- Email: [email protected]
The Transcription Terminator Rho: A First Bacterial Prion
TIMI 1446 No. of Pages 3
Forum
class. The conformational promiscuity of yeast prions is encoded in specific regions of their sequences, known as prion domains (PrDs). PrDs are both sufficient and necessary for prion conversion and usually correspond to long and intrinsically disordered protein segments of low complexity [3].
proteins and are associated with essential biological processes such as DNA-templated transcription and termination or translation initiation. These activities might allow the rewiring of gene expression in response to environmental fluctuations, facilitating the development of novel and better adapted phenotypes.
Dozens of yeast proteins have been shown to behave as prions, but do other organisms also harbour analogous functional prion-like proteins? The knowledge of the structural and sequential features shared by PrDs in yeast has stimulated the development of bioinformatics tools aimed at answering this question. The search for similar domains in the proteomes of more than 3000 organisms has both revealed the existence of new prion-based phenotypes and led to the identification of thousands of new potential prion-like proteins in organisms Functional Amyloids and Prionbelonging to all taxonomic divisions, suglike Proteins. gesting that the sustained mechanism of Amyloids were first discovered as protein functional prion-like assembly might be deposits associated with human diseases. more prevalent in nature than previously They are insoluble fibrillar structures assumed [4]. formed by the assembly of proteins and peptides into intermolecular b-sheets. The Discovering Putative Prion term ‘functional amyloid’ was coined upon Sequences in Bacteria the discovery of the amyloid nature of the A bioinformatics survey of prion-like procurli fibres of Escherichia coli and their role teins in all complete bacterial proteomes in facilitating the surface attachment and identified more than 2000 candidates in biofilm development of bacteria [1]. Since these microorganisms [4]. Further analythen, an increasing number of functional sis of the functions and structures assoamyloids have been identified in a wide ciated with these polypeptides indicated variety of organisms, including humans, that many of them contain multiple funcshowing that, despite their potential toxictionally associated domains [5], which ity, protein aggregates can be exploited for suggests that the embedded prion beneficial functions [2]. domains may modulate the function of other domains within the proteins that Prions are a singular set of proteins that contain them. Yeast prions are usually can switch between a soluble conformainvolved in pathways that regulate the tion and a self-perpetuating amyloid flow of genetic information in the cell, state. In yeast, prion conformational consuch as transcription, RNA processing, version results in heritable phenotypic and translation [6]. Thus, it was not surchanges. Although these changes are prising to identify nucleic acid binding as sometimes detrimental, on other one of the most enriched molecular funcoccasions they provide a way of adapting tions in bacterial prion-like proteins [5]. to fluctuating environments, which places The identified polypeptides include both yeast prions in the functional amyloid transcription factors and RNA-binding
Bacterial prion-like candidates were also found to be enriched in proteins involved in invasion and virulence, as well as in stimulus to response [5]. Indeed, a fraction of PrD-containing proteins are located at the cell periphery and predicted to play a role in cell wall dynamics and in the formation of biofilms, where cells cooperatively stick to each other in response to various external factors. These activities are reminiscent of the ones performed by certain yeast prions, which promote the expression of cell-surface adhesion proteins, allowing cells to form multicellular communities in response to environmental stress.
The Transcription Terminator Rho: A First Bacterial Prion Irantzu Pallarès1,2,* and Salvador Ventura1,2,* Traditionally associated with neurodegenerative diseases, prions are increasingly recognized for their potential to confer beneficial traits on eukaryotic organisms. The discovery of the first bacterial prion suggests that the sustained mechanism of prion assembly is an ancient molecular tool aimed at providing fast and persistent adaptation to changing environments.
Interestingly, pathogenic species seem to have a much higher prion load than nonpathogenic ones, suggesting that these malleable proteins may contribute to the ability of microbes to survive in hostile environments and thus to their persistence in host tissues. Overall, computational predictions suggested that prion-like conformational conversion might confer heritable bacterial adaptation when faced with changing conditions, as it does in yeast [7] and mammals [8].
Rho, the First Prion Discovered in Bacteria Bacteria can propagate the prionic state of the heterologous yeast translation termination factor Sup35p [9]. Interestingly, the transcription termination factor Rho, a protein whose architecture resembles Sup35p (Figure 1A), was top ranked among the predicted prion-like proteins of more than 20 different bacterial species [5]. Rho is a highly conserved hexameric
Trends in Microbiology, Month Year, Vol. xx, No. yy
1
TIMI 1446 No. of Pages 3
(B)
(A)
[rho−]
Translaon terminaon factor Sup35 EFTUD2
GTP_EFTU
PrD
EFTU-D3
685
[RHO+]
Stop
Translaon terminaon factor Rho Rho_ N
PrD
Rho_RNA _bind
ATP-synt_ab
541
Terminator readthrough
(C) Environment 1
Environment 2 Stress
Change prion states
Change phenotypes
Daughter cells ClpB
Fitness enrichment
Figure 1. Prions: Epigenetic Heritable Phenotypic Diversity Devices. (A) Clostridium botulinum Rho and the yeast prion protein Sup35 promote phenotypic conversion acting at the transcriptional and translational level, respectively. Both proteins display prion domains (PrDs) at their N [56_TD$IF]terminus. Identified Pfam domains and predicted PrDs are shown in violet and black, respectively. (B) The [RHO+] prion phenotype. In [rho ] cells, Rho acts as a transcription termination factor. In [RHO+] cells, Rho aggregates, resulting in termination readthrough and triggering genome-wide changes in the transcriptome. (C) Prions confer heritable phenotypic diversity that provides fitness advantages under stress conditions. Pink circles and green pentagons indicate two different prion proteins in their soluble states. These proteins can respond to stress, switching their conformation to a prionogenic state (pink triangles and green squares, respectively) generating a new ClpB-dependent selfpropagating phenotype.
the N-terminal portion of the protein, embedded in a low-complexity region and contiguous with the RNA-binding domain (Figure 1A). This organization is conserved in many Rho orthologues and is found in many eukaryotic prion-like proteins [6]. Recently, two studies have validated Rho as the first bona fide prion found in bacteria [11,12]. RhoPrD has the ability to self-assemble into thioflavin-T-positive, b-sheet-enriched, highly ordered amyloid fibrils in the absence of other factors and, similar to other functional amyloids, contains a short amyloiThe predicted PrD in Clostridium botu- dogenic segment that can nucleate its linum Rho factor (RhoPrD) is localized at assembly [11]. RhoPrD can functionally helicase that catalyses the disassociation of mRNA from genomic DNA and the RNA polymerase promoting transcription termination. Mounting evidence indicates that, in addition to being a housekeeping gene, Rho has the ability to regulate termination efficiency in response to multiple physiological signals [10]. Indeed, mutations increasing the aggregation propensity of this gene expression regulator provide adaptive properties when faced with stress, which itself suggests a prionlike activity.
2
Trends in Microbiology, Month Year, Vol. xx, No. yy
substitute for Sup35 PrD in yeast, promoting a heritable phenotypic switch in yeast, whose propagation is strictly dependent on the chaperone Hsp104 [12], as has been observed for most fungal prions [2]. A strong piece of evidence within this study supporting the action of RhoPrD as a prion domain is provided by the infectious nature of Rho bacterial aggregates, which induce phenotypic conversion when introduced into nonprionic yeast cells expressing the RhoPrD-Sup35 fusion [12]. Although a definitive prion-mediated mechanism of activity of RhoPrD could
TIMI 1446 No. of Pages 3
not be confirmed in its natural host, C. botulinum, experiments in Escherichia coli demonstrated that Rho can access alternative protein conformations in prokaryotes, including a self-perpetuating prion state with decreased Rho activity that results in genome-wide changes at the transcriptome level [12] (Figure 1B). This newly acquired phenotype was persistent but could be ‘cured' by overproduction of the disaggregase ClpB (the bacterial orthologue of Hsp104), which, together with additional evidence, pointed to aggregated Rho as the causative agent behind phenotypic conversion. Terminator readthrough caused gene expression rewiring in cells bearing the prion Rho state, allowing them to adapt better to specific stress-induced conditions than cells displaying fully functional Rho (Figure 1C). Together, these results show that Rho is a bacterial protein capable of switching into an archetypical functional amyloid-like prion conformation.
persistence of bacterial infections (Figure 1C). Due to their ability to propagate conformational assembly, even across species, prions may operate as cell-to-cell communication elements, developing important roles in the formation of socially organized structures and transforming microbial community dynamics. The discovery of a first bacterial prion supports the idea of prions being versatile molecular tools exploited by cells at the early evolutionary stages of signalling systems, before the divergence of Bacteria and Eukaryota. Importantly, the study of protein-based heredity in the bacterial domain of life might open new and unexpected avenues for the treatment of bacterial infections, now that the golden age of antibiotics is coming to an end. Acknowledgments This work was funded by the Spanish Ministry of
Concluding Remarks Prions may constitute an epigenetic inheritance bet-hedging strategy in bacteria by driving phenotypic diversity, contributing to rapid adaptation to fluctuating environments, and enhancing the evolution of new traits and the
Economy
and
CompetitivenessBIO2016-783-
78310-R to S.V and by ICREA, ICREA-Academia
*Correspondence: [email protected] (I. Pallarès) and [email protected] (S. Ventura). http://dx.doi.org/10.1016/j.tim.2017.03.008 References 1. Chapman, M.R. et al. (2002) Role of E. coli curli operons in directing amyloid fiber formation. Science 295, 851–855 2. Fowler, D.M. et al. (2007) Functional amyloid – from bacteria to humans. Trends Biochem. Sci. 32, 217–224 3. Masison, D.C. and Wickner, R.B. (1995) Prion-inducing domain of yeast Ure2p and protease resistance of Ure2p in prion-containing cells. Science 270, 93–95 4. Espinosa Angarica, V. et al. (2013) Discovering putative prion sequences in complete proteomes using probabilistic representations of Q/N-rich domains. BMC Genom. 14, 316 5. Iglesias, V. et al. (2015) Computational analysis of candidate prion-like proteins in bacteria and their role. Front. Microbiol. Published online October 15, 2015. http://dx. doi.org/10.3389/fmicb.2015.01123 6. Malinovska, L. et al. (2013) Protein disorder, prion propensities, and self-organizing macromolecular collectives. Biochim. Biophys. Acta 1834, 918–931 7. Newby, G.A. and Lindquist, S. (2013) Blessings in disguise: biological benefits of prion-like mechanisms. Trends Cell Biol. 23, 251–259 8. Hou, F. et al. (2011) MAVS Forms functional prion-like aggregates to activate and propagate antiviral innate immune response. Cell 146, 448–461 9. Yuan, A.H. et al. (2014) Prion propagation can occur in a prokaryote and requires the ClpB chaperone. Elife 3, e02949 10. Kriner, M.A. et al. (2016) Learning from the leaders: gene regulation by the transcription termination factor rho. Trends Biochem. Sci. 41, 690–699
1
11. Pallarès, I. et al. (2016) The Rho termination factor of Clostridium botulinum contains a prion-like domain with a highly amyloidogenic core. Front. Microbiol. 6, 1516
2
12. Yuan, A.H. and Hochschild, A. (2016) A bacterial global regulator forms a prion. Science 355, 198–201
2015 to S.V. Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
Trends in Microbiology, Month Year, Vol. xx, No. yy
3
Forum
class. The conformational promiscuity of yeast prions is encoded in specific regions of their sequences, known as prion domains (PrDs). PrDs are both sufficient and necessary for prion conversion and usually correspond to long and intrinsically disordered protein segments of low complexity [3].
proteins and are associated with essential biological processes such as DNA-templated transcription and termination or translation initiation. These activities might allow the rewiring of gene expression in response to environmental fluctuations, facilitating the development of novel and better adapted phenotypes.
Dozens of yeast proteins have been shown to behave as prions, but do other organisms also harbour analogous functional prion-like proteins? The knowledge of the structural and sequential features shared by PrDs in yeast has stimulated the development of bioinformatics tools aimed at answering this question. The search for similar domains in the proteomes of more than 3000 organisms has both revealed the existence of new prion-based phenotypes and led to the identification of thousands of new potential prion-like proteins in organisms Functional Amyloids and Prionbelonging to all taxonomic divisions, suglike Proteins. gesting that the sustained mechanism of Amyloids were first discovered as protein functional prion-like assembly might be deposits associated with human diseases. more prevalent in nature than previously They are insoluble fibrillar structures assumed [4]. formed by the assembly of proteins and peptides into intermolecular b-sheets. The Discovering Putative Prion term ‘functional amyloid’ was coined upon Sequences in Bacteria the discovery of the amyloid nature of the A bioinformatics survey of prion-like procurli fibres of Escherichia coli and their role teins in all complete bacterial proteomes in facilitating the surface attachment and identified more than 2000 candidates in biofilm development of bacteria [1]. Since these microorganisms [4]. Further analythen, an increasing number of functional sis of the functions and structures assoamyloids have been identified in a wide ciated with these polypeptides indicated variety of organisms, including humans, that many of them contain multiple funcshowing that, despite their potential toxictionally associated domains [5], which ity, protein aggregates can be exploited for suggests that the embedded prion beneficial functions [2]. domains may modulate the function of other domains within the proteins that Prions are a singular set of proteins that contain them. Yeast prions are usually can switch between a soluble conformainvolved in pathways that regulate the tion and a self-perpetuating amyloid flow of genetic information in the cell, state. In yeast, prion conformational consuch as transcription, RNA processing, version results in heritable phenotypic and translation [6]. Thus, it was not surchanges. Although these changes are prising to identify nucleic acid binding as sometimes detrimental, on other one of the most enriched molecular funcoccasions they provide a way of adapting tions in bacterial prion-like proteins [5]. to fluctuating environments, which places The identified polypeptides include both yeast prions in the functional amyloid transcription factors and RNA-binding
Bacterial prion-like candidates were also found to be enriched in proteins involved in invasion and virulence, as well as in stimulus to response [5]. Indeed, a fraction of PrD-containing proteins are located at the cell periphery and predicted to play a role in cell wall dynamics and in the formation of biofilms, where cells cooperatively stick to each other in response to various external factors. These activities are reminiscent of the ones performed by certain yeast prions, which promote the expression of cell-surface adhesion proteins, allowing cells to form multicellular communities in response to environmental stress.
The Transcription Terminator Rho: A First Bacterial Prion Irantzu Pallarès1,2,* and Salvador Ventura1,2,* Traditionally associated with neurodegenerative diseases, prions are increasingly recognized for their potential to confer beneficial traits on eukaryotic organisms. The discovery of the first bacterial prion suggests that the sustained mechanism of prion assembly is an ancient molecular tool aimed at providing fast and persistent adaptation to changing environments.
Interestingly, pathogenic species seem to have a much higher prion load than nonpathogenic ones, suggesting that these malleable proteins may contribute to the ability of microbes to survive in hostile environments and thus to their persistence in host tissues. Overall, computational predictions suggested that prion-like conformational conversion might confer heritable bacterial adaptation when faced with changing conditions, as it does in yeast [7] and mammals [8].
Rho, the First Prion Discovered in Bacteria Bacteria can propagate the prionic state of the heterologous yeast translation termination factor Sup35p [9]. Interestingly, the transcription termination factor Rho, a protein whose architecture resembles Sup35p (Figure 1A), was top ranked among the predicted prion-like proteins of more than 20 different bacterial species [5]. Rho is a highly conserved hexameric
Trends in Microbiology, Month Year, Vol. xx, No. yy
1
TIMI 1446 No. of Pages 3
(B)
(A)
[rho−]
Translaon terminaon factor Sup35 EFTUD2
GTP_EFTU
PrD
EFTU-D3
685
[RHO+]
Stop
Translaon terminaon factor Rho Rho_ N
PrD
Rho_RNA _bind
ATP-synt_ab
541
Terminator readthrough
(C) Environment 1
Environment 2 Stress
Change prion states
Change phenotypes
Daughter cells ClpB
Fitness enrichment
Figure 1. Prions: Epigenetic Heritable Phenotypic Diversity Devices. (A) Clostridium botulinum Rho and the yeast prion protein Sup35 promote phenotypic conversion acting at the transcriptional and translational level, respectively. Both proteins display prion domains (PrDs) at their N [56_TD$IF]terminus. Identified Pfam domains and predicted PrDs are shown in violet and black, respectively. (B) The [RHO+] prion phenotype. In [rho ] cells, Rho acts as a transcription termination factor. In [RHO+] cells, Rho aggregates, resulting in termination readthrough and triggering genome-wide changes in the transcriptome. (C) Prions confer heritable phenotypic diversity that provides fitness advantages under stress conditions. Pink circles and green pentagons indicate two different prion proteins in their soluble states. These proteins can respond to stress, switching their conformation to a prionogenic state (pink triangles and green squares, respectively) generating a new ClpB-dependent selfpropagating phenotype.
the N-terminal portion of the protein, embedded in a low-complexity region and contiguous with the RNA-binding domain (Figure 1A). This organization is conserved in many Rho orthologues and is found in many eukaryotic prion-like proteins [6]. Recently, two studies have validated Rho as the first bona fide prion found in bacteria [11,12]. RhoPrD has the ability to self-assemble into thioflavin-T-positive, b-sheet-enriched, highly ordered amyloid fibrils in the absence of other factors and, similar to other functional amyloids, contains a short amyloiThe predicted PrD in Clostridium botu- dogenic segment that can nucleate its linum Rho factor (RhoPrD) is localized at assembly [11]. RhoPrD can functionally helicase that catalyses the disassociation of mRNA from genomic DNA and the RNA polymerase promoting transcription termination. Mounting evidence indicates that, in addition to being a housekeeping gene, Rho has the ability to regulate termination efficiency in response to multiple physiological signals [10]. Indeed, mutations increasing the aggregation propensity of this gene expression regulator provide adaptive properties when faced with stress, which itself suggests a prionlike activity.
2
Trends in Microbiology, Month Year, Vol. xx, No. yy
substitute for Sup35 PrD in yeast, promoting a heritable phenotypic switch in yeast, whose propagation is strictly dependent on the chaperone Hsp104 [12], as has been observed for most fungal prions [2]. A strong piece of evidence within this study supporting the action of RhoPrD as a prion domain is provided by the infectious nature of Rho bacterial aggregates, which induce phenotypic conversion when introduced into nonprionic yeast cells expressing the RhoPrD-Sup35 fusion [12]. Although a definitive prion-mediated mechanism of activity of RhoPrD could
TIMI 1446 No. of Pages 3
not be confirmed in its natural host, C. botulinum, experiments in Escherichia coli demonstrated that Rho can access alternative protein conformations in prokaryotes, including a self-perpetuating prion state with decreased Rho activity that results in genome-wide changes at the transcriptome level [12] (Figure 1B). This newly acquired phenotype was persistent but could be ‘cured' by overproduction of the disaggregase ClpB (the bacterial orthologue of Hsp104), which, together with additional evidence, pointed to aggregated Rho as the causative agent behind phenotypic conversion. Terminator readthrough caused gene expression rewiring in cells bearing the prion Rho state, allowing them to adapt better to specific stress-induced conditions than cells displaying fully functional Rho (Figure 1C). Together, these results show that Rho is a bacterial protein capable of switching into an archetypical functional amyloid-like prion conformation.
persistence of bacterial infections (Figure 1C). Due to their ability to propagate conformational assembly, even across species, prions may operate as cell-to-cell communication elements, developing important roles in the formation of socially organized structures and transforming microbial community dynamics. The discovery of a first bacterial prion supports the idea of prions being versatile molecular tools exploited by cells at the early evolutionary stages of signalling systems, before the divergence of Bacteria and Eukaryota. Importantly, the study of protein-based heredity in the bacterial domain of life might open new and unexpected avenues for the treatment of bacterial infections, now that the golden age of antibiotics is coming to an end. Acknowledgments This work was funded by the Spanish Ministry of
Concluding Remarks Prions may constitute an epigenetic inheritance bet-hedging strategy in bacteria by driving phenotypic diversity, contributing to rapid adaptation to fluctuating environments, and enhancing the evolution of new traits and the
Economy
and
CompetitivenessBIO2016-783-
78310-R to S.V and by ICREA, ICREA-Academia
*Correspondence: [email protected] (I. Pallarès) and [email protected] (S. Ventura). http://dx.doi.org/10.1016/j.tim.2017.03.008 References 1. Chapman, M.R. et al. (2002) Role of E. coli curli operons in directing amyloid fiber formation. Science 295, 851–855 2. Fowler, D.M. et al. (2007) Functional amyloid – from bacteria to humans. Trends Biochem. Sci. 32, 217–224 3. Masison, D.C. and Wickner, R.B. (1995) Prion-inducing domain of yeast Ure2p and protease resistance of Ure2p in prion-containing cells. Science 270, 93–95 4. Espinosa Angarica, V. et al. (2013) Discovering putative prion sequences in complete proteomes using probabilistic representations of Q/N-rich domains. BMC Genom. 14, 316 5. Iglesias, V. et al. (2015) Computational analysis of candidate prion-like proteins in bacteria and their role. Front. Microbiol. Published online October 15, 2015. http://dx. doi.org/10.3389/fmicb.2015.01123 6. Malinovska, L. et al. (2013) Protein disorder, prion propensities, and self-organizing macromolecular collectives. Biochim. Biophys. Acta 1834, 918–931 7. Newby, G.A. and Lindquist, S. (2013) Blessings in disguise: biological benefits of prion-like mechanisms. Trends Cell Biol. 23, 251–259 8. Hou, F. et al. (2011) MAVS Forms functional prion-like aggregates to activate and propagate antiviral innate immune response. Cell 146, 448–461 9. Yuan, A.H. et al. (2014) Prion propagation can occur in a prokaryote and requires the ClpB chaperone. Elife 3, e02949 10. Kriner, M.A. et al. (2016) Learning from the leaders: gene regulation by the transcription termination factor rho. Trends Biochem. Sci. 41, 690–699
1
11. Pallarès, I. et al. (2016) The Rho termination factor of Clostridium botulinum contains a prion-like domain with a highly amyloidogenic core. Front. Microbiol. 6, 1516
2
12. Yuan, A.H. and Hochschild, A. (2016) A bacterial global regulator forms a prion. Science 355, 198–201
2015 to S.V. Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
Trends in Microbiology, Month Year, Vol. xx, No. yy
3