Unfolding of metastable linker region is at the core of Hsp33 activation as a redox-regulated chaperone

The cold atmospheric pressure plasma-generated species superoxide, singlet oxygen and atomic oxygen activate the molecular chaperone Hsp33

Cold atmospheric pressure plasmas are used for surface decontamination or disinfection, e.g. in clinical settings. Protein aggregation has been shown to significantly contribute to the antibacterial mechanisms of plasma. To investigate the potential role of the redox-activated zinc-binding chaperone Hsp33 in preventing protein aggregation and thus mediating plasma resistance, we compared the plasma sensitivity of wild-type E. coli to that of an hslO deletion mutant lacking Hsp33 as well as an over-producing strain. Over-production of Hsp33 increased plasma survival rates above wild-type levels. Hsp33 was previously shown to be activated by plasma in vitro. For the PlasmaDerm source applied in dermatology, reversible activation of Hsp33 was confirmed. Thiol oxidation and Hsp33 unfolding, both crucial for Hsp33 activation, occurred during plasma treatment. After prolonged plasma exposure, however, unspecific protein oxidation was detected, the ability of Hsp33 to bind zinc ions was decreased without direct modifications of the zinc-binding motif, and the protein was inactivated. To identify chemical species of potential relevance for plasma-induced Hsp33 activation, reactive oxygen species were tested for their ability to activate Hsp33 in vitro. Superoxide, singlet oxygen and potentially atomic oxygen activate Hsp33, while no evidence was found for activation by ozone, peroxynitrite or hydroxyl radicals.

The Cdc48 N-terminal domain has a molecular switch that mediates the Npl4-Ufd1-Cdc48 complex formation

Cdc48 (VCP/p97) is a major AAA-ATPase involved in protein quality control, along with its canonical cofactors Ufd1 and Npl4 (UN). Here, we present novel structural insights into the interactions within the Cdc48-Npl4-Ufd1 ternary complex. Using integrative modeling, we combine subunit structures with crosslinking mass spectrometry (XL-MS) to map the interaction between Npl4 and Ufd1, alone and in complex with Cdc48. We describe the stabilization of the UN assembly upon binding with the N-terminal-domain (NTD) of Cdc48 and identify a highly conserved cysteine, C115, at the Cdc48-Npl4-binding interface which is central to the stability of the Cdc48-Npl4-Ufd1 complex. Mutation of Cys115 to serine disrupts the interaction between Cdc48-NTD and Npl4-Ufd1 and leads to a moderate decrease in cellular growth and protein quality control in yeast. Our results provide structural insight into the architecture of the Cdc48-Npl4-Ufd1 complex as well as its in vivo implications.

ATP-Independent Chaperones

The folding of proteins into their native structure is crucial for the functioning of all biological processes. Molecular chaperones are guardians of the proteome that assist in protein folding and prevent the accumulation of aberrant protein conformations that can lead to proteotoxicity. ATP-independent chaperones do not require ATP to regulate their functional cycle. Although these chaperones have been traditionally regarded as passive holdases that merely prevent aggregation, recent work has shown that they can directly affect the folding energy landscape by tuning their affinity to various folding states of the client. This review focuses on emerging paradigms in the mechanism of action of ATP-independent chaperones and on the various modes of regulating client binding and release.

Molecular Effects of Elongation Factor Ts and Trigger Factor on the Unfolding and Aggregation of Elongation Factor Tu Induced by the Prokaryotic Molecular Chaperone Hsp33

Simple Summary

Proteins are versatile biological macromolecules involved in most biological processes. However, because of the highly labile nature of protein structures, protein quality control (PQC) to ensure proteostasis (i.e., protein homeostasis)is difficult. Therefore, proteins of a specialized class (i.e., molecular chaperones) are required that assist in proper folding and prevent aberrant folding of other proteins. Hsp33 was originally discovered as a holding chaperone that is overexpressed upon heat shock and activated by oxidation to prevent the misfolding of client proteins. Recently, an unfoldase/aggregase activity of Hsp33 was identified in its reduced state against a specific substrate, EF-Tu, which plays a key role in protein biosynthesis in cells. The present study demonstrates that EF-Tu unfolding/aggregation by Hsp33 can be accelerated by another molecular chaperone trigger factor. Given that the unfolded/aggregated EF-Tu is finally degraded by another chaperone, Lon protease, it is likely that a chaperone network dysregulating EF-Tu operates in heat shock to attenuate protein biosynthesis, which is harmful to cell survival under stressed conditions. Therefore, the apparently contradictory chaperone function (i.e., promotion of client misfolding) of Hsp33 can also be associated with the PQC processes to ensure proteostasis in cells.

Abstract

Hsp33, a prokaryotic redox-regulated holding chaperone, has been recently identified to be able to exhibit an unfoldase and aggregase activity against elongation factor Tu (EF-Tu) in its reduced state. In this study, we investigated the effect of elongation factor Ts (EF-Ts) and trigger factor (TF) on Hsp33-mediated EF-Tu unfolding and aggregation using gel filtration, light scattering, circular dichroism, and isothermal titration calorimetry. We found that EF-Tu unfolding and subsequent aggregation induced by Hsp33 were evident even in its complex state with EF-Ts, which enhanced EF-Tu stability. In addition, although TF alone had no substantial effect on the stability of EF-Tu, it markedly amplified the Hsp33-mediated EF-Tu unfolding and aggregation. Collectively, the present results constitute the first example of synergistic unfoldase/aggregase activity of molecular chaperones and suggest that the stability of EF-Tu is modulated by a sophisticated network of molecular chaperones to regulate protein biosynthesis in cells under stress conditions.

The Central Role of Redox-Regulated Switch Proteins in Bacteria

Bacteria possess the ability to adapt to changing environments. To enable this, cells use reversible post-translational modifications on key proteins to modulate their behavior, metabolism, defense mechanisms and adaptation of bacteria to stress. In this review, we focus on bacterial protein switches that are activated during exposure to oxidative stress. Such protein switches are triggered by either exogenous reactive oxygen species (ROS) or endogenous ROS generated as by-products of the aerobic lifestyle. Both thiol switches and metal centers have been shown to be the primary targets of ROS. Cells take advantage of such reactivity to use these reactive sites as redox sensors to detect and combat oxidative stress conditions. This in turn may induce expression of genes involved in antioxidant strategies and thus protect the proteome against stress conditions. We further describe the well-characterized mechanism of selected proteins that are regulated by redox switches. We highlight the diversity of mechanisms and functions (as well as common features) across different switches, while also presenting integrative methodologies used in discovering new members of this family. Finally, we point to future challenges in this field, both in uncovering new types of switches, as well as defining novel additional functions.

The Cys Sense: Thiol Redox Switches Mediate Life Cycles of Cellular Proteins

Protein homeostasis is an essential component of proper cellular function; however, sustaining protein health is a challenging task, especially during the aerobic lifestyle. Natural cellular oxidants may be involved in cell signaling and antibacterial defense; however, imbalanced levels can lead to protein misfolding, cell damage, and death. This merges together the processes of protein homeostasis and redox regulation. At the heart of this process are redox-regulated proteins or thiol-based switches, which carefully mediate various steps of protein homeostasis across folding, localization, quality control, and degradation pathways. In this review, we discuss the "redox code" of the proteostasis network, which shapes protein health during cell growth and aging. We describe the sources and types of thiol modifications and elaborate on diverse strategies of evolving antioxidant proteins in proteostasis networks during oxidative stress conditions. We also highlight the involvement of cysteines in protein degradation across varying levels, showcasing the importance of cysteine thiols in proteostasis at large. The individual examples and mechanisms raised open the door for extensive future research exploring the interplay between the redox and protein homeostasis systems. Understanding this interplay will enable us to re-write the redox code of cells and use it for biotechnological and therapeutic purposes.

Redox regulation in host-pathogen interactions: thiol switches and beyond

Our organism is exposed to pathogens on a daily basis. Owing to this age-old interaction, both pathogen and host evolved strategies to cope with these encounters. Here, we focus on the consequences of the direct encounter of cells of the innate immune system with bacteria. First, we will discuss the bacterial strategies to counteract powerful reactive species. Our emphasis lies on the effects of hypochlorous acid (HOCl), arguably the most powerful oxidant produced inside the phagolysosome of professional phagocytes. We will highlight individual examples of proteins in gram-negative bacteria activated by HOCl via thiol-disulfide switches, methionine sulfoxidation, and N-chlorination of basic amino acid side chains. Second, we will discuss the effects of HOCl on proteins of the host. Recent studies have shown that both host and bacteria address failing protein homeostasis by activation of chaperone-like holdases through N-chlorination. After discussing the role of individual proteins in the HOCl-defense, we will turn our attention to the examination of effects on host and pathogen on a systemic level. Recent studies using genetically encoded redox probes and redox proteomics highlight differences in redox homeostasis in host and pathogen and give first hints at potential cellular HOCl signaling beyond thiol-disulfide switch mechanisms.

Thiol-based switching mechanisms of stress-sensing chaperones

Thiol-based redox switches evolved as efficient post-translational regulatory mechanisms that enable individual proteins to rapidly respond to sudden environmental changes. While some protein functions need to be switched off to save resources and avoid potentially error-prone processes, protective functions become essential and need to be switched on. In this review, we focus on thiol-based activation mechanisms of stress-sensing chaperones. Upon stress exposure, these chaperones convert into high affinity binding platforms for unfolding proteins and protect cells against the accumulation of potentially toxic protein aggregates. Their chaperone activity is independent of ATP, a feature that becomes especially important under oxidative stress conditions, where cellular ATP levels drop and canonical ATP-dependent chaperones no longer operate. Vice versa, reductive inactivation and substrate release require the restoration of ATP levels, which ensures refolding of client proteins by ATP-dependent foldases. We will give an overview over the different strategies that cells evolved to rapidly increase the pool of ATP-independent chaperones upon oxidative stress and provide mechanistic insights into how stress conditions are used to convert abundant cellular proteins into ATP-independent holding chaperones.

Regulation of chaperone function by coupled folding and oligomerization

The homotrimeric molecular chaperone Skp of Gram-negative bacteria facilitates the transport of outer membrane proteins across the periplasm. It has been unclear how its activity is modulated during its functional cycle. Here, we report an atomic-resolution characterization of the Escherichia coli Skp monomer-trimer transition. We find that the monomeric state of Skp is intrinsically disordered and that formation of the oligomerization interface initiates folding of the α-helical coiled-coil arms via a unique "stapling" mechanism, resulting in the formation of active trimeric Skp. Native client proteins contact all three Skp subunits simultaneously, and accordingly, their binding shifts the Skp population toward the active trimer. This activation mechanism is shown to be essential for Salmonella fitness in a mouse infection model. The coupled mechanism is a unique example of how an ATP-independent chaperone can modulate its activity as a function of the presence of client proteins.

Multiple Functions of Spectrin: Convergent Effects

Spectrin is a multifunctional, multi-domain protein most well known in the membrane skeleton of mature human erythrocytes. Here we review the literature on the crosstalk of the chaperone activity of spectrin with its other functionalities. We hypothesize that the chaperone activity is derived from the surface exposed hydrophobic patches present in individual "spectrin-repeat" domains and show a competition between the membrane phospholipid binding functionality and chaperone activity of spectrin. Moreover, we show that post-translational modifications such as glycation which shield these surface exposed hydrophobic patches, reduce the chaperone function. On the other hand, oligomerization which is linked to increase of hydrophobicity is seen to increase it. We note that spectrin seems to prefer haemoglobin as its chaperone client, binding with it preferentially over other denatured proteins. Spectrin is also known to interact with unstable haemoglobin variants with a higher affinity than in the case of normal haemoglobin. We propose that chaperone activity of spectrin could be important in the cellular biochemistry of haemoglobin, particularly in the context of diseases.

TrypOx, a Novel Eukaryotic Homolog of the Redox-Regulated Chaperone Hsp33 in Trypanosoma brucei

ATP-independent chaperones are widespread across all domains of life and serve as the first line of defense during protein unfolding stresses. One of the known crucial chaperones for bacterial survival in a hostile environment (e.g., heat and oxidative stress) is the highly conserved, redox-regulated ATP-independent bacterial chaperone Hsp33. Using a bioinformatic analysis, we describe novel eukaryotic homologs of Hsp33 identified in eukaryotic pathogens belonging to the kinetoplastids, a family responsible for lethal human diseases such as Chagas disease as caused by Trypanosoma cruzi, African sleeping sickness caused by Trypanosoma brucei spp., and leishmaniasis pathologies delivered by various Leishmania species. During their pathogenic life cycle, kinetoplastids need to cope with elevated temperatures and oxidative stress, the same conditions which convert Hsp33 into a powerful chaperone in bacteria, thus preventing aggregation of a wide range of misfolded proteins. Here, we focused on a functional characterization of the Hsp33 homolog in one of the members of the kinetoplastid family, T. brucei, (Tb927.6.2630), which we have named TrypOx. RNAi silencing of TrypOx led to a significant decrease in the survival of T. brucei under mild oxidative stress conditions, implying a protective role of TrypOx during the Trypanosomes growth. We then adopted a proteomics-driven approach to investigate the role of TrypOx in defining the oxidative stress response. Depletion of TrypOx significantly altered the abundance of proteins mediating redox homeostasis, linking TrypOx with the antioxidant system. Using biochemical approaches, we identified the redox-switch domain of TrypOx, showing its modularity and oxidation-dependent structural plasticity. Kinetoplastid parasites such as T. brucei need to cope with high levels of oxidants produced by the innate immune system, such that parasite-specific antioxidant proteins like TrypOx - which are depleted in mammals - are highly promising candidates for drug targeting.

Características comunes de las chaperonas pequeñas y diméricas

Las chaperonas moleculares constituyen un mecanismo importante para evitar la muerte celular provocada por la agregación de proteínas. Las chaperonas independientes del ATP son un grupo de proteínas de bajo peso molecular que pueden proteger y ayudar a alcanzar la estructura nativa de las proteínas desplegadas o mal plegadas sin necesidad de un gasto energético. Hemos encontrado que el dominio C-terminal de las catalasas de subunidad grande tiene actividad de chaperona. Por ello, en esta revisión analizamos las características más comunes de las chaperonas pequeñas y más estudiadas como: αB-cristalina, Hsp20, Spy, Hsp33 y Hsp31. En particular, se examina la participación de los aminoácidos hidrofóbicos y de los aminoácidos con carga en el reconocimiento de las proteínas sustrato, así como el papel que tiene la forma dimérica y su oligomerización en la actividad de chaperona. En cada una de esas chaperonas revisaremos la estructura de la proteína, su función, localización celular e importancia para la célula.

The metastable states of proteins

The intriguing process of protein folding comprises discrete steps that stabilize the protein molecules in different conformations. The metastable state of protein is represented by specific conformational characteristics, which place the protein in a local free energy minimum state of the energy landscape. The native-to-metastable structural transitions are governed by transient or long-lived thermodynamic and kinetic fluctuations of the intrinsic interactions of the protein molecules. Depiction of the structural and functional properties of metastable proteins is not only required to understand the complexity of folding patterns but also to comprehend the mechanisms of anomalous aggregation of different proteins. In this article, we review the properties of metastable proteins in context of their stability and capability of undergoing atypical aggregation in physiological conditions.

The Anti-Aggregation Holdase Hsp33 Promotes the Formation of Folded Protein Structures

Holdase chaperones are known to be central to suppressing aggregation, but how they affect substrate conformations remains poorly understood. Here, we use optical tweezers to study how the holdase Hsp33 alters folding transitions within single maltose binding proteins and aggregation transitions between maltose binding protein substrates. Surprisingly, we find that Hsp33 not only suppresses aggregation but also guides the folding process. Two modes of action underlie these effects. First, Hsp33 binds unfolded chains, which suppresses aggregation between substrates and folding transitions within substrates. Second, Hsp33 binding promotes substrate states in which most of the chain is folded and modifies their structure, possibly by intercalating its intrinsically disordered regions. A statistical ensemble model shows how Hsp33 function results from the competition between these two contrasting effects. Our findings reveal an unexpectedly comprehensive functional repertoire for Hsp33 that may be more prevalent among holdases and dispels the notion of a strict chaperone hierarchy.

Orchestration of algal metabolism by protein disorder

Intrinsically disordered proteins (IDPs) are proteins that provide many functional advantages in a large number of metabolic and signalling pathways. Because of their high flexibility that endows them with pressure-, heat- and acid-resistance, IDPs are valuable metabolic regulators that help algae to cope with extreme conditions of pH, temperature, pressure and light. They have, however, been overlooked in these organisms. In this review, we present some well-known algal IDPs, including the conditionally disordered CP12, a protein involved in the regulation of CO₂ assimilation, as probably the best known example, whose disorder content is strongly dependent on the redox conditions, and the essential pyrenoid component 1 that serves as a scaffold for ribulose-1, 5-bisphosphate carboxylase/oxygenase. We also describe how some enzymes are regulated by protein regions, called intrinsically disordered regions (IDRs), such as ribulose-1, 5-bisphosphate carboxylase/oxygenase activase, the A₂B₂ form of glyceraldehyde-3-phosphate dehydrogenase and the adenylate kinase. Several molecular chaperones, which are crucial for cell proteostasis, also display significant disorder propensities such as the algal heat shock proteins HSP33, HSP70 and HSP90. This review confirms the wide distribution of IDPs in algae but highlights that further studies are needed to uncover their full role in orchestrating algal metabolism.

The molecular chaperone Hsp33 is activated by atmospheric-pressure plasma protecting proteins from aggregation

Non-equilibrium atmospheric-pressure plasmas are an alternative means to sterilize and disinfect. Plasma-mediated protein aggregation has been identified as one of the mechanisms responsible for the antibacterial features of plasma. Heat shock protein 33 (Hsp33) is a chaperone with holdase function that is activated when oxidative stress and unfolding conditions coincide. In its active form, it binds unfolded proteins and prevents their aggregation. Here we analyse the influence of plasma on the structure and function of Hsp33 of Escherichia coli using a dielectric barrier discharge plasma. While most other proteins studied so far were rapidly inactivated by atmospheric-pressure plasma, exposure to plasma activated Hsp33. Both, oxidation of cysteine residues and partial unfolding of Hsp33 were observed after plasma treatment. Plasma-mediated activation of Hsp33 was reversible by reducing agents, indicating that cysteine residues critical for regulation of Hsp33 activity were not irreversibly oxidized. However, the reduction yielded a protein that did not regain its original fold. Nevertheless, a second round of plasma treatment resulted again in a fully active protein that was unfolded to an even higher degree. These conformational states were not previously observed after chemical activation with HOCl. Thus, although we could detect the formation of HOCl in the liquid phase during plasma treatment, we conclude that other species must be involved in plasma activation of Hsp33. E. coli cells over-expressing the Hsp33-encoding gene hslO from a plasmid showed increased survival rates when treated with plasma while an hslO deletion mutant was hypersensitive emphasizing the importance of protein aggregation as an inactivation mechanism of plasma.

Defining Hsp33's Redox-regulated Chaperone Activity and Mapping Conformational Changes on Hsp33 Using Hydrogen-deuterium Exchange Mass Spectrometry

Living organisms regularly need to cope with fluctuating environments during their life cycle, including changes in temperature, pH, the accumulation of reactive oxygen species, and more. These fluctuations can lead to a widespread protein unfolding, aggregation, and cell death. Therefore, cells have evolved a dynamic and stress-specific network of molecular chaperones, which maintain a "healthy" proteome during stress conditions. ATP-independent chaperones constitute one major class of molecular chaperones, which serve as first-line defense molecules, protecting against protein aggregation in a stress-dependent manner. One feature these chaperones have in common is their ability to utilize structural plasticity for their stress-specific activation, recognition, and release of the misfolded client. In this paper, we focus on the functional and structural analysis of one such intrinsically disordered chaperone, the bacterial redox-regulated Hsp33, which protects proteins against aggregation during oxidative stress. Here, we present a toolbox of diverse techniques for studying redox-regulated chaperone activity, as well as for mapping conformational changes of the chaperone, underlying its activity. Specifically, we describe a workflow which includes the preparation of fully reduced and fully oxidized proteins, followed by an analysis of the chaperone anti-aggregation activity in vitro using light-scattering, focusing on the degree of the anti-aggregation activity and its kinetics. To overcome frequent outliers accumulated during aggregation assays, we describe the usage of Kfits, a novel graphical tool which allows easy processing of kinetic measurements. This tool can be easily applied to other types of kinetic measurements for removing outliers and fitting kinetic parameters. To correlate the function with the protein structure, we describe the setup and workflow of a structural mass spectrometry technique, hydrogen-deuterium exchange mass spectrometry, that allows the mapping of conformational changes on the chaperone and substrate during different stages of Hsp33 activity. The same methodology can be applied to other protein-protein and protein-ligand interactions.

Exploring intrinsically disordered proteins in Chlamydomonas reinhardtii

The content of intrinsically disordered protein (IDP) is related to organism complexity, evolution, and regulation. In the Plantae, despite their high complexity, experimental investigation of IDP content is lacking. We identified by mass spectrometry 682 heat-resistant proteins from the green alga, Chlamydomonas reinhardtii. Using a phosphoproteome database, we found that 331 of these proteins are targets of phosphorylation. We analyzed the flexibility propensity of the heat-resistant proteins and their specific features as well as those of predicted IDPs from the same organism. Their mean percentage of disorder was about 20%. Most of the IDPs (~70%) were addressed to other compartments than mitochondrion and chloroplast. Their amino acid composition was biased compared to other classic IDPs. Their molecular functions were diverse; the predominant ones were nucleic acid binding and unfolded protein binding and the less abundant one was catalytic activity. The most represented proteins were ribosomal proteins, proteins associated to flagella, chaperones and histones. We also found CP12, the only experimental IDP from C. reinhardtii that is referenced in disordered protein database. This is the first experimental investigation of IDPs in C. reinhardtii that also combines in silico analysis.

A Role of Metastable Regions and Their Connectivity in the Inactivation of a Redox-Regulated Chaperone and Its Inter-Chaperone Crosstalk

AIMS

A recently discovered group of conditionally disordered chaperones share a very unique feature; they need to lose structure to become active as chaperones. This activation mechanism makes these chaperones particularly suited to respond to protein-unfolding stress conditions, such as oxidative unfolding. However, the role of this disorder in stress-related activation, chaperone function, and the crosstalk with other chaperone systems is not yet clear. Here, we focus on one of the members of the conditionally disordered chaperones, a thiol-redox switch of the bacterial proteostasis system, Hsp33.

RESULTS

By modifying the Hsp33's sequence, we reveal that the metastable region has evolved to abolish redox-dependent chaperone activity, rather than enhance binding affinity for client proteins. The intrinsically disordered region of Hsp33 serves as an anchor for the reduced, inactive state of Hsp33, and it dramatically affects the crosstalk with the synergetic chaperone system, DnaK/J. Using mass spectrometry, we describe the role that the metastable region plays in determining client specificity during normal and oxidative stress conditions in the cell. Innovation and Conclusion: We uncover a new role of protein plasticity in Hsp33's inactivation, client specificity, crosstalk with the synergistic chaperone system DnaK/J, and oxidative stress-specific interactions in bacteria. Our results also suggest that Hsp33 might serve as a member of the house-keeping proteostasis machinery, tasked with maintaining a "healthy" proteome during normal conditions, and that this function does not depend on the metastable linker region. Antioxid. Redox Signal. 27, 1252-1267.

Stress-Activated Chaperones: A First Line of Defense

Proteins are constantly challenged by environmental stress conditions that threaten their structure and function. Especially problematic are oxidative, acid, and severe heat stress which induce very rapid and widespread protein unfolding and generate conditions that make canonical chaperones and/or transcriptional responses inadequate to protect the proteome. We review here recent advances in identifying and characterizing stress-activated chaperones which are inactive under non-stress conditions but become potent chaperones under specific protein-unfolding stress conditions. We discuss the post-translational mechanisms by which these chaperones sense stress, and consider the role that intrinsic disorder plays in their regulation and function. We examine their physiological roles under both non-stress and stress conditions, their integration into the cellular proteostasis network, and their potential as novel therapeutic targets.

Near diffusion-controlled reaction of a Zn(Cys)4 zinc finger with hypochlorous acid

Reaction rate constants of HOCl with zinc-bound cysteines are determined, demonstrating that zinc fingers are potent targets for HOCl and may serve as HOCl sensors.

Hypochlorous acid (HOCl) is one of the strongest oxidants produced in mammals to kill invading microorganisms. The bacterial response to HOCl involves proteins that are able to sense HOCl using methionine, free cysteines or zinc-bound cysteines of zinc finger sites. Although the reactivity of methionine or free cysteine with HOCl is well documented at the molecular level, this is not the case for zinc-bound cysteines. We present here a study that aims at filling this gap. Using a model peptide of the Zn(Cys)₄ zinc finger site of the chaperone Hsp33, a protein involved in the defence against HOCl in bacteria, we show that HOCl oxidation of this model leads to the formation of two disulfides. A detailed mechanistic and kinetic study of this reaction, relying on stopped-flow measurements and competitive oxidation with methionine, reveals very high rate constants: the absolute second-order rate constants for the reaction of the model zinc finger with HOCl and its conjugated base ClO^– are (9.3 ± 0.8) × 10⁸ M^–1 s^–1 and (1.2 ± 0.2) × 10⁴ M^–1 s^–1, the former approaching the diffusion limit. Revised values of the second-order rate constants for the reaction of methionine with HOCl and ClO^– were also determined to be (5.5 ± 0.8) × 10⁸ M^–1 s^–1 and (7 ± 5) × 10² M^–1 s^–1, respectively. At physiological pH, the zinc finger site reacts faster with HOCl than methionine and glutathione or cysteine. This study demonstrates that zinc fingers are potent targets for HOCl and confirms that they may serve as HOCl sensors as proposed for Hsp33.

Are the curli proteins CsgE and CsgF intrinsically disordered?

Curli are a type of proteinaceous cell surface filament produced by enteric bacteria such as Escherichia and Salmonella that facilitate cell adhesion and invasion, bio-film formation, and environmental persistence. Curli assembly involves 6 proteins encoded by the curli specific genes A, B, C, E, F, and G. Although CsgA is the major structural component of curli, CsgE, and CsgF, are thought to play important chaperone like functions in the assembly of CsgA into curli. Given that some proteins with chaperone like function have been observed to contain disordered regions, sequence analysis and circular dichroism spectroscopy was used to investigate the possibility that structures of CsgE and CsgF were also disordered. Sequence analysis based on charge and hydrophobicity, as well as using the disorder prediction software PONDR, indicates that both proteins have significant regions of disorder. The secondary structure and unfolding, of CsgE and CsgF, analyzed using circular dichroism spectroscopy suggests that both proteins lack a well defined and stable structure. These observations support the hypothesis that the curli assembly proteins CsgE and CsgF are disordered proteins containing intrinsically disordered regions.

Protein unfolding as a switch from self-recognition to high-affinity client binding

Stress-specific activation of the chaperone Hsp33 requires the unfolding of a central linker region. This activation mechanism suggests an intriguing functional relationship between the chaperone's own partial unfolding and its ability to bind other partially folded client proteins. However, identifying where Hsp33 binds its clients has remained a major gap in our understanding of Hsp33's working mechanism. By using site-specific Fluorine-19 nuclear magnetic resonance experiments guided by in vivo crosslinking studies, we now reveal that the partial unfolding of Hsp33's linker region facilitates client binding to an amphipathic docking surface on Hsp33. Furthermore, our results provide experimental evidence for the direct involvement of conditionally disordered regions in unfolded protein binding. The observed structural similarities between Hsp33's own metastable linker region and client proteins present a possible model for how Hsp33 uses protein unfolding as a switch from self-recognition to high-affinity client binding.

Under stress conditions the molecular chaperone Hsp33 is activated to process unfolded proteins. Here, the authors use in vivo and in vitro crosslinking and ¹⁹F-NMR to elucidate the binding site for misfolded proteins and are able to propose a model for its mechanism of action.

HSP33 in eukaryotes - an evolutionary tale of a chaperone adapted to photosynthetic organisms

HSP33 was originally identified in bacteria as a redox-sensitive chaperone that protects unfolded proteins from aggregation. Here, we describe a eukaryote ortholog of HSP33 from the green algae Chlamydomonas reinhardtii, which appears to play a protective role under light-induced oxidizing conditions. The algal HSP33 exhibits chaperone activity, as shown by citrate synthase aggregation assays. Studies from the Jakob laboratory established that activation of the bacterial HSP33 upon its oxidation initiates by the release of pre-bound Zn from the well conserved Zn-binding motif Cys-X-Cys-Xn -Cys-X-X-Cys, and is followed by significant structural changes (Reichmann et al., ). Unlike the bacterial protein, the HSP33 from C. reinhardtii had lost the first cysteine residue of its center, diminishing Zn-binding activity under all conditions. As a result, the algal protein can be easily activated by minor structural changes in response to oxidation and/or excess heat. An attempt to restore the missing first cysteine did not have a major effect on Zn-binding and on the mode of activation. Replacement of all remaining cysteines abolished completely any residual Zn binding, although the chaperone activation was maintained. A phylogenetic analysis of the algal HSP33 showed that it clusters with the cyanobacterial protein, in line with its biochemical localization to the chloroplast. Indeed, expression of the algal HSP33 increases in response to light-induced oxidative stress, which is experienced routinely by photosynthetic organisms. Despite the fact that no ortholog could be found in higher eukaryotes, its abundance in all algal species examined could have a biotechnological relevance.

Protein quality control under oxidative stress conditions

Accumulation of reactive oxygen and chlorine species (RO/CS) is generally regarded to be a toxic and highly undesirable event, which serves as contributing factor in aging and many age-related diseases. However, it is also put to excellent use during host defense, when high levels of RO/CS are produced to kill invading microorganisms and regulate bacterial colonization. Biochemical and cell biological studies of how bacteria and other microorganisms deal with RO/CS have now provided important new insights into the physiological consequences of oxidative stress, the major targets that need protection, and the cellular strategies employed by organisms to mitigate the damage. This review examines the redox-regulated mechanisms by which cells maintain a functional proteome during oxidative stress. We will discuss the well-characterized redox-regulated chaperone Hsp33, and we will review recent discoveries demonstrating that oxidative stress-specific activation of chaperone function is a much more widespread phenomenon than previously anticipated. New members of this group include the cytosolic ATPase Get3 in yeast, the Escherichia coli protein RidA, and the mammalian protein α2-macroglobulin. We will conclude our review with recent evidence showing that inorganic polyphosphate (polyP), whose accumulation significantly increases bacterial oxidative stress resistance, works by a protein-like chaperone mechanism. Understanding the relationship between oxidative and proteotoxic stresses will improve our understanding of both host-microbe interactions and how mammalian cells combat the damaging side effects of uncontrolled RO/CS production, a hallmark of inflammation.

Thiol-based redox switches

Regulation of protein function through thiol-based redox switches plays an important role in the response and adaptation to local and global changes in the cellular levels of reactive oxygen species (ROS). Redox regulation is used by first responder proteins, such as ROS-specific transcriptional regulators, chaperones or metabolic enzymes to protect cells against mounting levels of oxidants, repair the damage and restore redox homeostasis. Redox regulation of phosphatases and kinases is used to control the activity of select eukaryotic signaling pathways, making reactive oxygen species important second messengers that regulate growth, development and differentiation. In this review we will compare different types of reversible protein thiol modifications, elaborate on their structural and functional consequences and discuss their role in oxidative stress response and ROS adaptation. This article is part of a Special Issue entitled: Thiol-Based Redox Processes.

Bile salts act as effective protein-unfolding agents and instigators of disulfide stress in vivo

Commensal and pathogenic bacteria must deal with many different stress conditions to survive in and colonize the human gastrointestinal tract. One major challenge that bacteria encounter in the gut is the high concentration of bile salts, which not only aid in food absorption but also act as effective physiological antimicrobials. The mechanism by which bile salts limit bacterial growth is still largely unknown. Here, we show that bile salts cause widespread protein unfolding and aggregation, affecting many essential proteins. Simultaneously, the bacterial cytosol becomes highly oxidizing, indicative of disulfide stress. Strains defective in reducing oxidative thiol modifications, restoring redox homeostasis, or preventing irreversible protein aggregation under disulfide stress conditions are sensitive to bile salt treatment. Surprisingly, cholate and deoxycholate, two of the most abundant and very closely related physiological bile salts, vary substantially in their destabilizing effects on proteins in vitro and cause protein unfolding of different subsets of proteins in vivo. Our results provide a potential mechanistic explanation for the antimicrobial effects of bile salts, help explain the beneficial effects of bile salt mixtures, and suggest that we have identified a physiological source of protein-unfolding disulfide stress conditions in bacteria.

Disorder in the lifetime of a protein

Intrinsic disorder is everywhere and is inevitable. The non-folding propensity is inherent for numerous natural polypeptide chains, and many functional proteins and protein regions are intrinsically disordered. Furthermore, at particular moments in their life, most notably during their synthesis and degradation, all ordered proteins are at least partially unfolded (disordered). Also, there is a widely spread phenomenon of conditional (functional or transient) disorder, where functions of many ordered proteins require local or even global unfolding of their unique structures. Finally, extrinsic disorder (i.e., intrinsic disorder in functional partners of ordered proteins) should be taken into account too. Therefore, even if a protein is completely devoid of intrinsically disordered regions in its mature form (which is a rather exceptional situation), it faces different forms of disorder (intrinsic, extrinsic, or induced disorder) at all the stages of its functional life, from birth to death. The goal of this article is to briefly introduce this concept of disorder in the lifetime of a protein.

Analysis of Arabidopsis thioredoxin-h isotypes identifies discrete domains that confer specific structural and functional properties

In this study, we identified specific domains and amino acids responsible for the structural and functional properties of AtTrx-hs (Arabidopsis h-type thioredoxins). Specific domains and amino acids for the chaperone function of AtTrx-hs played a critical role in heat-shock-resistance in vivo.

Recognition and binding of apocytochrome c to P. aeruginosa CcmI, a component of cytochrome c maturation machinery

The biogenesis of c-type cytochromes (Cytc) is a process that in Gram-negative bacteria demands the coordinated action of different periplasmic proteins (CcmA-I), whose specific roles are still being investigated. Activities of Ccm proteins span from the chaperoning of heme b in the periplasm to the specific reduction of oxidized apocytochrome (apoCyt) cysteine residues and to chaperoning and recognition of the unfolded apoCyt before covalent attachment of the heme to the cysteine thiols can occur. We present here the functional characterization of the periplasmic domain of CcmI from the pathogen Pseudomonas aeruginosa (Pa-CcmI*). Pa-CcmI* is composed of a TPR domain and a peculiar C-terminal domain. Pa-CcmI* fulfills both the ability to recognize and bind to P. aeruginosa apo-cytochrome c551 (Pa-apoCyt) and a chaperoning activity towards unfolded proteins, as it prevents citrate synthase aggregation in a concentration-dependent manner. Equilibrium and kinetic experiments with Pa-CcmI*, or its isolated domains, with peptides mimicking portions of Pa-apoCyt sequence allow us to quantify the molecular details of the interaction between Pa-apoCyt and Pa-CcmI*. Binding experiments show that the interaction occurs at the level of the TPR domain and that the recognition is mediated mainly by the C-terminal sequence of Pa-apoCyt. The affinity of Pa-CcmI* to full-length Pa-apoCyt or to its C-terminal sequence is in the range expected for a component of a multi-protein complex, whose task is to receive the apoCyt and to deliver it to other components of the apoCyt:heme b ligation protein machinery.

The roles of conditional disorder in redox proteins

Cells are constantly exposed to various oxidants, either generated endogenously due to metabolic activity or exogenously. One way that cells respond to oxidants is through the action of redox-regulated proteins. These proteins also play important roles in oxidant signaling and protein biogenesis events. The key sensors built into redox-regulated proteins are cysteines, which undergo reversible thiol oxidation in response to changes in the oxidation status of the cellular environment. In this review, we discuss three examples of redox-regulated proteins found in bacteria, mitochondria, and chloroplasts. These proteins use oxidation of their redox-sensitive cysteines to reversibly convert large structural domains into more disordered regions or vice versa. These massive structural rearrangements are directly implicated in the functions of these proteins.

Regulated unfolding of proteins in signaling

The transduction of biological signals often involves structural rearrangements of proteins in response to input signals, which leads to functional outputs. This review discusses the role of regulated partial and complete protein unfolding as a mechanism of controlling protein function and the prevalence of this regulatory mechanism in signal transduction pathways. The principles of regulated unfolding, the stimuli that trigger unfolding, and the coupling of unfolding with other well characterized regulatory mechanism are discussed.

Hsp33 controls elongation factor-Tu stability and allows Escherichia coli growth in the absence of the major DnaK and trigger factor chaperones

Intracellular de novo protein folding is assisted by cellular networks of molecular chaperones. In Escherichia coli, cooperation between the chaperones trigger factor (TF) and DnaK is central to this process. Accordingly, the simultaneous deletion of both chaperone-encoding genes leads to severe growth and protein folding defects. Herein, we took advantage of such defective phenotypes to further elucidate the interactions of chaperone networks in vivo. We show that disruption of the TF/DnaK chaperone pathway is efficiently rescued by overexpression of the redox-regulated chaperone Hsp33. Consistent with this observation, the deletion of hslO, the Hsp33 structural gene, is no longer tolerated in the absence of the TF/DnaK pathway. However, in contrast with other chaperones like GroEL or SecB, suppression by Hsp33 was not attributed to its potential overlapping general chaperone function(s). Instead, we show that overexpressed Hsp33 specifically binds to elongation factor-Tu (EF-Tu) and targets it for degradation by the protease Lon. This synergistic action of Hsp33 and Lon was responsible for the rescue of bacterial growth in the absence of TF and DnaK, by presumably restoring the coupling between translation and the downstream folding capacity of the cell. In support of this hypothesis, we show that overexpression of the stress-responsive toxin HipA, which inhibits EF-Tu, also rescues bacterial growth and protein folding in the absence of TF and DnaK. The relevance for such a convergence of networks of chaperones and proteases acting directly on EF-Tu to modulate the intracellular rate of protein synthesis in response to protein aggregation is discussed.

Conditional disorder in chaperone action

Protein disorder remains an intrinsically fuzzy concept. Its role in protein function is difficult to conceptualize and its experimental study is challenging. Although a wide variety of roles for protein disorder have been proposed, establishing that disorder is functionally important, particularly in vivo, is not a trivial task. Several molecular chaperones have now been identified as conditionally disordered proteins; fully folded and chaperone-inactive under non-stress conditions, they adopt a partially disordered conformation upon exposure to distinct stress conditions. This disorder appears to be vital for their ability to bind multiple aggregation-sensitive client proteins and to protect cells against the stressors. The study of these conditionally disordered chaperones should prove useful in understanding the functional role for protein disorder in molecular recognition.

Moonlighting by different stressors: crystal structure of the chaperone species of a 2-Cys peroxiredoxin

2-Cys peroxiredoxins (Prxs) play two different roles depending on the physiological status of the cell. They are thioredoxin-dependent peroxidases under low oxidative stress and ATP-independent chaperones upon exposure to high peroxide concentrations. These alternative functions have been associated with changes in the oligomerization state from low-(LMW) to high-molecular-weight (HMW) species. Here we present the structures of Schistosoma mansoni PrxI in both states: the LMW decamer and the HMW 20-mer formed by two stacked decamers. The latter is the structure of a 2-Cys Prx chaperonic form. Comparison of the structures sheds light on the mechanism by which chemical stressors, such as high H(2)O(2) concentration and acidic pH, are sensed and translated into a functional switch in this protein family. We also propose a model to account for the in vivo formation of long filaments of stacked Prx rings.

Order out of disorder: working cycle of an intrinsically unfolded chaperone

The redox-regulated chaperone Hsp33 protects organisms against oxidative stress that leads to protein unfolding. Activation of Hsp33 is triggered by the oxidative unfolding of its own redox-sensor domain, making Hsp33 a member of a recently discovered class of chaperones that require partial unfolding for full chaperone activity. Here we address the long-standing question of how chaperones recognize client proteins. We show that Hsp33 uses its own intrinsically disordered regions to discriminate between unfolded and partially structured folding intermediates. Binding to secondary structure elements in client proteins stabilizes Hsp33's intrinsically disordered regions, and this stabilization appears to mediate Hsp33's high affinity for structured folding intermediates. Return to nonstress conditions reduces Hsp33's disulfide bonds, which then significantly destabilizes the bound client proteins and in doing so converts them into less-structured, folding-competent client proteins of ATP-dependent foldases. We propose a model in which energy-independent chaperones use internal order-to-disorder transitions to control substrate binding and release.

Structure of Hsp33/YOR391Cp from the yeast Saccharomyces cerevisiae

Saccharomyces cerevisiae Hsp33/YOR391Cp is a member of the ThiI/DJ-1/PfpI superfamily. Hsp33 was overexpressed in Escherichia coli and its crystal structure was determined at 2.40 Å resolution. Structural comparison revealed that Hsp33 adopts an α/β-hydrolase fold and possesses the putative Cys-His-Glu catalytic triad common to the Hsp31 family, suggesting that Hsp33 and Hsp31 share similar aminopeptidase activity, while structural deviations in helices α2-α3 of the core domain might be responsible for the access of different peptide substrates.