Molecular Biology最新文献

{"title":"Modeling Protein–Protein Interaction of the KNOTTED-LIKE HOMEOBOX 3 Protein Involved in Symbiotic Nodule Development in Medicago truncatula","authors":"M. Azarakhsh, M. Lebedeva, V. K. Vishvakarma","doi":"10.1134/s0026893324020031","DOIUrl":"https://doi.org/10.1134/s0026893324020031","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>KNOTTED-LIKE HOMEOBOX (KNOX) proteins are homeodomain containing transcription factors, and regulate many aspects of plant development through homo or heterodimerization with another group of TALE transcription factors known as BELL. In <i>Medicago truncatula</i> the <i>MtKNOX3</i> gene is involved in nodule development. In this work, we hypothesized that MtKNOX3 involvement in the activation of cytokinin signaling during nodule development could be through heterodimerization with BELL proteins. Thereby, the expression of different <i>BELL</i> genes in <i>Medicago</i> was analyzed, and it was shown that the expression of <i>Medtr8g078480</i> and <i>Medtr8g098815</i> genes increases during nodule development. Besides, the <i>Medtr8g078480</i> shows a co-expression pattern with MtKNOX3 at different developmental stages of nodule development. Afterward, the interaction of MtKNOX3 with the MtBELL1-2 (Medtr8g078480) protein was shown using docking, and their stability was analyzed by molecular dynamic simulation and mmpbsa methods. Moreover, the stability of MtKNOX3- Medtr8g078480 heterodimers was compared with the MtKNOX3 homodimer.</p>","PeriodicalId":18734,"journal":{"name":"Molecular Biology","volume":"267 1","pages":""},"PeriodicalIF":1.2,"publicationDate":"2024-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139561577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ischemia–Reperfusion Injury: Molecular Mechanisms of Pathogenesis and Methods of Their Correction","authors":"R. G. Goncharov, M. G. Sharapov","doi":"10.1134/s0026893323060067","DOIUrl":"https://doi.org/10.1134/s0026893323060067","url":null,"abstract":"<p><b>Abstract</b>—Ischemia–reperfusion is a cascade of complex and interrelated pathological processes underlying many human diseases, including such socially significant diseases as stroke, myocardial infarction, acute renal failure, etc. The present review considers modern ideas about the main biochemical and signal-regulatory processes in the cell under conditions of ischemia–reperfusion. Both generally accepted and newly developed ways of ischemia–reperfusion lesion correction aimed at different chains of this pathological process are considered.</p>","PeriodicalId":18734,"journal":{"name":"Molecular Biology","volume":"72 3 1","pages":""},"PeriodicalIF":1.2,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138555981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Long Noncoding RNAs MEG3, TUG1, and hsa-miR-21-3p Are Potential Diagnostic Biomarkers for Coronary Artery Disease","authors":"M. Abdelgawad, H. Y. Abdallah, A. Fareed, A. E. Ahmed","doi":"10.1134/s0026893324010126","DOIUrl":"https://doi.org/10.1134/s0026893324010126","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>Peripheral blood biomarkers are of particular importance to diagnose certain diseases including coronary artery disease (CAD) due to their non-invasiveness. Investigating the expression of noncoding RNAs (ncRNAs) paves the way to early disease diagnosis, prognosis, and treatment. Consequently, in this research, we aimed to investigate a panel of ncRNAs as potential biomarkers in patients with coronary artery disease. Two different groups have been designed (control and CAD). All participants were subjected to interviews and clinical examinations. Peripheral blood samples were collected, and plasma was extracted. At the same time, target ncRNAs have been selected based on literature review and bioinformatic analysis, and later they underwent investigation using quantitative real-time PCR. The selected panel encompassed the long non-coding RNAs (lncRNAs) MEG3, TUG1, and SRA1, and one related microRNA (miRNA): hsa-miR-21-3p. We observed statistically significant upregulation in MEG3, TUG1<i>,</i> and hsa-miR21-3p in CAD patients compared to control participants (<i>p</i>-value &lt; 0.01). Nevertheless, SRA1 exhibited downregulation with no statistical significance (<i>p</i>-value &gt; 0.05). All ncRNAs under study displayed a significantly strong correlation with disease incidence, age, and smoking. Network construction revealed a strong relationship between MEG3 and TUG1. ROC analysis indicated high potentiality for hsa-miR-21-3p to be a promising biomarker for CAD. Moreover, MEG3 and TUG1 displayed distinguished diagnostic discrimination but less than hsa-miR-21-3p, all of them exhibited strong statistical significance differences between CAD and control groups. Conclusively, this research pinpointed that MEG3, TUG1, and hsa-miR-21-3p are potential biomarkers of CAD incidence and diagnosis.</p>","PeriodicalId":18734,"journal":{"name":"Molecular Biology","volume":"5 1","pages":""},"PeriodicalIF":1.2,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138556304","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Protein Repeats Show Clade-Specific Volatility in Aves","authors":"S. Sharma, L. Teekas, N. Vijay","doi":"10.1134/s0026893324010163","DOIUrl":"https://doi.org/10.1134/s0026893324010163","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>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 <i>RUNX2</i> 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 <i>PCDH20</i> 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.</p>","PeriodicalId":18734,"journal":{"name":"Molecular Biology","volume":"165 1","pages":""},"PeriodicalIF":1.2,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138556309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interaction of SENP6 with PINK1 Promotes Temozolomide Resistance in Neuroglioma Cells via Inducing the Mitophagy","authors":"Y. W. Wang, K. G. Jia, H. J. Xing, Y. Pan, C. S. Zeng, L. Chen, Q. J. Su, W. T. Shen, J. Chen, C. Chen, Q. Cao, Y. Y. Wang","doi":"10.1134/s0026893324010175","DOIUrl":"https://doi.org/10.1134/s0026893324010175","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>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.</p>","PeriodicalId":18734,"journal":{"name":"Molecular Biology","volume":"23 1","pages":""},"PeriodicalIF":1.2,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138556311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Protective Action of Hsp70 and Hydrogen Sulfide Donors in THP-1 Macrophages in the Lipopolysaccharide-Induced Inflammatory Response by Modulating Endocytosis","authors":"M. M. Yurinskaya, D. G. Garbuz, M. B. Evgen’ev, M. G. Vinokurov","doi":"10.1134/s0026893323060213","DOIUrl":"https://doi.org/10.1134/s0026893323060213","url":null,"abstract":"<p><b>Abstract</b>—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.</p>","PeriodicalId":18734,"journal":{"name":"Molecular Biology","volume":"1 1","pages":""},"PeriodicalIF":1.2,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138555977","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolic Heterogeneity of Tumors","authors":"M. V. Shirmanova, S. D. Sinyushkina, A. D. Komarova","doi":"10.1134/s002689332306016x","DOIUrl":"https://doi.org/10.1134/s002689332306016x","url":null,"abstract":"<p><b>Abstract</b>—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.</p>","PeriodicalId":18734,"journal":{"name":"Molecular Biology","volume":"82 1","pages":""},"PeriodicalIF":1.2,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138556308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Heat Shock Proteins in Plant Protection from Oxidative Stress","authors":"N. P. Yurina","doi":"10.1134/s0026893323060201","DOIUrl":"https://doi.org/10.1134/s0026893323060201","url":null,"abstract":"<p>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 <i>Hsp</i> 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 <i>Arabidodpsis</i>, rice, poplar, lettuce, and wheat revealed a complex network of interaction between the <i>Hsps</i> and <i>Hsfs</i> 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.</p>","PeriodicalId":18734,"journal":{"name":"Molecular Biology","volume":"34 1","pages":""},"PeriodicalIF":1.2,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138555980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Changes in the Activity of Antioxidant Systems of Escherichia coli under Phosphate Starvation","authors":"G. V. Smirnova, A. V. Tyulenev, N. G. Muzyka, L. V. Sutormina, O. N. Oktyabrsky","doi":"10.1134/s0026893323060171","DOIUrl":"https://doi.org/10.1134/s0026893323060171","url":null,"abstract":"<p><b>Abstract</b>—Changes in the activity of antioxidant systems in <i>Escherichia coli</i> 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 <i>katG</i> and <i>katE</i> 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 <i>E. coli</i> 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 <i>gor trxB</i> 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 <i>katG</i>::<i>lacZ</i>, 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 <i>E. coli</i> cells can maintain high viability for a long period of time, which allows them to quickly resume growth after the addition of phosphate.</p>","PeriodicalId":18734,"journal":{"name":"Molecular Biology","volume":"77 1","pages":""},"PeriodicalIF":1.2,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138556312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Effects of the Hydrogen Sulfide Donor GYY4137 on the Proteasome Pool of Colorectal Cancer Cells","authors":"E. V. Grigorieva, T. M. Astakhova, A. V. Burov, V. L. Karpov, A. V. Morozov","doi":"10.1134/s0026893323060079","DOIUrl":"https://doi.org/10.1134/s0026893323060079","url":null,"abstract":"<p><b>Abstract</b>—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.</p>","PeriodicalId":18734,"journal":{"name":"Molecular Biology","volume":"17 1","pages":""},"PeriodicalIF":1.2,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138563666","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}