Protein Homeostasis Database: protein quality control in E.coli

Abstract Motivation In vivo protein folding is governed by molecular chaperones, that escort proteins from their translational birth to their proteolytic degradation. In E.coli the main classes of chaperones that interact with the nascent chain are trigger factor, DnaK/J and GroEL/ES and several authors have performed whole-genome experiments to construct exhaustive client lists for each of these. Results We constructed a database collecting all publicly available data of experimental chaperone-interaction and -dependency data for the E.coli proteome, and enriched it with an extensive set of protein-specific as well as cell context-dependent proteostatic parameters. We made this publicly accessible via a web interface that allows to search for proteins or chaperone client lists, but also to profile user-specified datasets against all the collected parameters. We hope this will accelerate research in this field by quickly identifying differentiating features in datasets. Availability and implementation The Protein Homeostasis Database is freely available without any registration requirement at http://PHDB.switchlab.org/.

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DNAJ Proteins in neurodegeneration: essential and protective factors

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2016.0534 ◽

2017 ◽

Vol 373 (1738) ◽

pp. 20160534 ◽

Cited By ~ 33

Author(s):

Christina Zarouchlioti ◽

David A. Parfitt ◽

Wenwen Li ◽

Lauren M. Gittings ◽

Michael E. Cheetham

Keyword(s):

Quality Control ◽

Neurodegenerative Diseases ◽

Conformational Changes ◽

Molecular Chaperones ◽

Protein Quality ◽

Misfolded Proteins ◽

Protein Homeostasis ◽

Polyglutamine Expansion ◽

Binding Domains

Maintenance of protein homeostasis is vitally important in post-mitotic cells, particularly neurons. Neurodegenerative diseases such as polyglutamine expansion disorders—like Huntington's disease or spinocerebellar ataxia (SCA), Alzheimer's disease, fronto-temporal dementia (FTD), amyotrophic lateral sclerosis (ALS) and Parkinson's disease—are often characterized by the presence of inclusions of aggregated protein. Neurons contain complex protein networks dedicated to protein quality control and maintaining protein homeostasis, or proteostasis. Molecular chaperones are a class of proteins with prominent roles in maintaining proteostasis, which act to bind and shield hydrophobic regions of nascent or misfolded proteins while allowing correct folding, conformational changes and enabling quality control. There are many different families of molecular chaperones with multiple functions in proteostasis. The DNAJ family of molecular chaperones is the largest chaperone family and is defined by the J-domain, which regulates the function of HSP70 chaperones. DNAJ proteins can also have multiple other protein domains such as ubiquitin-interacting motifs or clathrin-binding domains leading to diverse and specific roles in the cell, including targeting client proteins for degradation via the proteasome, chaperone-mediated autophagy and uncoating clathrin-coated vesicles. DNAJ proteins can also contain ER-signal peptides or mitochondrial leader sequences, targeting them to specific organelles in the cell. In this review, we discuss the multiple roles of DNAJ proteins and in particular focus on the role of DNAJ proteins in protecting against neurodegenerative diseases caused by misfolded proteins. We also discuss the role of DNAJ proteins as direct causes of inherited neurodegeneration via mutations in DNAJ family genes. This article is part of the theme issue ‘Heat shock proteins as modulators and therapeutic targets of chronic disease: an integrated perspective’.

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Identification and characterization of mutations responsible for the β-lactam resistance in oxacillin-susceptible mecA-positive Staphylococcus aureus

Scientific Reports ◽

10.1038/s41598-020-73796-5 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Tanit Boonsiri ◽

Shinya Watanabe ◽

Xin-Ee Tan ◽

Kanate Thitiananpakorn ◽

Ryu Narimatsu ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Quality Control ◽

Protein Quality ◽

Stringent Response ◽

Protein Quality Control ◽

Purine Biosynthesis ◽

Genome Comparison ◽

Whole Genome ◽

Intergenic Regions ◽

Mrsa Strains

Abstract Staphylococcus aureus strains that are susceptible to the β-lactam antibiotic oxacillin despite carrying mecA (OS-MRSA) cause serious clinical problems globally because of their ability to easily acquire β-lactam resistance. Understanding the genetic mechanism(s) of acquisition of the resistance is therefore crucial for infection control management. For this purpose, a whole-genome sequencing-based analysis was performed using 43 clinical OS-MRSA strains and 100 mutants with reduced susceptibility to oxacillin (MICs 1.0–256 µg/mL) generated from 26 representative OS-MRSA strains. Genome comparison between the mutants and their respective parent strains identified a total of 141 mutations in 46 genes and 8 intergenic regions. Among them, the mutations are frequently found in genes related to RNA polymerase (rpoBC), purine biosynthesis (guaA, prs, hprT), (p)ppGpp synthesis (relSau), glycolysis (pykA, fbaA, fruB), protein quality control (clpXP, ftsH), and tRNA synthase (lysS, gltX), whereas no mutations existed in mec and bla operons. Whole-genome transcriptional profile of the resistant mutants demonstrated that expression of genes associated with purine biosynthesis, protein quality control, and tRNA synthesis were significantly inhibited similar to the massive transcription downregulation seen in S. aureus during the stringent response, while the levels of mecA expression and PBP2a production were varied. We conclude that a combination effect of mecA upregulation and stringent-like response may play an important role in acquisition of β-lactam resistance in OS-MRSA.

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CHIP phosphorylation by protein kinase G enhances protein quality control and attenuates cardiac ischemic injury

Nature Communications ◽

10.1038/s41467-020-18980-x ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Mark J. Ranek ◽

Christian Oeing ◽

Rebekah Sanchez-Hodge ◽

Kristen M. Kokkonen-Simon ◽

Danielle Dillard ◽

...

Keyword(s):

Quality Control ◽

Protein Kinase ◽

Protein Quality ◽

Therapeutic Potential ◽

Protein Quality Control ◽

Ischemic Injury ◽

Protein Kinase G ◽

Interacting Protein ◽

Important Regulator

Abstract Proteotoxicity from insufficient clearance of misfolded/damaged proteins underlies many diseases. Carboxyl terminus of Hsc70-interacting protein (CHIP) is an important regulator of proteostasis in many cells, having E3-ligase and chaperone functions and often directing damaged proteins towards proteasome recycling. While enhancing CHIP functionality has broad therapeutic potential, prior efforts have all relied on genetic upregulation. Here we report that CHIP-mediated protein turnover is markedly post-translationally enhanced by direct protein kinase G (PKG) phosphorylation at S20 (mouse, S19 human). This increases CHIP binding affinity to Hsc70, CHIP protein half-life, and consequent clearance of stress-induced ubiquitinated-insoluble proteins. PKG-mediated CHIP-pS20 or expressing CHIP-S20E (phosphomimetic) reduces ischemic proteo- and cytotoxicity, whereas a phospho-silenced CHIP-S20A amplifies both. In vivo, depressing PKG activity lowers CHIP-S20 phosphorylation and protein, exacerbating proteotoxicity and heart dysfunction after ischemic injury. CHIP-S20E knock-in mice better clear ubiquitinated proteins and are cardio-protected. PKG activation provides post-translational enhancement of protein quality control via CHIP.

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In vivo analysis of protein quality control in response to aging using transgenic mice

Acta Ophthalmologica ◽

10.1111/j.1755-3768.2013.s076.x ◽

2013 ◽

Vol 91 ◽

pp. 0-0

Author(s):

C MARQUES ◽

P MATAFOME ◽

A SANTOS ◽

C LOBO ◽

F SHANG ◽

...

Keyword(s):

Quality Control ◽

Transgenic Mice ◽

Protein Quality ◽

Protein Quality Control ◽

In Vivo Analysis

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Molecular chaperones and stress-inducible protein-sorting factors coordinate the spatiotemporal distribution of protein aggregates

Molecular Biology of the Cell ◽

10.1091/mbc.e12-03-0194 ◽

2012 ◽

Vol 23 (16) ◽

pp. 3041-3056 ◽

Cited By ~ 126

Author(s):

Liliana Malinovska ◽

Sonja Kroschwald ◽

Matthias C. Munder ◽

Doris Richter ◽

Simon Alberti

Keyword(s):

Quality Control ◽

Molecular Chaperones ◽

Cellular Response ◽

Protein Quality ◽

Acute Stress ◽

Protein Sorting ◽

Protein Quality Control ◽

Normal Growth ◽

Small Heat Shock Protein ◽

Misfolded Proteins

Acute stress causes a rapid redistribution of protein quality control components and aggregation-prone proteins to diverse subcellular compartments. How these remarkable changes come about is not well understood. Using a phenotypic reporter for a synthetic yeast prion, we identified two protein-sorting factors of the Hook family, termed Btn2 and Cur1, as key regulators of spatial protein quality control in Saccharomyces cerevisiae. Btn2 and Cur1 are undetectable under normal growth conditions but accumulate in stressed cells due to increased gene expression and reduced proteasomal turnover. Newly synthesized Btn2 can associate with the small heat shock protein Hsp42 to promote the sorting of misfolded proteins to a peripheral protein deposition site. Alternatively, Btn2 can bind to the chaperone Sis1 to facilitate the targeting of misfolded proteins to a juxtanuclear compartment. Protein redistribution by Btn2 is accompanied by a gradual depletion of Sis1 from the cytosol, which is mediated by the sorting factor Cur1. On the basis of these findings, we propose a dynamic model that explains the subcellular distribution of misfolded proteins as a function of the cytosolic concentrations of molecular chaperones and protein-sorting factors. Our model suggests that protein aggregation is not a haphazard process but rather an orchestrated cellular response that adjusts the flux of misfolded proteins to the capacities of the protein quality control system.

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The Cochaperone HspBP1 Inhibits the CHIP Ubiquitin Ligase and Stimulates the Maturation of the Cystic Fibrosis Transmembrane Conductance Regulator

Molecular Biology of the Cell ◽

10.1091/mbc.e04-04-0293 ◽

2004 ◽

Vol 15 (9) ◽

pp. 4003-4010 ◽

Cited By ~ 116

Author(s):

Simon Alberti ◽

Karsten Böhse ◽

Verena Arndt ◽

Anton Schmitz ◽

Jörg Höhfeld

Keyword(s):

Cystic Fibrosis ◽

Quality Control ◽

Ubiquitin Ligase ◽

Molecular Chaperones ◽

Protein Quality ◽

Regulatory Mechanism ◽

Transmembrane Conductance Regulator ◽

Transmembrane Conductance ◽

Ubiquitin Ligase Activity ◽

Cystic Fibrosis Transmembrane

The CHIP ubiquitin ligase turns molecular chaperones into protein degradation factors. CHIP associates with the chaperones Hsc70 and Hsp90 during the regulation of signaling pathways and during protein quality control, and directs chaperone-bound clients to the proteasome for degradation. Obviously, this destructive activity should be carefully controlled. Here, we identify the cochaperone HspBP1 as an inhibitor of CHIP. HspBP1 attenuates the ubiquitin ligase activity of CHIP when complexed with Hsc70. As a consequence, HspBP1 interferes with the CHIP-induced degradation of immature forms of the cystic fibrosis transmembrane conductance regulator (CFTR) and stimulates CFTR maturation. Our data reveal a novel regulatory mechanism that determines folding and degradation activities of molecular chaperones.

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Integrated protein quality-control pathways regulate free α-globin in murine β-thalassemia

Blood ◽

10.1182/blood-2011-12-397729 ◽

2012 ◽

Vol 119 (22) ◽

pp. 5265-5275 ◽

Cited By ~ 41

Author(s):

Eugene Khandros ◽

Christopher S. Thom ◽

Janine D'Souza ◽

Mitchell J. Weiss

Keyword(s):

Quality Control ◽

Stress Response ◽

Protein Quality ◽

Transcriptional Profiling ◽

Globin Gene ◽

Gene Mutations ◽

Protein Quality Control ◽

Proteasome Inhibition ◽

Protective Mechanisms

Cells remove unstable polypeptides through protein quality-control (PQC) pathways such as ubiquitin-mediated proteolysis and autophagy. In the present study, we investigated how these pathways are used in β-thalassemia, a common hemoglobinopathy in which β-globin gene mutations cause the accumulation and precipitation of cytotoxic α-globin subunits. In β-thalassemic erythrocyte precursors, free α-globin was polyubiquitinated and degraded by the proteasome. These cells exhibited enhanced proteasome activity, and transcriptional profiling revealed coordinated induction of most proteasome subunits that was mediated by the stress-response transcription factor Nrf1. In isolated thalassemic cells, short-term proteasome inhibition blocked the degradation of free α-globin. In contrast, prolonged in vivo treatment of β-thalassemic mice with the proteasome inhibitor bortezomib did not enhance the accumulation of free α-globin. Rather, systemic proteasome inhibition activated compensatory proteotoxic stress-response mechanisms, including autophagy, which cooperated with ubiquitin-mediated proteolysis to degrade free α-globin in erythroid cells. Our findings show that multiple interregulated PQC responses degrade excess α-globin. Therefore, β-thalassemia fits into the broader framework of protein-aggregation disorders that use PQC pathways as cell-protective mechanisms.

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Quality Control of a Transcriptional Regulator by SUMO-Targeted Degradation

Molecular and Cellular Biology ◽

10.1128/mcb.01470-08 ◽

2009 ◽

Vol 29 (7) ◽

pp. 1694-1706 ◽

Cited By ~ 55

Author(s):

Zheng Wang ◽

Gregory Prelich

Keyword(s):

Quality Control ◽

Protein Quality ◽

Temperature Sensitive ◽

Wild Type ◽

Physiological Importance ◽

Sensitive Allele ◽

Quality Control Mechanism ◽

Mutant Phenotypes

ABSTRACT Slx5 and Slx8 are heterodimeric RING domain-containing proteins that possess SUMO-targeted ubiquitin ligase (STUbL) activity in vitro. Slx5-Slx8 and its orthologs are proposed to target SUMO conjugates for ubiquitin-mediated proteolysis, but the only in vivo substrate identified to date is mammalian PML, and the physiological importance of SUMO-targeted ubiquitylation remains largely unknown. We previously identified mutations in SLX5 and SLX8 by selecting for suppressors of a temperature-sensitive allele of MOT1, which encodes a regulator of TATA-binding protein. Here, we demonstrate that Mot1 is SUMOylated in vivo and that disrupting the Slx5-Slx8 pathway by mutation of the target lysines in Mot1, by deletion of SLX5 or the ubiquitin E2 UBC4, or by inhibition of the proteosome suppresses mot1-301 mutant phenotypes and increases the stability of the Mot1-301 protein. The Mot1-301 mutant protein is targeted for proteolysis by SUMOylation to a much greater extent than wild-type Mot1, suggesting a quality control mechanism. In support of this idea, growth of Saccharomyces cerevisiae in the presence of the arginine analog canavanine results in increased SUMOylation and Slx5-Slx8-mediated degradation of wild-type Mot1. These results therefore demonstrate that Mot1 is an in vivo STUbL target in yeast and suggest a role for SUMO-targeted degradation in protein quality control.

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The chaperone Tsr2 regulates Rps26 release and reincorporation from mature ribosomes to enable a reversible, ribosome-mediated response to stress

10.1101/2021.04.05.438496 ◽

2021 ◽

Author(s):

Yoon-Mo Yang ◽

Katrin Karbstein

Keyword(s):

Quality Control ◽

Energy Input ◽

Energy Levels ◽

Ribosome Assembly ◽

Protein Homeostasis ◽

Control Mechanisms ◽

Diamond Blackfan Anemia ◽

Response To Stress

Although ribosome assembly is quality controlled to maintain protein homeostasis, different ribosome populations have been described. How these form, especially under stress conditions that impact energy levels and stop the energy-intensive production of ribosomes, remains unknown. Here we demonstrate how a physiologically relevant ribosome population arises during high Na+ and pH stress via dissociation of Rps26 from fully assembled ribosomes to enable a translational response to these stresses. The chaperone Tsr2 releases Rps26 in the presence of high Na or pH in vitro and is required for Rps26 release in vivo. Moreover, Tsr2 stores free Rps26 and promotes re-incorporation of the protein, thereby repairing the subunit after the stress subsides. Our data implicate a residue in Rps26 involved in Diamond Blackfan Anemia in mediating the effects of Na+. These data demonstrate how different ribosome populations can arise rapidly, without major energy input, and without bypass of quality control mechanisms.

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Molecular Chaperones in Protein Quality Control

BMB Reports ◽

10.5483/bmbrep.2005.38.3.259 ◽

2005 ◽

Vol 38 (3) ◽

pp. 259-265 ◽

Cited By ~ 25

Author(s):

Suk-Yeong Lee ◽

Francis T.F. Tsai

Keyword(s):

Quality Control ◽

Molecular Chaperones ◽

Protein Quality ◽

Protein Quality Control

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