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Article ; Online: Autorepression of yeast Hsp70 cochaperones by intramolecular interactions involving their J-domains.

Rebeaud, Mathieu E / Tiwari, Satyam / Fauvet, Bruno / Mohr, Adelaïde / Goloubinoff, Pierre / De Los Rios, Paolo

2024 Volume 29, Issue 2, Page(s) 338–348

Abstract: The 70 kDa heat shock protein (Hsp70) chaperones control protein homeostasis in all ATP-containing cellular compartments. J-domain proteins (JDPs) coevolved with Hsp70s to trigger ATP hydrolysis and catalytically upload various substrate polypeptides in ... ...

Abstract	The 70 kDa heat shock protein (Hsp70) chaperones control protein homeostasis in all ATP-containing cellular compartments. J-domain proteins (JDPs) coevolved with Hsp70s to trigger ATP hydrolysis and catalytically upload various substrate polypeptides in need to be structurally modified by the chaperone. Here, we measured the protein disaggregation and refolding activities of the main yeast cytosolic Hsp70, Ssa1, in the presence of its most abundant JDPs, Sis1 and Ydj1, and two swap mutants, in which the J-domains have been interchanged. The observed differences by which the four constructs differently cooperate with Ssa1 and cooperate with each other, as well as their observed intrinsic ability to bind misfolded substrates and trigger Ssa1's ATPase, indicate the presence of yet uncharacterized intramolecular dynamic interactions between the J-domains and the remaining C-terminal segments of these proteins. Taken together, the data suggest an autoregulatory role to these intramolecular interactions within both type A and B JDPs, which might have evolved to reduce energy-costly ATPase cycles by the Ssa1-4 chaperones that are the most abundant Hsp70s in the yeast cytosol.
MeSH term(s)	Saccharomyces cerevisiae/metabolism ; HSP40 Heat-Shock Proteins/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Protein Binding ; HSP70 Heat-Shock Proteins/metabolism ; Molecular Chaperones/metabolism ; Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/metabolism
Chemical Substances	HSP40 Heat-Shock Proteins ; Saccharomyces cerevisiae Proteins ; HSP70 Heat-Shock Proteins ; Molecular Chaperones ; Adenosine Triphosphatases (EC 3.6.1.-) ; Adenosine Triphosphate (8L70Q75FXE)
Language	English
Publishing date	2024-03-21
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1362749-1
ISSN	1466-1268 ; 1355-8145
ISSN (online)	1466-1268
ISSN	1355-8145
DOI	10.1016/j.cstres.2024.03.008
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Article ; Online: Author Correction: A fluorescent multi-domain protein reveals the unfolding mechanism of Hsp70.

Tiwari, Satyam / Fauvet, Bruno / Assenza, Salvatore / De Los Rios, Paolo / Goloubinoff, Pierre

Nature chemical biology

2023 Volume 19, Issue 4, Page(s) 529

Language	English
Publishing date	2023-03-09
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2202962-X
ISSN	1552-4469 ; 1552-4450
ISSN (online)	1552-4469
ISSN	1552-4450
DOI	10.1038/s41589-023-01296-4
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Article ; Online: ABC transporters are billion-year-old Maxwell Demons.

Flatt, Solange / Busiello, Daniel Maria / Zamuner, Stefano / De Los Rios, Paolo

Communications physics

2023 Volume 6, Issue 1, Page(s) 205

Abstract: ATP-Binding Cassette (ABC) transporters are a broad family of biological machines, found in most prokaryotic and eukaryotic cells, performing the crucial import or export of substrates through both plasma and organellar membranes, and maintaining a ... ...

Abstract	ATP-Binding Cassette (ABC) transporters are a broad family of biological machines, found in most prokaryotic and eukaryotic cells, performing the crucial import or export of substrates through both plasma and organellar membranes, and maintaining a steady concentration gradient driven by ATP hydrolysis. Building upon the present biophysical and biochemical characterization of ABC transporters, we propose here a model whose solution reveals that these machines are an exact molecular realization of the autonomous Maxwell Demon, a century-old abstract device that uses an energy source to drive systems away from thermodynamic equilibrium. In particular, the Maxwell Demon does not perform any direct mechanical work on the system, but simply selects which spontaneous processes to allow and which ones to forbid based on information that it collects and processes. In its autonomous version, the measurement device is embedded in the system itself. In the molecular model introduced here, the different operations that characterize Maxwell Demons (measurement, feedback, resetting) are features that emerge from the biochemical and structural properties of ABC transporters, revealing the crucial role of allostery to process information. Our framework allows us to develop an explicit bridge between the molecular-level description and the higher-level language of information theory for ABC transporters.
Language	English
Publishing date	2023-08-08
Publishing country	England
Document type	Journal Article
ISSN	2399-3650
ISSN (online)	2399-3650
DOI	10.1038/s42005-023-01320-y
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Article ; Online: Dissipation-Driven Selection under Finite Diffusion: Hints from Equilibrium and Separation of Time Scales.

Liang, Shiling / De Los Rios, Paolo / Busiello, Daniel Maria

Entropy (Basel, Switzerland)

2021 Volume 23, Issue 8

Abstract: When exposed to a thermal gradient, reaction networks can convert thermal energy into the chemical selection of states that would be unfavourable at equilibrium. The kinetics of reaction paths, and thus how fast they dissipate available energy, might be ... ...

Abstract	When exposed to a thermal gradient, reaction networks can convert thermal energy into the chemical selection of states that would be unfavourable at equilibrium. The kinetics of reaction paths, and thus how fast they dissipate available energy, might be dominant in dictating the stationary populations of all chemical states out of equilibrium. This phenomenology has been theoretically explored mainly in the infinite diffusion limit. Here, we show that the regime in which the diffusion rate is finite, and also slower than some chemical reactions, might bring about interesting features, such as the maximisation of selection or the switch of the selected state at stationarity. We introduce a framework, rooted in a time-scale separation analysis, which is able to capture leading non-equilibrium features using only equilibrium arguments under well-defined conditions. In particular, it is possible to identify fast-dissipation sub-networks of reactions whose Boltzmann equilibrium dominates the steady-state of the entire system as a whole. Finally, we also show that the dissipated heat (and so the entropy production) can be estimated, under some approximations, through the heat capacity of fast-dissipation sub-networks. This work provides a tool to develop an intuitive equilibrium-based grasp on complex non-isothermal reaction networks, which are important paradigms to understand the emergence of complex structures from basic building blocks.
Language	English
Publishing date	2021-08-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2014734-X
ISSN	1099-4300 ; 1099-4300
ISSN (online)	1099-4300
ISSN	1099-4300
DOI	10.3390/e23081068
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Article ; Online: A fluorescent multi-domain protein reveals the unfolding mechanism of Hsp70.

Tiwari, Satyam / Fauvet, Bruno / Assenza, Salvatore / De Los Rios, Paolo / Goloubinoff, Pierre

Nature chemical biology

2022 Volume 19, Issue 2, Page(s) 198–205

Abstract: Detailed understanding of the mechanism by which Hsp70 chaperones protect cells against protein aggregation is hampered by the lack of a comprehensive characterization of the aggregates, which are typically heterogeneous. Here we designed a reporter ... ...

Abstract	Detailed understanding of the mechanism by which Hsp70 chaperones protect cells against protein aggregation is hampered by the lack of a comprehensive characterization of the aggregates, which are typically heterogeneous. Here we designed a reporter chaperone substrate, MLucV, composed of a stress-labile luciferase flanked by stress-resistant fluorescent domains, which upon denaturation formed a discrete population of small aggregates. Combining Förster resonance energy transfer and enzymatic activity measurements provided unprecedented details on the aggregated, unfolded, Hsp70-bound and native MLucV conformations. The Hsp70 mechanism first involved ATP-fueled disaggregation and unfolding of the stable pre-aggregated substrate, which stretched MLucV beyond simply unfolded conformations, followed by native refolding. The ATP-fueled unfolding and refolding action of Hsp70 on MLucV aggregates could accumulate native MLucV species under elevated denaturing temperatures highly adverse to the native state. These results unambiguously exclude binding and preventing of aggregation from the non-equilibrium mechanism by which Hsp70 converts stable aggregates into metastable native proteins.
MeSH term(s)	Protein Folding ; HSP70 Heat-Shock Proteins/chemistry ; Molecular Chaperones/chemistry ; Luciferases/metabolism ; Adenosine Triphosphate ; Protein Denaturation ; Protein Unfolding
Chemical Substances	HSP70 Heat-Shock Proteins ; Molecular Chaperones ; Luciferases (EC 1.13.12.-) ; Adenosine Triphosphate (8L70Q75FXE)
Language	English
Publishing date	2022-10-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2202962-X
ISSN	1552-4469 ; 1552-4450
ISSN (online)	1552-4469
ISSN	1552-4450
DOI	10.1038/s41589-022-01162-9
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Article ; Online: Data-driven large-scale genomic analysis reveals an intricate phylogenetic and functional landscape in J-domain proteins.

Malinverni, Duccio / Zamuner, Stefano / Rebeaud, Mathieu E / Barducci, Alessandro / Nillegoda, Nadinath B / De Los Rios, Paolo

Proceedings of the National Academy of Sciences of the United States of America

2023 Volume 120, Issue 32, Page(s) e2218217120

Abstract: The 70-kD heat shock protein (Hsp70) chaperone system is a central hub of the proteostasis network that helps maintain protein homeostasis in all organisms. The recruitment of Hsp70 to perform different and specific cellular functions is regulated by the ...

Abstract	The 70-kD heat shock protein (Hsp70) chaperone system is a central hub of the proteostasis network that helps maintain protein homeostasis in all organisms. The recruitment of Hsp70 to perform different and specific cellular functions is regulated by the J-domain protein (JDP) co-chaperone family carrying the small namesake J-domain, required to interact and drive the ATPase cycle of Hsp70s. Besides the J-domain, prokaryotic and eukaryotic JDPs display a staggering diversity in domain architecture, function, and cellular localization. Very little is known about the overall JDP family, despite their essential role in cellular proteostasis, development, and its link to a broad range of human diseases. In this work, we leverage the exponentially increasing number of JDP gene sequences identified across all kingdoms owing to the advancements in sequencing technology and provide a broad overview of the JDP repertoire. Using an automated classification scheme based on artificial neural networks (ANNs), we demonstrate that the sequences of J-domains carry sufficient discriminatory information to reliably recover the phylogeny, localization, and domain composition of the corresponding full-length JDP. By harnessing the interpretability of the ANNs, we find that many of the discriminatory sequence positions match residues that form the interaction interface between the J-domain and Hsp70. This reveals that key residues within the J-domains have coevolved with their obligatory Hsp70 partners to build chaperone circuits for specific functions in cells.
MeSH term(s)	Humans ; Amino Acid Sequence ; Genomics ; HSP40 Heat-Shock Proteins/metabolism ; HSP70 Heat-Shock Proteins/metabolism ; Molecular Chaperones/metabolism ; Phylogeny
Chemical Substances	HSP40 Heat-Shock Proteins ; HSP70 Heat-Shock Proteins ; Molecular Chaperones
Language	English
Publishing date	2023-07-31
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2218217120
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Article: Membraneless organelles: phasing out of equilibrium.

Hondele, Maria / Heinrich, Stephanie / De Los Rios, Paolo / Weis, Karsten

Emerging topics in life sciences

2020 Volume 4, Issue 3, Page(s) 331–342

Abstract: Over the past years, liquid-liquid phase separation (LLPS) has emerged as a ubiquitous principle of cellular organization implicated in many biological processes ranging from gene expression to cell division. The formation of biological condensates, like ...

Abstract	Over the past years, liquid-liquid phase separation (LLPS) has emerged as a ubiquitous principle of cellular organization implicated in many biological processes ranging from gene expression to cell division. The formation of biological condensates, like the nucleolus or stress granules, by LLPS is at its core a thermodynamic equilibrium process. However, life does not operate at equilibrium, and cells have evolved multiple strategies to keep condensates in a non-equilibrium state. In this review, we discuss how these non-equilibrium drivers counteract solidification and potentially detrimental aggregation, and at the same time enable biological condensates to perform work and control the flux of substrates and information in a spatial and temporal manner.
MeSH term(s)	Cell Nucleolus ; Gene Expression ; Organelles ; Thermodynamics
Language	English
Publishing date	2020-08-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2882721-1
ISSN	2397-8554 ; 2397-8554 ; 2397-8562
ISSN (online)	2397-8554
ISSN	2397-8554 ; 2397-8562
DOI	10.1042/ETLS20190190
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Article: Repair or Degrade: the Thermodynamic Dilemma of Cellular Protein Quality-Control.

Fauvet, Bruno / Rebeaud, Mathieu E / Tiwari, Satyam / De Los Rios, Paolo / Goloubinoff, Pierre

Frontiers in molecular biosciences

2021 Volume 8, Page(s) 768888

Abstract: Life is a non-equilibrium phenomenon. Owing to their high free energy content, the macromolecules of life tend to spontaneously react with ambient oxygen and water and turn into more stable inorganic molecules. A similar thermodynamic picture applies to ... ...

Abstract	Life is a non-equilibrium phenomenon. Owing to their high free energy content, the macromolecules of life tend to spontaneously react with ambient oxygen and water and turn into more stable inorganic molecules. A similar thermodynamic picture applies to the complex shapes of proteins: While a polypeptide is emerging unfolded from the ribosome, it may spontaneously acquire secondary structures and collapse into its functional native conformation. The spontaneity of this process is evidence that the free energy of the unstructured state is higher than that of the structured native state. Yet, under stress or because of mutations, complex polypeptides may fail to reach their native conformation and form instead thermodynamically stable aggregates devoid of biological activity. Cells have evolved molecular chaperones to actively counteract the misfolding of stress-labile proteins dictated by equilibrium thermodynamics. HSP60, HSP70 and HSP100 can inject energy from ATP hydrolysis into the forceful unfolding of stable misfolded structures in proteins and convert them into unstable intermediates that can collapse into the native state, even under conditions inauspicious for that state. Aggregates and misfolded proteins may also be forcefully unfolded and degraded by chaperone-gated endo-cellular proteases, and in eukaryotes also by chaperone-mediated autophagy, paving the way for their replacement by new, unaltered functional proteins. The greater energy cost of degrading and replacing a polypeptide, with respect to the cost of its chaperone-mediated repair represents a thermodynamic dilemma: some easily repairable proteins are better to be processed by chaperones, while it can be wasteful to uselessly try recover overly compromised molecules, which should instead be degraded and replaced. Evolution has solved this conundrum by creating a host of unfolding chaperones and degradation machines and by tuning their cellular amounts and activity rates.
Language	English
Publishing date	2021-10-27
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2021.768888
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Article ; Online: Dissipation-driven selection of states in non-equilibrium chemical networks.

Busiello, Daniel Maria / Liang, Shiling / Piazza, Francesco / De Los Rios, Paolo

Communications chemistry

2021 Volume 4, Issue 1, Page(s) 16

Abstract: Life has most likely originated as a consequence of processes taking place in non-equilibrium conditions (e.g. in the proximity of deep-sea thermal vents) selecting states of matter that would have been otherwise unfavorable at equilibrium. Here we ... ...

Abstract	Life has most likely originated as a consequence of processes taking place in non-equilibrium conditions (e.g. in the proximity of deep-sea thermal vents) selecting states of matter that would have been otherwise unfavorable at equilibrium. Here we present a simple chemical network in which the selection of states is driven by the thermodynamic necessity of dissipating heat as rapidly as possible in the presence of a thermal gradient: states participating to faster reactions contribute the most to the dissipation rate, and are the most populated ones in non-equilibrium steady-state conditions. Building upon these results, we show that, as the complexity of the chemical network increases, the velocity of the reaction path leading to a given state determines its selection, giving rise to non-trivial localization phenomena in state space. A byproduct of our studies is that, in the presence of a temperature gradient, thermophoresis-like behavior inevitably appears depending on the transport properties of each individual state, thus hinting at a possible microscopic explanation of this intriguing yet still not fully understood phenomenon.
Language	English
Publishing date	2021-02-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2929562-2
ISSN	2399-3669 ; 2399-3669
ISSN (online)	2399-3669
ISSN	2399-3669
DOI	10.1038/s42004-021-00454-w
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Article ; Online: Equilibrium and non-equilibrium furanose selection in the ribose isomerisation network.

Dass, Avinash Vicholous / Georgelin, Thomas / Westall, Frances / Foucher, Frédéric / De Los Rios, Paolo / Busiello, Daniel Maria / Liang, Shiling / Piazza, Francesco

Nature communications

2021 Volume 12, Issue 1, Page(s) 2749

Abstract: The exclusive presence of β-D-ribofuranose in nucleic acids is still a conundrum in prebiotic chemistry, given that pyranose species are substantially more stable at equilibrium. However, a precise characterisation of the relative furanose/pyranose ... ...

Abstract	The exclusive presence of β-D-ribofuranose in nucleic acids is still a conundrum in prebiotic chemistry, given that pyranose species are substantially more stable at equilibrium. However, a precise characterisation of the relative furanose/pyranose fraction at temperatures higher than about 50 °C is still lacking. Here, we employ a combination of NMR measurements and statistical mechanics modelling to predict a population inversion between furanose and pyranose at equilibrium at high temperatures. More importantly, we show that a steady temperature gradient may steer an open isomerisation network into a non-equilibrium steady state where furanose is boosted beyond the limits set by equilibrium thermodynamics. Moreover, we demonstrate that nonequilibrium selection of furanose is maximum at optimal dissipation, as gauged by the temperature gradient and energy barriers for isomerisation. The predicted optimum is compatible with temperature drops found in hydrothermal vents associated with extremely fresh lava flows on the seafloor.
Language	English
Publishing date	2021-05-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-22818-5
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