1
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Antonazzi F, Di Felice F, Camilloni G. GCN5 enables HSP12 induction promoting chromatin remodeling not histone acetylation. Biochem Cell Biol 2021; 99:700-706. [PMID: 34102063 DOI: 10.1139/bcb-2020-0620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Regulation of stress responsive genes represents one of the best examples of gene induction and the relevance and involvement of different regulators may change for a given gene depending on the challenging stimulus. HSP12 gene is induced by very different stimuli, however the molecular response to the stress has been characterized in detail only for heat shock treatments. In this work we want to verify whether, the regulation of transcription induced by oxidative stress, utilizes the same epigenetic solutions relative to those employed in heat shock response. We also monitored HSP12 induction employing spermidine, a known acetyltransferase inhibitor, and observed an oxidative stress that synergizes with spermidine treatment. Our data show that during transcriptional response to H2O2, histone acetylation and chromatin remodeling occur. However, when the relevance of Gcn5p on these processes was studied, we observed that induction of transcription is GCN5 dependent and this does not rely on histone acetylation by Gcn5p despite its HAT activity. Chromatin remodeling accompanying gene activation is rather GCN5 dependent. Thus, GCN5 controls HSP12 transcription after H2O2 treatment by allowing chromatin remodeling and it is only partially involved in HSP12 histone acetylation regardless its HAT activity.
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Affiliation(s)
- Francesca Antonazzi
- Università degli Studi di Roma La Sapienza, 9311, Dipartimento di Biologia e Biotecnologie, Roma, Lazio, Italy;
| | - Francesca Di Felice
- Università degli Studi di Roma La Sapienza, 9311, Dipartimento di Biologia e Biotecnologie, Roma, Lazio, Italy;
| | - Giorgio Camilloni
- Università degli Studi di Roma La Sapienza, 9311, Dipartimento di Biologia e Biotecnologie, Piazzale A. Moro 5, Roma, Italy, 00185;
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2
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Abstract
This chronologue seeks to document the discovery and development of an understanding of oligomeric ring protein assemblies known as chaperonins that assist protein folding in the cell. It provides detail regarding genetic, physiologic, biochemical, and biophysical studies of these ATP-utilizing machines from both in vivo and in vitro observations. The chronologue is organized into various topics of physiology and mechanism, for each of which a chronologic order is generally followed. The text is liberally illustrated to provide firsthand inspection of the key pieces of experimental data that propelled this field. Because of the length and depth of this piece, the use of the outline as a guide for selected reading is encouraged, but it should also be of help in pursuing the text in direct order.
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3
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Gupta A, Lloyd-Price J, Ribeiro AS. In silico analysis of division times of Escherichia coli populations as a function of the partitioning scheme of non-functional proteins. In Silico Biol 2016; 12:9-21. [PMID: 25318468 PMCID: PMC4923715 DOI: 10.3233/isb-140462] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Recent evidence suggests that cells employ functionally asymmetric partitioning schemes in division to cope with aging. We explore various schemes in silico, with a stochastic model of Escherichia coli that includes gene expression, non-functional proteins generation, aggregation and polar retention, and molecule partitioning in division. The model is implemented in SGNS2, which allows stochastic, multi-delayed reactions within hierarchical, transient, interlinked compartments. After setting parameter values of non-functional proteins’ generation and effects that reproduce realistic intracellular and population dynamics, we investigate how the spatial organization of non-functional proteins affects mean division times of cell populations in lineages and, thus, mean cell numbers over time. We find that division times decrease for increasingly asymmetric partitioning. Also, increasing the clustering of non-functional proteins decreases division times. Increasing the bias in polar segregation further decreases division times, particularly if the bias favors the older pole and aggregates’ polar retention is robust. Finally, we show that the non-energy consuming retention of inherited non-functional proteins at the older pole via nucleoid occlusion is a source of functional asymmetries and, thus, is advantageous. Our results suggest that the mechanisms of intracellular organization of non-functional proteins, including clustering and polar retention, affect the vitality of E. coli populations.
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Affiliation(s)
| | | | - Andre S. Ribeiro
- Corresponding author: Andre S. Ribeiro, Department of Signal Processing, Tampere University of Technology, P.O. Box 553, 33101 Tampere, Finland. Tel.: +358 408490736; Fax: +358 331154989;
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4
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Maleki F, Khosravi A, Nasser A, Taghinejad H, Azizian M. Bacterial Heat Shock Protein Activity. J Clin Diagn Res 2016; 10:BE01-3. [PMID: 27134861 DOI: 10.7860/jcdr/2016/14568.7444] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/28/2015] [Indexed: 01/09/2023]
Abstract
Bacteria are exposed to different types of stress in their growth conditions. They have developed appropriate responses, modulated by the re-modeling of protein complexes and by phosphorylation dependent signal transduction systems, to adapt and to survive in a variety range of nature. Proteins are essential components for biologic activity in the eukaryotic and prokaryotic cell. Heat Shock Proteins (HSP) have been identified from various organisms and have critical role in cell hemostasis. Chaperone can sense environment and have different potential role in the organism evolution.
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Affiliation(s)
- Farajollah Maleki
- Lecturer, Clinical Microbiology Research Center, Ilam University of Medical Science , Ilam, Iran
| | - Afra Khosravi
- Professor, Department of Immunology, Faculty of Medicine, Ilam University of Medical Sciences , Ilam, Iran
| | - Ahmad Nasser
- Lecturer, Clinical Microbiology Research Center, Ilam University of Medical Science , Ilam, Iran
| | - Hamid Taghinejad
- Assistant Professor, Department of Nursing, Faculty of Nursing and Midwifery, Ilam University of Medical Sciences , Ilam, Iran
| | - Mitra Azizian
- Lecturer, Clinical Microbiology Research Center, Ilam University of Medical Science , Ilam, Iran
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5
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Guenther I, Zolkiewski M, Kędzierska-Mieszkowska S. Cooperation between two ClpB isoforms enhances the recovery of the recombinant β-galactosidase from inclusion bodies. Biochem Biophys Res Commun 2012; 426:596-600. [PMID: 22982305 DOI: 10.1016/j.bbrc.2012.08.135] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 08/28/2012] [Indexed: 10/27/2022]
Abstract
Bacterial ClpB is a molecular chaperone that solubilizes and reactivates aggregated proteins in cooperation with the DnaK chaperone system. The mechanism of protein disaggregation mediated by ClpB is linked to translocation of substrates through the central channel within the ring-hexameric structure of ClpB. Two isoforms of ClpB are produced in vivo: the full-length ClpB95 and the truncated ClpB80 (ClpBΔN), which does not contain the N-terminal domain. The functional specificity of the two ClpB isoforms and the biological role of the N-terminal domain are still not fully understood. Recently, it has been demonstrated that ClpB may achieve its full potential as an aggregate-reactivating chaperone through the functional interaction and synergistic cooperation of its two isoforms. It has been found that the most efficient resolubilization and reactivation of stress-aggregated proteins occurred in the presence of both ClpB95 and ClpB80. In this work, we asked if the two ClpB isoforms functionally cooperate in the solubilization and reactivation of proteins from insoluble inclusion bodies (IBs) in Escherichia coli cells. Using the model β-galactosidase fusion protein (VP1LAC), we found that solubilization and reactivation of enzymes entrapped in IBs occurred more efficiently in the presence of ClpB95 with ClpB80 than with either ClpB95 or ClpB80 alone. The two isoforms of ClpB chaperone acting together enhanced the solubility and enzymatic activity of β-galactosidase sequestered into IBs. Both ClpB isoforms were associated with IBs of β-galactosidase, what demonstrates their affinity to this type of aggregates. These results demonstrate a synergistic cooperation between the two isoforms of ClpB chaperone. In addition, no significant recovery of the β-galactosidase from IBs in ΔclpB mutant cells suggests that ClpB is a key chaperone in IB protein release.
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Affiliation(s)
- Izabela Guenther
- Department of Biochemistry, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
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6
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Balamurugan S, Dugan MER. Growth temperature associated protein expression and membrane fatty acid composition profiles of Salmonella enterica serovar Typhimurium. J Basic Microbiol 2011; 50:507-18. [PMID: 20806250 DOI: 10.1002/jobm.201000037] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Total cellular proteins and fatty acid composition profiles of mid-log phase cells of Salmonella enterica serovar Typhimurium grown at 8, 25, 37 or 42 °C were separated by 2D-PAGE and FAME analysis. Growth temperature associated protein expression can be grouped into 3 thermal classes which include proteins whose expression is: I) optimal at 37 °C, meaning their expression peaked at 37 °C; II) up-regulated with an increase in growth temperature; III) down-regulated with increase in growth temperature; meaning their expression peaked at 8 °C. At higher growth temperatures, proteins belonging to the functional groups of amino acid transport and metabolism, nucleotide metabolism, energy metabolism and post-translation modifications (chaperones) are present in substantially higher amounts. This increase in abundance is regulated in a temperature dependent manner. It is important to point out that proteins involved in energy metabolism observed in higher amounts at higher growth temperatures all belong to the glycolysis pathway, while at 8 °C they belonged to the TCA cycle. Increase in growth temperatures results in a decrease in membrane fatty acid unsaturation and an increase in saturated and cyclic fatty acids. These results provide an insight into the dynamic molecular and physiological responses of Salmonella Typhimurium during growth at different temperatures.
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7
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Richter K, Haslbeck M, Buchner J. The heat shock response: life on the verge of death. Mol Cell 2010; 40:253-66. [PMID: 20965420 DOI: 10.1016/j.molcel.2010.10.006] [Citation(s) in RCA: 1247] [Impact Index Per Article: 89.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 10/03/2010] [Accepted: 10/05/2010] [Indexed: 12/16/2022]
Abstract
Organisms must survive a variety of stressful conditions, including sudden temperature increases that damage important cellular structures and interfere with essential functions. In response to heat stress, cells activate an ancient signaling pathway leading to the transient expression of heat shock or heat stress proteins (Hsps). Hsps exhibit sophisticated protection mechanisms, and the most conserved Hsps are molecular chaperones that prevent the formation of nonspecific protein aggregates and assist proteins in the acquisition of their native structures. In this Review, we summarize the concepts of the protective Hsp network.
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Affiliation(s)
- Klaus Richter
- Munich Center for Integrated Protein Science, Department Chemie Technische Universität München, 85747 Garching, Germany
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8
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Abstract
The aggregation of misfolded proteins is associated with the perturbation of cellular function, ageing and various human disorders. Mounting evidence suggests that protein aggregation is often part of the cellular response to an imbalanced protein homeostasis rather than an unspecific and uncontrolled dead-end pathway. It is a regulated process in cells from bacteria to humans, leading to the deposition of aggregates at specific sites. The sequestration of misfolded proteins in such a way is protective for cell function as it allows for their efficient solubilization and refolding or degradation by components of the protein quality-control network. The organized aggregation of misfolded proteins might also allow their asymmetric distribution to daughter cells during cell division.
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9
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Welker S, Rudolph B, Frenzel E, Hagn F, Liebisch G, Schmitz G, Scheuring J, Kerth A, Blume A, Weinkauf S, Haslbeck M, Kessler H, Buchner J. Hsp12 Is an Intrinsically Unstructured Stress Protein that Folds upon Membrane Association and Modulates Membrane Function. Mol Cell 2010; 39:507-20. [DOI: 10.1016/j.molcel.2010.08.001] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Revised: 07/02/2010] [Accepted: 08/04/2010] [Indexed: 11/27/2022]
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10
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11
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Protein misfolding and cellular defense mechanisms in neurodegenerative diseases. NEURODEGENER DIS 2005. [DOI: 10.1017/cbo9780511544873.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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12
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Pope WH, Haase-Pettingell C, King J. Protein folding failure sets high-temperature limit on growth of phage P22 in Salmonella enterica serovar Typhimurium. Appl Environ Microbiol 2004; 70:4840-7. [PMID: 15294822 PMCID: PMC492335 DOI: 10.1128/aem.70.8.4840-4847.2004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The high-temperature limit for growth of microorganisms differs greatly depending on their species and habitat. The importance of an organism's ability to manage thermal stress is reflected in the ubiquitous distribution of the heat shock chaperones. Although many chaperones function to reduce protein folding defects, it has been difficult to identify the specific protein folding pathways that set the high-temperature limit of growth for a given microorganism. We have investigated this for a simple system, phage P22 infection of Salmonella enterica serovar Typhimurium. Production of infectious particles exhibited a broad maximum of 150 phage per cell when host cells were grown at between 30 and 39 degrees C in minimal medium. Production of infectious phage declined sharply in the range of 40 to 41 degrees C, and at 42 degrees C, production had fallen to less than 1% of the maximum rate. The host cells maintained optimal division rates at these temperatures. The decrease in phage infectivity was steeper than the loss of physical particles, suggesting that noninfectious particles were formed at higher temperatures. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a decrease in the tailspike adhesins assembled on phage particles purified from cultures incubated at higher temperatures. The infectivity of these particles was restored by in vitro incubation with soluble tailspike trimers. Examination of tailspike folding and assembly in lysates of phage-infected cells confirmed that the fraction of polypeptide chains able to reach the native state in vivo decreased with increasing temperature, indicating a thermal folding defect rather than a particle assembly defect. Thus, we believe that the folding pathway of the tailspike adhesin sets the high-temperature limit for P22 formation in Salmonella serovar Typhimurium.
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Affiliation(s)
- Welkin H Pope
- Massachusetts Institute of Technology, 77 Massachusetts Ave. 68-330, Cambridge, MA 02139, USA
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13
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Lee KH, Hwang YH, Lee CT, Kim YW, Han SK, Shim YS, Yoo CG. The heat-shock-induced suppression of the IkappaB/NF-kappaB cascade is due to inactivation of upstream regulators of IkappaBalpha through insolubilization. Exp Cell Res 2004; 299:49-56. [PMID: 15302572 DOI: 10.1016/j.yexcr.2004.05.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2004] [Revised: 05/10/2004] [Indexed: 10/26/2022]
Abstract
Heat shock (HS) was found to suppress the IkappaB/NF-kappaB cascade via the inhibition of IkappaB kinase (IKK) activity; however, the mechanism has not been clear. This study was undertaken to elucidate the detail of the mechanism involved. TNF-alpha-induced activation of IKK was suppressed by HS in human bronchial epithelial cells, and this was associated with the absence of IKK in the immunoprecipitates. It was not due to a degradation of IKK, but due to a conversion of IKK from a soluble to an insoluble form. IKK lost its activity rapidly upon exposure to HS in vitro. The time course of the insolubilization of IKK coincided with the decrease in IKK activity. However, inhibition of IKK insolubilization by the induction of thermotolerance did not reverse the HS-induced suppression of IKK activation and IkappaBalpha degradation. Upstream activators of IKK, such as NF-kappaB-inducing kinase (NIK) and IL-1R-associated kinase (IRAK) were also insolubilized by HS. The HS-induced insolubilization of NIK was not blocked by the induction of thermotolerance. Overexpression of NIK resumed TNF-alpha-induced activation of IKK in thermotolerant cells. These results indicate that the loss of activity of NIK, IRAK, and IKK through insolubilization is responsible for the HS-induced suppression of IkappaB/NF-kappaB pathway.
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Affiliation(s)
- Kyoung-Hee Lee
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
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14
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Kedzierska S, Matuszewska E. The effect of co-overproduction of DnaK/DnaJ/GrpE and ClpB proteins on the removal of heat-aggregated proteins from Escherichia coli DeltaclpB mutant cells--new insight into the role of Hsp70 in a functional cooperation with Hsp100. FEMS Microbiol Lett 2001; 204:355-60. [PMID: 11731148 DOI: 10.1111/j.1574-6968.2001.tb10910.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The effect of overproduction of the Hsp70 system proteins (DnaK, DnaJ, GrpE) and/or ClpB (Hsp100) from plasmids on the process of formation and removal of heat-aggregated proteins from Escherichia coli cells (the S fraction) was investigated by sucrose density gradient centrifugation. Two plasmids were employed: pKJE7 carrying the dnaK/dnaJ/grpE genes under the control of the araB promoter and pClpB carrying the clpB gene under the control of its own promoter (sigma(32)-dependent). In the wild-type cells the S fraction after 15 min of heat shock amounted to 21% of cellular insoluble proteins (IP), and disappeared 10 min after transfer of the culture to 37 degrees C. In contrast to this, in the clpB mutant the S fraction was larger (35% IP) and its elimination was retarded, nearly 60% of the aggregated proteins remained stable 30 min after heat shock. This result points to the importance of ClpB in removal of the heat-aggregated proteins from cells. Overproduction of the Hsp70 system proteins (exceeding by about 1.5-fold that of wild-type) in wild-type and DeltaclpB cells completely prevented the formation of the S fraction during heat shock. Overproduction of ClpB (exceeding by about eight-fold that of wild-type) in the same background did not prevent protein aggregation after heat shock and only partly compensated for the effect of the mutation in the clpB gene. Monitoring the S fraction during co-production of DnaK/DnaJ/GrpE and ClpB in the DeltaclpB mutant revealed that both the levels of expression and the ratios of ClpB to Hsp70 system proteins had a significant effect on the formation and removal of protein aggregates in heat-shocked E. coli cells. In the presence of excess ClpB, an increase in the levels of DnaK, DnaJ and GrpE was required to prevent aggregate formation upon heat shock or to efficiently remove protein aggregates after heat shock. Therefore, it is supposed that a high level of ClpB under some conditions, especially at insufficient levels of Hsp70 system proteins, may support protein aggregation resulting from heat shock and may lead to stabilization of hydrophobic aggregates.
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Affiliation(s)
- S Kedzierska
- Department of Biochemistry, University of Gdansk, Kladki 24, 80-822, Gdansk, Poland.
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15
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Abstract
Protein folding in the cell, long thought to be a spontaneous process, in fact often requires the assistance of molecular chaperones. This is thought to be largely because of the danger of incorrect folding and aggregation of proteins, which is a particular problem in the crowded environment of the cell. Molecular chaperones are involved in numerous processes in bacterial cells, including assisting the folding of newly synthesized proteins, both during and after translation; assisting in protein secretion, preventing aggregation of proteins on heat shock, and repairing proteins that have been damaged or misfolded by stresses such as a heat shock. Within the cell, a balance has to be found between refolding of proteins and their proteolytic degradation, and molecular chaperones play a key role in this. In this review, the evidence for the existence and role of the major cytoplasmic molecular chaperones will be discussed, mainly from the physiological point of view but also in relationship to their known structure, function and mechanism of action. The two major chaperone systems in bacterial cells (as typified by Escherichia coli) are the GroE and DnaK chaperones, and the contrasting roles and mechanisms of these chaperones will be presented. The GroE chaperone machine acts by providing a protected environment in which protein folding of individual protein molecules can proceed, whereas the DnaK chaperones act by binding and protecting exposed regions on unfolded or partially folded protein chains. DnaK chaperones interact with trigger factor in protein translation and with ClpB in reactivating proteins which have become aggregated after heat shock. The nature of the other cytoplasmic chaperones in the cell will also be reviewed, including those for which a clear function has not yet been determined, and those where an in vivo chaperone function has still to be proven, such as the small heat shock proteins IbpA and IbpB. The regulation of expression of the genes of the heat shock response will also be discussed, particularly in the light of the signals that are needed to induce the response. The major signals for induction of the heat shock response are elevated temperature and the presence of unfolded protein within the cell, but these are sensed and transduced differently by different bacteria. The best characterized example is the sigma 32 subunit of RNA polymerase from E. coli, which is both more efficiently translated and also transiently stabilized following heat shock. The DnaK chaperones modulate this effect. However, a more widely conserved system appears to be typified by the HrcA repressor in Bacillus subtilis, the activity of which is modulated by the GroE chaperone machine. Other examples of regulation of molecular chaperones will also be discussed. Finally, the likely future research directions for molecular chaperone biology in the post-genomic era will be briefly evaluated.
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Affiliation(s)
- P A Lund
- School of BioSciences, University of Birmingham, Birmingham B15 2TT, UK
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16
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Meriin AB, Mabuchi K, Gabai VL, Yaglom JA, Kazantsev A, Sherman MY. Intracellular aggregation of polypeptides with expanded polyglutamine domain is stimulated by stress-activated kinase MEKK1. J Cell Biol 2001; 153:851-64. [PMID: 11352944 PMCID: PMC2192371 DOI: 10.1083/jcb.153.4.851] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Abnormal proteins, which escape chaperone-mediated refolding or proteasome-dependent degradation, aggregate and form inclusion bodies (IBs). In several neurodegenerative diseases, such IBs can be formed by proteins with expanded polyglutamine (polyQ) domains (e.g., huntingtin). This work studies the regulation of intracellular IB formation using an NH2-terminal fragment of huntingtin with expanded polyQ domain. We demonstrate that the active form of MEKK1, a protein kinase that regulates several stress-activated signaling cascades, stimulates formation of the IBs. This function of MEKK1 requires kinase activity, as the kinase-dead mutant of MEKK1 cannot stimulate this process. Exposure of cells to UV irradiation or cisplatin, both of which activate MEKK1, also augmented the formation of IBs. The polyQ-containing huntingtin fragment exists in cells in two distinct forms: (a) in a discrete soluble complex, and (b) in association with insoluble fraction. MEKK1 strongly stimulated recruitment of polyQ polypeptides into the particulate fraction. Notably, a large portion of the active form of MEKK1 was associated with the insoluble fraction, concentrating in discrete sites, and polyQ-containing IBs always colocalized with them. We suggest that MEKK1 is involved in a process of IB nucleation. MEKK1 also stimulated formation of IBs with two abnormal polypeptides lacking the polyQ domain, indicating that this kinase has a general effect on protein aggregation.
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Affiliation(s)
- Anatoli B. Meriin
- Boston Biomedical Research Institute, Watertown, Massachusetts 02472
| | - Katsuhide Mabuchi
- Boston Biomedical Research Institute, Watertown, Massachusetts 02472
| | - Vladimir L. Gabai
- Boston Biomedical Research Institute, Watertown, Massachusetts 02472
| | - Julia A. Yaglom
- Boston Biomedical Research Institute, Watertown, Massachusetts 02472
| | - Alex Kazantsev
- Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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17
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Tomoyasu T, Mogk A, Langen H, Goloubinoff P, Bukau B. Genetic dissection of the roles of chaperones and proteases in protein folding and degradation in the Escherichia coli cytosol. Mol Microbiol 2001; 40:397-413. [PMID: 11309122 DOI: 10.1046/j.1365-2958.2001.02383.x] [Citation(s) in RCA: 272] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We investigated the roles of chaperones and proteases in quality control of proteins in the Escherichia coli cytosol. In DeltarpoH mutants, which lack the heat shock transcription factor and therefore have low levels of all major cytosolic proteases and chaperones except GroEL and trigger factor, 5-10% and 20-30% of total protein aggregated at 30 degrees C and 42 degrees C respectively. The aggregates contained 350-400 protein species, of which 93 were identified by mass spectrometry. The aggregated protein species were similar at both temperatures, indicating that thermolabile proteins require folding assistance by chaperones already at 30 degrees C, and showed strong overlap with previously identified DnaK substrates. Overproduction of the DnaK system, or low-level production of the DnaK system and ClpB, prevented aggregation and provided thermotolerance to DeltarpoH mutants, indicating key roles for these chaperones in protein quality control and stress survival. In rpoH+ cells, DnaK depletion did not lead to protein aggregation at 30 degrees C, which is probably the result of high levels of proteases and thus suggests that DnaK is not a prerequisite for proteolysis of misfolded proteins. Lon was the most efficient protease in degrading misfolded proteins in DnaK-depleted cells. At 42 degrees C, ClpXP and Lon became essential for viability of cells with low DnaK levels, indicating synergistic action of proteases and the DnaK system, which is essential for cell growth at 42 degrees C.
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Affiliation(s)
- T Tomoyasu
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, Hermann-Herder-Str. 7, D-79104 Freiburg, Germany
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18
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Sherman MY, Goldberg AL. Cellular defenses against unfolded proteins: a cell biologist thinks about neurodegenerative diseases. Neuron 2001; 29:15-32. [PMID: 11182078 DOI: 10.1016/s0896-6273(01)00177-5] [Citation(s) in RCA: 729] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- M Y Sherman
- Boston Biomedical Research Institute, 64 Grove Street, Watertown, MA 02472, USA.
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19
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Mayer MP, Rüdiger S, Bukau B. Molecular basis for interactions of the DnaK chaperone with substrates. Biol Chem 2000; 381:877-85. [PMID: 11076019 DOI: 10.1515/bc.2000.109] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Hsp70 chaperones assist a large variety of protein folding processes in the cell by transient association with short peptide segments of proteins. The substrate binding and release cycle is driven by the switching between the low affinity ATP bound state and the high affinity ADP bound state of Hsp70. Considerable progress has been made recently by the identification of in vivo substrates for the Escherichia coli homolog, DnaK, and the molecular mechanisms which govern the DnaK-substrate interactions. Here we review the processes that generate DnaK substrates in vivo and the properties of these substrates, and we describe insights gained from structural and kinetic analysis of DnaK-substrate interaction.
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Affiliation(s)
- M P Mayer
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, Germany
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20
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Affiliation(s)
- G Georgiou
- Department of Chemical Engineering, University of Texas, Austin 78712, USA
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21
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Kedzierska S, Staniszewska M, Potrykus J, Wegrzyn G. The effect of some antibiotic-resistance-conferring plasmids on the removal of the heat-aggregated proteins from Escherichia coli cells. FEMS Microbiol Lett 1999; 176:279-84. [PMID: 10427710 DOI: 10.1111/j.1574-6968.1999.tb13673.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We found that the presence of plasmids expressing tetracycline resistance or chloramphenicol resistance genes, but not those expressing ampicillin resistance or kanamycin resistance genes, in Escherichia coli led to the retardation of the process of removal of the heat-aggregated proteins (i.e. the S fraction) from the bacterial cells. The presence of chloramphenicol acetyltransferase in the S fraction is demonstrated. Moreover, we observed that the expression of T7 RNA polymerase gene had an influence on S fraction removal. These results suggest that high level production of some heterologous proteins which are accumulated in the cytoplasm, but not proteins exported through the cell membranes, may cause overloading of the S fraction and delay in the removal of heat-aggregated proteins from bacterial cells.
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Affiliation(s)
- S Kedzierska
- Department of Biochemistry, University of Gdańsk, Poland.
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22
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Kedzierska S, Staniszewska M, Wegrzyn A, Taylor A. The role of DnaK/DnaJ and GroEL/GroES systems in the removal of endogenous proteins aggregated by heat-shock from Escherichia coli cells. FEBS Lett 1999; 446:331-7. [PMID: 10100869 DOI: 10.1016/s0014-5793(99)00154-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The submission of Escherichia coli cells to heat-shock (45 degrees C, 15 min) caused the intracellular aggregation of endogenous proteins. In the wt cells the aggregates (the S fraction) disappeared 10 min after transfer to 37 degrees C. In contrast, the S fraction in the dnaK and dnaJ mutant strains was stable during approximately one generation time (45 min). This demonstrated that neither the renaturation nor the degradation of the denatured proteins was possible in the absence of DnaK and DnaJ. The groEL44 and groES619 mutations stabilised the aggregates to a lesser extent. It was shown by the use of cloned genes, dnaK/dnaJ or groEL/groES, producing the corresponding proteins in about 4-fold excess, that the appearance of the S fraction in the wt strain resulted from a transiently insufficient supply of the heat-shock proteins. Overproduction of the GroEL/GroES proteins in dnaK756 or dnaJ259 background prevented the aggregation, however, overproduction of the DnaK/DnaJ proteins did not prevent the aggregation in the groEL44 or groES619 mutant cells although it accelerated the disappearance of the aggregates. The properties of the aggregated proteins are discussed from the point of view of their competence to renaturation/degradation by the heat-shock system.
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Affiliation(s)
- S Kedzierska
- Department of Biochemistry, University of Gdańsk, Poland
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23
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Grallert H, Rutkat K, Buchner J. GroEL traps dimeric and monomeric unfolding intermediates of citrate synthase. J Biol Chem 1998; 273:33305-10. [PMID: 9837903 DOI: 10.1074/jbc.273.50.33305] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The prokaryotic molecular chaperone GroE is increasingly expressed under heat shock conditions. GroE protects cells by preventing the irreversible aggregation of thermally unfolding proteins. Here, the interaction of GroE with thermally unfolding citrate synthase (CS) was dissected into several steps that occur before irreversible aggregation, and the conformational states of the unfolding protein recognized by GroEL were determined. The kinetic analysis of CS unfolding revealed the formation of inactive dimeric and monomeric intermediates. GroEL binds both intermediates without affecting the unfolding pathway. Furthermore, the dimeric intermediates are not protected against dissociation in the presence of GroEL. Monomeric CS is stably associated with GroEL, thus preventing further irreversible unfolding steps and subsequent aggregation. During refolding, monomeric CS is encapsulated inside the cavity of GroEL. GroES complexes. Taken together our results suggest that for protection of cells against heat stress both the ability of GroEL to interact with a large variety of nonnative conformations of proteins and the active, GroES-dependent refolding of highly unfolded species are important.
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Affiliation(s)
- H Grallert
- Institut für Biophysik & Physikalische Biochemie, Universität Regensburg, 93040 Regensburg, Germany
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24
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Hesterkamp T, Bukau B. Role of the DnaK and HscA homologs of Hsp70 chaperones in protein folding in E.coli. EMBO J 1998; 17:4818-28. [PMID: 9707441 PMCID: PMC1170811 DOI: 10.1093/emboj/17.16.4818] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Folding of newly synthesized cytosolic proteins has been proposed to require assistance by Hsp70 chaperones. We investigated whether two Hsp70 homologs of Escherichia coli, DnaK and HscA, have this role in vivo. Double mutants lacking dnaK and hscA were viable and lacked defects in protein folding at intermediate temperature. After heat shock, a subpopulation of pre-existing proteins slowly aggregated in mutants lacking DnaK, but not HscA, whereas the bulk of newly synthesized proteins displayed wild-type solubility. For thermolabile firefly luciferase, DnaK was dispensable for de novo folding at 30 degrees C, but essential for aggregation prevention during heat shock and subsequent refolding. DnaK and HscA are thus not strictly essential for folding of newly synthesized proteins. DnaK instead has functions in refolding of misfolded proteins that are essential under stress.
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Affiliation(s)
- T Hesterkamp
- Institut für Biochemie und Molekularbiologie, Universität Freiburg, Hermann Herder Strasse 7, D-79104 Freiburg, Germany
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25
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Jaenicke R. Protein folding and association: in vitro studies for self-organization and targeting in the cell. CURRENT TOPICS IN CELLULAR REGULATION 1996; 34:209-314. [PMID: 8646849 DOI: 10.1016/s0070-2137(96)80008-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- R Jaenicke
- Institut für Biophysik und Physikalische Biochemie, Universität Regensburg, Germany
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26
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Jakob U, Lilie H, Meyer I, Buchner J. Transient interaction of Hsp90 with early unfolding intermediates of citrate synthase. Implications for heat shock in vivo. J Biol Chem 1995; 270:7288-94. [PMID: 7706269 DOI: 10.1074/jbc.270.13.7288] [Citation(s) in RCA: 283] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
At normal temperatures, Hsp90 is one of the most abundant proteins in the cytosol of various eucaryotic cells. Upon heat shock, the level of Hsp90 is increased even more, suggesting that it is important for helping cells to survive under these conditions. However, studies so far have been almost exclusively concerned with the function of Hsp90 under non-stress conditions, and therefore only little is known about the role of Hsp90 during heat shock. As a model for heat shock in vitro, we have monitored the inactivation and subsequent aggregation of dimeric citrate synthase (CS) at elevated temperatures. Hsp90 effectively "stabilized" CS under conditions where the enzyme is normally inactivated and finally aggregates very rapidly. A kinetic dissection of the unfolding pathway of CS succeeded in revealing two intermediates which form and subsequently undergo irreversible aggregation reactions. Hsp90 apparently interacts transiently with these highly structured early unfolding intermediates. Binding and subsequent release of the intermediates favorably influences the kinetic partitioning between two competing processes, the further unfolding of CS and the productive refolding to the native state. As a consequence, CS is effectively stabilized in the presence of Hsp90. The significance of this interaction is especially evident in the suppression of aggregation, the major end result of thermal unfolding events in vivo and in vitro. These effects, which are ATP-independent, seem to be a general function of members of the Hsp90 family, since yeast and bovine Hsp90 as well as the Hsp90 homologue from Escherichia coli gave similar results. It seems likely that this function also reflects the role of Hsp90 under heat shock conditions in vivo. We therefore propose that members of the Hsp90 family convey thermotolerance by transiently binding to highly structured early unfolding intermediates, thereby preventing their irreversible aggregation and stabilizing the active species.
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Affiliation(s)
- U Jakob
- Institut für Biophysik & Physikalische Biochemie, Universität Regensburg, Federal Republic of Germany
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27
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Gaitanaris GA, Vysokanov A, Hung SC, Gottesman ME, Gragerov A. Successive action of Escherichia coli chaperones in vivo. Mol Microbiol 1994; 14:861-9. [PMID: 7715448 DOI: 10.1111/j.1365-2958.1994.tb01322.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Escherichia coli DnaK, DnaJ and GrpE are required for renaturation of heat-inactivated lambda Cl857 repressor (Gaitanaris et al., 1990). Here we demonstrate that in addition to the above three proteins, GroEL and GroES are necessary for the Cl857 repressor to acquire full activity at the permissive temperature. Although full-length soluble repressor is present at normal amounts, the protein has reduced specific activity and migrates abnormally on native gels. To determine where the different chaperones act in protein folding, we identified their cellular locations. DnaK and DnaJ are associated with nascent polypeptide chains in translating ribosomes. In contrast, GroEL, although it is transiently associated with newly synthesized proteins, is absent from the ribosomes. This suggests that DnaK and DnaJ play an early role in protein maturation, whereas GroEL acts at a later stage.
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Affiliation(s)
- G A Gaitanaris
- Institute of Cancer Research, College of Physicians and Surgeons of Columbia University, New York, New York 10032
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28
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Gragerov A, Nudler E, Komissarova N, Gaitanaris GA, Gottesman ME, Nikiforov V. Cooperation of GroEL/GroES and DnaK/DnaJ heat shock proteins in preventing protein misfolding in Escherichia coli. Proc Natl Acad Sci U S A 1992; 89:10341-4. [PMID: 1359538 PMCID: PMC50334 DOI: 10.1073/pnas.89.21.10341] [Citation(s) in RCA: 165] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Newly synthesized proteins aggregate extensively in Escherichia coli rpoH mutants, which are deficient in the heat shock proteins (hsp). Overproduction of either GroEL and GroES or DnaK and DnaJ prevents aggregation. If expressed together, the four hsp are effective at physiological concentrations. Our data suggest that the GroEL and GroES proteins and the DnaK and DnaJ proteins have complementary functions in the folding and assembly of most proteins.
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Affiliation(s)
- A Gragerov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow
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Abstract
It is becoming increasingly evident that intermediates observed in protein folding in vitro may be closely related to conformational states that are important in various intracellular processes. This review focuses on recent advances in in vitro protein-folding studies with particular reference to the molten globule state, which is purported to be a common and distinct intermediate of protein folding.
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Affiliation(s)
- K Kuwajima
- Department of Physics, Faculty of Science, University of Tokyo, Japan
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