Publications

WIRES RNA Cover Image (Art by Nisansala)

Publications (For most updated pubs, visit Google Scholar and pubmed bibliography)

Mallikaarachchi KS, Huang JL, Madras S, Cuellar RA, Huang Z, Gega A, Rathnayaka-Mudiyanselage IW, Al-Husini N, Saldaña-Rivera N, Ma LH, Ng E, Chen JC, Schrader JM. Sinorhizobium meliloti BR-bodies promote fitness during host colonization. bioRxiv. 2024
Rathnayaka-Mudiyanselage IW, Nandana V, Schrader JM. Proteomic composition of eukaryotic and bacterial RNA decay condensates suggests convergent evolution. Curr Opin Microbiol. 2024
Nandana V, Al-Husini N, Vaishnav A, Dilrangi KH, Schrader JM. Caulobacter crescentus RNase E condensation contributes to autoregulation and fitness. bioRxiv. 2023
de Araújo HL, Picinato BA, Lorenzetti APR, Muthunayake NS, Rathnayaka-Mudiyanselage IW, Dos Santos NM, Schrader J, Koide T, Marques MV. The DEAD-box RNA helicase RhlB is required for efficient RNA processing at low temperature in Caulobacter. Microbiol Spectr. 2023
Nandana V, Rathnayaka-Mudiyanselage IW, Muthunayake NS, Hatami A, Mousseau CB, Ortiz-Rodríguez LA, Vaishnav J, Collins M, Gega A, Mallikaarachchi KS, Yassine H, Ghosh A, Biteen JS, Zhu Y, Champion MM, Childers WS, Schrader JM. The BR-body proteome contains a complex network of protein-protein and protein-RNA interactions. Cell Rep. 2023
Collins MJ, Tomares DT, Nandana V, Schrader JM, Childers WS. RNase E biomolecular condensates stimulate PNPase activity. Sci Rep. 2023
Nandana, V., Schrader, J.M. Roles of liquid-liquid phase separation in bacterial RNA metabolism. Curr Opin Microbiol. 2021
Muthunayake, N.S., Al-Husini, N., and Schrader, J. M. Differential centrifugation to enrich Bacterial Ribonucleoprotein bodies (BR-bodies) from Caulobacter crescentus. STAR Protocols. 2020
Bharmal, M.-H.M., Aretakis, J.M., Schrader, J.M. An improved Caulobacter crescentus operon annotation based on transcriptome data. MRA. 2020
Bharmal, M.-H.M., Gega, A., Schrader, J.M. A combinatorial model predicts leaderless mRNA start codon selection in C. crescentus. NAR Genom Bioinform, 2021.
Muthunayake, N.S., Tomares, D. T. , Childers, W. S., and Schrader, J. M. Phase-Separated Bacterial Ribonucleoprotein Bodies (BR-bodies) Organize mRNA Decay. WIREs RNA 2020.
Al-Husini, N., D. T. Tomares, Z. Pfaffenberger, N. S. Muthunayake, M. A. Samad, T. Zuo, O. Bitar, J. R. Aretakis, M.-H. M. Bharmal, A. Gega, J. S. Biteen, W. S. Childers and J. M. Schrader. BR-bodies provide selectively permeable condensates that stimulate mRNA decay and prevent release of decay intermediates. Molecular Cell 2020. BioRxiv, 2019.
Munoz-Dorado, J., A. Moraleda-Muñoz, F. J. Marcos-Torres, F. J. Contreras-Moreno, A. B. Martin-Cuadrado, J. M. Schrader, P. I. Higgs and J. Perez. Transcriptome dynamics of the Myxococcus xanthus multicellular developmental program. eLife, 2019.
Aretakis, J.R., Gega, A., Schrader, J.M. Absolute measurements of mRNA translation in C. crescentus reveal important fitness costs of vitamin B12 scavenging. mSystems, 2019, BioRxiv, 2019.
Aretakis, J.R, Al-Husini, N., Schrader, J.M. Methodology for ribosome profiling of key stages of the Caulobacter crescentus cell cycle. Methods in Enzymology, 2018.
Al-Husini, N., Tomares, D.T., Bitar, O., Childers, W.S., Schrader, J.M. α-proteobacterial RNA degradosomes assemble liquid-liquid phase separated RNP bodies. Molecular Cell, 2018.
Uhlenbeck, O.C. and Schrader, J.M. Evolutionary tuning impacts the design of bacterial tRNAs for the incorporation of unnatural amino acids by ribosomes. Current Opinion in Chemical Biology, 2018.
Bayas, C.A., Wang, J., Lee, M.K., Schrader, J.M., Shapiro, L., Moerner, W.E. Spatial organization and dynamics of RNase E and ribosomes in Caulobacter crescentus. Proceedings of the National Academy of Sciences, 2018.
Schrader, J.M., Li, G.W., Childers, W.S., Perez, A., Weissman, J.S., Shapiro, L., McAdams, H.H. Dynamic translational regulation in Caulobacter cell cycle control. Proceedings of the National Academy of Sciences 2016.
Lasker, K.*, Schrader, J.M.*, Men, Y., Marshik, T., Dill, D.L., McAdams, H.H., Shapiro, L. CauloBrowser: a systems biology resource for Caulobacter crescentus. Nucleic Acids Research, 2016. *Equal contribution
Zhou, B.*, Schrader, J.M.*, Kalogeraki, V.S., Abeliuk, E.A., Dinh, C.B., McAdams, H.H., Shapiro, L. The global regulatory architecture of transcription during the Caulobacter cell cycle. PLOS Genetics, 2015. *Equal contribution
Schrader, J.M., Shapiro, L. Synchronization of Caulobacter crescentus for investigation of the bacterial cell cycle. JoVE, 2014.
Liu, W., Kavaliauskas, D., Schrader, J.M., Perla-Kajan, J., Mandecki, W., Uhlenbeck, O.C., Knudsen, C.R., Goldman, Y.E., Cooperman, B.S. Labeled EF-Tus for rapid kinetic studies of pre-translocation complex formation. ACS Chemical Biology, 2014.
Yikilmaz, E., Chapman, S.J., Schrader, J.M., Uhlenbeck, O.C. The interface between Escherichia coli Elongation Factor Tu and aminoacyl-tRNA. Biochemistry, 2014.
Schrader, J.M., Zhou, B., Li, G., Lasker, K., Childers, W.S., Williams, B., Long, T., Crosson, S., McAdams, H.H., Weissman, J.S., Shapiro, L. The coding and noncoding architecture of the Caulobacter crescentus genome. PLOS Genetics, 2014.
Chapman, S.J., Schrader, J.M., Uhlenbeck, O.C. Histidine 66 in E. coli elongation factor Tu selectively stabilizes aminoacyl-tRNAs. Journal of Biological Chemistry, 2011.
Schrader, J.M., Uhlenbeck, O.C. Is the sequence-specific binding of aminoacyl-tRNAs by EF-Tu universal among bacteria?. Nucleic Acids Research, 2011.
Schrader, J.M.,Chapman, S.J., Uhlenbeck, O.C. Tuning the affinity of aminoacyl-tRNA to elongation factor Tu for optimal decoding. Proceedings of the National Academy of Sciences, 2011.
Schrader, J.M., Saks, M.E., Uhlenbeck, O.C. The specific interaction between aminoacyl-tRNAs and elongation factor Tu. Chapter 15. Ribosomes: Structure, Function, and Dynamics, 2010.
Schrader, J.M.,Chapman, S.J., Uhlenbeck, O.C. Understanding the sequence specificity of tRNA binding to elongation factor Tu using tRNA mutagenesis. Journal of Molecular Biology, 2009.