Degradation Of Macromolecules Research Articles

A Fluorescence-Microscopic System for Monitoring the Turnover of the Autophagic Substrate p62/SQSTM1.

In conditions of cellular stress and nutrient shortage, macroautophagy (hereafter referred to as autophagy) assures the degradation of dysfunctional macromolecules and organelles as it liberates energy resources via the breakdown of dispensable cellular components. Morphologically, autophagy is characterized by the formation of double-membraned autophagosomes that facilitate the isolation of autophagic cargo for subsequent lysosomal degradation at low pH. Sequestosome-1 (SQSTM1, better known as ubiquitin-binding protein p62), is an autophagosomal cargo receptor that targets proteins for selective autophagic degradation. Indeed, the redistribution of tandem mCherry and enhanced green fluorescent protein (mCherry-EGFP)-conjugated p62 from the cytosol into nascent autophagosomes constitutes a phenotype applicable to microscopic analysis. Furthermore, the differential pH sensitivity of mCherry and EGFP allows the visualization of autophagic flux due to the selective decrease of the EGFP signal upon fusion of autophagosomes with lysosomes. Here, we describe a method employing automated confocal cellular imaging for the study of autophagic degradation that is amenable to systems biology approaches.

Use of Microfluidics Chambers to Image Axonal transport in Adult Sensory Neurons.

Transport of cargoes along axons is crucial for ensuring effective neuronal function and survival. Lysosomes, which are membrane-bound organelles responsible for the degradation of macromolecules, are among the many cargoes being transported. Compartmentalized systems that allow for the separation of the somatic compartment from the axonal network, are widely used in the field of neurobiology and in the study of axonal transport in particular. Among the various solutions available, microfluidics chambers that take advantage of fluidic separation between different compartments, have seen widespread adoption. Said chambers are made of polydimethylsiloxane (PDMS), a transparent, gas permeable compound, which is compatible with fluorescence microscopy, and have significantly positively impacted cellular neuroscience, drastically increasing our understanding of axonal peripheral signaling. Here we describe a two-layered microfluidics chamber, engineered to allow for the culture of adult sensory neurons. This device was designed to promote the proper placement of adult sensory neurons in the somatic chamber in proximity of the microgrooves. We detail the production of the master mold, how to fabricate and assemble the device and how to disaggregate and load the cells in it. In addition, we provide details on how to conduct and analyze an axonal transport experiment using a custom made script in MATLAB designed by our laboratory.

Extracellular Enzyme Activities and Carbon/Nitrogen Utilization in Mycorrhizal Fungi Isolated From Epiphytic and Terrestrial Orchids.

Fungi employ extracellular enzymes to initiate the degradation of organic macromolecules into smaller units and to acquire the nutrients for their growth. As such, these enzymes represent important functional components in terrestrial ecosystems. While it is well-known that the regulation and efficiency of extracellular enzymes to degrade organic macromolecules and nutrient-acquisition patterns strongly differ between major fungal groups, less is known about variation in enzymatic activity and carbon/nitrogen preference in mycorrhizal fungi. In this research, we investigated variation in extracellular enzyme activities and carbon/nitrogen preferences in orchid mycorrhizal fungi (OMF). Previous research has shown that the mycorrhizal fungi associating with terrestrial orchids often differ from those associating with epiphytic orchids, but whether extracellular enzyme activities and carbon/nitrogen preference differ between growth forms remains largely unknown. To fill this gap, we compared the activities of five extracellular enzymes [cellulase, xylanase, lignin peroxidase, laccase, and superoxide dismutase (SOD)] between fungi isolated from epiphytic and terrestrial orchids. In total, 24 fungal strains belonging to Tulasnellaceae were investigated. Cellulase and xylanase activities were significantly higher in fungi isolated from terrestrial orchids (0.050 ± 0.006 U/ml and 0.531 ± 0.071 U/ml, respectively) than those from epiphytic orchids (0.043 ± 0.003 U/ml and 0.295 ± 0.067 U/ml, respectively), while SOD activity was significantly higher in OMF from epiphytic orchids (5.663 ± 0.164 U/ml) than those from terrestrial orchids (3.780 ± 0.180 U/ml). Carboxymethyl cellulose was more efficiently used by fungi from terrestrial orchids, while starch and arginine were more suitable for fungi from epiphytic orchids. Overall, the results of this study show that extracellular enzyme activities and to a lesser extent carbon/nitrogen preferences differ between fungi isolated from terrestrial and epiphytic orchids and may indicate functional differentiation and ecological adaptation of OMF to local growth conditions.

Microbial Community Response to Polysaccharide Amendment in Anoxic Hydrothermal Sediments of the Guaymas Basin.

Organic-rich, hydrothermal sediments of the Guaymas Basin are inhabited by diverse microbial communities including many uncultured lineages with unknown metabolic potential. Here we investigated the short-term effect of polysaccharide amendment on a sediment microbial community to identify taxa involved in the initial stage of macromolecule degradation. We incubated anoxic sediment with cellulose, chitin, laminarin, and starch and analyzed the total and active microbial communities using bioorthogonal non-canonical amino acid tagging (BONCAT) combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Our results show a response of an initially minor but diverse population of Clostridia particularly after amendment with the lower molecular weight polymers starch and laminarin. Thus, Clostridia may readily become key contributors to the heterotrophic community in Guaymas Basin sediments when substrate availability and temperature range permit their metabolic activity and growth, which expands our appreciation of the potential diversity and niche differentiation of heterotrophs in hydrothermally influenced sediments. BONCAT-FACS, although challenging in its application to complex samples, detected metabolic responses prior to growth and thus can provide complementary insight into a microbial community’s metabolic potential and succession pattern. As a primary application of BONCAT-FACS on a diverse deep-sea sediment community, our study highlights important considerations and demonstrates inherent limitations associated with this experimental approach.

Multiple Layers of Regulation on Leaf Senescence: New Advances and Perspectives.

Leaf senescence is the last stage of leaf development and is an orderly biological process accompanied by degradation of macromolecules and nutrient recycling, which contributes to plant fitness. Forward genetic mutant screening and reverse genetic studies of senescence-associated genes (SAGs) have revealed that leaf senescence is a genetically regulated process, and the initiation and progression of leaf senescence are influenced by an array of internal and external factors. Recently, multi-omics techniques have revealed that leaf senescence is subjected to multiple layers of regulation, including chromatin, transcriptional and post-transcriptional, as well as translational and post-translational levels. Although impressive progress has been made in plant senescence research, especially the identification and functional analysis of a large number of SAGs in crop plants, we still have not unraveled the mystery of plant senescence, and there are some urgent scientific questions in this field, such as when plant senescence is initiated and how senescence signals are transmitted. This paper reviews recent advances in the multiple layers of regulation on leaf senescence, especially in post-transcriptional regulation such as alternative splicing.

The effect of lactic acid bacteria and co-culture on structural, rheological, and textural profile of corn dough.

This study is aimed at assessing the effect of lactic acid bacteria (LAB) on corn flour using dynamic characterization methods including RVA, TPA, Rheometer, SEM, and DSC along with co‐culture technique in order to enhance its applicability by evaluating the variations in rheological, textural, morphological, thermal, and structural properties. Our findings suggested that bacterial incorporation both individually and in combination (co‐culture) revealed an improved corn dough profile with better properties. SEM showed irregular shape of particles having more grooves, indentations, and cracks. RVA demonstrated different pasting behavior on the dough. Bacterial inoculation in flour attributed to increase the TO (68.61–71.18), TP (73.74–78.42), TC (78.78–85.36), melting temperature (10.17–15.19), and ΔH (2.72–5.40). The hardness of corn was found approximately 75% of native dough. In treated corn, an increase was noted in both loss and storage modulus in correspondence with changes in the starch configuration and leaching of constituents. The results from DSC presented an increased melting temperature range and gelatinization enthalpy owing to bacterial treatment accredited to diversified morphological characteristics. The outcomes concluded in demonstration of a novel influence on structural, thermal, morphological, and rheological capabilities and capacities of corn dough. Lactic acid bacteria hydrolyzed part of the corn and flour had smaller, irregularly shaped particles with more holes in them, resulting in a reduced water retaining capacity. Textural, thermal, and pasting profile has also been improved due to degradation of macromolecules. Furthermore, the insight alterations induce various changes leading to improved corn flour. It may also develop the associations about the upright insurgence in the corn dough profile and its potential usage in industry and homes.

Efficacy and self-similarity of SARS-CoV-2 thermal decontamination

Dry heat decontamination has been shown to effectively inactivate viruses without compromising the integrity of delicate personal protective equipment (PPE), allowing safe reuse and helping to alleviate shortages of PPE that have arisen due to COVID-19. Unfortunately, current thermal decontamination guidelines rely on empirical data which are often sparse, limited to a specific virus, and unable to provide fundamental insight into the underlying inactivation reaction. In this work, we experimentally quantified dry heat decontamination of SARS-CoV-2 on disposable masks and validated a model that treats the inactivation reaction as thermal degradation of macromolecules. Furthermore, upon nondimensionalization, all of the experimental data collapse onto a unified curve, revealing that the thermally driven decontamination process exhibits self-similar behavior. Our results show that heating surgical masks to 70 °C for 5 min inactivates over 99.9% of SARS-CoV-2. We also characterized the chemical and physical properties of disposable masks after heat treatment and did not observe degradation. The model presented in this work enables extrapolation of results beyond specific temperatures to provide guidelines for safe PPE decontamination. The modeling framework and self-similar behavior are expected to extend to most viruses—including yet-unencountered novel viruses—while accounting for a range of environmental conditions.

Regulation of autophagy protects against liver injury in liver surgery-induced ischaemia/reperfusion.

Transient ischaemia and reperfusion in liver tissue induce hepatic ischaemia/reperfusion (I/R) tissue injury and a profound inflammatory response in vivo. Hepatic I/R can be classified into warm I/R and cold I/R and is characterized by three main types of cell death, apoptosis, necrosis and autophagy, in rodents or patients following I/R. Warm I/R is observed in patients or animal models undergoing liver resection, haemorrhagic shock, trauma, cardiac arrest or hepatic sinusoidal obstruction syndrome when vascular occlusion inhibits normal blood perfusion in liver tissue. Cold I/R is a condition that affects only patients who have undergone liver transplantation (LT) and is caused by donated liver graft preservation in a hypothermic environment prior to entering a warm reperfusion phase. Under stress conditions, autophagy plays a critical role in promoting cell survival and maintaining liver homeostasis by generating new adenosine triphosphate (ATP) and organelle components after the degradation of macromolecules and organelles in liver tissue. This role of autophagy may contribute to the protection of hepatic I/R‐induced liver injury; however, a considerable amount of evidence has shown that autophagy inhibition also protects against hepatic I/R injury by inhibiting autophagic cell death under specific circumstances. In this review, we comprehensively discuss current strategies and underlying mechanisms of autophagy regulation that alleviates I/R injury after liver resection and LT. Directed autophagy regulation can maintain liver homeostasis and improve liver function in individuals undergoing warm or cold I/R. In this way, autophagy regulation can contribute to improving the prognosis of patients undergoing liver resection or LT.

The Biology of Colicin M and Its Orthologs.

The misuse of antibiotics during the last decades led to the emergence of multidrug resistant pathogenic bacteria. This phenomenon constitutes a major public health issue. Consequently, the discovery of new antibacterials in the short term is crucial. Colicins, due to their antibacterial properties, thus constitute good candidates. These toxin proteins, produced by E. coli to kill enteric relative competitors, exhibit cytotoxicity through ionophoric activity or essential macromolecule degradation. Among the 25 colicin types known to date, colicin M (ColM) is the only one colicin interfering with peptidoglycan biosynthesis. Accordingly, ColM develops its lethal activity in E. coli periplasm by hydrolyzing the last peptidoglycan precursor, lipid II, into two dead-end products, thereby leading to cell lysis. Since the discovery of its unusual mode of action, several ColM orthologs have also been identified based on sequence alignments; all of the characterized ColM-like proteins display the same enzymatic activity of lipid II degradation and narrow antibacterial spectra. This publication aims at being an exhaustive review of the current knowledge on this new family of antibacterial enzymes as well as on their potential use as food preservatives or therapeutic agents.

Ethephon-Induced Ethylene Enhances Starch Degradation and Sucrose Transport with an Interactive Abscisic Acid-Mediated Manner in Mature Leaves of Oilseed rape (Brassica napus L.).

The leaf senescence process is characterized by the degradation of macromolecules in mature leaves and the remobilization of degradation products via phloem transport. The phytohormone ethylene mediates leaf senescence. This study aimed to investigate the ethephon-induced ethylene effects on starch degradation and sucrose remobilization through their interactive regulation with other hormones. Ethephon (2-chloroethylphosphonic acid) was used as an ethylene-generating agent. Endogenous hormonal status, carbohydrate compounds, starch degradation-related gene expression, sucrose transporter gene expression, and phloem sucrose loading were compared between the ethephon-treated plants and controls. Foliar ethephon spray enhanced the endogenous ethylene concentration and accelerated leaf senescence, as evidenced by reduced chlorophyll content and enhanced expression of the senescence-related gene SAG12. Ethephon-enhanced ethylene prominently enhanced the endogenous abscisic acid (ABA) level. accompanied with upregulation of ABA synthesis gene 9-cis-epoxycarotenoid dioxygenase (NCED3), ABA receptor gene pyrabactin resistance 1 (PYR1), and ABA signaling genes sucrose non-fermenting 1 (Snf1)-related protein kinase 2 (SnRK2), ABA-responsive element binding 2 (AREB2), and basic-helix-loop-helix (bHLH) transcription factor (MYC2).) Ethephon treatment decreased starch content by enhancing expression of the starch degradation-related genes α-amylase 3 (AMY3) and β-amylase 1 (BAM1), resulting in an increase in sucrose content in phloem exudates with enhanced expression of sucrose transporters, SUT1, SUT4, and SWEET11. These results suggest that a synergistic interaction between ethylene and ABA might account for sucrose accumulation, mainly due to starch degradation in mature leaves and sucrose phloem loading in the ethephon-induced senescent leaves.

Autophagy in Xp11 translocation renal cell carcinoma: from bench to bedside.

Xp11 translocation renal cell carcinoma (tRCC) characterized by the rearrangement of the TFE3 is recently identified as a unique subtype of RCC that urgently requires effective prevention and treatment strategies. Therefore, determining suitable therapeutic targets and fully understanding the biological significance of tRCC is essential. The importance of autophagy is increasingly acknowledged because it shows carcinogenic activity or suppressor effect. Autophagy is a physiological cellular process critical to maintaining cell homeostasis, which is involved in the lysosomal degradation of cytoplasmic organelles and macromolecules via the lysosomal pathway, suggesting that targeting autophagy is a potential therapeutic approach for cancer therapies. However, the underlying mechanism of autophagy in tRCC is still ambiguous. In this review, we summarize the autophagy-related signaling pathways associated with tRCC. Moreover, we examine the roles of autophagy and the immune response in tumorigenesis and investigate how these factors interact to facilitate or prevent tumorigenesis. Besides, we review the findings regarding the treatment of tRCC via induction or inhibition of autophagy. Hopefully, this study will shed some light on the functions and implications of autophagy and emphasize its role as a potential molecular target for therapeutic intervention in tRCC.

Influence of sludge organic matter on elimination of polycyclic aromatic hydrocarbons (PAHs) from waste activated sludge by ozonation: Controversy over aromatic compounds

Ozonation has been widely used as a viable advanced oxidation process (AOP) for elimination of PAHs in waste activated sludge through effective sludge disintegration and abatement of organic pollutants. However, sludge organic matter (SOM) influences PAHs degradation during ozone treatment is still rarely understood. In this study, we investigated such an influence with the aid of solid-state 13C nuclear magnetic resonance (NMR) spectroscopy and the corresponding two-dimensional correlation analysis (2D-COS) strategy. The results showed that the degradation of SOM macromolecules in the order of aromatic substances > aliphatic carbon > α carbon > amides groups > O-alkyl upon ozone treatment. Moreover, the PAHs removal efficiency was positively correlated with the aromaticity of sludge (R2 = 0.84–0.98), while negative associated with its aliphaticity (R2 = 0.81–0.95). Lastly, humic acid (HA) was used as a proxy of aromatic SOM to further explore their interaction with PAHs in sludge matrix. The results revealed that freely dissolved (HA-D) and suspended particulates (HA-S) imposed distinctively different influence on ozone-based PAHs degradation. The HA-S facilitated the elimination of PAHs by 7.95 ± 0.11%, while those HA-D reduced the removal efficiency by 16.70 ± 0.13%.

Dried Blood Spot (DBS) Methodology Study for Biomarker Discovery in Lysosomal Storage Disease (LSD).

Lysosomal storage diseases (LSDs) are a heterogeneous group of inherited metabolic diseases caused by mutations in genes encoding for proteins involved in the lysosomal degradation of macromolecules. They occur in approximately 1 in 5000 live births and pose a lifelong risk. Therefore, to achieve the maximum benefit from LSDs therapies, a fast and early diagnosis of the disease is required. In this framework, biomarker discovery is a significant factor in disease diagnosis and in predicting its outcomes. On the other hand, the dried blood spot (DBS) based metabolomics platform can open up new pathways for studying non-directional hypothesis approaches to biomarker discovery. This study aims to increase the efficiency of the developed methods for biomarker development in the context of rare diseases, with an improved impact on the reliability of the detected compounds. Thereby, we conducted two independent experiments and integrated them into the screening of the human blood metabolome: (1) comparison of EDTA blood and filter cards in terms of their suitability for metabolomics studies; (2) optimization of the extraction method: a side-by-side comparison of a series of buffers to the best utility to the disease of interest. The findings were compared to previous studies across parameters such as metabolite coverage, sample type suitability, and stability. The results indicate that measurements of metabolites are susceptible to differences in pre-analytical conditions and extraction solvents. This proposed approach can increase the positive rate of the future development of biomarkers. Altogether, the procedure can be easily adapted and applied to other studies, where the limited number of samples is a common barrier.

Particle-associated and free-living bacterial communities in an oligotrophic sea are affected by different environmental factors.

In the oceans and seas, environmental conditions change over multiple temporal and spatial scales. Here, we ask what factors affect the bacterial community structure across time, depth and size fraction during six seasonal cruises (2 years) in the ultra-oligotrophic Eastern Mediterranean Sea. The bacterial community varied most between size fractions (free-living (FL) vs. particle-associated), followed by depth and finally season. The FL community was taxonomically richer and more stable than the particle-associated (PA) one, which was characterized by recurrent 'blooms' of heterotrophic bacteria such as Alteromonas and Ralstonia. The heterotrophic FL and PA communities were also correlated with different environmental parameters: the FL population correlated with depth and phytoplankton, whereas PA bacteria were correlated primarily with the time of sampling. A significant part of the variability in community structure could, however, not be explained by the measured parameters. The metabolic potential of the PA community, predicted from 16S rRNA amplicon data using PICRUSt, was enriched in pathways associated with the degradation and utilization of biological macromolecules, as well as plastics, other petroleum products and herbicides. The FL community was enriched in predicted pathways for the metabolism of inositol phosphate, a potential phosphorus source, and of polycyclic aromatic hydrocarbons.

Degradation of biological macromolecules supports uncultured microbial populations in Guaymas Basin hydrothermal sediments

Hydrothermal sediments contain large numbers of uncultured heterotrophic microbial lineages. Here, we amended Guaymas Basin sediments with proteins, polysaccharides, nucleic acids or lipids under different redox conditions and cultivated heterotrophic thermophiles with the genomic potential for macromolecule degradation. We reconstructed 20 metagenome-assembled genomes (MAGs) of uncultured lineages affiliating with known archaeal and bacterial phyla, including endospore-forming Bacilli and candidate phylum Marinisomatota. One Marinisomatota MAG had 35 different glycoside hydrolases often in multiple copies, seven extracellular CAZymes, six polysaccharide lyases, and multiple sugar transporters. This population has the potential to degrade a broad spectrum of polysaccharides including chitin, cellulose, pectin, alginate, chondroitin, and carrageenan. We also describe thermophiles affiliating with the genera Thermosyntropha, Thermovirga, and Kosmotoga with the capability to make a living on nucleic acids, lipids, or multiple macromolecule classes, respectively. Several populations seemed to lack extracellular enzyme machinery and thus likely scavenged oligo- or monomers (e.g., MAGs affiliating with Archaeoglobus) or metabolic products like hydrogen (e.g., MAGs affiliating with Thermodesulfobacterium or Desulforudaceae). The growth of methanogens or the production of methane was not observed in any condition, indicating that the tested macromolecules are not degraded into substrates for methanogenesis in hydrothermal sediments. We provide new insights into the niches, and genomes of microorganisms that actively degrade abundant necromass macromolecules under oxic, sulfate-reducing, and fermentative thermophilic conditions. These findings improve our understanding of the carbon flow across trophic levels and indicate how primary produced biomass sustains complex and productive ecosystems.

Characterization of humic acids produced from fungal liquefaction of low-grade Thar coal

Fungal liquefaction of coal is a promising technology to convert low rank coal into value-added products such as humic acids (HAs) that are extensively used as fertilizer. Use of Pakistani Thar lignite for humic acid extraction can promote agriculture industry in Pakistan. In this study, fifty-five fungal strains were isolated from Thar lignite and screened for their lignite solubilization efficiency. Isolates M13 and MI exhibited highest capacity for lignite solubilization and HA was extracted with 67.4 ± 4.3 percent (w/w) yield. Elemental analysis showed increased nitrogen (0.72–1.39 percent) and oxygen (41.7–48 percent), and decreased carbon (51.8–46.1 percent) and sulphur (1.18–0.73 percent) contents in bio-extracted HA (bHA) compared to chemically extracted HA (cHA). UV/Vis spectroscopy showed increased E4/E6 value from 5.6 ± 0.39 (cHA) to 6.28 ± 0.35 (bHA) indicating reduced molecular mass and aromaticity and increased bioactivity of molecule. FTIR analysis also confirmed these results. HPLC analysis of bHA and cHA showed typical choromatogram of humic acids. Enzyme activity staining indicated the presence of fungal cellulase and xylanase on SDS-PAGE gel. The degradation of lignite macromolecules by lignin degrading fungi is a complex process dependent on alkaline substances, chelators, surfactants and extracellular fungal enzymes.

Relationship between the index of protein modification (Kolbach index) and degradation of macromolecules in wheat malt.

Kolbach index (KI) is an important index to evaluate the qualities of malt, which will affect protein molecular composition, enzyme activity, and other macromolecules degradation during wheat malting. In this paper, the relationship between wheat (Triticum aestivum L.) malts KI and the (i) characterization of albumins, globulins, gliadins, and glutenins and their hydrolysis and (ii) the enzymatic breakdown of starch and arabinoxylans during malting were studied. As malt KI values increased, all fractions of glutenins and gliadins were extensively hydrolyzed. The higher Mw globulins (36.6 to 70.8kDa) were also increasingly degraded at higher KI values, but the concentration of smaller globulin fractions (14.9 to 35.0kDa) had increased significantly. As for albumins, although their overall concentration had increased as KI increased, changes in the concentration of individual albumin fractions was more complex. While there were significant increases in the concentration of some new albumin proteins (43.8 and 84.4kDa), the concentration of some albumins decreased (21.1 to 64.3kDa), and some fractions had completely disappeared (28.8 and 64.3kDa). Following mashing, the hydrophobicity of the worts had decreased significantly at higher KI values. At malt KI values between 39.5% and 42.7%, the enzymatic activity was at its highest, the degradation of starch was adequate and stable, and the concentration of water-soluble arabinoxylans was optimal. A KI value of about 39.5% to 42.7% was therefore considered optimal for the production of wheat malts with superior quality attributes. PRACTICAL APPLICATION: The findings from this study will be valuable to beer companies; a more precise control of the malting and brewing parameters, fundamental for the production of high-quality wheat malts and wheat beer, can be achieved.

The influence of circular RNAs on autophagy and disease progression

ABSTRACT Circular RNAs (circRNAs) are non-coding RNAs that have attracted considerable attention in recent years. Owing to their distinct circular structure, circRNAs are stable in cells. Autophagy is a catabolic process that helps in the degradation and recycling of harmful or inessential biological macromolecules in cells and enables cells to adapt to stress and changes in the internal and external environments. Evidence has shown that circRNAs influence the course of a disease by regulating autophagy, which indicates that autophagy is involved in the onset and development of various diseases and can affect drug resistance (for example, it affects cisplatin resistance in tumors). In this review, we summarized the role of circRNAs in autophagy and their influence on disease onset and progression as well as drug resistance. The review will expand our understanding of tumors as well as cardiovascular and neurological diseases and also suggest novel therapeutic strategies. Abbreviations: ACR: autophagy-related circRNA; ADSCs: adipogenic mesenchymal stem cells; AMPK: AMP-activated protein kinase; ATG: autophagy related; BCL2: BCL2 apoptosis regulator; BECN1: beclin 1; ceRNA: competing endogenous RNA; circRNA: circular RNA; CMA: chaperone-mediated autophagy; EPCs: endothelial progenitor cells; LE/MVBs: late endosomes/multivesicular bodies; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MTOR: mechanistic target of rapamycin kinase; NSCLC: non-small cell lung cancer; PDLSCs: periodontal ligament stem cells; PE: phosphatidylethanolamine; PtdIns: phosphatidylinositol; PtdIns3K: phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate 1,2-dipalmitoyl; PTEN: phosphatase and tensin homolog; RBPs: RNA-binding proteins; SiO2: silicon dioxide; TFEB: transcription factor EB; ULK: unc-51 like autophagy activating kinase 1

Potential of genistein-induced autophagy in the treatment of neurodegenerative diseases

Development of therapies for neurodegenerative diseases, disorders characterized by progressing loss of neurons, is a great challenge for current medicine. Searching for drugs for these diseases is being proceeded in many laboratories in the world. To date, several therapeutical strategies have been proposed which, however, are either of insufficient efficacy or at the early preclinical stages. One of the newest concepts is elevated efficiency of degradation of protein aggregates which are causes of 70% of these diseases. Autophagy, i.e. lysosomal degradation of macromolecules, is a process which could be employed in such a strategy Searching for a compound which would not only stimulate autophagy but also reveal safety in a long-term usage and be able to cross the blood-brain-barrier led to studies on one of flavonoids, genistein which occurs at high concentrations in soy. Experiments with this compound indicated its enormous efficiency in removing protein aggregated formed by beta-amyloid, hyperphosphorylated tau protein, and mutant huntingtin. Moreover, using animal models of these diseases, correction of cognitive and motoric symptoms was demonstrated. Considering safety of genistein as well as its ability to crossing the blood-brain-barrier, one may assume that this molecule is a candidate for an effective drug in therapies of not only Alzheimer disease and Huntington disease, but also other disorders caused be protein aggregates. In this article, recent results of studies on the use of genistein in different models of neurodegenerative diseases are summarized, with special emphasis on its autophagy-dependent action.

S6K1 Is Indispensible for Stress-Induced Microtubule Acetylation and Autophagic Flux.

Autophagy is a specific macromolecule and organelle degradation process. The target macromolecule or organelle is first enclosed in an autophagosome, and then delivered along acetylated microtubules to the lysosome. Autophagy is triggered by stress and largely contributes to cell survival. We have previously shown that S6K1 kinase is essential for autophagic flux under stress conditions. Here, we aimed to elucidate the underlying mechanism of S6K1 involvement in autophagy. We stimulated autophagy in S6K1/2 double-knockout mouse embryonic fibroblasts by exposing them to different stress conditions. Transient gene overexpression or silencing, immunoblotting, immunofluorescence, flow cytometry, and ratiometric fluorescence analyses revealed that the perturbation of autophagic flux in S6K1-deficient cells did not stem from impaired lysosomal function. Instead, the absence of S6K1 abolished stress-induced tubulin acetylation and disrupted the acetylated microtubule network, in turn impairing the autophagosome-lysosome fusion. S6K1 overexpression restored tubulin acetylation and autophagic flux in stressed S6K1/2-deficient cells. Similar effect of S6K1 status was observed in prostate cancer cells. Furthermore, overexpression of an acetylation-mimicking, but not acetylation-resistant, tubulin variant effectively restored autophagic flux in stressed S6K1/2-deficient cells. Collectively, S6K1 controls tubulin acetylation, hence contributing to the autophagic flux induced by different stress conditions and in different cells.