Molecular Biology最新文献

Abstract

Protein repeats are a source of rapid evolutionary and functional novelty. Repeats are crucial in development, neurogenesis, immunity, and disease. Repeat length variability and purity can alter the outcome of a pathway by altering the protein structure and affecting the protein−protein interaction affinity. Such rampant alterations can facilitate species to rapidly adapt to new environments or acquire various morphological/physiological features. With more than 11000 species, the avian clade is one of the most speciose vertebrate clades, with near-ubiquitous distribution globally. Explosive adaptive radiation and functional diversification facilitated the birds to occupy various habitats. High diversity in morphology, physiology, flight pattern, behavior, coloration, and life histories make birds ideal for studying protein repeats’ role in evolutionary novelty. Our results demonstrate a similar repeat diversity and proportion of repeats across all the avian orders considered, implying an essential role of repeats in necessary pathways. We detected positively selected sites (PSS) in the polyQ repeat of RUNX2 in the avian clade; and considerable repeat length contraction in the Psittacopasserae. The repeats show a species-wide bias towards a contraction in Galloanseriformes. Interestingly, we detected the length contrast of polyS repeat in PCDH20 between Galliformes and Anseriformes. We speculate the length variability of serine repeat and its interaction with β-catenin in the Wnt/β-catenin signaling pathway could have facilitated fowls to adapt to their respective environmental conditions. We believe our study emphasizes the role of protein repeats in functional/morphological diversification in birds. We also provide an extensive list of genes with considerable repeat length contrast to further explore the role of length volatility in evolutionary novelty and rapid functional diversification.

Abstract

Temozolomide resistance is a major cause of recurrence and poor prognosis in neuroglioma. Recently, growing evidence has suggested that mitophagy is involved in drug resistance in various tumor types. However, the role and molecular mechanisms of mitophagy in temozolomide resistance in glioma remain unclear. In this study, mitophagy levels in temozolomide-resistant and -sensitive cell lines were evaluated. The mechanisms underlying the regulation of mitophagy were explored through RNA sequencing, and the roles of differentially expressed genes in mitophagy and temozolomide resistance were investigated. We found that mitophagy promotes temozolomide resistance in glioma. Specifically, small ubiquitin-like modifier specific protease 6 (SENP6) promoted temozolomide resistance in glioma by inducing mitophagy. Protein-protein interactions between SENP6 and the mitophagy executive protein PTEN-induced kinase 1 (PINK1) resulted in a reduction in small ubiquitin-like modifier 2 (SUMO2)ylation of PINK1, thereby enhancing mitophagy. Our study demonstrates that by inducing mitophagy, the interaction of SENP6 with PINK1 promotes temozolomide resistance in glioblastoma. Therefore, targeting SENP6 or directly regulating mitophagy could be a potential and novel therapeutic target for reversing temozolomide resistance in glioma.

Abstract—Hsp70 and hydrogen sulfide donors reduce inflammatory processes in human and animal cells. The biological action mediated by Hsp70 and H₂S donors (GYY4137 and sodium thiosulfate) depends on their protection kinetics from cell activation by lipopolysaccharides. However, the molecular mechanisms of action of Hsp70 and H₂S are not well understood. We studied the effect of human recombinant Hsp70 and H₂S donors on the formation of reactive oxygen species and tumor necrosis factor-alpha induced in human cells (THP-1) by lipopolysaccharides. Transcriptomic changes occurring in these cells after LPS administration in combination with GYY4137 pretreatment were investigated. The results we obtained showed that Hsp70 and hydrogen sulfide donors reduce inflammatory processes in cells activated by the action of LPS. Hsp70 and H₂S donors differed in the kinetics of the protective action, while hydrogen sulfide donors turned out to be more effective. The role of endocytosis in the mechanisms of protection of cells by H₂S and Hsp70 donors from the action of LPS was studied. It has been found that GYY4137 pretreatment of LPS-exposed cells reduces the LPS-induced induction of various pro-inflammatory genes and affects the expression of genes of various intracellular signaling pathways.

Abstract—Currently, much attention in oncology is devoted to the issues of tumor heterogeneity, which creates serious problems in the diagnosis and therapy of malignant neoplasms. Intertumoral and intratumoral differences relate to various characteristics and aspects of the vital activity of tumor cells, including cellular metabolism. This review provides general information about the tumor metabolic heterogeneity with a focus on energy metabolism, its causes, mechanisms and research methods. Among the methods, fluorescence lifetime imaging is described in more detail as a new promising method for observing metabolic heterogeneity at the cellular level. The review demonstrates the importance of studying the features of tumor metabolism and identifying intra- and intertumoral metabolic differences.

Abstract—This review considers the recent progress on the role of heat shock proteins (HSPs), as well as transcription factors of heat shock proteins genes (HSFs) in protecting plants from oxidative stress induced by various types of abiotic and biotic stresses. HSPs are pleiotropic proteins involved in various intracellular processes and performing many important functions. In particular, HSPs increase plant resistance to stress by protecting the structure and activity of proteins of the antioxidant system. Overexpression of Hsp genes under stressful conditions, leading to an increased content of HSPs, can be used as a marker of oxidative stress. Plant HSFs are encoded by large gene families with variable sequences, expression and function. Plant HSFs regulate transcription of a wide range of stress-induced genes, including HSPs and other chaperones, reactive oxygen species scavengers, enzymes involved in protective metabolic reactions and osmolytic biosynthesis, or other transcriptional factors. Genome-wide analysis of Arabidodpsis, rice, poplar, lettuce, and wheat revealed a complex network of interaction between the Hsps and Hsfs gene families that form plant protection against oxidative stress. Plant protection systems are discussed, with special emphasis on the role of HSPs and HSFs in plant responses to stress, which will be useful for the development of technologies to increase productivity and stress resistance of plant crops.

Abstract—Changes in the activity of antioxidant systems in Escherichia coli during phosphate starvation have been studied. It is shown that starvation was accompanied by a decrease in the intensity of respiration, an increase in the rate of superoxide production, and a decrease in the level of ATP. Simultaneously, there was a decrease in H₂O₂ in the medium and a significant increase in the expression of the katG and katE genes which encode the HPI and HPII catalases, respectively. At the same time, there was no drop in the membrane potential, which may indicate the retention of normal membrane activity in starving cells. It has been shown for the first time that the transition of E. coli to phosphate starvation is accompanied by significant changes in the status of glutathione. The most important of these are associated with a decrease in the level of reduced glutathione in the medium (GSH_out) and with a simultaneous increase in its content in the cytoplasm (GSH_in), as well as a shift in the GSH_in to oxidized glutathione form (GSSG_in) ratio towards reductive values, and GSH_out/GSSG_out towards oxidative values. Among the mutants used in the work, the gor trxB double mutant, which is deficient in the synthesis of glutathione reductase and thioredoxin reductase, showed the most pronounced distinctive features. Compared to the parental strain, this mutant showed a multiple higher expression of katG::lacZ, the highest level of oxidized intra- and extracellular glutathione, and, accordingly, the lowest GSH/GSSG ratio in both compartments. In general, the data we obtained indicate that during phosphate starvation the interaction of the glutathione redox-system and regulons that control protection against reactive oxygen species creates conditions that allow maintaining the concentration of ROS below the toxic level. As a result, phosphate-starved E. coli cells can maintain high viability for a long period of time, which allows them to quickly resume growth after the addition of phosphate.

Abstract—Cancer cells are characterized by an increased level of metabolism and are highly dependent on the correct functioning of the processes that ensure homeostasis. Reactive sulfur species (RSS) are important molecular modulators of metabolic processes in both healthy and tumor cells. The effect of RSS and, in particular, H₂S, on key cellular systems, including the ubiquitin–proteasome system (UPS), which provides the destruction of most intracellular proteins, has been shown. The main components of the UPS are proteasomes, multisubunit protein complexes, within which proteolysis occurs. At the same time, data on the effect of H₂S directly on the pool of proteasomes in tumor cells are insufficient. Here, we studied the effect of incubation of SW620B8-mCherry colorectal adenocarcinoma cells expressing a fluorescently labeled proteasome subunit with 50, 100, and 200 µM of the hydrogen sulfide donor GYY4137. The effect of the substance on the proteasome pool was assessed 6, 24, 48, and 72 h after administration. It was shown that the chymotrypsin-like and caspase-like proteasome activity decreases in cells incubated with 200 µM of the GYY4137 for 24 h. This coincided with an increase in the expression of proteasome subunit genes. In lysates of cells incubated with 200 µM GYY4137 for 48 h an increase in the content of the constitutive β5 subunit was observed and the activity of proteasomes leveled off. Following prolonged incubation with GYY4137 (72h), an increase in the expression levels of some proteasome genes was also observed, although this did not have a significant effect on the activity and subunit composition of proteasomes. Thus, the obtained data indicate the modulation of proteasome activity by the hydrogen sulfide donor and the effect of GYY4137 on transcription and translation of proteasome genes.

Abstract—Metabolic stress caused by a lack of glucose significantly affects the state of red blood cells, where glycolysis is the main pathway for the production of ATP. Hypoglycemia can be both physiological (occurring during fasting and heavy physical exertion) and pathological (accompanying a number of diseases, such as diabetes mellitus). In this study, we have characterized the state of isolated erythrocytes under metabolic stress caused by the absence of glucose. It was established that 24 h of incubation of the erythrocytes in a glucose-free medium to simulate blood plasma led to a two-fold decrease in the ATP level into them. The cell size, as well as intracellular sodium concentration increased. These findings could be the result of a disruption in ion transporter functioning because of a decrease in the ATP level. The calcium level remained unchanged. With a lack of glucose in the medium of isolated erythrocytes, there was no increase in ROS and a significant change in the level of nitric oxide, while the level of the main low-molecular weight thiol of cells, glutathione (GSH) decreased by almost 2 times. It was found that the metabolic stress of isolated red blood cells induced hemoglobin glutathionylation despite the absence of ROS growth. The cause was the lack of ATP, which led to a decrease in the level of GSH because of the inhibition of its synthesis and, probably, due to a decrease in the NADPH level required for glutathione (GSSG) reduction and protein deglutathionylation. Thus, erythrocyte metabolic stress induced hemoglobin glutathionylation, which is not associated with an increase in ROS. This may have an important physiological significance, since glutathionylation of hemoglobin changes its affinity for oxygen.

Abstract—One of the key regulators of hematopoietic stem cell (HSC) maintenance is cellular metabolism. Resting HSCs use anaerobic glycolysis as the main source of energy. During expansion and differentiation under conditions of steady state hematopoiesis, the energy needs of activated HSCs increase by many fold. To meet the increased demands, cells switch to mitochondrial oxidative phosphorylation, which is accompanied by an increase in reactive oxygen species (ROS) production. Here, the molecular mechanisms maintaining glycolysis in HSCs, as well as the factors determining the increase in metabolic activity and the transition to mitochondrial biogenesis during HSC activation are discussed. We focus on the role of HIF (hypoxia-inducible factor) proteins as key mediators of the cellular response to hypoxia, and also consider the phenomenon of extraphysiological oxygen shock (EPHOSS), leading to the forced differentiation of HSCs as well as methods of overcoming it. Finally, the role of fatty acid oxidation (FAO) in hematopoiesis is discussed. Understanding the metabolic needs of normal HSCs and precursors is crucial for the development of new treatments for diseases related to the hematopoietic and immune systems.

Abstract—NO is a gaseous signaling redox-active molecule that functions in various eukaryotes. However, its synthesis, turnover, and effects in cells are specific in plants in several aspects. Compared with higher plants, the role of NO in Chlorophyta has not been investigated enough. However, some of the mechanisms for controlling the levels of this signaling molecule have been characterized in model green algae. In Chlamydomonas reinhardtii, NO synthesis is carried out by a dual system of nitrate reductase and NO-forming nitrite reductase. Other mechanisms that might produce NO from nitrite are associated with components of the mitochondrial electron-transport chain. In addition, NO formation in some green algae proceeds by an oxidative mechanism similar to that in mammals. The recent discovery of L-arginine-dependent NO synthesis in the colorless alga Polytomella parva suggests the existence of a protein complex with enzyme activities that are similar to animal nitric oxide synthase. This latter finding paves the way for further research into potential members of the NO synthases family in Chlorophyta. Beyond synthesis, the regulatory processes to maintain intracellular NO levels are also an integral part for its function in cells. Members of the truncated hemoglobins family with dioxygenase activity can convert NO to nitrate, as was shown for C. reinhardtii. In addition, the implication of NO reductases in NO scavenging has also been described. Even more intriguing, unlike in animals, the typical NO/cGMP signaling module appears not to be used by green algae. S-nitrosylated glutathione, which is considered the main reservoir for NO, provides NO signals to proteins. In Chlorophyta, protein S-nitrosation is one of the key mechanisms of action of the redox molecule. In this review, we discuss the current state-of-the-art and possible future directions related to the biology of NO in green algae.