GroEL and the GroEL-GroES Complex

Tolerance to NSAIDs in Actinobacteria From a Mexican Volcano Crater: Genomics and Bioremediation Potential

Non-steroidal anti-inflammatory drugs (NSAIDs) are emerging contaminants that pose significant health and environmental risks due to their persistence, including their presence in drinking water. Bioremediation, particularly through microorganisms such as actinobacteria, offers a sustainable approach to mitigate these pollutants. Actinobacteria from poly-extreme environments exhibit unique genetic and metabolic adaptations, enabling resistance to and degradation of various contaminants. This study aimed to evaluate the tolerance of actinobacteria to NSAIDs and conduct a genomic analysis of a selected strain. Actinobacteria were isolated from the crater of the Chichonal volcano [Chiapas, Mexico), resulting in 16 isolates. Among these, Micrococcus luteus P8SUE1, Micrococcus yunnanensis P9AGU1, and Kocuria rhizophila P1AGU3 demonstrated tolerance to diclofenac, ibuprofen, and paracetamol at concentrations of 1 ppm, 10 ppm, and 100 ppm, respectively. Whole-genome sequencing of M. yunnanensis P9AGU1 identified genes linked to the degradation of aromatic compounds and adaptations to extreme environmental conditions, highlighting its potential for bioremediation applications.

Co-purification of the GroEL chaperone during outer membrane vesicle purification: insights from Aeromonas salmonicida subsp. salmonicida

Outer membrane vesicles (OMVs) are naturally produced by Gram-negative bacteria and originate from their outer membrane. They can be extracted using ultracentrifugation or ultrafiltration using concentration columns, followed by purification with a density gradient. However, these methods may co-purify contaminants with similar physical properties. Several studies have identified GroEL, a chaperonin, as a major protein in OMV preparations. Using Aeromonas salmonicida subsp. salmonicida as a model, we detected GroEL by mass spectrometry and observed it in transmission electron microscopy images as separate from OMVs. As a cytoplasmic protein complex, GroEL is more likely a contaminant resulting from bacterial lysis during growth rather than an intrinsic OMV component. The model A. salmonicida subsp. salmonicida proved valuable in reaching this conclusion because it produces high levels of extracellular GroEL and low amounts of OMVs. This study emphasizes the need for caution when interpreting the presence of GroEL in OMV preparations and highlights the importance of rigorous purification methods to ensure OMV purity.

Evaluation of Maltose-based Mixtures With Lanthanoid Acetates as Electron Staining Reagents for Transmission Electron Microscopy of Extracellular Vesicles and Liposomes

Extracellular vesicles (EVs), including exosomes, have attracted interest as vehicles for intercellular communication. Recognition of EVs as bio-derived nanocolloids allows for advanced fractionation and preparation methods that preserve their integrity. Direct observation of EVs is critical, and negative staining with heavy metal salts is a standard technique in biological transmission electron microscopy for routine morphological analysis and experimental optimization. However, customizations are often required for specific objectives. Uranyl acetate, widely used for its excellent electron scattering properties, allows clear visualization of ultrafine structures but is limited by strict global regulations and its harsh effects on biological membranes. To overcome these challenges, the author investigated lanthanoid series heavy metal salts as alternatives. Among various maltose-based mixtures, a combination of lanthanum and samarium acetates proved effective for observing EV morphology. In addition, replacing maltose with trehalose, which is known to increase water retention, resulted in improved staining characteristics with lanthanum and samarium acetates.

Molecular dynamics simulations suggest novel allosteric modes in the Hsp70 chaperone protein

The Hsp70 chaperone protein system is an essential component of the protein folding and homeostasis machinery in E.Coli. Hsp70 is a three domain, 70 kDa protein which functions as an allosteric system cycling between an ADP-bound state where the three domains are loosely coupled via a flexible interdomain linker and an ATP-bound state where they are tightly coupled into a single entity. The structure-function model of this protein proposes an allosteric connection between the 45 kDa Nucleotide Binding Domain (NBD) and the 25 kDa Substrate Binding Domain (SBD) and Lid Domain which operates through the inter NBD-SBD linker. X-Ray crystallography and NMR spectroscopy have provided structures of the end states of the functional cycle of this protein, bound to ADP and ATP. We have used MD simulations to study the transitions between these end states and allosteric communication in this system. Our results largely validate the experimentally derived allosteric model of function, but shed additional light on the flow of allosteric information in the SBD + Lid. Specifically, we find that the Lid domain has a double-hinged structure with the potential for greater conformational flexibility than was hitherto expected.Communicated by Ramaswamy H. Sarma.

Exploring Novel Antibiotics by Targeting the GroEL/GroES Chaperonin System

Infectious diseases have affected 13.7 million patients, placing a heavy burden on society. Furthermore, inappropriate and unrequited utilization of antibiotics has led to antimicrobial resistance worldwide. However, well-established targeted screening of environmental isolates or compound libraries has produced limited new drugs. The current situation, in which drug development is delayed, bacterial evolution is occurring, and drug resistance is emerging, requires the development of new targets and/or new strategies to combat infections. Some novel antibacterial strategies have been proposed, among which disruption of protein balance by inhibiting transcription and translation machinery is one of the proven effective antimicrobial strategies. Molecular chaperonins could mediate the correct folding of proteins, especially under conditions such as high temperature and pressure. The GroEL/ES system has been confirmed as one of the key molecular chaperones for bacterial viability. Recent data have revealed the antibacterial activities of GroEL/ES-targeted compounds, highlighting the potential role of GroEL/ES in the development of novel antibiotics. In this brief review, we discuss the function of the GroEL/ES system and summarize the inhibitors of the GroEL/ES system. The GroEL/ES system may represent a promising drug target for the exploration of novel antibiotics.

Molecular dynamics simulations shows real-time lid opening in Hsp70 chaperone

The stress-inducible mammalian heat shock protein Hsp70 and its bacterial orthologue DnaK are highly conserved molecular chaperones and a crucial part of the machinery responsible for protein folding and homeostasis. Hsp70 is a three-domain, 70 kDa protein that cycles between an ATP-bound state in which all three domains are securely coupled into one unit and an ADP-bound state in which they are loosely attached via a flexible interdomain linker. The Hsp70 presents an alluring novel therapeutic target since it is crucial for maintaining cellular proteostasis and is particularly crucial to cancer cells. We have performed molecular dynamics simulations of the SBD (substrate binding domain) along with the Lid domain in response to experimental efforts to identify small molecule inhibitors that impair the functioning of Hsp70. Our intent has been to characterize the motion of the SBD/Lid allosteric machinery and in, addition, to identify the effect of the PET16 molecule on this motion. Interestingly, we noticed the opening of the entire Lid domain in the apo-form of the dimer. The configuration of the open structure was very different from previously published structures (PDB 4JN4) of the open and docked conformation of the ATP bound form. MD simulations revealed the Lid to be capable of far greater dynamical excursions than has been anticipated by experimental structural biology. This is of value in future drug discovery efforts targeted to modulating Hsp70 activity. The PET16 molecule appears to be weakly bound and its effect on the dynamics of the complex is yet to be elucidated.

Immunogens in Balamuthia mandrillaris: a proteomic exploration

Balamuthia mandrillaris is the causative agent of granulomatous amoebic encephalitis, a rare and often fatal infection affecting the central nervous system. The amoeba is isolated from diverse environmental sources and can cause severe infections in both immunocompromised and immunocompetent individuals. Given the limited understanding of B. mandrillaris, our research aimed to explore its protein profile, identifying potential immunogens crucial for early granulomatous amoebic encephalitis diagnosis. Cultures of B. mandrillaris and other amoebas were grown under axenic conditions, and total amoebic extracts were obtained. Proteomic analyses, including two-dimensional electrophoresis and mass spectrometry, were performed. A 50-kDa band showed a robust recognition of antibodies from immunized BALB/c mice; peptides contained in this band were matched with elongation factor-1 alpha, which emerged as a putative key immunogen. Besides, lectin blotting revealed the presence of glycoproteins in B. mandrillaris, and confocal microscopy demonstrated the focal distribution of the 50-kDa band throughout trophozoites. Cumulatively, these observations suggest the participation of the 50-kDa band in adhesion and recognition mechanisms. Thus, these collective findings demonstrate some protein characteristics of B. mandrillaris, opening avenues for understanding its pathogenicity and developing diagnostic and therapeutic strategies.

C-shaped dipper: A novel useful auxiliary tool for preparation of specimen grids for transmission electron microscopy

The transmission electron microscopy (TEM) has played a pivotal role in visualizing and detailing the morphology of nanoscale objects of observation, but care must be taken to ensure that the object is in its original, unperturbed state. This is because not all objects under the observation are necessarily robust and structurally stable, and if the object being observed is so delicate and easily changeable in shape, one may be observing structural artifacts leading to wrong interpretations. I here present a novel prototype of an easy-to-use and reliable auxiliary tool, the C-shaped dipper, developed for the preparation of specimen grids for TEM, along with its handling instructions for diverse applications. Some nanostructures are so delicate and fragile that their nanocomplexes are easily destroyed when aspirated by a pipette with a narrow tip diameter. Using the C-shaped dipper, the observation objects can be scooped up in a droplet formed by the surface tension of the liquid, keeping their intact shapes, and placed on a grid precovered with a support film. The C-shaped dipper has proven to be excellent for handling soft assemblies having delicate structures, such as nano-scale composites, for facilitating thin layered formations with molecular constituent blocks, and for preparing a grid individually covered with a collodion film or an amorphous carbon support film.

Function and Fiber-Type Specific Distribution of Hsp60 and αB-Crystallin in Skeletal Muscles: Role of Physical Exercise

Simple Summary

Skeletal muscle represents about 40% of the body mass in humans and it is a copious and plastic tissue, rich in proteins that are subject to continuous rearrangements. Physical exercise is considered a physiological stressor for different organs, in particular for skeletal muscle, and it is a factor able to stimulate the cellular remodeling processes related to the phenomenon of adaptation. All cells respond to various stress conditions by up-regulating the expression and/or activation of a group of proteins called heat shock proteins (HSPs). Although their expression is induced by several stimuli, they are commonly recognized as HSPs due to the first experiments showing their increased transcription after application of heat shock. These proteins are molecular chaperones mainly involved in assisting protein transport and folding, assembling multimolecular complexes, and triggering protein degradation by proteasome. Among the HSPs, a special attention needs to be devoted to Hsp60 and αB-crystallin, proteins constitutively expressed in the skeletal muscle, where they are known to be important in muscle physiopathology. Therefore, here we provide a critical update on their role in skeletal muscle fibers after physical exercise, highlighting the control of their expression, their biological function, and their specific distribution within skeletal muscle fiber-types.

Abstract

Skeletal muscle is a plastic and complex tissue, rich in proteins that are subject to continuous rearrangements. Skeletal muscle homeostasis can be affected by different types of stresses, including physical activity, a physiological stressor able to stimulate a robust increase in different heat shock proteins (HSPs). The modulation of these proteins appears to be fundamental in facilitating the cellular remodeling processes related to the phenomenon of training adaptations such as hypertrophy, increased oxidative capacity, and mitochondrial activity. Among the HSPs, a special attention needs to be devoted to Hsp60 and αB-crystallin (CRYAB), proteins constitutively expressed in the skeletal muscle, where their specific features could be highly relevant in understanding the impact of different volumes of training regimes on myofiber types and in explaining the complex picture of exercise-induced mechanical strain and damaging conditions on fiber population. This knowledge could lead to a better personalization of training protocols with an optimal non-harmful workload in populations of individuals with different needs and healthy status. Here, we introduce for the first time to the reader these peculiar HSPs from the perspective of exercise response, highlighting the control of their expression, biological function, and specific distribution within skeletal muscle fiber-types.

Stress proteins: the biological functions in virus infection, present and challenges for target-based antiviral drug development

Stress proteins (SPs) including heat-shock proteins (HSPs), RNA chaperones, and ER associated stress proteins are molecular chaperones essential for cellular homeostasis. The major functions of HSPs include chaperoning misfolded or unfolded polypeptides, protecting cells from toxic stress, and presenting immune and inflammatory cytokines. Regarded as a double-edged sword, HSPs also cooperate with numerous viruses and cancer cells to promote their survival. RNA chaperones are a group of heterogeneous nuclear ribonucleoproteins (hnRNPs), which are essential factors for manipulating both the functions and metabolisms of pre-mRNAs/hnRNAs transcribed by RNA polymerase II. hnRNPs involve in a large number of cellular processes, including chromatin remodelling, transcription regulation, RNP assembly and stabilization, RNA export, virus replication, histone-like nucleoid structuring, and even intracellular immunity. Dysregulation of stress proteins is associated with many human diseases including human cancer, cardiovascular diseases, neurodegenerative diseases (e.g., Parkinson’s diseases, Alzheimer disease), stroke and infectious diseases. In this review, we summarized the biologic function of stress proteins, and current progress on their mechanisms related to virus reproduction and diseases caused by virus infections. As SPs also attract a great interest as potential antiviral targets (e.g., COVID-19), we also discuss the present progress and challenges in this area of HSP-based drug development, as well as with compounds already under clinical evaluation.

Global mRNA decay and 23S rRNA fragmentation in Gluconobacter oxydans 621H

Background

Gluconobacter oxydans is a strictly aerobic Gram-negative acetic acid bacterium used industrially for oxidative biotransformations due to its exceptional type of catabolism. It incompletely oxidizes a wide variety of carbohydrates regio- and stereoselectively in the periplasm using membrane-bound dehydrogenases with accumulation of the products in the medium. As a consequence, only a small fraction of the carbon and energy source enters the cell, resulting in a low biomass yield. Additionally, central carbon metabolism is characterized by the absence of a functional glycolysis and absence of a functional tricarboxylic acid (TCA) cycle. Due to these features, G. oxydans is a highly interesting model organism. Here we analyzed global mRNA decay in G. oxydans to describe its characteristic features and to identify short-lived mRNAs representing potential bottlenecks in the metabolism for further growth improvement by metabolic engineering.

Results

Using DNA microarrays we estimated the mRNA half-lives in G. oxydans. Overall, the mRNA half-lives ranged mainly from 3 min to 25 min with a global mean of 5.7 min. The transcripts encoding GroES and GroEL required for proper protein folding ranked at the top among transcripts exhibiting both long half-lives and high abundance. The F-type H⁺-ATP synthase transcripts involved in energy metabolism ranked among the transcripts with the shortest mRNA half-lives. RNAseq analysis revealed low expression levels for genes of the incomplete TCA cycle and also the mRNA half-lives of several of those were short and below the global mean. The mRNA decay analysis also revealed an apparent instability of full-length 23S rRNA. Further analysis of the ribosome-associated rRNA revealed a 23S rRNA fragmentation pattern exhibiting new cleavage regions in 23S rRNAs which were previously not known.

Conclusions

The very short mRNA half-lives of the H⁺-ATP synthase, which is likely responsible for the ATP-proton motive force interconversion in G. oxydans under many or most conditions, is notably in contrast to mRNA decay data from other bacteria. Together with the short mRNA half-lives and low expression of some other central metabolic genes it could limit intended improvements of G. oxydans’ biomass yield by metabolic engineering. Also, further studies are needed to unravel the multistep process of the 23S rRNA fragmentation in G. oxydans.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5111-1) contains supplementary material, which is available to authorized users.

Chaperonin of Group I: Oligomeric Spectrum and Biochemical and Biological Implications

Chaperonins play various physiological roles and can also be pathogenic. Elucidation of their structure, e.g., oligomeric status and post-translational modifications (PTM), is necessary to understand their functions and mechanisms of action in health and disease. Group I chaperonins form tetradecamers with two stacked heptameric rings. The tetradecamer is considered the typical functional complex for folding of client polypeptides. However, other forms such as the monomer and oligomers with smaller number of subunits than the classical tetradecamer, also occur in cells. The properties and functions of the monomer and oligomers, and their roles in chaperonin-associated diseases are still incompletely understood. Chaperonin I in eukaryotes occurs in various locations, not just the mitochondrion, which is its canonical place of residence and function. Eukaryotic Chaperonin I, namely Hsp60 (designated HSP60 or HSPD1 in humans) has, indeed, been found in the cytosol; the plasma-cell membrane; on the outer surface of cells; in the intercellular space; in biological liquids such as lymph, blood, and cerebrospinal fluid; and in secretions, for instance saliva and urine. Hsp60 has also been found in cell-derived vesicles such as exosomes. The functions of Hsp60 in all these non-canonical locales are still poorly characterized and one of the questions not yet answered is in what form, i.e., monomer or oligomer, is the chaperonin present in these non-canonical locations. In view of the steady increase in interest on chaperonopathies over the last several years, we have studied human HSP60 to determine its role in various diseases, its locations in cells and tissues and migrations in the body, and its post-translational modifications that might have an impact on its location and function. We also carried out experiments to characterize the oligomeric status of extramitochondrial of HSP60 in solution. Here, we provide an overview of our results, focusing on the oligomeric equilibrium and stability of the various forms of HSP60 in comparison with GroEL. We also discuss post-translational modifications associated with anti-cancer drugs to indicate the potential of Hsp60 in Medicine, as a biomarker and etiopathogenic factor.

Heat Shock Proteins in Histoplasma and Paracoccidioides

Heat shock proteins (Hsps) are highly conserved biomolecules that are constitutively expressed and generally upregulated in response to various stress conditions (biotic and abiotic). Hsps have diverse functions, categorizations, and classifications. Their adaptive expression in fungi indicates their significance in these diverse species, particularly in dimorphic pathogens. Histoplasma capsulatum and Paracoccidioides species are dimorphic fungi that are the causative agents of histoplasmosis and paracoccidioidomycosis, respectively. This minireview focuses on the pathobiology of Hsps, with particular emphasis on their roles in the morphogenesis and virulence of Histoplasma and Paracoccidioides and the potential roles of active and passive immunization against Hsps in protection against infection with these fungi.