scholarly journals PDZ Domains in Microorganisms: Link Between Stress Response and Protein Synthesis

2017 ◽  
Author(s):  
Vijaykumar Yogesh Muley ◽  
Sanjeev Galande

AbstractThe PSD-95/Dlg-A/ZO-1 (PDZ) domain is highly expanded and diversified in metazoan where it is known to assemble diverse signalling components by virtue of interactions with other proteins in sequence-specific manner. In contrast, in bacteria it monitors protein quality control during stress response. The distribution, functions and origin of PDZ domain-containing proteins in prokaryotes are largely unknown. We analyzed 7,852 PDZ domain-containing proteins in 1,474 prokaryotes and fungi. PDZ domains are abundant in eubacteria; and, this study confirms their occurrence also in archaea and fungi. Of all eubacterial PDZ domain-containing proteins, 89% are predicted to be membrane and periplasmic, explaining the depletion of bacterial domain forms in metazoan. Planctomycetes, myxobacteria and other eubacteria occupying terrestrial and aquatic niches encode more domain copies, which may have contributed towards multi-cellularity and prokaryotic-eukaryotic transition. Over 93% of the 7,852 PDZ-containing proteins classified into 12 families including 6 novel families. Out of these 88% harbour eight different protease domains, suggesting their substrate-specificity is guided by PDZ domains. The genomic context provides tantalizing insight towards the functions associated with PDZ domains and reinforces their involvement in protein synthesis. We propose that the highly variable PDZ domain of the uncharacterized Fe-S oxidoreductase superfamily, exclusively found in gladobacteria and several anaerobes and acetogens, may have preceded all existing PDZ domains.

Blood ◽  
2012 ◽  
Vol 119 (22) ◽  
pp. 5265-5275 ◽  
Author(s):  
Eugene Khandros ◽  
Christopher S. Thom ◽  
Janine D'Souza ◽  
Mitchell J. Weiss

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.


iScience ◽  
2020 ◽  
Vol 23 (11) ◽  
pp. 101725 ◽  
Author(s):  
Susanna Boronat ◽  
Luis Marte ◽  
Montserrat Vega ◽  
Sarela García-Santamarina ◽  
Margarita Cabrera ◽  
...  

mBio ◽  
2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Antoine Delhaye ◽  
Jean-François Collet ◽  
Géraldine Laloux

ABSTRACTThe envelope of Gram-negative bacteria is an essential compartment that constitutes a protective and permeability barrier between the cell and its environment. The envelope also hosts the cell wall, a mesh-like structure made of peptidoglycan (PG) that determines cell shape and provides osmotic protection. Since the PG must grow and divide in a cell-cycle-synchronized manner, its synthesis and remodeling are tightly regulated. Here, we discovered that PG homeostasis is intimately linked to the levels of activation of the Cpx system, an envelope stress response system traditionally viewed as being involved in protein quality control in the envelope. We first show that Cpx is activated when PG integrity is challenged and that this activation provides protection to cells exposed to antibiotics inhibiting PG synthesis. By rerouting the outer membrane lipoprotein NlpE, a known Cpx activator, to a different envelope subcompartment, we managed to manipulate Cpx activation levels. We found that Cpx overactivation leads to aberrant cellular morphologies, to an increased sensitivity to β-lactams, and to dramatic division and growth defects, consistent with a loss of PG homeostasis. Remarkably, these phenotypes were largely abrogated by the deletion ofldtD, a Cpx-induced gene involved in noncanonical PG cross-linkage, suggesting that this transpeptidase is an important link between PG homeostasis and the Cpx system.Altogether our data show that fine-tuning of an envelope quality control system constitutes an important layer of regulation of the highly organized cell wall structure.IMPORTANCEThe envelope of Gram-negative bacteria is essential for viability. First, it includes the cell wall, a continuous polymer of peptidoglycan (PG) that determines cell morphology and protects against osmotic stress. Moreover, the envelope constitutes a protective barrier between the cell interior and the environment. Therefore, mechanisms called envelope stress response systems (ESRS) exist to monitor and defend envelope integrity against harmful conditions. Cpx is a major ESRS that detects and manages the accumulation of misfolded proteins in the envelope ofEscherichia coli. We found that this protein quality control system also plays a fundamental role in the regulation of PG assembly. Strikingly, the level of Cpx response is critical, as an excessive activation leads to phenotypes associated with a loss of cell wall integrity. Thus, by contributing to PG homeostasis, the Cpx system lies at the crossroads between key processes of bacterial life, including cell shape, growth, division, and antibiotic resistance.


2020 ◽  
Author(s):  
Darius Šulskis ◽  
Johannes Thoma ◽  
Björn M. Burmann

AbstractProtein quality control is an essential cellular function and it is mainly executed by a large array of proteases and molecular chaperones. One of the bacterial HtrA protein family members, the homo-oligomeric DegP-protease, plays a crucial role in the Escherichia coli (E. coli) protein quality control machinery by removing unfolded proteins or preventing them from aggregation and chaperoning them until they are properly folded within the periplasm. DegP contains two regulatory PDZ domains, which play key roles in substrate recognition as well as in the transformation of DegP to proteolytic cage-like structures. Here, we analyse the interaction and dynamics of the PDZ-domains of DegP underlying this transformation in solution by high-resolution NMR spectroscopy. We identify an interdomain molecular lock guiding the interactions between both PDZ domains, regulated by fine-tuned protein dynamics and potentially conserved in proteins harboring tandem PDZ domains.


2013 ◽  
Vol 3 (10) ◽  
pp. 400 ◽  
Author(s):  
Kohta Ohnishi ◽  
Kazuhiro Irie ◽  
Akira Murakami

Background: Phytochemicals are secondary metabolites of plants that are produced for their defense against environmental stresses, such as polyphenols, which are considered to play a major role in protection against ultraviolet (UV) light-induced oxidative damage, as well as anti-fungal and anti-microbial activities. In addition, there is a great body of evidence showing that phytochemicals exhibit a wide array of physiological activities in humans. Accumulated data show that the bioavailability of most, if not all, phytochemicals is quite poor and their substantial biotransformation after ingestion has also been noted. Thus, they are characterized as non-nutritive xenobiotics in animals, and the question of why phytochemicals, which are produced for plant self-defense, have beneficial effects in humans is quite intriguing. Meanwhile, stress-induced denaturing of cellular proteins greatly affects their tertiary structure and critically disrupts their biological functions, occasionally leading to aggregation for the onset of some pathology. Many recent studies have indicated that protein quality control (PQC) systems play key roles in counteracting ‘proteo-stress’, which is comprised of several processes, including protein refolding by heat shock proteins (HSPs) and degradation of abnormal proteins by the ubiquitin-proteasome system as well as autophagy.Objective: Phytochemicals are xenobiotics, thus their biochemical interactions with animal proteins are considered to occur in a non-specific manner, which raises the possibility that some phytochemicals cause proteo-stress for activating PQC systems. Because their status is thought to be a critical determinant of homeostasis, the physiological functions of phytochemicals may be partially mediated through those unique systems. The present study was thus undertaken to address this possibility. Methods and Results: We focused on zerumbone (ZER), an electrophilic sesquiterpene present in Zingiber zerumbet Smith (shampoo ginger). This agent has been reported to exhibit various bioactivities, including anti-inflammation and cancer prevention[1,2]. Treatment of Hepa1c1c7 mouse hepatoma cells with ZER resulted in marked up-regulation of multiple HSPs, such as HSP40 and HSP70. Furthermore, oral administration to the nematode Caenorhabditis elegans and SD rats increased the expressions of some HSPs[3]. Interestingly, ZER also increased proteasome activity in Hepa1c1c7 cells, which was accompanied with up-regulation of 5, a major proteasome functional protein. In addition, the agent notably up-regulated the expressions of several pro-autophagic markers, including p62 and microtubule-associated protein 1 light-chain 3 (LC3)-II[4]. Experiments with biotin-labeled ZER as well as a specific antibody against ZER-adduct proteins revealed that it binds numerous cellular proteins in a non-specific manner. Along a similar line, incubation with ZER led to formations of p62-conjugated proteins and aggresomes. Together, these results suggest that ZER causes proteo-stress for potentiating the integrity of PQC systems. In support of this notion, ZER-bound proteins have been suggested to be partially recognized by HSP90, leading to dissociation of heat shok factor 1 (HSF1) from HSP90 for inducing multiple HSP genes. Next we speculated that mild chemical stress by ZER may exert beneficial effects, since ZER-bound proteins were time-dependently degraded, suggesting that defense capacity was amplified to a great level as compared with the non-treated condition. As expected, ZER conferred thermoresistance to Caenorhabditis elegans (C. elegans) and suppressed the proteo-toxicity of 4-hydroxy-2-nonenal, a potent electrophile produced through a lipid peroxidation process, in a p62-dependent manner. We then screened a number of nutrients and phytochemicals for their HSP70 inducibility, and found that certain phytochemicals, such as curcumin, phenethyl isothiocyanate, ursolic acid, and lycopene, were significantly active, whereas most nutrients were virtually inactive. These results may be associated with the fact that phytochemicals, but not nutrients, are foreign chemicals to animals, as noted above.Conclusion: Up-regulation of antioxidant and xenobiotics metabolizing enzymes has been reported to be an adaptive response in animals exposed to phytochemicals. Our present results imply that the process also increases the capacity to counteract proteo-stresses through activation of PQC systems. This putative phenomenon, representing the concept of hormesis[5], may be associated with mechanisms underlying the physiological functions of phytochemicals. Therefore, chronic ingestion of this class of chemicals may result in ‘chemical training’, in which self-defense systems are continuously activated for adaptation to phytochemical-driven stresses.Key words: heat shock proteins, ubiquitin-proteasome system, autophagy, C. elegans


2020 ◽  
Vol 48 (7) ◽  
pp. 3888-3905
Author(s):  
Arnab Ghosh ◽  
Loren Dean Williams ◽  
Dimitri G Pestov ◽  
Natalia Shcherbik

Abstract Cells continuously monitor protein synthesis to prevent accumulation of aberrant polypeptides. Insufficient capacity of cellular degradative systems, chaperone shortage or high levels of mistranslation by ribosomes can result in proteotoxic stress and endanger proteostasis. One of the least explored reasons for mistranslation is the incorrect functioning of the ribosome itself. To understand how cells deal with ribosome malfunction, we introduced mutations in the Expansion Segment 7 (ES7L) of 25S rRNA that allowed the formation of mature, translationally active ribosomes but induced proteotoxic stress and compromised cell viability. The ES7L-mutated ribosomes escaped nonfunctional rRNA Decay (NRD) and remained stable. Remarkably, ES7L-mutated ribosomes showed increased segregation into cytoplasmic foci containing soluble misfolded proteins. This ribosome entrapment pathway, termed TRAP (Translational Relocalization with Aberrant Polypeptides), was generalizable beyond the ES7L mutation, as wild-type ribosomes also showed increased relocalization into the same compartments in cells exposed to proteotoxic stressors. We propose that during TRAP, assembled ribosomes associated with misfolded nascent chains move into cytoplasmic compartments enriched in factors that facilitate protein quality control. In addition, TRAP may help to keep translation at its peak efficiency by preventing malfunctioning ribosomes from active duty in translation.


2019 ◽  
Vol 2 (1) ◽  
pp. e201800219 ◽  
Author(s):  
Uwe Richter ◽  
Kah Ying Ng ◽  
Fumi Suomi ◽  
Paula Marttinen ◽  
Taina Turunen ◽  
...  

Mitochondria have a compartmentalized gene expression system dedicated to the synthesis of membrane proteins essential for oxidative phosphorylation. Responsive quality control mechanisms are needed to ensure that aberrant protein synthesis does not disrupt mitochondrial function. Pathogenic mutations that impede the function of the mitochondrial matrix quality control protease complex composed of AFG3L2 and paraplegin cause a multifaceted clinical syndrome. At the cell and molecular level, defects to this quality control complex are defined by impairment to mitochondrial form and function. Here, we establish the etiology of these phenotypes. We show how disruptions to the quality control of mitochondrial protein synthesis trigger a sequential stress response characterized first by OMA1 activation followed by loss of mitochondrial ribosomes and by remodelling of mitochondrial inner membrane ultrastructure. Inhibiting mitochondrial protein synthesis with chloramphenicol completely blocks this stress response. Together, our data establish a mechanism linking major cell biological phenotypes of AFG3L2 pathogenesis and show how modulation of mitochondrial protein synthesis can exert a beneficial effect on organelle homeostasis.


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