Interrogation of RNA-protein interaction dynamics in bacterial growth.
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Springer Nature
https://doi.org/10.1038/s44320-024-00031-y
https://doi.org/10.1038/s44320-024-00031-y
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Acknowledgements: The authors would like to thank Dr Caia DS Duncan and Prof Juan Mata for kindly letting us access the MP FastPrep-24 5 G Tissue Homogenizer (MP Biomedicals) and Prof Pietro Cicuta for microscopy access. Mass spectrometry analysis was performed at the Proteomics Facility of the Medical Research Council Toxicology Unit University of Cambridge, Cambridge, UK by Catarina Franco and Rayner Queiroz. The authors additionally thank Mike Deery at CCP for his assistance with MS sample preparation and analysis. The authors also thank Dr. Maria Marti Solano for her assistance during the manuscript writing and Dr. Xiaoteng Jiang for his inputs and manuscript proofreading. In addition, Bini Ramchandran, Yagnesh Umrania and Julie Howard Murkin for help in proteomic file management and submission. Finally, the authors thank Dr. Sergey Moshkovksiy and Prof. Urlaub Henning for their help and support in interpreting the MS data. MM is supported by the Medical Research Council, grant number 5TR00. LM is supported by a Herchel Smith Postdoctoral. CSD is supported by a Herchel Smith PhD Research Studentship. KD is supported by UK DRI at King’s College London. EV was supported by Wellcome Trust, grant numbers 110071/Z/15/Z awarded to KSL. The contribution of KD, CC and JU research was funded by the European Union’s Horizon 2020 research and innovation programme (835300-RNPdynamics). The Francis Crick Institute receives its core funding from Cancer Research UK (FC001110), the UK Medical Research Council (FC001110), and the Wellcome Trust (FC001110). RH and GHT were supported by InnovateUK and the Biotechnology and Biological Sciences Research Council through the Industrial Biotechnology Catalyst grant BB/N01040X/1. For the purpose of Open Access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.
Funder: Herchel Smith Postoctoral Fellowship
Funder: Herchel Smith PhD Research Studenship
Characterising RNA-protein interaction dynamics is fundamental to understand how bacteria respond to their environment. In this study, we have analysed the dynamics of 91% of the Escherichia coli expressed proteome and the RNA-interaction properties of 271 RNA-binding proteins (RBPs) at different growth phases. We find that 68% of RBPs differentially bind RNA across growth phases and characterise 17 previously unannotated proteins as bacterial RBPs including YfiF, a ncRNA-binding protein. While these new RBPs are mostly present in Proteobacteria, two of them are orthologs of human mitochondrial proteins associated with rare metabolic disorders. Moreover, we reveal novel RBP functions for proteins such as the chaperone HtpG, a new stationary phase tRNA-binding protein. For the first time, the dynamics of the bacterial RBPome have been interrogated, showcasing how this approach can reveal the function of uncharacterised proteins and identify critical RNA-protein interactions for cell growth which could inform new antimicrobial therapies.
Funder: Herchel Smith Postoctoral Fellowship
Funder: Herchel Smith PhD Research Studenship
Characterising RNA-protein interaction dynamics is fundamental to understand how bacteria respond to their environment. In this study, we have analysed the dynamics of 91% of the Escherichia coli expressed proteome and the RNA-interaction properties of 271 RNA-binding proteins (RBPs) at different growth phases. We find that 68% of RBPs differentially bind RNA across growth phases and characterise 17 previously unannotated proteins as bacterial RBPs including YfiF, a ncRNA-binding protein. While these new RBPs are mostly present in Proteobacteria, two of them are orthologs of human mitochondrial proteins associated with rare metabolic disorders. Moreover, we reveal novel RBP functions for proteins such as the chaperone HtpG, a new stationary phase tRNA-binding protein. For the first time, the dynamics of the bacterial RBPome have been interrogated, showcasing how this approach can reveal the function of uncharacterised proteins and identify critical RNA-protein interactions for cell growth which could inform new antimicrobial therapies.