Publications

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

• Kulathungage, H*, Aretakis, JR*, Vaidya, K, Al-Husini, N, Muthunayake, NS, Kim, S, Schrader, JM. Rif-seq reveals Caulobacter crescentus mRNA decay is globally coordinated with transcription and translation.  Manuscript in Preparation. *These authors contributed equally

• Passos, C*, Tomares, DT*, Yassine, H, Schnorr, WE, Hunter, H, Wolfe-Feichter, HK, Veiler, J, Dzurik, KG, Grillos, J, Gega, A, Saxena, SK, Schrader, JM, Childers, WS. BR-bodies Facilitate Adaptive Responses and Survival During Copper Stress in Caulobacter crescentus. bioRxiv 2025 *These authors contributed equally

• Ortiz-Rodrĺguez, LA, Yassine, H, Nandaha, V, Azaldegui, CA, Cheng, J., Schrader, JM, Biteen, JS. Stress Changes the Bacterial Biomolecular Condensate Material State and Shifts Function from mRNA Decay to Storage. bioRxiv 2024

• Yassine, H, Schrader, JM. APEX2 proximity labeling of RNA in bacteria.  bioRxiv 2024 

• 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. Current Opinion Microbiology 2024 

• Nandana V, Al-Husini N, Vaishnav A, Dilrangi KH, Schrader JM. Caulobacter crescentus RNase E condensation contributes to autoregulation and fitness. Molecular Biology of the Cell 2024 

• 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. Microbiology Spectrum 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 Reports 2023 *These authors contributed equally

• Ghosh, A.*, Bharmal, M.-H.M.*, Ghaleb, A., Nandana, V., , Schrader, J.M. Initiator AUGs Are Discriminated from Elongator AUGs Predominantly through mRNA Accessibility in C. crescentus. J Bacteriology 2023 *These authors contributed equally

• Collins MJ, Tomares DT, Nandana V, Schrader JM, Childers WS. RNase E biomolecular condensates stimulate PNPase activity. Scientific Reports 2023 

• Nandana, V., Schrader, J.M. Roles of liquid-liquid phase separation in bacterial RNA metabolism. Current Opinion Microbiology 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 Genomics and Bioinformatics 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