BR-Bodies Provide Selectively Permeable Condensates that Stimulate mRNA Decay and Prevent Release of Decay Intermediates

Al-Husini, Nadra; Tomares, Dylan T.; Pfaffenberger, Zechariah; Muthunayake, Nisansala S.; Samad, Mohammad Abdus; Zuo, Tiancheng; Bitar, Obaidah; Aretakis, James R.; Bharmal, Mohammed-Husain M.; Gega, Alisa; Biteen, Julie S.; Childers, W. Seth; Schrader, Jared M.

doi:10.1016/j.molcel.2020.04.001

Cited by 70 publications

(83 citation statements)

References 86 publications

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“…Characteristics of RNAs enriched in P-bodies, stress granules, and germ granules (Table 1) pertain to other RNA granules as well. For example, bacterial RNP-bodies (BR-bodies) "prefer" long and non-translating mRNAs [119]. Similarly, fragile X mental-retardation protein FMRP, an mRNA-binding protein that forms granules in mammalian neurons [120,121], also selects for longer, translationally-repressed mRNAs [122].…”

Section: Conserved Rna Properties Of Diverse Rna Granulesmentioning

confidence: 99%

RNA Granules: A View from the RNA Perspective

2020

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RNA granules are ubiquitous. Composed of RNA-binding proteins and RNAs, they provide functional compartmentalization within cells. They are inextricably linked with RNA biology and as such are often referred to as the hubs for post-transcriptional regulation. Much of the attention has been given to the proteins that form these condensates and thus many fundamental questions about the biology of RNA granules remain poorly understood: How and which RNAs enrich in RNA granules, how are transcripts regulated in them, and how do granule-enriched mRNAs shape the biology of a cell? In this review, we discuss the imaging, genetic, and biochemical data, which have revealed that some aspects of the RNA biology within granules are carried out by the RNA itself rather than the granule proteins. Interestingly, the RNA structure has emerged as an important feature in the post-transcriptional control of granule transcripts. This review is part of the Special Issue in the Frontiers in RNA structure in the journal Molecules.

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Section: Conserved Rna Properties Of Diverse Rna Granulesmentioning

confidence: 99%

RNA Granules: A View from the RNA Perspective

2020

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“…Note that the Y-axis scales are different between the two samples. Figure from Al-Husini et al. (2020 ).…”

Section: Expected Outcomesmentioning

confidence: 99%

“… Note: Importantly, as native BR bodies are highly labile and not detectible in a cell lysate, this protocol utilizes a strain with an RNase E active site mutation (ASM, JS299 NA1000 vanA::RNE (ASM) YFP RNE::pXRNEssrAC GentR KanR ) to stabilize the bodies. As a negative control, a strain harboring an RNase E C-terminal domain truncation (JS221 NA1000 vanA::RNE(NTD)-YFP RNE::pXRNEssrAC GentR KanR ) that cannot assemble BR bodies can be utilized ( Al-Husini et al., 2020 ). Note: All Caulobacter crescentus strains used in this study were derived from the wild-type strain NA1000 ( Evinger and Agabian, 1977 ) and were grown at 28°C in PYE medium.…”

Section: Before You Beginmentioning

confidence: 99%

“…As native BR bodies are highly labile and dissociate by degrading internal mRNAs, an active site mutant of RNase E, which blocks dissolution of BR bodies, allows BR-body stabilization during enrichment. For complete details on the use and execution of this protocol, please refer to Al-Husini et al. (2020 ).…”

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confidence: 99%

“…For complete details on the use and execution of this protocol, please refer to Al-Husini et al. (2020 ).…”

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Differential Centrifugation to Enrich Bacterial Ribonucleoprotein Bodies (BR bodies) from Caulobacter crescentus

2020

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Summary Bacterial RNP bodies (BR bodies) contain the mRNA decay machinery, but the collection of associated RNAs and proteins are poorly defined. Here, we present a protocol for the rapid differential centrifugation-based enrichment of BR bodies from Caulobacter crescentus cells. As native BR bodies are highly labile and dissociate by degrading internal mRNAs, an active site mutant of RNase E, which blocks dissolution of BR bodies, allows BR-body stabilization during enrichment. For complete details on the use and execution of this protocol, please refer to Al-Husini et al. (2020 ).

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Biomolecular Condensates: From Bacterial Compartments to Incubator Spaces of Emergent Chemical Systems in Matter‐to‐Life Transitions

Schnorr,

Childers

2024

ChemSystemsChem

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At the earliest development of prebiotic chemistry, bacterial cells were primarily viewed as “bags of molecules.” This longstanding viewpoint shaped and biased early research about life’s origins, setting an initial target when considering the path from prebiotic chemistry to modern life. The two fields of systems chemistry and bacterial cell biology seem like oil and water, but each brings their own perspectives and methods to consider “what is life?”. Here, we review the most recent discoveries in bacterial cell biology, focusing on biomolecular condensates to consider how they may impact our thinking of matter‐to‐life transitions. The presence of condensate compartments in the bacterial domain of life strengthens the hypothesis that condensates play roles in coordinating chemical systems in life’s origins. Bacterial condensates have been shown to enhance enzymatic reactions, tune substrate specificity, and be responsive to environmental conditions and metabolites. Systems chemistry studies have further illuminated the unique chemical environment within condensates and strategies for logically tying chemical processes to the formation and dissolution of condensates. We consider the potential of biomolecular condensates to provide “incubator spaces” where new chemistries can develop and examine future challenges regarding the capability of condensates to yield emergent chemical systems capable of selection.

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BR-Bodies Provide Selectively Permeable Condensates that Stimulate mRNA Decay and Prevent Release of Decay Intermediates

Cited by 70 publications

References 86 publications

RNA Granules: A View from the RNA Perspective

RNA Granules: A View from the RNA Perspective

Differential Centrifugation to Enrich Bacterial Ribonucleoprotein Bodies (BR bodies) from Caulobacter crescentus

Biomolecular Condensates: From Bacterial Compartments to Incubator Spaces of Emergent Chemical Systems in Matter‐to‐Life Transitions

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