Abstract
Bacterial ribonuclease E (RNase E) plays a crucial role in the processing and decay of RNAs. A small protein named RraA negatively regulates the activity of RNase E via protein-protein interaction in various bacteria. Recently, RraAS1 and RraAS2, which are functional homologs of RraA from Escherichia coli, were identified in the Gram-positive species Streptomyces coelicolor. RraAS1 and RraAS2 inhibit RNase ES ribonuclease activity in S. coelicolor. RraAS1 and RraAS2 have a C-terminal extension region unlike typical bacterial RraA proteins. In this study, we present the crystal structure of RraAS2, exhibiting a hexamer arranged in a dimer of trimers, consistent with size exclusion chromatographic results. Importantly, the C-terminal extension region formed a long α-helix at the junction of the neighboring subunit, which is similar to the trimeric RraA orthologs from Saccharomyces cerevisiae. Truncation of the C-terminal extension region resulted in loss of RNase ES inhibition, demonstrating its crucial role. Our findings present the first bacterial RraA that has a hexameric assembly with a C-terminal extension α-helical region, which plays an essential role in the regulation of RNase ES activity in S. coelicolor.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Adams, P.D., Afonine, P.V., Bunkoczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.W., Kapral, G.J., Grosse-Kunstleve, R.W., et al. 2010. Phenix: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221.
Ahn, S., Shin, E., Yeom, J.H., and Lee, K. 2008. Modulation of Escherichia coli RNase E activity by RraAS2, a Streptomyces coelicolor ortholog of RraA. Korean J. Microbiolol. 44, 93–97.
Badger, J., Sauder, J.M., Adams, J.M., Antonysamy, S., Bain, K., Bergseid, M.G., Buchanan, S.G., Buchanan, M.D., Batiyenko, Y., Christopher, J.A., et al. 2005. Structural analysis of a set of proteins resulting from a bacterial genomics project. Proteins 60, 787–796.
Callaghan, A.J., Aurikko, J.P., Ilag, L.L., Gunter Grossmann, J., Chandran, V., Kuhnel, K., Poljak, L., Carpousis, A.J., Robinson, C.V., Symmons, M.F., et al. 2004. Studies of the RNA degradosome-organizing domain of the Escherichia coli ribonuclease RNase E. J. Mol. Biol. 340, 965–979.
Cohen, S.N. and McDowall, K.J. 1997. RNase E: still a wonderfully mysterious enzyme. J. Mol. Biol. 23, 1099–1106.
Emsley, P., Lohkamp, B., Scott, W.G., and Cowtan, K. 2010. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501.
Gao, J., Lee, K., Zhao, M., Qiu, J., Zhan, X., Saxena, A., Moore, C.J., Cohen, S.N., and Georgiou, G. 2006. Differential modulation of E. coli mRNA abundance by inhibitory proteins that alter the composition of the degradosome. Mol. Microbiol. 61, 394–406.
Ghora, B.K. and Apirion, D. 1978. Structural analysis and in vitro processing to p5 rRNA of a 9S RNA molecule isolated from an rne mutant of E. coli. Cell 15, 1055–1066.
Gorna, M.W., Pietras, Z., Tsai, Y.C., Callaghan, A.J., Hernandez, H., Robinson, C.V., and Luisi, B.F. 2010. The regulatory protein RraA modulates RNA-binding and helicase activities of the E. coli RNA degradosome. RNA 16, 553–562.
Heo, J., Kim, D., Joo, M., Lee, B., Seo, S., Lee, J., Song, S., Yeom, J.H., Ha, N.C., and Lee, K. 2016. RraAS2 requires both scaffold domains of RNase ESfor high-affinity binding and inhibitory action on the ribonucleolytic activity. J. Microbiol. 54, 660–666.
Kim, D., Kim, Y.H., Jang, J., Yeom, J.H., Jun, J.W., Hyun, S., and Lee, K. 2016. Functional Analysis of Vibrio vulnificus Orthologs of Escherichia coli RraA and RNase E. Curr. Microbiol. 72, 716–722.
Lee, K. and Cohen, S.N. 2003. A Streptomyces coelicolor functional orthologue of Escherichia coli RNase E shows shuffling of catalytic and PNPase-binding domains. Mol. Microbiol. 48, 349–360.
Lee, K., Zhan, X., Gao, J., Qiu, J., Feng, Y., Meganathan, R., Cohen, S.N., and Georgiou, G. 2003. RraA. a protein inhibitor of RNase E activity that globally modulates RNA abundance in E. coli. Cell 114, 623–634.
Lee, M., Yeom, J.H., Sim, S.H., Ahn, S., and Lee, K. 2009. Effects of Escherichia coli RraA orthologs of Vibrio vulnificus on the ribonucleolytic activity of RNase E in vivo. Curr. Microbiol. 58, 349–353.
Leulliot, N., Quevillon-Cheruel, S., Graille, M., Schiltz, M., Blondeau, K., Janin, J., and Van Tilbeurgh, H. 2005. Crystal structure of yeast YER010Cp, a knotable member of the RraA protein family. Protein Sci. 14, 2751–2758.
Li, Z. and Deutscher, M.P. 2002. RNase E plays an essential role in the maturation of Escherichia coli tRNA precursors. RNA 8, 97–109.
Mazurkewich, S., Wang, W., and Seah, S.Y. 2014. Biochemical and structural analysis of RraA proteins to decipher their relationships with 4-hydroxy-4-methyl-2-oxoglutarate/4-carboxy-4-hydroxy-2-oxoadipate aldolases. Biochemistry 53, 542–553.
Monzingo, A.F., Gao, J., Qiu, J., Georgiou, G., and Robertus, J.D. 2003. The X-ray structure of Escherichia coli RraA (MenG), A protein inhibitor of RNA processing. J. Mol. Biol. 332, 1015–1024.
Otwinowski, Z. and Minor, W. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326.
Park, S., Ha, S., and Kim, Y. 2017. The protein crystallography beamlines at the pohang light source ll. Biodesign 5, 30–34.
Rehse, P.H., Kuroishi, C., and Tahirov, T.H. 2004. Structure of the RNA-processing inhibitor RraA from Thermus thermophilis. Acta Crystallogr. D Biol. Crystallogr. 60, 1997–2002.
Seo, S., Kim, D., Song, W., Heo, J., Joo, M., Lim, Y., Yeom, J.H., and Lee, K. 2017. RraAS1 inhibits the ribonucleolytic activity of RNase ESby interacting with its catalytic domain in Streptomyces coelicolor. J. Microbiol. 55, 37–43.
Sigle, S., Ladwig, N., Wohlleben, W., and Muth, G. 2015. Synthesis of the spore envelope in the developmental life cycle of Streptomyces coelicolor. Int. J. Med. Microbiol. 305, 183–189.
Tang, J., Luo, M., Niu, S., Zhou, H., Cai, X., Zhang, W., Hu, Y., Yin, Y., Huang, A., and Wang, D. 2010. The crystal structure of hexamer RraA from Pseudomonas aeruginosa reveals six conserved protein-protein interaction sites. Protein J. 29, 583–590.
Yeom, J.H., Go, H., Shin, E., Kim, H.L., Han, S.H., Moore, C.J., Bae, J., and Lee, K. 2008. Inhibitory effects of RraA and RraB on RNAse E-related enzymes imply conserved functions in the regulated enzymatic cleavage of RNA. FEMS Microbiol. Lett. 285, 10–15.
Author information
Authors and Affiliations
Corresponding authors
Rights and permissions
About this article
Cite this article
Park, N., Heo, J., Song, S. et al. Crystal structure of Streptomyces coelicolor RraAS2, an unusual member of the RNase E inhibitor RraA protein family. J Microbiol. 55, 388–395 (2017). https://doi.org/10.1007/s12275-017-7053-8
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12275-017-7053-8