The BR-body proteome contains a complex network of protein-protein and protein-RNA interactions
Vidhyadhar Nandana,
Imalka W. Rathnayaka-Mudiyanselage,
Nisansala S. Muthunayake,
Ali Hatami,
C. Bruce Mousseau,
Luis A. Ortiz-Rodríguez,
Jamuna Vaishnav,
Michael Collins,
Alisa Gega,
Kaveendya S. Mallikaarachchi,
Hadi Yassine,
Aishwarya Ghosh,
Julie S. Biteen,
Yingxi Zhu,
Matthew M. Champion,
W. Seth Childers,
Jared M. Schrader
Affiliations
Vidhyadhar Nandana
Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
Imalka W. Rathnayaka-Mudiyanselage
Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA; Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
Nisansala S. Muthunayake
Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
Ali Hatami
Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI 48202, USA
C. Bruce Mousseau
Department of Chemistry, University of Notre Dame, Notre Dame, IN 46556, USA
Luis A. Ortiz-Rodríguez
Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
Jamuna Vaishnav
Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI 48202, USA
Michael Collins
Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
Alisa Gega
Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
Kaveendya S. Mallikaarachchi
Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
Hadi Yassine
Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
Aishwarya Ghosh
Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
Julie S. Biteen
Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
Yingxi Zhu
Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI 48202, USA
Matthew M. Champion
Department of Chemistry, University of Notre Dame, Notre Dame, IN 46556, USA
W. Seth Childers
Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
Jared M. Schrader
Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA; Corresponding author
Summary: Bacterial ribonucleoprotein bodies (BR-bodies) are non-membrane-bound structures that facilitate mRNA decay by concentrating mRNA substrates with RNase E and the associated RNA degradosome machinery. However, the full complement of proteins enriched in BR-bodies has not been defined. Here, we define the protein components of BR-bodies through enrichment of the bodies followed by mass spectrometry-based proteomic analysis. We find 111 BR-body-enriched proteins showing that BR-bodies are more complex than previously assumed. We identify five BR-body-enriched proteins that undergo RNA-dependent phase separation in vitro with a complex network of condensate mixing. We observe that some RNP condensates co-assemble with preferred directionality, suggesting that RNA may be trafficked through RNP condensates in an ordered manner to facilitate mRNA processing/decay, and that some BR-body-associated proteins have the capacity to dissolve the condensate. Altogether, these results suggest that a complex network of protein-protein and protein-RNA interactions controls BR-body phase separation and RNA processing.
