Spatiotemporal Organization of the E. coli Transcriptome: Translation Independence and Engagement in Regulation

Shanmugapriya Kannaiah, Jonathan Livny, Orna Amster-Choder*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

48 Scopus citations

Abstract

Despite reports that bacteria are capable of localizing RNAs to specific subcellular sites, the global prevalence of this phenomenon remained unknown. Kannaiah et al. show uneven distribution of the E. coli transcriptome and a significant translation-independent RNA localization. The unique population at the poles highlights them as hubs for regulation.

Original languageAmerican English
Pages (from-to)574-589.e7
JournalMolecular Cell
Volume76
Issue number4
DOIs
StatePublished - 21 Nov 2019

Bibliographical note

Funding Information:
We thank Anat Nussbaum-Shochat for construction of strains and plasmids and Omer Goldberger and Mikel Irastorza for technical help. We are grateful to Hanah Margalit and her group members for helpful advice on preparation of cDNA libraries and data analysis. We appreciate the advice of Yuval Nevo from the Computational Center, and Michal Bronstein, director of the Center for Genomic Technologies, Hebrew University, on RNA sequencing and data analysis. We thank Yael Feinstein-Rotkopf from the Core Research Facility, Faculty of Medicine at The Hebrew University for help with FRAP microscopy. We thank Susan Gottesman and Kumari Kavita for providing strains that express Hfq mutant proteins in E. coli MG1655 and Agamemnon Carpousis for providing strain Kti164. We appreciate helpful discussions with members of the Amster-Choder lab. We are grateful to Richard Losick for critical reading of the manuscript. This research was supported by the Israel Science Foundation (ISF) founded by the Israel Academy of Sciences and Humanities and the Deutsch-Israeli Project Cooperation (DIP).

Funding Information:
We thank Anat Nussbaum-Shochat for construction of strains and plasmids and Omer Goldberger and Mikel Irastorza for technical help. We are grateful to Hanah Margalit and her group members for helpful advice on preparation of cDNA libraries and data analysis. We appreciate the advice of Yuval Nevo from the Computational Center, and Michal Bronstein, director of the Center for Genomic Technologies, Hebrew University, on RNA sequencing and data analysis. We thank Yael Feinstein-Rotkopf from the Core Research Facility, Faculty of Medicine at The Hebrew University for help with FRAP microscopy. We thank Susan Gottesman and Kumari Kavita for providing strains that express Hfq mutant proteins in E. coli MG1655 and Agamemnon Carpousis for providing strain Kti164. We appreciate helpful discussions with members of the Amster-Choder lab. We are grateful to Richard Losick for critical reading of the manuscript. This research was supported by the Israel Science Foundation (ISF) founded by the Israel Academy of Sciences and Humanities and the Deutsch-Israeli Project Cooperation (DIP). S.K. and O.A.-C. prepared the libraries for RNA-seq. J.L. and S.K. analyzed the RNA-seq data and carried out bioinformatics analyses. S.K. conducted the experiments. O.A.-C. and J.L. provided advice and contributed to experimental design. S.K. J.L. and O.A.-C. designed the study, analyzed data, and wrote manuscript. The authors declare no competing interests.

Publisher Copyright:
© 2019 Elsevier Inc.

Keywords

  • E. coli
  • RNA localization
  • RNA sequencing
  • bacteria
  • cell fractionation
  • live-cell microscopy
  • small RNAs
  • spatial organization

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