1
|
Singh A, Rief M, Žoldák G. Direct observation of chemo-mechanical coupling in DnaK by single-molecule force experiments. Biophys J 2022; 121:4729-4739. [PMID: 36196054 PMCID: PMC9748191 DOI: 10.1016/j.bpj.2022.09.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/16/2022] [Accepted: 09/29/2022] [Indexed: 12/15/2022] Open
Abstract
Protein allostery requires a communication channel for functional regulation between distal sites within a protein. In the molecular chaperone Hsp70, a two-domain enzyme, the ATP/ADP status of an N-terminal nucleotide-binding domain regulates the substrate affinity of a C-terminal substrate-binding domain. Recently available three-dimensional structures of Hsp70 in ATP/ADP states have provided deep insights into molecular pathways of allosteric signals. However, direct mechanical probing of long-range allosteric coupling between the ATP hydrolysis step and domain states is missing. Using laser optical tweezers, we examined the mechanical properties of a truncated two-domain DnaK(1-552ye) in apo/ADP/ATP- and peptide-bound states. We find that in the apo and ADP states, DnaK domains are mechanically stable and rigid. However, in the ATP state, substrate-binding domain (SBD)∗ye is mechanically destabilized as the result of interdomain docking followed by the unfolding of the α-helical lid. By observing the folding state of the SBD, we could observe the continuous ATP/ADP cycling of the enzyme in real time with a single molecule. The SBD lid closure is strictly coupled to the chemical steps of the ATP hydrolysis cycle even in the presence of peptide substrate.
Collapse
Affiliation(s)
- Anubhuti Singh
- Center for Functional Protein Assemblies (CPA), Physik Department, Technische Universität München, Garching, Germany
| | - Matthias Rief
- Center for Functional Protein Assemblies (CPA), Physik Department, Technische Universität München, Garching, Germany.
| | - Gabriel Žoldák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P. J. Šafárik University, Košice, Slovakia; Center for Interdisciplinary Biosciences, Cassovia New Industry Cluster (CNIC), Trieda SNP 1, 040 11, Košice, Slovakia.
| |
Collapse
|
2
|
Differential expression of gut protein genes and population density of Arsenophonus contributes to sex-biased transmission of Bemisia tabaci vectored Cotton leaf curl virus. PLoS One 2021; 16:e0259374. [PMID: 34843507 PMCID: PMC8629229 DOI: 10.1371/journal.pone.0259374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/18/2021] [Indexed: 11/19/2022] Open
Abstract
Whitefly, Bemisia tabaci (Gennadius) is an important pest of cotton causing direct damage as sap feeder and vector of Cotton leaf curl virus (CLCuV). Previous few studies suggest that female whiteflies are more efficient vector of begomovirusthan males, however the sex-biased transmission efficiency is still not clearly understood. Present studies with B. tabaci AsiaII-1 haplotype showed higher virus transmission efficiency of females compared to males. This variable begomovirus transmission efficiency has been related to previously identifiedkey factors associated with B. tabaci. The higher density of endosymbiont Arsenophonus and variable expression of some midgut proteins genes i.e. Cyclophilin, Knottin, Hsp40, Hsp70 may be possibly imparting higher vector competency to the females compared to males. The present studies suggest low abundance of Arsenophonus spp. as well as lower expressionof Cyclophilin genein males as compared to females. This is further supplemented by overexpression of Knottin, Hsp40, and Hsp70 genes in males compared to females and thus collectively all these factors might be playing a key role in low virus transmission efficiency of males. The relative density of Arsenophonus spp. and expression of midgut proteins genes in male and female whitefly first time enriches our understanding about sex-biased transmission efficiency of begomovirus.
Collapse
|
3
|
Gundersen CB. Cysteine string proteins. Prog Neurobiol 2020; 188:101758. [DOI: 10.1016/j.pneurobio.2020.101758] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 01/06/2020] [Accepted: 01/13/2020] [Indexed: 12/17/2022]
|
4
|
Kaur R, Gupta M, Singh S, Joshi N, Sharma A. Enhancing RNAi Efficiency to Decipher the Functional Response of Potential Genes in Bemisia tabaci AsiaII-1 (Gennadius) Through dsRNA Feeding Assays. Front Physiol 2020; 11:123. [PMID: 32194431 PMCID: PMC7061899 DOI: 10.3389/fphys.2020.00123] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/03/2020] [Indexed: 01/09/2023] Open
Abstract
Whitefly Bemisia tabaci is a global invasive pest that causes substantial losses to agricultural crops worldwide either by direct feeding or vectoring numerous plant viruses. Management with insecticides remains a big challenge due to its rapid resistance development potential as well as the impact of these chemicals on non-target organisms. Thus, in search of alternate and novel pest management strategies RNA interference (RNAi) has come up as potential future tool in this direction. The present study targets nine potential genes (Aquaporin (AQP), Calcitonin (CAL), CyclophilinB (CYCP), Knottin-1 (k-1), Heat shock proteins (Hsp20, Hsp40 and Hsp70), SWItch/Sucrose Non-fermentable (SNF7) and inhibitor of apoptosis (IAP) of whitefly that have been implicated to play a role in various vital physiological functions and virus transmission. The RNAi mediated knockdown efficiency of these genes has been improved through the conjugation of respective target gene dsRNA with CQD (carbon quantum dots) nanoparticles or simultaneous knockdown of dsRNA specific gut nucleases. The studies revealed that feeding of dsRNA (40 μg/ml sucrose diet) of the target gene(s) either conjugated with CQD or along with dsRNA against dsRNase (dsdsRNase) (40 μg/ml sucrose diet) enhanced the RNAi efficiency by 24-89% compared to whiteflies fed with naked dsRNA of the same target gene. The studies provide insights about the functional role of various genes in whitefly, which can possibly be exploited for the management of this pest in the future.
Collapse
Affiliation(s)
- Ramandeep Kaur
- Department of Microbiology, Punjab Agricultural University, Ludhiana, India
| | - Mridula Gupta
- Regional Research Station, Punjab Agricultural University, Faridkot, India
| | - Satnam Singh
- Regional Research Station, Punjab Agricultural University, Faridkot, India
| | - Neelam Joshi
- Department of Entomology, Punjab Agricultural University, Ludhiana, India
| | - Abhishek Sharma
- Department of Vegetable Sciences, Punjab Agricultural University, Ludhiana, India
| |
Collapse
|
5
|
Mukherjee M, Sabir S, O'Regan L, Sampson J, Richards MW, Huguenin-Dezot N, Ault JR, Chin JW, Zhuravleva A, Fry AM, Bayliss R. Mitotic phosphorylation regulates Hsp72 spindle localization by uncoupling ATP binding from substrate release. Sci Signal 2018; 11:11/543/eaao2464. [PMID: 30108182 DOI: 10.1126/scisignal.aao2464] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Hsp72 is a member of the 70-kDa heat shock family of molecular chaperones (Hsp70s) that comprise a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD) connected by a linker that couples the exchange of adenosine diphosphate (ADP) for adenosine triphosphate (ATP) with the release of the protein substrate. Mitotic phosphorylation of Hsp72 by the kinase NEK6 at Thr66 located in the NBD promotes the localization of Hsp72 to the mitotic spindle and is required for efficient spindle assembly and chromosome congression and segregation. We determined the crystal structure of the Hsp72 NBD containing a genetically encoded phosphoserine at position 66. This revealed structural changes that stabilized interactions between subdomains within the NBD. ATP binding to the NBD of unmodified Hsp72 resulted in the release of substrate from the SBD, but phosphorylated Hsp72 retained substrate in the presence of ATP. Mutations that prevented phosphorylation-dependent subdomain interactions restored the connection between ATP binding and substrate release. Thus, phosphorylation of Thr66 is a reversible mechanism that decouples the allosteric connection between nucleotide binding and substrate release, providing further insight into the regulation of the Hsp70 family. We propose that phosphorylation of Hsp72 on Thr66 by NEK6 during mitosis promotes its localization to the spindle by stabilizing its interactions with components of the mitotic spindle.
Collapse
Affiliation(s)
- Manjeet Mukherjee
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Sarah Sabir
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Laura O'Regan
- Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Josephina Sampson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Mark W Richards
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Nicolas Huguenin-Dezot
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - James R Ault
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Anastasia Zhuravleva
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Andrew M Fry
- Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Richard Bayliss
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| |
Collapse
|
6
|
Sekhar A, Velyvis A, Zoltsman G, Rosenzweig R, Bouvignies G, Kay LE. Conserved conformational selection mechanism of Hsp70 chaperone-substrate interactions. eLife 2018; 7:32764. [PMID: 29460778 PMCID: PMC5819949 DOI: 10.7554/elife.32764] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/27/2017] [Indexed: 12/17/2022] Open
Abstract
Molecular recognition is integral to biological function and frequently involves preferred binding of a molecule to one of several exchanging ligand conformations in solution. In such a process the bound structure can be selected from the ensemble of interconverting ligands a priori (conformational selection, CS) or may form once the ligand is bound (induced fit, IF). Here we focus on the ubiquitous and conserved Hsp70 chaperone which oversees the integrity of the cellular proteome through its ATP-dependent interaction with client proteins. We directly quantify the flux along CS and IF pathways using solution NMR spectroscopy that exploits a methyl TROSY effect and selective isotope-labeling methodologies. Our measurements establish that both bacterial and human Hsp70 chaperones interact with clients by selecting the unfolded state from a pre-existing array of interconverting structures, suggesting a conserved mode of client recognition among Hsp70s and highlighting the importance of molecular dynamics in this recognition event. Proteins are the workhorses of a cell and are involved in almost all biological processes. Newly made proteins need to ‘fold’ into precise three-dimensional shapes in order to carry out their roles. However, proteins sometimes fold incorrectly or unfold. These protein forms are not able to work effectively and in some cases may even cause diseases. Chaperone proteins help other proteins to fold correctly and are found in living organisms ranging in complexity from bacteria to humans. There are many different types of chaperones that play different roles inside cells. One, called Hsp70, binds to proteins that are incorrectly folded to help them to mature into their correct structures. However, it was not clear whether Hsp70 can also associate with the mature, correctly folded form of the proteins. A technique called Nuclear Magnetic Resonance (NMR) spectroscopy can distinguish between mature, unfolded and chaperone-bound forms of the same protein. Sekhar et al. therefore used NMR to investigate which forms of a protein Hsp70 binds to. This revealed that both the bacterial and human versions of the Hsp70 chaperone interact only with unfolded proteins. The results presented by Sekhar et al. also explain why Hsp70 does not disrupt the routine workings of the cell: because it does not bind to mature forms of proteins. These observations extend our understanding of how chaperones assist in folding proteins, and fit into a broader research theme exploring how proteins recognize one another. It will now be interesting to see whether the same mechanism holds for more complex forms of proteins, such as aggregates, or larger protein structures with regions of both folded and unfolded elements.
Collapse
Affiliation(s)
- Ashok Sekhar
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Chemistry, University of Toronto, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Algirdas Velyvis
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Chemistry, University of Toronto, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Guy Zoltsman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rina Rosenzweig
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Chemistry, University of Toronto, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Canada.,Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Guillaume Bouvignies
- Laboratoire des Biomolécules, Département de chimie, École normale supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, Paris, France.,Sorbonne Universités, UPMC Univ. Paris 06, École normale supérieure, CNRS, Laboratoire des Biomolécules, Paris, France
| | - Lewis E Kay
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Chemistry, University of Toronto, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Canada.,Hospital for Sick Children, Program in Molecular Medicine, University Avenue, Toronto, Canada
| |
Collapse
|
7
|
Bascos NAD, Mayer MP, Bukau B, Landry SJ. The Hsp40 J-domain modulates Hsp70 conformation and ATPase activity with a semi-elliptical spring. Protein Sci 2017; 26:1838-1851. [PMID: 28685898 DOI: 10.1002/pro.3223] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 06/22/2017] [Accepted: 06/29/2017] [Indexed: 11/12/2022]
Abstract
Regulatory protein interactions are commonly attributed to lock-and-key associations that bring interacting domains together. However, studies in some systems suggest that regulation is not achieved by binding interactions alone. We report our investigations on specific physical characteristics required of the Hsp40 J-domain to stimulate ATP hydrolysis in the Hsp40-Hsp70 molecular chaperone machine. Biophysical analysis using isothermal titration calorimetry, and nuclear magnetic resonance spectroscopy reveals the importance of helix rigidity for the maintenance of Hsp40 function. Our results suggest that the functional J-domain acts like a semi-elliptical spring, wherein the resistance to bending upon binding to the Hsp70 ATPase modulates the ATPase domain conformational change and promotes ATP hydrolysis.
Collapse
Affiliation(s)
- Neil Andrew D Bascos
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, 70112
| | - Matthias P Mayer
- Center for Molecular Biology of the University of Heidelberg (ZMBH), Im Neuenheimer Feld 282, Heidelberg, 69120, Germany
| | - Bernd Bukau
- Center for Molecular Biology of the University of Heidelberg (ZMBH), Im Neuenheimer Feld 282, Heidelberg, 69120, Germany
| | - Samuel J Landry
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, 70112
| |
Collapse
|
8
|
Tryptophan Codon-Dependent Transcription in Chlamydia pneumoniae during Gamma Interferon-Mediated Tryptophan Limitation. Infect Immun 2016; 84:2703-13. [PMID: 27400720 DOI: 10.1128/iai.00377-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/05/2016] [Indexed: 12/16/2022] Open
Abstract
In evolving to an obligate intracellular niche, Chlamydia has streamlined its genome by eliminating superfluous genes as it relies on the host cell for a variety of nutritional needs like amino acids. However, Chlamydia can experience amino acid starvation when the human host cell in which the bacteria reside is exposed to interferon gamma (IFN-γ), which leads to a tryptophan (Trp)-limiting environment via induction of the enzyme indoleamine-2,3-dioxygenase (IDO). The stringent response is used to respond to amino acid starvation in most bacteria but is missing from Chlamydia Thus, how Chlamydia, a Trp auxotroph, responds to Trp starvation in the absence of a stringent response is an intriguing question. We previously observed that C. pneumoniae responds to this stress by globally increasing transcription while globally decreasing translation, an unusual response. Here, we sought to understand this and hypothesized that the Trp codon content of a given gene would determine its transcription level. We quantified transcripts from C. pneumoniae genes that were either rich or poor in Trp codons and found that Trp codon-rich transcripts were increased, whereas those that lacked Trp codons were unchanged or even decreased. There were exceptions, and these involved operons or large genes with multiple Trp codons: downstream transcripts were less abundant after Trp codon-rich sequences. These data suggest that ribosome stalling on Trp codons causes a negative polar effect on downstream sequences. Finally, reassessing previous C. pneumoniae microarray data based on codon content, we found that upregulated transcripts were enriched in Trp codons, thus supporting our hypothesis.
Collapse
|
9
|
Ajit Tamadaddi C, Sahi C. J domain independent functions of J proteins. Cell Stress Chaperones 2016; 21:563-70. [PMID: 27145962 PMCID: PMC4908003 DOI: 10.1007/s12192-016-0697-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/04/2016] [Accepted: 04/25/2016] [Indexed: 01/19/2023] Open
Abstract
Heat shock proteins of 40 kDa (Hsp40s), also called J proteins, are obligate partners of Hsp70s. Via their highly conserved and functionally critical J domain, J proteins interact and modulate the activity of their Hsp70 partners. Mutations in the critical residues in the J domain often result in the null phenotype for the J protein in question. However, as more J proteins have been characterized, it is becoming increasingly clear that a significant number of J proteins do not "completely" rely on their J domains to carry out their cellular functions, as previously thought. In some cases, regions outside the highly conserved J domain have become more important making the J domain dispensable for some, if not for all functions of a J protein. This has profound effects on the evolution of such J proteins. Here we present selected examples of J proteins that perform J domain independent functions and discuss this in the context of evolution of J proteins with dispensable J domains and J-like proteins in eukaryotes.
Collapse
Affiliation(s)
- Chetana Ajit Tamadaddi
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Chandan Sahi
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.
| |
Collapse
|
10
|
Overproduction and biophysical characterization of human HSP70 proteins. Protein Expr Purif 2014; 106:57-65. [PMID: 25266791 DOI: 10.1016/j.pep.2014.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/16/2014] [Accepted: 09/18/2014] [Indexed: 11/20/2022]
Abstract
Heat shock proteins (HSP) perform vital cellular functions and modulate cell response pathways to physical and chemical stressors. A key feature of HSP function is the ability to interact with a broad array of protein binding partners as a means to potentiate downstream response pathways or facilitate protein folding. These binding interactions are driven by ATP-dependent conformational rearrangements in HSP proteins. The HSP70 family is evolutionarily conserved and is associated with diabetes and cancer progression and the etiopathogenesis of hepatic, cardiovascular, and neurological disorders in humans. However, functional characterization of human HSP70s has been stymied by difficulties in obtaining large quantities of purified protein. Studies of purified human HSP70 proteins are essential for downstream investigations of protein-protein interactions and in the rational design of novel family-specific therapeutics. Within this work, we present optimized protocols for the heterologous overexpression and purification of either the nucleotide binding domain (NBD) or the nucleotide and substrate binding domains of human HSPA9, HSPA8, and HSPA5 in either Escherichia coli or Saccharomyces cerevisiae. We also include initial biophysical characterization of HSPA9 and HSPA8. This work provides the basis for future biochemical studies of human HSP70 protein function and structure.
Collapse
|
11
|
Samaddar M, Goswami AV, Purushotham J, Hegde P, D'Silva P. Role of the loop L4,5 in allosteric regulation in mtHsp70s: in vivo significance of domain communication and its implications in protein translocation. Mol Biol Cell 2014; 25:2129-42. [PMID: 24829379 PMCID: PMC4091826 DOI: 10.1091/mbc.e14-03-0821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The SBD loop L4,5 in mtHsp70s functions synergistically with the linker region to maintain the interdomain interface governing protein translocation and mitochondrial biogenesis. Intragenic suppressors of a communication-impaired L4,5 mutant reveal molecular insights into the allosteric regulation of mtHsp70s at the in vivo level. Mitochondrial Hsp70 (mtHsp70) is essential for a vast repertoire of functions, including protein import, and requires effective interdomain communication for efficient partner-protein interactions. However, the in vivo functional significance of allosteric regulation in eukaryotes is poorly defined. Using integrated biochemical and yeast genetic approaches, we provide compelling evidence that a conserved substrate-binding domain (SBD) loop, L4,5, plays a critical role in allosteric communication governing mtHsp70 chaperone functions across species. In yeast, a temperature-sensitive L4,5 mutation (E467A) disrupts bidirectional domain communication, leading to compromised protein import and mitochondrial function. Loop L4,5 functions synergistically with the linker in modulating the allosteric interface and conformational transitions between SBD and the nucleotide-binding domain (NBD), thus regulating interdomain communication. Second-site intragenic suppressors of E467A isolated within the SBD suppress domain communication defects by conformationally altering the allosteric interface, thereby restoring import and growth phenotypes. Strikingly, the suppressor mutations highlight that restoration of communication from NBD to SBD alone is the minimum essential requirement for effective in vivo function when primed at higher basal ATPase activity, mimicking the J-protein–bound state. Together these findings provide the first mechanistic insights into critical regions within the SBD of mtHsp70s regulating interdomain communication, thus highlighting its importance in protein translocation and mitochondrial biogenesis.
Collapse
Affiliation(s)
- Madhuja Samaddar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | | | - Jaya Purushotham
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Pushpa Hegde
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Patrick D'Silva
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|
12
|
General IJ, Liu Y, Blackburn ME, Mao W, Gierasch LM, Bahar I. ATPase subdomain IA is a mediator of interdomain allostery in Hsp70 molecular chaperones. PLoS Comput Biol 2014; 10:e1003624. [PMID: 24831085 PMCID: PMC4022485 DOI: 10.1371/journal.pcbi.1003624] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 03/31/2014] [Indexed: 11/18/2022] Open
Abstract
The versatile functions of the heat shock protein 70 (Hsp70) family of molecular chaperones rely on allosteric interactions between their nucleotide-binding and substrate-binding domains, NBD and SBD. Understanding the mechanism of interdomain allostery is essential to rational design of Hsp70 modulators. Yet, despite significant progress in recent years, how the two Hsp70 domains regulate each other's activity remains elusive. Covariance data from experiments and computations emerged in recent years as valuable sources of information towards gaining insights into the molecular events that mediate allostery. In the present study, conservation and covariance properties derived from both sequence and structural dynamics data are integrated with results from Perturbation Response Scanning and in vivo functional assays, so as to establish the dynamical basis of interdomain signal transduction in Hsp70s. Our study highlights the critical roles of SBD residues D481 and T417 in mediating the coupled motions of the two domains, as well as that of G506 in enabling the movements of the α-helical lid with respect to the β-sandwich. It also draws attention to the distinctive role of the NBD subdomains: Subdomain IA acts as a key mediator of signal transduction between the ATP- and substrate-binding sites, this function being achieved by a cascade of interactions predominantly involving conserved residues such as V139, D148, R167 and K155. Subdomain IIA, on the other hand, is distinguished by strong coevolutionary signals (with the SBD) exhibited by a series of residues (D211, E217, L219, T383) implicated in DnaJ recognition. The occurrence of coevolving residues at the DnaJ recognition region parallels the behavior recently observed at the nucleotide-exchange-factor recognition region of subdomain IIB. These findings suggest that Hsp70 tends to adapt to co-chaperone recognition and activity via coevolving residues, whereas interdomain allostery, critical to chaperoning, is robustly enabled by conserved interactions.
Collapse
Affiliation(s)
- Ignacio J. General
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ying Liu
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Mandy E. Blackburn
- Department of Biochemistry & Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
| | - Wenzhi Mao
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Pharmacology, Tsinghua University, Beijing, China
| | - Lila M. Gierasch
- Department of Biochemistry & Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
13
|
Tiroli-Cepeda AO, Lima TB, Balbuena TS, Gozzo FC, Ramos CHI. Structural and functional characterization of the chaperone Hsp70 from sugarcane. Insights into conformational changes during cycling from cross-linking/mass spectrometry assays. J Proteomics 2014; 104:48-56. [PMID: 24530624 DOI: 10.1016/j.jprot.2014.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 01/28/2014] [Accepted: 02/02/2014] [Indexed: 01/20/2023]
Abstract
UNLABELLED Hsp70 cycles from an ATP-bound state, in which the affinity for unfolded polypeptides is low, to an ADP-bound state, in which the affinity for unfolded polypeptides is high, to assist with cell proteostasis. Such cycling also depends on co-chaperones because these proteins control both the Hsp70 ATPase activity and the delivery of unfolded polypeptide chains. Although it is very important, structural information on the entire protein is still scarce. This work describes the first cloning of a cDNA predicted to code for a cytosolic Saccharum spp. (sugarcane) Hsp70, named SsHsp70 here, the purification of the recombinant protein and the characterization of its structural conformation in solution by chemical cross-linking coupled to mass spectrometry. The in vivo expression of SsHsp70 in sugarcane extracts was confirmed by Western blot. Recombinant SsHsp70 was monomeric, both ADP and ATP binding increased its stability and it was efficient in cooperating with co-chaperones: ATPase activity was stimulated by Hsp40s, and it aided the refolding of an unfolded polypeptide delivered by a member of the small Hsp family. The structural conformation results favor a model in which nucleotide-free SsHsp70 is highly dynamic and may fluctuate among different conformations that may resemble those in which nucleotide is bound. BIOLOGICAL SIGNIFICANCE Validation of a sugarcane EST as a true mRNA that encodes a cytosolic Hsp70 (SsHsp70) as confirmed by in vivo expression and characterization of the structure and function of the recombinant protein. SsHsp70 was monomeric, both ADP and ATP binding increased its stability and was efficient in interacting and cooperating with co-chaperones to enhance ATPase activity and refold unfolded proteins. The conformation of nucleotide-free SsHsp70 in solution was much more dynamic than suggested by crystal structures of other Hsp70s. This article is part of a Special Issue entitled: Environmental and structural proteomics.
Collapse
Affiliation(s)
- Ana O Tiroli-Cepeda
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil; Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagem, Brazil
| | - Tatiani B Lima
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil
| | - Tiago S Balbuena
- Faculdade de Ciências Agrárias e Veterinárias, UNESP Universidade Estadual Paulista, Campus de Jaboticabal, Jaboticabal, SP 14884-900, Brazil
| | - Fábio C Gozzo
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil
| | - Carlos H I Ramos
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil; Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagem, Brazil.
| |
Collapse
|
14
|
Stricher F, Macri C, Ruff M, Muller S. HSPA8/HSC70 chaperone protein: structure, function, and chemical targeting. Autophagy 2013; 9:1937-54. [PMID: 24121476 DOI: 10.4161/auto.26448] [Citation(s) in RCA: 260] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
HSPA8/HSC70 protein is a fascinating chaperone protein. It represents a constitutively expressed, cognate protein of the HSP70 family, which is central in many cellular processes. In particular, its regulatory role in autophagy is decisive. We focused this review on HSC70 structure-function considerations and based on this, we put a particular emphasis on HSC70 targeting by small molecules and peptides in order to develop intervention strategies that deviate some of HSC70 properties for therapeutic purposes. Generating active biomolecules regulating autophagy via its effect on HSC70 can effectively be designed only if we understand the fine relationships between HSC70 structure and functions.
Collapse
Affiliation(s)
- François Stricher
- CNRS; Institut de Biologie Moléculaire et Cellulaire; Immunopathologie et Chimie Thérapeutique/Laboratory of Excellence Medalis; Strasbourg, France
| | | | | | | |
Collapse
|
15
|
Buck TM, Plavchak L, Roy A, Donnelly BF, Kashlan OB, Kleyman TR, Subramanya AR, Brodsky JL. The Lhs1/GRP170 chaperones facilitate the endoplasmic reticulum-associated degradation of the epithelial sodium channel. J Biol Chem 2013; 288:18366-80. [PMID: 23645669 DOI: 10.1074/jbc.m113.469882] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The epithelial sodium channel, ENaC, plays a critical role in maintaining salt and water homeostasis, and not surprisingly defects in ENaC function are associated with disease. Like many other membrane-spanning proteins, this trimeric protein complex folds and assembles inefficiently in the endoplasmic reticulum (ER), which results in a substantial percentage of the channel being targeted for ER-associated degradation (ERAD). Because the spectrum of factors that facilitates the degradation of ENaC is incomplete, we developed yeast expression systems for each ENaC subunit. We discovered that a conserved Hsp70-like chaperone, Lhs1, is required for maximal turnover of the ENaC α subunit. By expressing Lhs1 ATP binding mutants, we also found that the nucleotide exchange properties of this chaperone are dispensable for ENaC degradation. Consistent with the precipitation of an Lhs1-αENaC complex, Lhs1 holdase activity was instead most likely required to support the ERAD of αENaC. Moreover, a complex containing the mammalian Lhs1 homolog GRP170 and αENaC co-precipitated, and GRP170 also facilitated ENaC degradation in human, HEK293 cells, and in a Xenopus oocyte expression system. In both yeast and higher cell types, the effect of Lhs1 on the ERAD of αENaC was selective for the unglycosylated form of the protein. These data establish the first evidence that Lhs1/Grp170 chaperones can act as mediators of ERAD substrate selection.
Collapse
Affiliation(s)
- Teresa M Buck
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Introduction of a unique tryptophan residue into various positions of Bacillus licheniformis DnaK. Int J Biol Macromol 2012; 52:231-43. [PMID: 23085489 DOI: 10.1016/j.ijbiomac.2012.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/08/2012] [Accepted: 10/10/2012] [Indexed: 11/22/2022]
Abstract
Site-directed mutagenesis together with biochemical and biophysical techniques were used to probe effects of single-tryptophan-incorporated mutations on a bacterial molecular chaperone, Bacillus licheniformis DnaK (BlDnaK). Specifically, five phenylalanine residues (Phe(120), Phe(174), Phe(186), Phe(378) and Phe(396)) of BlDnaK were individually replaced by single tryptophans, thus creating site-specific probes for the fluorescence analysis of the protein. The steady-state ATPase activity for BlDnaK, F120W, F174W, F186W, F378W, and F396W was determined to be 76.01, 52.82, 25.32, 53.31, 58.84, and 47.53 nmol Pi/min/mg, respectively. Complementation test revealed that the single mutation at codons 120, 186, and 378 of the dnaK gene still allowed an Escherichia coli dnaK756-Ts strain to grow at a stringent temperature of 44°C. Simultaneous addition of co-chaperones and NR-peptide did not synergistically stimulate the ATPase activity of F174W and F396W, and these two proteins were unable to assist the refolding of GdnHCl-denatured luciferase. The heat-induced denaturation of all variants could be fitted adequately to a three-state model, in agreement with the observation for the wild-type protein. By CD spectral analysis, GdnHCl-induced unfolding transition for BlDnaK was 1.51 M corresponding to ΔG(N-U) of 1.69 kcal/mol; however, the transitions for mutant proteins were 1.07-1.55 M equivalent to ΔG(N-U) of 0.94-2.93 kcal/mol. The emission maximum of single-tryptophan-incorporated variants was in the range of 333.2-335.8 nm. Acrylamide quenching analysis showed that the mutant proteins had a dynamic quenching constant of 3.0-4.2 M(-1). Taken together, these results suggest that the molecular properties of BlDnaK have been significantly changed upon the individual replacement of selected phenylalanine residues by tryptophan.
Collapse
|
17
|
Jiao L, Fan M, Hua C, Wang S, Wei X. Expression of DnaJ Gene in Alicyclobacillus acidoterrestris under Stress Conditions by Quantitative Real-Time PCR. J Food Sci 2012; 77:M446-51. [DOI: 10.1111/j.1750-3841.2012.02790.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
18
|
Sun L, Edelmann FT, Kaiser CJO, Papsdorf K, Gaiser AM, Richter K. The lid domain of Caenorhabditis elegans Hsc70 influences ATP turnover, cofactor binding and protein folding activity. PLoS One 2012; 7:e33980. [PMID: 22479492 PMCID: PMC3315512 DOI: 10.1371/journal.pone.0033980] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 02/20/2012] [Indexed: 12/27/2022] Open
Abstract
Hsc70 is a conserved ATP-dependent molecular chaperone, which utilizes the energy of ATP hydrolysis to alter the folding state of its client proteins. In contrast to the Hsc70 systems of bacteria, yeast and humans, the Hsc70 system of C. elegans (CeHsc70) has not been studied to date. We find that CeHsc70 is characterized by a high ATP turnover rate and limited by post-hydrolysis nucleotide exchange. This rate-limiting step is defined by the helical lid domain at the C-terminus. A certain truncation in this domain (CeHsc70-Δ545) reduces the turnover rate and renders the hydrolysis step rate-limiting. The helical lid domain also affects cofactor affinities as the lidless mutant CeHsc70-Δ512 binds more strongly to DNJ-13, forming large protein complexes in the presence of ATP. Despite preserving the ability to hydrolyze ATP and interact with its cofactors DNJ-13 and BAG-1, the truncation of the helical lid domain leads to the loss of all protein folding activity, highlighting the requirement of this domain for the functionality of the nematode's Hsc70 protein.
Collapse
Affiliation(s)
| | | | | | | | | | - Klaus Richter
- Center for Integrated Protein Science Munich (CIPSM) and Department Chemie, Technische Universität München, Garching, Germany
- * E-mail:
| |
Collapse
|
19
|
Interactions Between Rnase L Ankyrin-Like Domain and ABC Transporters as a Possible Origin for Pain, Ion Transport, CNS and Immune Disorders of Chronic Fatigue Immune Dysfunction Syndrome. ACTA ACUST UNITED AC 2011. [DOI: 10.1300/j092v08n03_08] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
20
|
Clerico EM, Zhuravleva A, Smock RG, Gierasch LM. Segmental isotopic labeling of the Hsp70 molecular chaperone DnaK using expressed protein ligation. Biopolymers 2011; 94:742-52. [PMID: 20564022 DOI: 10.1002/bip.21426] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Introducing biophysical labels into specific regions of large and dynamic multidomain proteins greatly facilitates mechanistic analysis. Ligation of expressed domains that are labeled in a desired manner before assembly of the intact molecular machine provides such a strategy. We have elaborated an experimental route using expressed protein ligation (EPL) to create an Hsp70 molecular chaperone (the E. coli Hsp70, DnaK) where only one of the two constituent domains was labeled, in this case with NMR active isotopes, allowing visualization of the single domain in the context of the two domain protein. Several technical obstacles were overcome, including choice of site for ligation with retention of function, optimization of ligation yield, and purification from unreacted domains. Ligated semilabeled DnaK was successfully produced with a Cys residue at position 383, and the ligated product harboring the Cys mutation was confirmed to be functional and identical to an expressed Cys-containing two-domain construct. The NMR spectrum of the segmentally labeled protein was considerably simplified, enabling unequivocal assignment and enhanced analysis of dynamics, as a prelude to exploring the energy landscape for allostery in the Hsp70 family.
Collapse
Affiliation(s)
- Eugenia M Clerico
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst 01003, MA
| | | | | | | |
Collapse
|
21
|
Inserte J, Ruiz-Meana M, Rodríguez-Sinovas A, Barba I, Garcia-Dorado D. Contribution of delayed intracellular pH recovery to ischemic postconditioning protection. Antioxid Redox Signal 2011; 14:923-39. [PMID: 20578958 DOI: 10.1089/ars.2010.3312] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Ischemic postconditioning (PoCo) has been proven to be a feasible approach to attenuate reperfusion injury and enhance myocardial salvage in patients with acute myocardial infarction, but its mechanisms have not been completely elucidated yet. Recent studies demonstrate that PoCo may delay the recovery of intracellular pH during initial reperfusion, and that its ability to limit infarct size critically depends on this effect. Prolongation of postischemic intracellular acidosis inhibits hypercontracture, mitochondrial permeability transition, calpain-mediated proteolysis, and gap junction-mediated spread of injury during the first minutes of reflow. This role of prolonged acidosis does not exclude the participation of other pathways in PoCo-induced cardioprotection. On the contrary, it may allow these pathways to act by preventing immediate reperfusion-induced cell death. Moreover, the existence of interactions between intracellular acidosis and endogenous protection signaling cannot be excluded and needs to be investigated. The role of prolonged acidosis in PoCo cardioprotection has important implications in the design of optimal PoCo protocols and in the translation of cardioprotective strategies to patients with on-going myocardial infarction receiving coronary reperfusion.
Collapse
Affiliation(s)
- Javier Inserte
- Department of Cardiology, Vall d'Hebron University Hospital and Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | | | | | | |
Collapse
|
22
|
Endoplasmic reticulum associated protein degradation: a chaperone assisted journey to hell. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1803:694-705. [PMID: 20219571 DOI: 10.1016/j.bbamcr.2010.02.005] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Revised: 02/11/2010] [Accepted: 02/18/2010] [Indexed: 01/16/2023]
Abstract
Recognition and elimination of misfolded proteins are essential cellular processes. More than thirty percent of the cellular proteins are proteins of the secretory pathway. They fold in the lumen or membrane of the endoplasmic reticulum from where they are sorted to their site of action. The folding process, as well as any refolding after cell stress, depends on chaperone activity. In case proteins are unable to acquire their native conformation, chaperones with different substrate specificity and activity guide them to elimination. For most misfolded proteins of the endoplasmic reticulum this requires retro-translocation to the cytosol and polyubiquitylation of the misfolded protein by an endoplasmic reticulum associated machinery. Thereafter ubiquitylated proteins are guided to the proteasome for degradation. This review summarizes our up to date knowledge of chaperone classes and chaperone function in endoplasmic reticulum associated degradation of protein waste.
Collapse
|
23
|
del Castillo U, Fernández-Higuero JA, Pérez-Acebrón S, Moro F, Muga A. Nucleotide utilization requirements that render ClpB active as a chaperone. FEBS Lett 2010; 584:929-34. [PMID: 20085762 DOI: 10.1016/j.febslet.2010.01.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2009] [Revised: 12/28/2009] [Accepted: 01/12/2010] [Indexed: 11/26/2022]
Abstract
ClpB is a member of the AAA+ superfamily that forms a ring-shaped homohexamer. Each protomer contains two nucleotide binding domains arranged in two rings that hydrolyze ATP. We extend here previous studies on ClpB nucleotide utilization requirements by using an experimental approach that maximizes random incorporation of different subunits into the protein hexamer. Incorporation of one subunit unable to bind or hydrolyze ATP knocks down the chaperone activity, while the wt hexamer can accommodate two mutant subunits that hydrolyze ATP in only one protein ring. Four subunits seem to build the functional cooperative unit, provided that one of the protein rings contains active nucleotide binding sites.
Collapse
Affiliation(s)
- Urko del Castillo
- Unidad de Biofísica (CSIC-UPV/EHU), and Departamento de Bioquímica y BiologíaMolecular (UPV/EHU), Facultad de Ciencia y Tecnología, Universidad del País Vasco, P.O. Box 644, Bilbao, Spain
| | | | | | | | | |
Collapse
|
24
|
Sharma D, Masison DC. Hsp70 structure, function, regulation and influence on yeast prions. Protein Pept Lett 2009; 16:571-81. [PMID: 19519514 DOI: 10.2174/092986609788490230] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Heat shock proteins protect cells from various conditions of stress. Hsp70, the most ubiquitous and highly conserved Hsp, helps proteins adopt native conformation or regain function after misfolding. Various co-chaperones specify Hsp70 function and broaden its substrate range. We discuss Hsp70 structure and function, regulation by co-factors and influence on propagation of yeast prions.
Collapse
Affiliation(s)
- Deepak Sharma
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes, Digestive and Kidney Diseases, National institutes of Health, Bethesda, MD 20892-0851, USA
| | | |
Collapse
|
25
|
Acebrón SP, Martín I, del Castillo U, Moro F, Muga A. DnaK-mediated association of ClpB to protein aggregates. A bichaperone network at the aggregate surface. FEBS Lett 2009; 583:2991-6. [PMID: 19698713 DOI: 10.1016/j.febslet.2009.08.020] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Revised: 08/10/2009] [Accepted: 08/10/2009] [Indexed: 10/20/2022]
Abstract
Intracellular protein aggregates formed under severe thermal stress can be reactivated by the concerted action of the Hsp70 system and Hsp100 chaperones. We analyzed here the interaction of DnaJ/DnaK and ClpB with protein aggregates. We show that aggregate properties modulate chaperone binding, which in turn determines aggregate reactivation efficiency. ClpB binding strictly depends on previous DnaK association with the aggregate. The affinity of ClpB for the aggregate-DnaK complex is low (K(d)=5-10 microM), indicating a weak interaction. Therefore, formation of the DnaK-ClpB bichaperone network is a three step process. After initial DnaJ binding, the cochaperone drives association of DnaK to aggregates, and in the third step, as shown here, DnaK mediates ClpB interaction with the aggregate surface.
Collapse
Affiliation(s)
- Sergio P Acebrón
- Unidad de Biofísica (CSIC-UPV/EHU), and Departamento de Bioquímica y Biología Molecular (UPV/EHU), Facultad de Ciencia y Tecnología, Universidad del País Vasco, PO Box 644, Bilbao, Spain
| | | | | | | | | |
Collapse
|
26
|
Pleckaityte M, Mistinaite L, Mistiniene E, Dienys G, Zvirblis G. Biochemical properties of Hsp70 chaperone system fromMeiothermus ruber. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420500175812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
27
|
A 70-kDa molecular chaperone, DnaK, from the industrial bacterium Bacillus licheniformis: gene cloning, purification and molecular characterization of the recombinant protein. Indian J Microbiol 2009; 49:151-60. [PMID: 23100764 DOI: 10.1007/s12088-009-0029-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Accepted: 11/27/2008] [Indexed: 12/24/2022] Open
Abstract
The heat shock protein 70 (Hsp70/DnaK) gene of Bacillus licheniformis is 1,839 bp in length encoding a polypeptide of 612 amino acid residues. The deduced amino acid sequence of the gene shares high sequence identity with other Hsp70/DnaK proteins. The characteristic domains typical for Hsps/DnaKs are also well conserved in B. licheniformis DnaK (BlDnaK). BlDnaK was overexpressed in Escherichia coli using pQE expression system and the recombinant protein was purified to homogeneity by nickel-chelate chromatography. The optimal temperature for ATPase activity of the purified BlDnaK was 40°C in the presence of 100 mM KCl. The purified BlDnaK had a V(max) of 32.5 nmol Pi/min and a K(M) of 439 μM. In vivo, the dnaK gene allowed an E. coli dnaK756-ts mutant to grow at 44°C, suggesting that BlDnaK should be functional for survival of host cells under environmental changes especially higher temperature. We also described the use of circular dichroism to characterize the conformation change induced by ATP binding. Binding of ATP was not accompanied by a net change in secondary structure, but ATP together with Mg(2+) and K(+) ions had a greater enhancement in the stability of BlDnaK at stress temperatures. Simultaneous addition of DnaJ, GrpE, and NR-peptide (NRLLLTG) synergistically stimulates the ATPase activity of BlDnaK by 11.7-fold.
Collapse
|
28
|
Li Z, Xie Z. The Na/K-ATPase/Src complex and cardiotonic steroid-activated protein kinase cascades. Pflugers Arch 2008; 457:635-44. [DOI: 10.1007/s00424-008-0470-0] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Revised: 01/24/2008] [Accepted: 01/29/2008] [Indexed: 01/01/2023]
|
29
|
Kamiguchi K, Torigoe T, Fujiwara O, Ohshima S, Hirohashi Y, Sahara H, Hirai I, Kohgo Y, Sato N. Disruption of the association of 73 kDa heat shock cognate protein with transporters associated with antigen processing (TAP) decreases TAP-dependent translocation of antigenic peptides into the endoplasmic reticulum. Microbiol Immunol 2008; 52:94-106. [DOI: 10.1111/j.1348-0421.2008.00017.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
30
|
Buck TM, Wright CM, Brodsky JL. The activities and function of molecular chaperones in the endoplasmic reticulum. Semin Cell Dev Biol 2007; 18:751-61. [PMID: 17964199 PMCID: PMC2175536 DOI: 10.1016/j.semcdb.2007.09.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Revised: 07/22/2007] [Accepted: 09/05/2007] [Indexed: 01/23/2023]
Abstract
Most proteins in the secretory pathway are translated, folded, and subjected to quality control at the endoplasmic reticulum (ER). These processes must be flexible enough to process diverse protein conformations, yet specific enough to recognize when a protein should be degraded. Molecular chaperones are responsible for this decision making process. ER associated chaperones assist in polypeptide translocation, protein folding, and ER associated degradation (ERAD). Nevertheless, we are only beginning to understand how chaperones function, how they are recruited to specific substrates and assist in folding/degradation, and how unique chaperone classes make quality control "decisions".
Collapse
Affiliation(s)
- Teresa M Buck
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States.
| | | | | |
Collapse
|
31
|
Swain JF, Dinler G, Sivendran R, Montgomery DL, Stotz M, Gierasch LM. Hsp70 chaperone ligands control domain association via an allosteric mechanism mediated by the interdomain linker. Mol Cell 2007; 26:27-39. [PMID: 17434124 PMCID: PMC1894942 DOI: 10.1016/j.molcel.2007.02.020] [Citation(s) in RCA: 239] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Revised: 01/24/2007] [Accepted: 02/20/2007] [Indexed: 11/16/2022]
Abstract
Hsp70 chaperones assist in protein folding, disaggregation, and membrane translocation by binding to substrate proteins with an ATP-regulated affinity that relies on allosteric coupling between ATP-binding and substrate-binding domains. We have studied single- and two-domain versions of the E. coli Hsp70, DnaK, to explore the mechanism of interdomain communication. We show that the interdomain linker controls ATPase activity by binding to a hydrophobic cleft between subdomains IA and IIA. Furthermore, the domains of DnaK dock only when ATP binds and behave independently when ADP is bound. Major conformational changes in both domains accompany ATP-induced docking: of particular importance, some regions of the substrate-binding domain are stabilized, while those near the substrate-binding site become destabilized. Thus, the energy of ATP binding is used to form a stable interface between the nucleotide- and substrate-binding domains, which results in destabilization of regions of the latter domain and consequent weaker substrate binding.
Collapse
Affiliation(s)
- Joanna F. Swain
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, Amherst, Massachusetts 01003 USA
| | - Gizem Dinler
- Department of Chemistry, University of Massachusetts, Amherst, Amherst, Massachusetts 01003 USA
| | - Renuka Sivendran
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, Amherst, Massachusetts 01003 USA
| | - Diana L. Montgomery
- Department of Chemistry, University of Massachusetts, Amherst, Amherst, Massachusetts 01003 USA
| | - Mathias Stotz
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, Amherst, Massachusetts 01003 USA
| | - Lila M. Gierasch
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, Amherst, Massachusetts 01003 USA
- Department of Chemistry, University of Massachusetts, Amherst, Amherst, Massachusetts 01003 USA
- *To whom correspondence should be addressed at: , phone: 413-545-6094, fax: 413-545-1289
| |
Collapse
|
32
|
Fernández-Sáiz V, Moro F, Arizmendi JM, Acebrón SP, Muga A. Ionic contacts at DnaK substrate binding domain involved in the allosteric regulation of lid dynamics. J Biol Chem 2006; 281:7479-88. [PMID: 16415343 DOI: 10.1074/jbc.m512744200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To gain further insight into the interactions involved in the allosteric transition of DnaK we have characterized wild-type (wt) protein and three mutants in which ionic interactions at the interface between the two subdomains of the substrate binding domain, and within the lid subdomain have been disrupted. Our data show that ionic contacts, most likely forming an electrically charged network, between the N-terminal region of helix B and an inner loop of the beta-sandwich are involved in maintaining the position of the lid relative to the beta-subdomain in the ADP state but not in the ATP state of the protein. Disruption of the ionic interactions between the C-terminal region of helix B and the outer loops of the beta-sandwich, known as the latch, does not have the same conformational consequences but results equally in an inactive protein. This indicates that a variety of mechanisms can inactivate this complex allosteric machine. Our results identify the ionic contacts at the subdomain and interdomain interfaces that are part of the hinge region involved in the ATP-induced allosteric displacement of the lid away from the peptide binding site. These interactions also stabilize peptide-Hsp70 complexes at physiological (37 degrees C) and stress (42 degrees C) temperatures, a requirement for productive substrate (re)folding.
Collapse
MESH Headings
- Adenosine Diphosphate/chemistry
- Adenosine Triphosphatases/chemistry
- Adenosine Triphosphate/chemistry
- Allosteric Regulation
- Allosteric Site
- Amino Acid Sequence
- Anisotropy
- Bacterial Proteins/chemistry
- Binding Sites
- Calorimetry, Differential Scanning
- Escherichia coli/metabolism
- Hot Temperature
- Ions
- Kinetics
- Luciferases/metabolism
- Mass Spectrometry
- Microscopy, Fluorescence
- Molecular Chaperones/chemistry
- Molecular Conformation
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Mutation
- Peptides/chemistry
- Protein Binding
- Protein Conformation
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Sequence Homology, Amino Acid
- Spectrometry, Mass, Electrospray Ionization
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Substrate Specificity
- Temperature
- Thermodynamics
- Time Factors
- Trypsin/chemistry
- Trypsin/pharmacology
Collapse
Affiliation(s)
- Vanesa Fernández-Sáiz
- Unidad de Biofísica (Consejo Superior de Investigaciones Científicas-Universidad del País Vasco, Euskal Herriko Unibertsitatea), 48080 Bilbao, Spain
| | | | | | | | | |
Collapse
|
33
|
Moro F, Fernández-Sáiz V, Muga A. The allosteric transition in DnaK probed by infrared difference spectroscopy. Concerted ATP-induced rearrangement of the substrate binding domain. Protein Sci 2005; 15:223-33. [PMID: 16384998 PMCID: PMC2242457 DOI: 10.1110/ps.051732706] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The biological activity of DnaK, the bacterial representative of the Hsp70 protein family, is regulated by the allosteric interaction between its nucleotide and peptide substrate binding domains. Despite the importance of the nucleotide-induced cycling of DnaK between substrate-accepting and releasing states, the heterotropic allosteric mechanism remains as yet undefined. To further characterize this mechanism, the nucleotide-induced absorbance changes in the vibrational spectrum of wild-type DnaK was characterized. To assign the conformation sensitive absorption bands, two deletion mutants (one lacking the C-terminal alpha-helical subdomain and another comprising only the N-terminal ATPase domain), and a single-point DnaK mutant (T199A) with strongly reduced ATPase activity, were investigated by time-resolved infrared difference spectroscopy combined with the use of caged-nucleotides. The results indicate that (1) ATP, but not ADP, binding promotes a conformational change in both subdomains of the peptide binding domain that can be individually resolved; (2) these conformational changes are kinetically coupled, most likely to ensure a decrease in the affinity of DnaK for peptide substrates and a concomitant displacement of the lid away from the peptide binding site that would promote efficient diffusion of the released peptide to the medium; and (3) the alpha-helical subdomain contributes to stabilize the interdomain interface against the thermal challenge and allows bidirectional transmission of the allosteric signal between the ATPase and substrate binding domains at stress temperatures (42 degrees C).
Collapse
Affiliation(s)
- Fernando Moro
- Unidad de Biofísica (CSIC/UPV-EHU) y Departamento de Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Apartado 644, 48080 Bilbao, Spain
| | | | | |
Collapse
|
34
|
Groemping Y, Seidel R, Reinstein J. Balance of ATPase stimulation and nucleotide exchange is not required for efficient refolding activity of the DnaK chaperone. FEBS Lett 2005; 579:5713-7. [PMID: 16225874 DOI: 10.1016/j.febslet.2005.09.056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2005] [Revised: 09/22/2005] [Accepted: 09/22/2005] [Indexed: 11/22/2022]
Abstract
The DnaK system from Thermus thermophilus (DnaK(Tth)) exhibits pronounced differences in organisation and regulation to its mesophile counterpart from Escherichia coli (DnaK(Eco)). While the ATPase cycle of DnaK(Eco) is tightly regulated by the concerted action of the two cofactors DnaJ(Eco) and GrpE(Eco), the DnaK(Tth) system features an imbalance in this cochaperone mediated regulation. GrpE(Tth) considerably accelerates the ATP/ADP exchange, but DnaJ(Tth) only slightly stimulates ATPase activity, believed to be a key step for chaperone activity of DnaK(Eco). By in vitro complementation assays, we could not detect significant ATPase-stimulation of orthologous DnaJ(Tth) . DnaKEco or DnaJ(Eco). DnaK(Tth)-complexes as compared to the DnaK(Eco) system, although they were nevertheless active in luciferase refolding experiments. Assistance of protein recovery by DnaK thus seems to be uncoupled of the magnitude of DnaJ mediated ATPase-stimulation.
Collapse
Affiliation(s)
- Yvonne Groemping
- Max-Planck-Institute für medizinische Forschung, Abteilung Biomolekulare Mechanismen, Heidelberg, Germany
| | | | | |
Collapse
|
35
|
Swain JF, Schulz EG, Gierasch LM. Direct comparison of a stable isolated Hsp70 substrate-binding domain in the empty and substrate-bound states. J Biol Chem 2005; 281:1605-11. [PMID: 16275641 DOI: 10.1074/jbc.m509356200] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Hsp70 family of molecular chaperones acts to prevent protein misfolding, import proteins into organelles, unravel protein aggregates, and enhance cell survival under stress conditions. These activities are all mediated by recognition of diverse hydrophobic sequences via a C-terminal substrate-binding domain. ATP-binding/hydrolysis by the N-terminal ATPase domain regulates the interconversion of the substrate-binding domain between low and high affinity conformations. The empty state of the substrate-binding domain has been difficult to study because of its propensity to bind nearly any available protein chain, even if only modestly hydrophobic. We have generated a new stable construct of the substrate-binding domain from the Escherichia coli Hsp70, DnaK, which has enabled us to compare the empty and peptide-bound conformations using NMR chemical shift analysis and hydrogen-deuterium exchange. We have determined that the empty state is, overall, quite similar to the peptide-bound state, contrary to a previous report. Peptide binding leads to a subtle alteration in the packing of the alpha-helical lid relative to the beta-subdomain. Significantly, we have shown that the chemical shifts of the substrate-binding domain and the ATPase domain do not change when they are placed together in a two-domain construct, whether or not peptide is bound, suggesting that, in the absence of nucleotide, the two domains of E. coli DnaK do not interact. We conclude that the isolated substrate-binding domain exists in a stable high affinity state in the absence of influence from a nucleotide-bound ATPase domain.
Collapse
Affiliation(s)
- Joanna F Swain
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | | | | |
Collapse
|
36
|
Hennessy F, Nicoll WS, Zimmermann R, Cheetham ME, Blatch GL. Not all J domains are created equal: implications for the specificity of Hsp40-Hsp70 interactions. Protein Sci 2005; 14:1697-709. [PMID: 15987899 PMCID: PMC2253343 DOI: 10.1110/ps.051406805] [Citation(s) in RCA: 216] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Heat shock protein 40s (Hsp40s) and heat shock protein 70s (Hsp70s) form chaperone partnerships that are key components of cellular chaperone networks involved in facilitating the correct folding of a broad range of client proteins. While the Hsp40 family of proteins is highly diverse with multiple forms occurring in any particular cell or compartment, all its members are characterized by a J domain that directs their interaction with a partner Hsp70. Specific Hsp40-Hsp70 chaperone partnerships have been identified that are dedicated to the correct folding of distinct subsets of client proteins. The elucidation of the mechanism by which these specific Hsp40-Hsp70 partnerships are formed will greatly enhance our understanding of the way in which chaperone pathways are integrated into finely regulated protein folding networks. From in silico analyses, domain swapping and rational protein engineering experiments, evidence has accumulated that indicates that J domains contain key specificity determinants. This review will critically discuss the current understanding of the structural features of J domains that determine the specificity of interaction between Hsp40 proteins and their partner Hsp70s. We also propose a model in which the J domain is able to integrate specificity and chaperone activity.
Collapse
Affiliation(s)
- Fritha Hennessy
- Department of Biochemistry, Microbiology and Biotechnology, Rhodes University, Grahamstown, South Africa
| | | | | | | | | |
Collapse
|
37
|
Popp S, Packschies L, Radzwill N, Vogel KP, Steinhoff HJ, Reinstein J. Structural dynamics of the DnaK-peptide complex. J Mol Biol 2005; 347:1039-52. [PMID: 15784262 DOI: 10.1016/j.jmb.2005.02.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2004] [Revised: 02/04/2005] [Accepted: 02/09/2005] [Indexed: 10/25/2022]
Abstract
The molecular chaperone DnaK recognizes and binds substrate proteins via a stretch of seven amino acid residues that is usually only exposed in unfolded proteins. The binding kinetics are regulated by the nucleotide state of DnaK, which alternates between DnaK.ATP (fast exchange) and DnaK.ADP (slow exchange). These two forms cycle with a rate mainly determined by the ATPase activity of DnaK and nucleotide exchange. The different substrate binding properties of DnaK are mainly attributed to changes of the position and mobility of a helical region in the C-terminal peptide-binding domain, the so-called LID. It closes the peptide-binding pocket and thus makes peptide binding less dynamic in the ADP-bound state, but does not (strongly) interact with peptides directly. Here, we address the question if nucleotide-dependent structural changes may be observed in the peptide-binding region that could also be connected to peptide binding kinetics and more importantly could induce structural changes in peptide stretches using the energy available from ATP hydrolysis. Model peptides containing two cysteine residues at varying positions were derived from the structurally well-documented peptide NRLLLTG and labelled with electron spin sensitive probes. Measurements of distances and mobilities of these spin labels by electron paramagnetic resonance spectroscopy (EPR) of free peptides or peptides bound to the ATP and ADP-state of DnaK, respectively, showed no significant changes of mobility nor distance of the two labels. This indicates that no structural changes that could be sensed by the probes at the position of central leucine residues located in the center of the binding region occur due to different nucleotide states. We conclude from these studies that the ATPase activity of DnaK is not connected to structural changes of the peptide-binding pocket but rather only has an effect on the LID domain or other further remote residues.
Collapse
Affiliation(s)
- Simone Popp
- Department of Biomolecular Mechanisms, Max-Planck-Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | | | | | | | | | | |
Collapse
|
38
|
Boshoff A, Hennessy F, Blatch GL. The in vivo and in vitro characterization of DnaK from Agrobacterium tumefaciens RUOR. Protein Expr Purif 2005; 38:161-9. [PMID: 15555931 DOI: 10.1016/j.pep.2004.06.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2004] [Revised: 06/10/2004] [Indexed: 11/24/2022]
Abstract
Molecular chaperones of the heat shock protein 70 family (Hsp70; also called DnaK in prokaryotes) play an important role in the folding and functioning of cellular protein machinery. The dnaK gene from the plant pathogen Agrobacterium tumefaciens RUOR was amplified using the polymerase chain reaction and the DnaK protein (Agt DnaK) was over-produced as a His-tagged protein in Escherichia coli. The Agt DnaK amino acid sequence was 96% identical to the A. tumefaciens C58 DnaK sequence and 65% identical to the E. coli DnaK sequence. Agt DnaK was shown to be able to functionally replace E. coli DnaK in vivo using complementation assays with an E. coli dnaK756 mutant strain and a dnaK52 deletion strain. Over-production and purification of Agt DnaK was successful, and allowed for further characterization of the protein. Kinetic analysis of the basal ATPase activity of purified Agt DnaK revealed a Vmax of 1.3 nmol phosphate released per minute per milligram DnaK, and a Km of 62 microM ATP. Thus, this is the first study to provide both in vivo and in vitro evidence that Agt DnaK has the properties of a molecular chaperone of the Hsp70 family.
Collapse
Affiliation(s)
- Aileen Boshoff
- Department of Biochemistry, Microbiology and Biotechnology, Rhodes University, Grahamstown 6140, South Africa
| | | | | |
Collapse
|
39
|
Asan E, Drenckhahn D. Immunocytochemical characterization of two types of microvillar cells in rodent olfactory epithelium. Histochem Cell Biol 2005; 123:157-68. [PMID: 15856279 DOI: 10.1007/s00418-005-0759-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2004] [Indexed: 11/30/2022]
Abstract
Microvillar cells (MCs) have been identified in the olfactory epithelium of various mammalian species from rodents to humans. Studies on properties and functions of MCs to date have yielded partially controversial results, supporting alternatively an epithelial or a neuronal nature of these cells. In the present study, single and double immunolabeling investigations were carried out using antibodies against cytoskeletal and integral membrane proteins in order to further characterize MCs in rat and mouse olfactory epithelium. Application of antibodies against ankyrin (ANK), a protein that links integral membrane proteins to the submembrane cytoskeleton, led to intense labeling of the basolateral membranes of numerous cells with characteristic MC morphology. ANK-immunoreactive (ir) cells bore an apical tuft of beta-actin-ir microvilli, were filled with cytokeratin 18 (CK18)-ir filamentous network, and extended a basal process that appeared to end above the basal membrane. Immunoreactions for villin, an actin-crosslinking protein particularly prominently expressed in brush cells in the gastrointestinal and respiratory tract epithelia, and for the alpha-subunit of sodium-potassium ATPase (Na(+), K(+)-ATPase), revealed that ANK-ir MCs fall into two subpopulations. The less frequent type I MCs displayed villin immunoreactivity in their apical microvilli and underneath the basolateral membranes; the more numerous type II MCs were negative for villin but possessed intense basolateral immunoreactivity for Na(+), K(+)-ATPase. Strong reactivity for the epithelial-type integral membrane protein of adherens junctions, E-Cadherin, was localized in basolateral membranes of both types of MCs. Our results support an epithelial nature of ANK-ir MCs in rat and mouse olfactory epithelium. Type I MCs strongly resemble brush cells in their immunocytochemical characteristics, namely, their ANK reactivity, CK18 reactivity, and villin reactivity. The intense Na(+), K(+)-ATPase reactivity of type II MCs implicates these cells in transport processes.
Collapse
Affiliation(s)
- E Asan
- Institute of Anatomy and Cell Biology, University of Wuerzburg, Koellikerstr. 6, 97070 Wuerzburg, Germany.
| | | |
Collapse
|
40
|
Gur E, Katz C, Ron EZ. All three J-domain proteins of theEscherichia coliDnaK chaperone machinery are DNA binding proteins. FEBS Lett 2005; 579:1935-9. [PMID: 15792799 DOI: 10.1016/j.febslet.2005.01.084] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2004] [Revised: 01/30/2005] [Accepted: 01/31/2005] [Indexed: 11/21/2022]
Abstract
DnaJ, DjlA and CbpA are the J-domain proteins of DnaK, the major Hsp70 of Escherichia coli. CbpA was originally discovered as a DNA binding protein. Here, we show that DNA binding is a property of DnaJ and DjlA as well. Of special interest in this respect is DjlA, as this cytoplasmic protein is membrane bound and, as shown here, its affinity for DNA is extremely high. The finding that all the three J-proteins of DnaK are DNA binding proteins sheds new light on the cellular activity of these proteins.
Collapse
Affiliation(s)
- Eyal Gur
- Department of Molecular Microbiology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
| | | | | |
Collapse
|
41
|
Gruschus JM, Greene LE, Eisenberg E, Ferretti JA. Experimentally biased model structure of the Hsc70/auxilin complex: substrate transfer and interdomain structural change. Protein Sci 2005; 13:2029-44. [PMID: 15273304 PMCID: PMC2279835 DOI: 10.1110/ps.03390504] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A model structure of the Hsc70/auxilin complex has been constructed to gain insight into interprotein substrate transfer and ATP hydrolysis induced conformational changes in the multidomain Hsc70 structure. The Hsc70/auxilin system, which is a member of the Hsp70/Hsp40 chaperone system family, uncoats clathrin-coated vesicles in an ATP hydrolysis-driven process. Incorporating previous results from NMR and mutant binding studies, the auxilin J-domain was docked into the Hsc70 ATPase domain lower cleft using rigid backbone/flexible side chain molecular dynamics, and the Hsc70 substrate binding domain was docked by a similar procedure. For comparison, J-domain and substrate binding domain docking sites were obtained by the rigid-body docking programs DOT and ZDOCK, filtered and ranked by the program ClusPro, and relaxed using the same rigid backbone/flexible side chain dynamics. The substrate binding domain sites were assessed in terms of conserved surface complementarity and feasibility in the context of substrate transfer, both for auxilin and another Hsp40 protein, Hsc20. This assessment favors placement of the substrate binding domain near D152 on the ATPase domain surface adjacent to the J-domain invariant HPD segment, with the Hsc70 interdomain linker in the lower cleft. Examining Hsc70 interdomain energetics, we propose that long-range electrostatic interactions, perhaps due to a difference in the pKa values of bound ATP and ADP, could play a major role in the structural change induced by ATP hydrolysis. Interdomain electrostatic interactions also appear to play a role in stimulation of ATPase activity due to J-domain binding and substrate binding by Hsc70.
Collapse
Affiliation(s)
- James M Gruschus
- Laboratories of Biophysical Chemistry and Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892-8013, USA.
| | | | | | | |
Collapse
|
42
|
Hennessy F, Boshoff A, Blatch GL. Rational mutagenesis of a 40 kDa heat shock protein from Agrobacterium tumefaciens identifies amino acid residues critical to its in vivo function. Int J Biochem Cell Biol 2005; 37:177-91. [PMID: 15381160 DOI: 10.1016/j.biocel.2004.06.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2004] [Revised: 04/16/2004] [Accepted: 06/09/2004] [Indexed: 10/26/2022]
Abstract
Prokaryotic DnaJ and DnaK, homologous to the eukaryotic 40 and 70kDa heat shock proteins (Hsp40 and Hsp70) respectively, play an important role as molecular chaperones in assisted protein folding under both normal and stressed conditions. DnaJ-like proteins are defined by the presence of a 70 amino acid domain termed the J domain, similar to the initial 73 amino acids of the Escherichia coli protein DnaJ. The J domain comprises four alpha-helices and a loop region containing the invariant tripeptide of histidine, proline and aspartic acid (HPD motif). This motif and Helix II have been shown previously to be important for the interaction with partner Hsp70s. Conserved amino acid residues present in the J domain were identified, and substitutions of these residues were performed to examine their effect on the in vivo functioning of the J domain of Agrobacterium tumefaciens DnaJ. Three conserved, charged residues, and three conserved, hydrophobic residues, in addition to the HPD motif, were shown to be important for the correct functioning of A. tumefaciens DnaJ. These included Arg26 located on Helix II, Arg63 and Asp59 located on Helix IV, Tyr7 and Leu10 located on Helix I, and Leu57 located on Helix III. This study has identified charged and hydrophobic residues on all the structural elements of the J domain that were critical to the structure and function of DnaJ, and in particular shown that Helix IV may have an important role in the structure and function of DnaJs in general.
Collapse
Affiliation(s)
- Fritha Hennessy
- Department of Biochemistry, Microbiology and Biotechnology, Rhodes University, Grahamstown 6140, South Africa
| | | | | |
Collapse
|
43
|
Gur E, Biran D, Shechter N, Genevaux P, Georgopoulos C, Ron EZ. The Escherichia coli DjlA and CbpA proteins can substitute for DnaJ in DnaK-mediated protein disaggregation. J Bacteriol 2004; 186:7236-42. [PMID: 15489435 PMCID: PMC523209 DOI: 10.1128/jb.186.21.7236-7242.2004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The DnaJ (Hsp40) protein of Escherichia coli serves as a cochaperone of DnaK (Hsp70), whose activity is involved in protein folding, protein targeting for degradation, and rescue of proteins from aggregates. Two other E. coli proteins, CbpA and DjlA, which exhibit homology with DnaJ, are known to interact with DnaK and to stimulate its chaperone activity. Although it has been shown that in dnaJ mutants both CbpA and DjlA are essential for growth at temperatures above 37 degrees C, their in vivo role is poorly understood. Here we show that in a dnaJ mutant both CbpA and DjlA are required for efficient protein dissaggregation at 42 degrees C.
Collapse
Affiliation(s)
- Eyal Gur
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
| | | | | | | | | | | |
Collapse
|
44
|
D'Silva P, Liu Q, Walter W, Craig EA. Regulated interactions of mtHsp70 with Tim44 at the translocon in the mitochondrial inner membrane. Nat Struct Mol Biol 2004; 11:1084-91. [PMID: 15489862 DOI: 10.1038/nsmb846] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2004] [Accepted: 08/27/2004] [Indexed: 02/07/2023]
Abstract
Preproteins synthesized on cytosolic ribosomes, but destined for the mitochondrial matrix, pass through the presequence translocase of the inner membrane. Translocation is driven by the import motor, having at its core the essential chaperone mtHsp70 (Ssc1 in yeast). MtHsp70 is tethered to the translocon channel at the matrix side of the inner membrane by the peripheral membrane protein Tim44. A key question in mitochondrial import is how the mtHsp70-Tim44 interaction is regulated. Here we report that Tim44 interacts with both the ATPase and peptide-binding domains of mtHsp70. Disruption of these interactions upon binding of polypeptide substrates requires concerted conformational changes involving both domains of mtHsp70. Our results fit a model in which regulated interactions between Tim44 and mtHsp70, controlled by polypeptide binding, are required for efficient translocation across the mitochondrial inner membrane in vivo.
Collapse
Affiliation(s)
- Patrick D'Silva
- Department of Biochemistry, 433 Babcock Drive, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | | | | | | |
Collapse
|
45
|
Zmijewski MA, Kwiatkowska JM, Lipińska B. Complementation studies of the DnaK-DnaJ-GrpE chaperone machineries from Vibrio harveyi and Escherichia coli, both in vivo and in vitro. Arch Microbiol 2004; 182:436-49. [PMID: 15448982 DOI: 10.1007/s00203-004-0727-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2004] [Revised: 08/03/2004] [Accepted: 08/10/2004] [Indexed: 11/29/2022]
Abstract
The marine bacterium Vibrio harveyi is a potential indicator organism for evaluating marine environmental pollution. The DnaK-DnaJ-GrpE chaperone machinery of V. harveyi has been studied as a model of response to stress conditions and compared to the Escherichia coli DnaK system. The genes encoding DnaK, DnaJ and GrpE of V. harveyi were cloned into expression vectors and grpE was sequenced. It was found that V. harveyi possesses a unique organization of the hsp gene cluster (grpE-gltP-dnaK-dnaJ), which is present exclusively in marine Vibrio species. In vivo experiments showed that suppression of the E. coli dnaK mutation by V. harveyi DnaK protein was weak or absent, while suppression of the dnaJ and grpE mutations by V. harveyi DnaJ and GrpE proteins was efficient. These results suggest higher species-specificity of the DnaK chaperone than the GrpE and DnaJ cochaperones. Proteins of the DnaK chaperone machinery of V. harveyi were purified to homogeneity and their efficient cooperation with the E. coli chaperones in the luciferase refolding reaction and in stimulation of DnaK ATPase activity was demonstrated. Compared to the E. coli system, the purified DnaK-DnaJ-GrpE system of V. harveyi exhibited about 20% lower chaperoning activity in the luciferase reactivation assay. ATPase activity of V. harveyi DnaK protein was at least twofold higher than that of the E. coli model DnaK but its stimulation by the cochaperones DnaJ and GrpE was significantly (10 times) weaker. These results indicate that, despite their high structural identity (approximately 80%) and similar mechanisms of action, the DnaK chaperones of closely related V. harveyi and E.coli bacteria differ functionally.
Collapse
Affiliation(s)
- Michał A Zmijewski
- Department of Biochemistry, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | | | | |
Collapse
|
46
|
Zmijewski MA, Macario AJL, Lipińska B. Functional similarities and differences of an archaeal Hsp70(DnaK) stress protein compared with its homologue from the bacterium Escherichia coli. J Mol Biol 2004; 336:539-49. [PMID: 14757064 DOI: 10.1016/j.jmb.2003.12.053] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Archaea are prokaryotes but some of their chaperoning systems resemble those of eukaryotes. Also, not all archaea possess the stress protein Hsp70(DnaK), in contrast with bacteria and eukaryotes, which possess it without any known exception. Further, the primary structure of the archaeal DnaK resembles more the bacterial than the eukaryotic homologues. The work reported here addresses two questions: Is the archaeal Hsp70 protein a chaperone, like its homologues in the other two phylogenetic domains? And, if so, is the chaperoning mechanism of bacterial or eukaryotic type? The data have shown that the DnaK protein of the archaeon Methanosarcina mazei functions efficiently as a chaperone in luciferase renaturation in vitro, and that it requires DnaJ, and the other bacterial-type chaperone, GrpE, to perform its function. The M. mazei DnaK chaperone activity was enhanced by interaction with the bacterial co-chaperone DnaJ, but not by the eukaryotic homologue HDJ-2. Both the bacterial GrpE and DnaJ stimulated the ATPase activity of the M. mazei DnaK. The M. mazei DnaK-dependent chaperoning pathway in vitro is similar to that of the bacterium Escherichia coli used for comparison. However, in vivo analyses indicate that there are also significant differences. The M. mazei dnaJ and grpE genes rescued E.coli mutants lacking these genes, but E.coli dnaK mutants were not complemented by the M. mazei dnaK gene. Thus, while the data from in vitro tests demonstrate functional similarities between the M. mazei and E.coli DnaK proteins, in vivo results indicate that, intracellularly, the chaperones from the two species differ.
Collapse
Affiliation(s)
- Michał A Zmijewski
- Department of Biochemistry, University of Gdańsk, Klz.shtsls;adki 24, 80-822, Gdańsk, Poland
| | | | | |
Collapse
|
47
|
Hilge M, Siegal G, Vuister GW, Güntert P, Gloor SM, Abrahams JP. ATP-induced conformational changes of the nucleotide-binding domain of Na,K-ATPase. Nat Struct Mol Biol 2003; 10:468-74. [PMID: 12730684 DOI: 10.1038/nsb924] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2002] [Accepted: 03/31/2003] [Indexed: 11/08/2022]
Abstract
The Na,K-ATPase hydrolyzes ATP to drive the coupled extrusion and uptake of Na+ and K+ ions across the plasma membrane. Here, we report two high-resolution NMR structures of the 213-residue nucleotide-binding domain of rat alpha1 Na,K-ATPase, determined in the absence and the presence of ATP. The nucleotide binds in the anti conformation and shows a relative paucity of interactions with the protein, reflecting the low-affinity ATP-binding state. Binding of ATP induces substantial conformational changes in the binding pocket and in residues located in the hinge region connecting the N- and P-domains. Structural comparison with the Ca-ATPase stabilized by the inhibitor thapsigargin, E2(TG), and the model of the H-ATPase in the E1 form suggests that the observed changes may trigger the series of events necessary for the release of the K+ ions and/or disengagement of the A-domain, leading to the eventual transfer of the gamma-phosphate group to the invariant Asp369.
Collapse
Affiliation(s)
- Mark Hilge
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands.
| | | | | | | | | | | |
Collapse
|
48
|
Mehl AF, Heskett LD, Jain SS, Demeler B. Insights into dimerization and four-helix bundle formation found by dissection of the dimer interface of the GrpE protein from Escherichia coli. Protein Sci 2003; 12:1205-15. [PMID: 12761391 PMCID: PMC2323885 DOI: 10.1110/ps.0300803] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The GrpE heat shock protein from Escherichia coli has a homodimeric structure. The dimer interface encompasses two long alpha-helices at the NH(2)-terminal end from each monomer (forming a "tail"), which lead into a small four-helix bundle from which each monomer contributes two short sequential alpha-helices in an antiparallel topological arrangement. We have created a number of different deletion mutants of GrpE that have portions of the dimer interface to investigate requirements for dimerization and to study four-helix bundle formation. Using chemical crosslinking and analytical ultracentrifugation techniques to probe for multimeric states, we find that a mutant containing only the long alpha-helical tail portion (GrpE1-88) is unable to form a dimer, most likely due to a decrease in alpha-helical content as determined by circular dichroism spectroscopy, thus one reason for a dimeric structure for the GrpE protein is to support the tail region. Mutants containing both of the short alpha-helices (GrpE1-138 and GrpE88-197) are able to form a dimer and presumably the four-helix bundle at the dimer interface. These two mutants have equilibrium constants for the monomer-dimer equilibrium that are very similar to the full-length protein suggesting that the tail region does not contribute significantly to the stability of the dimer. Interestingly, one mutant that contains just one of the short alpha-helices (GrpE1-112) exists as a tetrameric species, which presumably is forming a four-helix bundle structure. A proposed model is discussed for this mutant and its relevance for factors influencing four-helix bundle formation.
Collapse
Affiliation(s)
- Andrew F Mehl
- Department of Chemistry, Knox College, Galesburg, Illinois 61401, USA.
| | | | | | | |
Collapse
|
49
|
Han W, Christen P. Interdomain communication in the molecular chaperone DnaK. Biochem J 2003; 369:627-34. [PMID: 12383055 PMCID: PMC1223109 DOI: 10.1042/bj20020943] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2002] [Revised: 10/02/2002] [Accepted: 10/17/2002] [Indexed: 11/17/2022]
Abstract
DnaK, a heat-shock protein 70 (Hsp70) homologue in Escherichia coli, possesses a single tryptophan residue in its ATPase domain. Changes in the intrinsic fluorescence of DnaK offer a simple means not only to follow the binding of ATP and of ADP plus the co-chaperone GrpE to the ATPase domain, but also to investigate the kinetics of peptide binding to the substrate-binding domain of ATP.DnaK and GrpE-liganded ADP.DnaK. Addition of ATP or of ADP plus GrpE to nucleotide-free DnaK resulted in a similar decrease in intrinsic fluorescence, indicating similar open conformations of the ATPase domain under these two conditions. Binding of peptide increased the intrinsic fluorescence of both ATP.DnaK and ADP.DnaK.GrpE and rendered their spectra similar to the spectrum of ADP.DnaK with closed conformation of the ATPase domain. These results, together with the differential kinetics of peptide binding to ADP.DnaK on the one hand, and to ATP.DnaK or ADP.DnaK.GrpE on the other, suggest that ligands for either domain, i.e. ATP or ADP plus GrpE for the ATPase domain and peptides for the substrate-binding domain, shift the conformational equilibrium of both domains of DnaK towards the open and closed forms, respectively, in a concerted and parallel manner.
Collapse
Affiliation(s)
- Wanjiang Han
- Biochemisches Institut der Universität Zürich, Switzerland
| | | |
Collapse
|
50
|
Moro F, Fernández V, Muga A. Interdomain interaction through helices A and B of DnaK peptide binding domain. FEBS Lett 2003; 533:119-23. [PMID: 12505170 DOI: 10.1016/s0014-5793(02)03752-3] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In order to better define the structural elements involved in allosteric signalling, wild-type DnaK and three deletion mutants of the peptide binding domain have been characterized by biophysical (steady-state and time-resolved fluorescence) and biochemical methods. In the presence of ATP the chemical environment of the single tryptophan residue of DnaK, located in the ATPase domain, becomes less polar, as seen by a blue shift of the emission maximum and a shortening of the fluorescence lifetime, and its accessibility to polar quenchers is drastically reduced. These nucleotide-dependent modifications are also observed for the deletion mutant DnaK1-537, but not for DnaK1-507 or DnaK1-385, and thus rely on the presence of residues 507-537 (helices A and the N-terminal half of B) of the peptide binding domain. These data indicate that alphaA and half alphaB contribute to the allosteric communication of DnaK. In the presence of ATP, they promote a conformational change that displaces a residue(s) of the peptide binding domain towards a region of the ATPase domain where the tryptophan residue (W102) is located. A putative role for these helical segments as regulators of the position of the lid is discussed.
Collapse
Affiliation(s)
- Fernando Moro
- Unidad de Biofísica (CSIC-UPV/EHU) and Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad del Pai;s Vasco, Aptdo. 644, 48080, Bilbao, Spain
| | | | | |
Collapse
|