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Cell Stress & Chaperones Sep 2023Chaperone proteins have crucial roles to play in all animal species and are involved in mediating both the folding of newly synthesized peptides into their mature... (Review)
Review
Chaperone proteins have crucial roles to play in all animal species and are involved in mediating both the folding of newly synthesized peptides into their mature conformation, the refolding of misfolded proteins, and the trafficking of proteins between subcellular compartments. These highly conserved proteins have particularly important roles to play in dealing with disruptions of the proteome as a result of environmental stress since abiotic factors, including temperature, pressure, oxygen, water availability, and pollutants can readily disrupt the conformation and/or function of all types of proteins, e.g., enzymes, transporters, and structural proteins. The current review provides an update on recent advances in understanding the roles and responses of chaperones in aiding animals to deal with environmental stress, offering new information on chaperone action in supporting survival strategies including torpor, hibernation, anaerobiosis, estivation, and cold/freeze tolerance among both vertebrate and invertebrate species.
Topics: Animals; Heat-Shock Proteins; Molecular Chaperones; Protein Folding; Cold Temperature; Temperature
PubMed: 36441380
DOI: 10.1007/s12192-022-01312-x -
International Journal of Molecular... May 2024Metals are dispersed in natural environments, particularly in the aquatic environment, and accumulate, causing adverse effects on aquatic life. Moreover, chronic... (Review)
Review
Metals are dispersed in natural environments, particularly in the aquatic environment, and accumulate, causing adverse effects on aquatic life. Moreover, chronic polymetallic water pollution is a common problem, and the biological effects of exposure to complex mixtures of metals are the most difficult to interpret. In this review, metal toxicity is examined with a focus on its impact on energy metabolism. Mechanisms regulating adenosine triphosphate (ATP) production and reactive oxygen species (ROS) emission are considered in their dual roles in the development of cytotoxicity and cytoprotection, and mitochondria may become target organelles of metal toxicity when the transmembrane potential is reduced below its phosphorylation level. One of the main consequences of metal toxicity is additional energy costs, and the metabolic load can lead to the disruption of oxidative metabolism and enhanced anaerobiosis.
Topics: Animals; Adenosine Triphosphate; Energy Metabolism; Fishes; Metals; Mitochondria; Oxidative Stress; Reactive Oxygen Species; Water Pollutants, Chemical
PubMed: 38732234
DOI: 10.3390/ijms25095015 -
Cellular & Molecular Biology Letters Jul 2023The preference for glucose oxidative mode has crucial impacts on various physiological activities, including determining stem cell fate. External mechanical factors can...
BACKGROUND
The preference for glucose oxidative mode has crucial impacts on various physiological activities, including determining stem cell fate. External mechanical factors can play a decisive role in regulating critical metabolic enzymes and pathways of stem cells. Periodontal ligament stem cells (PDLSCs) are momentous effector cells that transform mechanical force into biological signals during the reconstruction of alveolar bone. However, mechanical stimuli-induced alteration of oxidative characteristics in PDLSCs and the underlying mechanisms have not been fully elucidated.
METHODS
Herein, we examined the expression of LDH and COX4 by qRT-PCR, western blot, immunohistochemistry and immunofluorescence. We detected metabolites of lactic acid and reactive oxygen species for functional tests. We used tetramethylrhodamine methyl ester (TMRM) staining and a transmission electron microscope to clarify the mitochondrial status. After using western blot and immunofluorescence to clarify the change of DRP1, we further examined MFF, PINK1, and PARKIN by western blot. We used cyclosporin A (CsA) to confirm the regulation of mitophagy and ceased the stretching as a rescue experiment.
RESULTS
Herein, we ascertained that mechanical force could increase the level of LDH and decrease the expression of COX4 in PDLSCs. Simultaneously, the yield of reactive oxygen species (ROS) in PDLSC reduced after stretching, while lactate acid augmented significantly. Furthermore, mitochondrial function in PDLSCs was negatively affected by impaired mitochondrial membrane potential (MMP) under mechanical force, and the augment of mitochondrial fission further induced PRKN-dependent mitophagy, which was confirmed by the rescue experiments via blocking mitophagy. As a reversible physiological stimulation, the anaerobic preference of PDLSCs altered by mechanical force could restore after the cessation of force stimulation.
CONCLUSIONS
Altogether, our study demonstrates that PDLSCs under mechanical force preferred anaerobic oxidation induced by the affected mitochondrial dynamics, especially mitophagy. Our findings support an association between mechanical stimulation and the oxidative profile of stem cells, which may shed light on the mechanical guidance of stem cell maintenance and commitment, and lay a molecular foundation for periodontal tissue regeneration.
Topics: Periodontal Ligament; Anaerobiosis; Mitophagy; Reactive Oxygen Species; Oxidation-Reduction
PubMed: 37480044
DOI: 10.1186/s11658-023-00453-w -
MBio Aug 2023Polyphenols are abundant in nature, and their anaerobic biodegradation by gut and soil bacteria is a topic of great interest. The O requirement of phenol oxidases is...
Polyphenols are abundant in nature, and their anaerobic biodegradation by gut and soil bacteria is a topic of great interest. The O requirement of phenol oxidases is thought to explain the microbial inertness of phenolic compounds in anoxic environments, such as peatlands, termed the enzyme latch hypothesis. A caveat of this model is that certain phenols are known to be degraded by strict anaerobic bacteria, although the biochemical basis for this process is incompletely understood. Here, we report the discovery and characterization of a gene cluster in the environmental bacterium for the degradation phloroglucinol (1,3,5-trihydroxybenzene), a key intermediate in the anaerobic degradation of flavonoids and tannins, which constitute the most abundant polyphenols in nature. The gene cluster encodes the key C-C cleavage enzyme dihydrophloroglucinol cyclohydrolase, as well as ()-3-hydroxy-5-oxo-hexanoate dehydrogenase and triacetate acetoacetate-lyase, which enable phloroglucinol to be utilized as a carbon and energy source. Bioinformatics studies revealed the presence of this gene cluster in phylogenetically and metabolically diverse gut and environmental bacteria, with potential impacts on human health and carbon preservation in peat soils and other anaerobic environmental niches. IMPORTANCE This study provides novel insights into the microbiota's anaerobic metabolism of phloroglucinol, a critical intermediate in the degradation of polyphenols in plants. Elucidation of this anaerobic pathway reveals enzymatic mechanisms for the degradation of phloroglucinol into short-chain fatty acids and acetyl-CoA, which are used as a carbon and energy source for bacterium growth. Bioinformatics studies suggested the prevalence of this pathway in phylogenetically and metabolically diverse gut and environmental bacteria, with potential impacts on carbon preservation in peat soils and human gut health.
Topics: Humans; Phloroglucinol; Anaerobiosis; Bacteria; Bacteria, Anaerobic; Phenols; Polyphenols; Soil
PubMed: 37341492
DOI: 10.1128/mbio.01099-23 -
Applied and Environmental Microbiology Jun 2024In the next decades, the increasing material and energetic demand to support population growth and higher standards of living will amplify the current pressures on... (Review)
Review
In the next decades, the increasing material and energetic demand to support population growth and higher standards of living will amplify the current pressures on ecosystems and will call for greater investments in infrastructures and modern technologies. A valid approach to overcome such future challenges is the employment of sustainable bio-based technologies that explore the metabolic richness of microorganisms. Collectively, the metabolic capabilities of , spanning aerobic and anaerobic conditions, thermophilic adaptability, anoxygenic photosynthesis, and utilization of toxic compounds as electron acceptors, underscore the phylum's resilience and ecological significance. These diverse metabolic strategies, driven by the interplay between temperature, oxygen availability, and energy metabolism, exemplify the complex adaptations that enabled to colonize a wide range of ecological niches. In demonstrating the metabolic richness of the phylum, specific members exemplify the diverse capabilities of these microorganisms: showcases adaptability through its thermophilic and phototrophic growth, whereas members of the class are known for their role in the degradation of complex organic compounds, contributing significantly to the carbon cycle in anaerobic environments, highlighting the phylum's potential for biotechnological exploitation in varying environmental conditions. In this context, the metabolic diversity of must be considered a promising asset for a large range of applications. Currently, this bacterial phylum is organized into eight classes possessing different metabolic strategies to survive and thrive in a wide variety of extreme environments. This review correlates the ecological role of in such environments with the potential application of their metabolisms in biotechnological approaches.
Topics: Biotechnology; Chloroflexi; Anaerobiosis
PubMed: 38709098
DOI: 10.1128/aem.01756-23 -
Current Opinion in Microbiology Oct 2023Anaerobic and microaerophilic environments are pervasive in nature, providing essential contributions to the maintenance of human health, biogeochemical cycles and the... (Review)
Review
Anaerobic and microaerophilic environments are pervasive in nature, providing essential contributions to the maintenance of human health, biogeochemical cycles and the Earth's climate. These ecological niches are characterised by low free oxygen and oxidants, or lack thereof. Under these conditions, interactions between species are essential for supporting the growth of syntrophic species and maintaining thermodynamic feasibility of anaerobic fermentation. Kinetic models provide a simplified view of complex metabolic networks, while genome-scale metabolic models and flux-balance analysis (FBA) aim to unravel these systems as a whole. The target of this review is to outline the main similarities, differences and challenges associated with kinetic and metabolic modelling, and describe state-of-the-art modelling practices for studying syntrophies in the anaerobic digestion (AD) case study.
Topics: Humans; Anaerobiosis; Fermentation; Metabolic Networks and Pathways; Microbial Interactions
PubMed: 37542746
DOI: 10.1016/j.mib.2023.102363 -
Microbial Physiology 2024The denitrifying betaproteobacterium Aromatoleum aromaticum EbN1T is a facultative anaerobic degradation specialist and belongs to the environmental bacteria studied... (Review)
Review
The denitrifying betaproteobacterium Aromatoleum aromaticum EbN1T is a facultative anaerobic degradation specialist and belongs to the environmental bacteria studied best on the proteogenomic level. This review summarizes the current state of knowledge about the anaerobic and aerobic degradation (to CO2) of 47 organic growth substrates (23 aromatic, 21 aliphatic, and 3 amino acids) as well as the modes of respiratory energy conservation (denitrification vs. O2-respiration). The constructed catabolic network is comprised of 256 genes, which occupy ∼7.5% of the coding regions of the genome. In total, 219 encoded proteins have been identified by differential proteomics, yielding a proteome coverage of ∼74% of the network. Its degradation section is composed of 31 peripheral and 4 central pathways, with several peripheral modules (e.g., for 4-ethylphenol, 2-phenylethylamine, indoleacetate, and phenylpropanoids) discovered only after the complete genome [Arch Microbiol. 2005 Jan;183(1):27-36] and a first proteomic survey [Proteomics. 2007 Jun;7(13):2222-39] of A. aromaticum EbN1T were reported. The activation of recalcitrant aromatic compounds involves a suite of biochemically intriguing reactions ranging from C-H-bond activation (e.g., ethylbenzene dehydrogenase) via carboxylation (e.g., acetophenone carboxylase) to oxidative deamination (e.g., benzylamine), reductive dearomatization (benzoyl-CoA), and epoxide-forming oxygenases (e.g., phenylacetyl-CoA). The peripheral reaction sequences are substrate-specifically induced, mediated by specific transcriptional regulators with in vivo response thresholds in the nanomolar range. While lipophilic substrates (e.g., phenolics) enter the cells via passive diffusion, polar ones require active uptake that is driven by specific transporters. Next to the protein repertoire for canonical complexes I-III, denitrification, and O2-respiration (low- and high-affinity oxidases), the genome encodes an Ndh-II, a tetrathionate reductase, two ETF:quinone oxidoreductases, and two Rnf-type complexes, broadening the electron transfer flexibility of the strain. Taken together, the detailed catabolic network presented here forms a solid basis for future systems biology-level studies with A. aromaticum EbN1T.
Topics: Bacterial Proteins; Anaerobiosis; Metabolic Networks and Pathways; Aerobiosis; Proteome; Proteomics; Denitrification; Rhodocyclaceae
PubMed: 37816339
DOI: 10.1159/000534425 -
Environmental Science and Pollution... Aug 2023Sewage sludge is regarded by wastewater treatment plants as problematic, from a financial and managerial point of view. Thus, a variety of disposal routes are used, but... (Review)
Review
Sewage sludge is regarded by wastewater treatment plants as problematic, from a financial and managerial point of view. Thus, a variety of disposal routes are used, but the most popular is methane fermentation. The proportion of macromolecular compounds in sewage sludges varies, and substrates treated in methane fermentation provide different amounts of biogas with various quality and quantity. Depending on the equipment and financial capabilities for methane fermentation, different methods of sewage sludge pretreatment are available. This review presents the challenges associated with the recalcitrant structure of sewage sludge and the presence of process inhibitors. We also examined the diverse methods of sewage sludge pretreatment that increase methane yield. Moreover, in the field of biological sewage sludge treatment, three future study propositions are proposed: improved pretreatment of sewage sludge using biological methods, assess the changes in microbial consortia caused with pretreatment methods, and verification of microbial impact on biomass degradation.
Topics: Sewage; Anaerobiosis; Fermentation; Bioreactors; Methane; Biofuels; Waste Disposal, Fluid
PubMed: 37453013
DOI: 10.1007/s11356-023-28613-7 -
Journal of Experimental & Clinical... Dec 2023Within the tumor immune microenvironment (TME), tumor-associated macrophages (TAMs) are crucial in modulating polarization states to influence cancer development through...
BACKGROUND
Within the tumor immune microenvironment (TME), tumor-associated macrophages (TAMs) are crucial in modulating polarization states to influence cancer development through metabolic reprogramming. While long non-coding RNAs (lncRNAs) have been shown to play a pivotal role in the progression of various cancers, the underlying mechanisms by which lncRNAs alter M2 polarization through macrophage metabolism remodeling remain unelucidated.
METHODS
RNA sequencing was used to screen for differentially expressed lncRNAs in TAMs and normal tissue-resident macrophages (NTRMs) isolated from pancreatic ductal adenocarcinoma (PDAC) tissues, whilst RT-qPCR and FISH were employed to detect the expression level of SNHG17. Moreover, a series of in vivo and in vitro experiments were conducted to assess the functions of SNHG17 from TAMs in the polarization and glycolysis of M2-like macrophages and in the proliferation and metastasis of pancreatic cancer cells (PCs). Furthermore, Western blotting, RNA pull-down, mass spectrometry, RIP, and dual-luciferase assays were utilized to explore the underlying mechanism through which SNHG17 induces pro-tumor macrophage formation.
RESULTS
SNHG17 was substantially enriched in TAMs and was positively correlated with a worse prognosis in PDAC. Meanwhile, functional assays determined that SNHG17 promoted the malignant progression of PCs by enhancing M2 macrophage polarization and anaerobic glycolysis. Mechanistically, SNHG17 could sponge miR-628-5p to release PGK1 mRNA and concurrently interact with the PGK1 protein, activating the pro-tumorigenic function of PGK1 by enhancing phosphorylation at the T168A site of PGK1 through ERK1/2 recruitment. Lastly, SNHG17 knockdown could reverse the polarization status of macrophages in PDAC.
CONCLUSIONS
The present study illustrated the essential role of SNHG17 and its molecular mechanism in TAMs derived from PDAC, indicating that SNHG17 might be a viable target for PDAC immunotherapy.
Topics: Humans; Phosphorylation; RNA, Long Noncoding; Anaerobiosis; Cell Line, Tumor; Cell Proliferation; Pancreatic Neoplasms; Carcinoma, Pancreatic Ductal; Macrophages; Glycolysis; MicroRNAs; Tumor Microenvironment; Phosphoglycerate Kinase
PubMed: 38098044
DOI: 10.1186/s13046-023-02890-z -
The Journal of Biological Chemistry Aug 2023SIRT7 is a member of the sirtuin family proteins with nicotinamide adenine dinucleotide (NAD)-dependent histone deacetylase activity, which can inhibit the activity of...
SIRT7 is a member of the sirtuin family proteins with nicotinamide adenine dinucleotide (NAD)-dependent histone deacetylase activity, which can inhibit the activity of hypoxia-inducible factors independently of its enzymatic activity. However, the role of SIRT7 in affecting hypoxia signaling in vivo is still elusive. Here, we find that sirt7-null zebrafish are more resistant to hypoxic conditions, along with an increase of hypoxia-responsive gene expression and erythrocyte numbers, compared with their wildtype siblings. Overexpression of sirt7 suppresses the expression of hypoxia-responsive genes. Further assays indicate that sirt7 interacts with zebrafish hif-1αa, hif-1αb, hif-2αa, and hif-2αb to inhibit their transcriptional activity and mediate their protein degradation. In addition, sirt7 not only binds to the hypoxia responsive element of hypoxia-inducible gene promoters but also causes a reduction of H3K18Ac on these promoters. Sirt7 may regulate hypoxia-responsive gene expression through its enzymatic and nonenzymatic activities. This study provides novel insights into sirt7 function and sheds new light on the regulation of hypoxia signaling by sirt7.
Topics: Animals; Hypoxia-Inducible Factor 1, alpha Subunit; Proteolysis; Sirtuins; Zebrafish; Zebrafish Proteins; Anaerobiosis; Oxygen
PubMed: 37481210
DOI: 10.1016/j.jbc.2023.105074