Abstract
Biomolecular condensates play a key role in organizing RNAs and proteins into membraneless organelles. Bacterial RNP-bodies (BR-bodies) are a biomolecular condensate containing the RNA degradosome mRNA decay machinery, but the biochemical function of such organization remains poorly defined. Here, we define the RNA substrates of BR-bodies through enrichment of the bodies followed by RNA sequencing (RNA-seq). We find that long, poorly translated mRNAs, small RNAs, and antisense RNAs are the main substrates, while rRNA, tRNA, and other conserved non-coding RNAs (ncRNAs) are excluded from these bodies. BR-bodies stimulate the mRNA decay rate of enriched mRNAs, helping to reshape the cellular mRNA pool. We also observe that BR-body formation promotes complete mRNA decay, avoiding the buildup of toxic endo-cleaved mRNA decay intermediates. The combined selective permeability of BR-bodies for both enzymes and substrates together with the stimulation of the sub-steps of mRNA decay provide an effective organization strategy for bacterial mRNA decay.
Keywords:
BR-bodies; RNP granules; Ribonuclease E; biomolecular condensates; mRNA decay; phase separation; ribonucleoprotein.
Copyright © 2020 Elsevier Inc. All rights reserved.
Publication types
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Research Support, N.I.H., Extramural
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Research Support, Non-U.S. Gov't
MeSH terms
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Caulobacter crescentus / genetics
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Caulobacter crescentus / growth & development
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Caulobacter crescentus / metabolism*
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Endoribonucleases / genetics
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Endoribonucleases / metabolism*
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Escherichia coli / genetics
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Escherichia coli / growth & development
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Escherichia coli / metabolism*
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Humans
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Multienzyme Complexes / genetics
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Multienzyme Complexes / metabolism*
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Organelles / genetics
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Organelles / metabolism*
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Polyribonucleotide Nucleotidyltransferase / genetics
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Polyribonucleotide Nucleotidyltransferase / metabolism*
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RNA Helicases / genetics
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RNA Helicases / metabolism*
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RNA Stability*
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RNA, Antisense / genetics
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RNA, Antisense / metabolism
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RNA, Messenger / genetics
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RNA, Messenger / metabolism*
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RNA, Ribosomal / genetics
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RNA, Ribosomal / metabolism
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RNA, Small Untranslated / genetics
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RNA, Small Untranslated / metabolism
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RNA, Transfer / genetics
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RNA, Transfer / metabolism
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RNA, Untranslated / genetics
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RNA, Untranslated / metabolism
Substances
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Multienzyme Complexes
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RNA, Antisense
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RNA, Messenger
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RNA, Ribosomal
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RNA, Small Untranslated
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RNA, Untranslated
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degradosome
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RNA, Transfer
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Polyribonucleotide Nucleotidyltransferase
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Endoribonucleases
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RNA Helicases