCACCUCC sequence and binds helix 45 near the 3' end of 16S rRNA. Proc. Natl. Acad. Sci. USA 108: 10156-10161. https://doi.org/10.1073/pnas.1017679108