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Passing Through
Please cite this article in press as: McKnight, Passing Through, Trends in Biochemical Sciences (2019), https://doi.org/10.1016/j.tibs.2019.09.004
Spotlight
Passing Through Steven L. McKnight1,* mRNAs move to the right place in cells to facilitate localized translation. The pathway of mRNA movement involves nuclear and cytoplasmic puncta not surrounded by investing membranes. Discoveries reported by Hondele et al. explain how mRNA molecules can be passed from one puncta to another, forming a relay that directs mRNAs to their proper location.
In eukaryotic cells, the mRNAs encoded by nuclear genes are transcribed in the cell nucleus yet translated in its cytoplasm. Extensive evidence has confirmed that certain mRNAs are shipped to specific locations within the cytoplasm. In the large eggs of flies and worms, mRNAs are subject to sophisticated pathways leading to the formation of granular structures that effect spatial localization of mRNAs important for specification of the germ lineage [1,2]. Comprehensive genetic studies in these model organisms have led to the identification of dozens of genes whose products are required to properly localize germ cell-determining mRNAs. Equally compelling discoveries concerning mRNA localization have come from studies of synapse-restricted translation in nerve cells. Gene transcripts born in the nucleus of neurons are subject to regulatory phenomena that transport certain mRNA along dendritic processes such that translation is restricted to active synapses [3]. It has been hypothesized that this form of localized translation may be important for selectively strengthening subsets of synapses in a manner that may be important for learning, memory, or both.
The process of mRNA localization may be conceptually akin to that enacted by the Golgi apparatus in the control of protein sorting. Proteins destined for export from the cell, or for movement to specific subcellular structures, begin the process of ‘sorting’ upon translation in the Golgi network of cells. The field of science devoted to this subject is both sophisticated and mature. By contrast, we are only beginning to understand how cells move mRNAs to the proper cellular address. Just as the protein sorting field benefited from an understanding of the cellular apparatus within which trafficking is directed, biologists are beginning to understand the structures through which mRNAs pass on their journey from nucleus to their ultimate cellular address. Unlike the membrane-encased Golgi apparatus, the cellular assemblies involved in mRNA transport are not invested by surrounding membranes. These subcellular structures are variable in size and shape and are found in both the nuclear and cytoplasmic compartments of cells. mRNAs originate in puncta-like assemblies, variously called ‘hubs’ or ‘transcription factories’, housing components required for gene transcription. During or after the process of transcription, mRNAs transit speckle-like puncta enriched in the machinery required for pre-mRNA splicing. Egress of mature mRNAs from nuclei is enacted via nuclear pore complexes. Once delivered to the cytoplasm, mRNAs destined for specific cellular locations become incorporated into cytoplasmic granules that have been studied in worms, flies, yeast cells, and neurons. This hypothetical pathway of gene-to-message-toprotein ‘information flow’ is depicted schematically in Figure 1. The nuclear and cytoplasmic puncta through which mRNAs sequentially
pass between their birth and eventual translation are composed of both RNA and protein. The RNA components include, of course, the mRNAs that are themselves in transit. Nuclear puncta involved in mRNA maturation and movement from nucleus to cytoplasm also contain small nuclear RNAs required for pre-mRNA splicing and other forms of mRNA modification, as well, in some cases, as long noncoding RNAs [4]. Cytoplasmic granules involved in mRNA localization also contain forms of RNA other than the mRNA molecules subject to localized transport, including ribosomes [5]. Nuclear and cytoplasmic puncta involved in movement of mRNA to the proper cellular localization are, not surprisingly, enriched in RNA binding proteins. These granule-enriched RNA binding proteins are endowed with domains that fold into stable, threedimensional structures. Prototypic among these structures are domains required to directly bind RNA, such as RNA recognition motif domains. A second, equally prevalent structural domain found in proteins enriched in RNA granules is one required for forming ATP-dependent RNA helicase enzymes, generically termed DEAD box RNA helicases. Far more enigmatic is the fact that most constituents of the puncta involved in RNA localization contain protein domains that tend towards structural disorder. These domains are ‘gibberishlike’ in their primary sequences, being composed of only a small subset of the 20 amino acids typically required for proteins to fold into stable, threedimensional structure. An accidental technical advance to the field came upon recognition that these domains of low sequence complexity can selfassociate in a manner leading to phase transition [6,7]. Liquid- or gel-like
Trends in Biochemical Sciences, -- 2019, Vol. --, No. --
1
Please cite this article in press as: McKnight, Passing Through, Trends in Biochemical Sciences (2019), https://doi.org/10.1016/j.tibs.2019.09.004
Although rudimentary and reductionist, these experiments offer a glimpse at a distinct mechanistic reaction that may be at play during the passage of mRNA molecules from one cellular compartment to another during the process that enables properly localized translation. Quite by surprise, Hondele and colleagues found that DEAD box helicase enzymes may also control intracellular localization of RNA in bacterial cells. These observations hint towards the possibility that living systems, ranging from single bacterial cells to vertebrate neurons, care deeply about the precise place within cells where mRNAs are to be translated. The Hondele/Weis science predicts that the process of mRNA localization may be controlled by evolutionarily conserved RNA helicase enzymes universally attached to low complexity sequence domains endowed with the capacity to self-associate into distinct condensates that constitute zones of molecular identity/specificity within living cells. 1Department
Figure 1. Schematic Diagram of a Neuron Showing a Pathway of Information Flow from Gene to mRNA to Protein Pathway begins with gene expression within transcription factories (green), with mRNA transcripts then passing through nuclear speckles (orange) believed to facilitate pre-mRNA splicing. Mature, properly spliced mRNAs exit the nucleus via nuclear pores and enter a hypothetical, perinuclear mRNA sorting depot (blue) analogous in function to the Golgi apparatus. mRNAs encoding synaptic proteins are then segregated into neuronal transport granules (blue) such that the appropriate proteins can be synthesized locally at a position proximal to active synapses (orange dashed circle). Figure created with BioRender.
condensates prepared from low complexity domains have been studied as rudimentary surrogates of the cellular puncta through which mRNAs transit during the process of mRNA localization [8,9]. In a conceptually simple series of experiments, Hondele and colleagues [10] prepared phase separated droplets composed of a distinct mRNA, a distinct low complexity domain, and a 2
distinct RNA helicase enzyme. Upon exposure to a regulatory protein capable of activating ATP hydrolysis of the RNA helicase enzyme, the featured mRNA was released from the phase separated droplet. In a technically sophisticated extension of this line of experimentation, the authors demonstrated re-incorporation of the released RNA into distinct droplets formed from a different, phase-separated RNA binding protein.
Trends in Biochemical Sciences, -- 2019, Vol. --, No. --
of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA *Correspondence: [email protected] https://doi.org/10.1016/j.tibs.2019.09.004 ª 2019 Published by Elsevier Ltd.
References 1. Trcek, T. et al. (2015) Drosophila germ granules are structured and contain homotypic mRNA clusters. Nat. Commun. 6, 7962 2. Updike, D. and Strome, S. (2010) P granule assembly and function in Caenorhabditis elegans germ cells. J. Androl. 31, 53–60 3. Kiebler, M.A. and Bassell, G.J. (2006) Neuronal RNA granules: movers and makers. Neuron 51, 685–690 4. Naganuma, T. and Hirose, T. (2013) Paraspeckle formation during the biogenesis of long noncoding RNAs. RNA Biol 10, 456–461
Please cite this article in press as: McKnight, Passing Through, Trends in Biochemical Sciences (2019), https://doi.org/10.1016/j.tibs.2019.09.004
5. Teixeira, D. et al. (2005) Processing bodies require RNA for assembly and contain nontranslating mRNAs. RNA 11, 371–382
7. Han, T.W. et al. (2012) Cell-free formation of RNA granules: bound RNAs identify features and components of cellular assemblies. Cell 149, 768–779
6. Kato, M. et al. (2012) Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels. Cell 149, 753–767
8. Banani, S.F. et al. (2017) Biomolecular condensates: organizers of cellular biochemistry. Nat. Rev. Mol. Cell Biol. 18, 285–298
9. Kato, M. and McKnight, S. (2018) A solidstate conceptualization of information transfer from gene to message to protein. Annu. Rev. Biochem. 87, 351–390 10. Hondele, M. et al. (2019) DEAD-box ATPases are global regulators of phase-separated organelles. Nature 573, 144–148
Trends in Biochemical Sciences, -- 2019, Vol. --, No. --
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Spotlight
Passing Through Steven L. McKnight1,* mRNAs move to the right place in cells to facilitate localized translation. The pathway of mRNA movement involves nuclear and cytoplasmic puncta not surrounded by investing membranes. Discoveries reported by Hondele et al. explain how mRNA molecules can be passed from one puncta to another, forming a relay that directs mRNAs to their proper location.
In eukaryotic cells, the mRNAs encoded by nuclear genes are transcribed in the cell nucleus yet translated in its cytoplasm. Extensive evidence has confirmed that certain mRNAs are shipped to specific locations within the cytoplasm. In the large eggs of flies and worms, mRNAs are subject to sophisticated pathways leading to the formation of granular structures that effect spatial localization of mRNAs important for specification of the germ lineage [1,2]. Comprehensive genetic studies in these model organisms have led to the identification of dozens of genes whose products are required to properly localize germ cell-determining mRNAs. Equally compelling discoveries concerning mRNA localization have come from studies of synapse-restricted translation in nerve cells. Gene transcripts born in the nucleus of neurons are subject to regulatory phenomena that transport certain mRNA along dendritic processes such that translation is restricted to active synapses [3]. It has been hypothesized that this form of localized translation may be important for selectively strengthening subsets of synapses in a manner that may be important for learning, memory, or both.
The process of mRNA localization may be conceptually akin to that enacted by the Golgi apparatus in the control of protein sorting. Proteins destined for export from the cell, or for movement to specific subcellular structures, begin the process of ‘sorting’ upon translation in the Golgi network of cells. The field of science devoted to this subject is both sophisticated and mature. By contrast, we are only beginning to understand how cells move mRNAs to the proper cellular address. Just as the protein sorting field benefited from an understanding of the cellular apparatus within which trafficking is directed, biologists are beginning to understand the structures through which mRNAs pass on their journey from nucleus to their ultimate cellular address. Unlike the membrane-encased Golgi apparatus, the cellular assemblies involved in mRNA transport are not invested by surrounding membranes. These subcellular structures are variable in size and shape and are found in both the nuclear and cytoplasmic compartments of cells. mRNAs originate in puncta-like assemblies, variously called ‘hubs’ or ‘transcription factories’, housing components required for gene transcription. During or after the process of transcription, mRNAs transit speckle-like puncta enriched in the machinery required for pre-mRNA splicing. Egress of mature mRNAs from nuclei is enacted via nuclear pore complexes. Once delivered to the cytoplasm, mRNAs destined for specific cellular locations become incorporated into cytoplasmic granules that have been studied in worms, flies, yeast cells, and neurons. This hypothetical pathway of gene-to-message-toprotein ‘information flow’ is depicted schematically in Figure 1. The nuclear and cytoplasmic puncta through which mRNAs sequentially
pass between their birth and eventual translation are composed of both RNA and protein. The RNA components include, of course, the mRNAs that are themselves in transit. Nuclear puncta involved in mRNA maturation and movement from nucleus to cytoplasm also contain small nuclear RNAs required for pre-mRNA splicing and other forms of mRNA modification, as well, in some cases, as long noncoding RNAs [4]. Cytoplasmic granules involved in mRNA localization also contain forms of RNA other than the mRNA molecules subject to localized transport, including ribosomes [5]. Nuclear and cytoplasmic puncta involved in movement of mRNA to the proper cellular localization are, not surprisingly, enriched in RNA binding proteins. These granule-enriched RNA binding proteins are endowed with domains that fold into stable, threedimensional structures. Prototypic among these structures are domains required to directly bind RNA, such as RNA recognition motif domains. A second, equally prevalent structural domain found in proteins enriched in RNA granules is one required for forming ATP-dependent RNA helicase enzymes, generically termed DEAD box RNA helicases. Far more enigmatic is the fact that most constituents of the puncta involved in RNA localization contain protein domains that tend towards structural disorder. These domains are ‘gibberishlike’ in their primary sequences, being composed of only a small subset of the 20 amino acids typically required for proteins to fold into stable, threedimensional structure. An accidental technical advance to the field came upon recognition that these domains of low sequence complexity can selfassociate in a manner leading to phase transition [6,7]. Liquid- or gel-like
Trends in Biochemical Sciences, -- 2019, Vol. --, No. --
1
Please cite this article in press as: McKnight, Passing Through, Trends in Biochemical Sciences (2019), https://doi.org/10.1016/j.tibs.2019.09.004
Although rudimentary and reductionist, these experiments offer a glimpse at a distinct mechanistic reaction that may be at play during the passage of mRNA molecules from one cellular compartment to another during the process that enables properly localized translation. Quite by surprise, Hondele and colleagues found that DEAD box helicase enzymes may also control intracellular localization of RNA in bacterial cells. These observations hint towards the possibility that living systems, ranging from single bacterial cells to vertebrate neurons, care deeply about the precise place within cells where mRNAs are to be translated. The Hondele/Weis science predicts that the process of mRNA localization may be controlled by evolutionarily conserved RNA helicase enzymes universally attached to low complexity sequence domains endowed with the capacity to self-associate into distinct condensates that constitute zones of molecular identity/specificity within living cells. 1Department
Figure 1. Schematic Diagram of a Neuron Showing a Pathway of Information Flow from Gene to mRNA to Protein Pathway begins with gene expression within transcription factories (green), with mRNA transcripts then passing through nuclear speckles (orange) believed to facilitate pre-mRNA splicing. Mature, properly spliced mRNAs exit the nucleus via nuclear pores and enter a hypothetical, perinuclear mRNA sorting depot (blue) analogous in function to the Golgi apparatus. mRNAs encoding synaptic proteins are then segregated into neuronal transport granules (blue) such that the appropriate proteins can be synthesized locally at a position proximal to active synapses (orange dashed circle). Figure created with BioRender.
condensates prepared from low complexity domains have been studied as rudimentary surrogates of the cellular puncta through which mRNAs transit during the process of mRNA localization [8,9]. In a conceptually simple series of experiments, Hondele and colleagues [10] prepared phase separated droplets composed of a distinct mRNA, a distinct low complexity domain, and a 2
distinct RNA helicase enzyme. Upon exposure to a regulatory protein capable of activating ATP hydrolysis of the RNA helicase enzyme, the featured mRNA was released from the phase separated droplet. In a technically sophisticated extension of this line of experimentation, the authors demonstrated re-incorporation of the released RNA into distinct droplets formed from a different, phase-separated RNA binding protein.
Trends in Biochemical Sciences, -- 2019, Vol. --, No. --
of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA *Correspondence: [email protected] https://doi.org/10.1016/j.tibs.2019.09.004 ª 2019 Published by Elsevier Ltd.
References 1. Trcek, T. et al. (2015) Drosophila germ granules are structured and contain homotypic mRNA clusters. Nat. Commun. 6, 7962 2. Updike, D. and Strome, S. (2010) P granule assembly and function in Caenorhabditis elegans germ cells. J. Androl. 31, 53–60 3. Kiebler, M.A. and Bassell, G.J. (2006) Neuronal RNA granules: movers and makers. Neuron 51, 685–690 4. Naganuma, T. and Hirose, T. (2013) Paraspeckle formation during the biogenesis of long noncoding RNAs. RNA Biol 10, 456–461
Please cite this article in press as: McKnight, Passing Through, Trends in Biochemical Sciences (2019), https://doi.org/10.1016/j.tibs.2019.09.004
5. Teixeira, D. et al. (2005) Processing bodies require RNA for assembly and contain nontranslating mRNAs. RNA 11, 371–382
7. Han, T.W. et al. (2012) Cell-free formation of RNA granules: bound RNAs identify features and components of cellular assemblies. Cell 149, 768–779
6. Kato, M. et al. (2012) Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels. Cell 149, 753–767
8. Banani, S.F. et al. (2017) Biomolecular condensates: organizers of cellular biochemistry. Nat. Rev. Mol. Cell Biol. 18, 285–298
9. Kato, M. and McKnight, S. (2018) A solidstate conceptualization of information transfer from gene to message to protein. Annu. Rev. Biochem. 87, 351–390 10. Hondele, M. et al. (2019) DEAD-box ATPases are global regulators of phase-separated organelles. Nature 573, 144–148
Trends in Biochemical Sciences, -- 2019, Vol. --, No. --
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