J. Erenpreisa, K. Salmina, N. Vainshelbaum, I. Inashkina, T. Freivalds
The early stress response by AP-1 (FOS/JUN), supported by upregulation of c-Myc and involved in cell-fate changes and adaptation to hostile environments, is increased in cancer. The review shows the biphasic character of this response with negative feed-back typically lasting a few hours as a feature of the genome regulation by self-organising criticality. It involves rapid splitting of the pericentromeric heterochromatin clusters, opening of the active chromatin, and a massive transcription acceleration wave. Phylostratigraphic analysis revealed that AP-1 genes evolved in the Cambrian explosion ~500 Mya integrating the protein interaction networks of reproduction including proto-placenta intertwined with cytokine and immunity pathways, sex determination, oocyte maturation, and embryonal stemness. The peak of this response as part of accelerated cell senescence led by AP-1 and IL-1β was found in breast cancer cell-line resistant to doxorubicin. Adaptability of aggressive cancer to treatments can be explained by emergent stress response evolutionarily protecting reproduction
{"title":"Self-organisation of early stress response in the biology of cancer","authors":"J. Erenpreisa, K. Salmina, N. Vainshelbaum, I. Inashkina, T. Freivalds","doi":"10.18388/pb.2021_521","DOIUrl":"https://doi.org/10.18388/pb.2021_521","url":null,"abstract":"The early stress response by AP-1 (FOS/JUN), supported by upregulation of c-Myc and involved in cell-fate changes and adaptation to hostile environments, is increased in cancer. The review shows the biphasic character of this response with negative feed-back typically lasting a few hours as a feature of the genome regulation by self-organising criticality. It involves rapid splitting of the pericentromeric heterochromatin clusters, opening of the active chromatin, and a massive transcription acceleration wave. Phylostratigraphic analysis revealed that AP-1 genes evolved in the Cambrian explosion ~500 Mya integrating the protein interaction networks of reproduction including proto-placenta intertwined with cytokine and immunity pathways, sex determination, oocyte maturation, and embryonal stemness. The peak of this response as part of accelerated cell senescence led by AP-1 and IL-1β was found in breast cancer cell-line resistant to doxorubicin. Adaptability of aggressive cancer to treatments can be explained by emergent stress response evolutionarily protecting reproduction","PeriodicalId":20341,"journal":{"name":"Postępy Biochemii","volume":"88 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140232439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In 2024, it will be 140 years since the birth of Jan Karol Parnas, one of the most outstanding biochemists and one of the most outstanding Polish scientists of the first half of the 20th century. The article presents a synthetic biography of Prof. Parnas, his influence on the organization of scientific life in interwar Poland, and presents his students and collaborators who created the so-called "The School of Parnassus". It shows how this figure still influences the thinking of Polish biochemists about their Society and the attitude towards biochemical communities abroad, especially in Ukraine, which owes as much to Prof. Parnas as Poland does.
2024 年，20 世纪上半叶最杰出的生物化学家和波兰最杰出的科学家之一扬-卡罗尔-帕尔纳斯（Jan Karol Parnas）将诞辰 140 周年。文章介绍了帕尔纳斯教授的综合传记、他对战时波兰科学生活组织的影响，并介绍了他的学生和合作者，他们创建了所谓的 "帕尔纳斯学派"。文章展示了这位人物如何仍然影响着波兰生物化学家对其学会的思考，以及对国外生物化学家的态度，尤其是在乌克兰，乌克兰和波兰一样都要感谢帕尔纳斯教授。
{"title":"Profesor Jakub Karol Parnas: 140 rocznica urodzin","authors":"J. Barańska, A. Dżugaj, A. Szewczyk","doi":"10.18388/pb.2021_524","DOIUrl":"https://doi.org/10.18388/pb.2021_524","url":null,"abstract":"In 2024, it will be 140 years since the birth of Jan Karol Parnas, one of the most outstanding biochemists and one of the most outstanding Polish scientists of the first half of the 20th century. The article presents a synthetic biography of Prof. Parnas, his influence on the organization of scientific life in interwar Poland, and presents his students and collaborators who created the so-called \"The School of Parnassus\". It shows how this figure still influences the thinking of Polish biochemists about their Society and the attitude towards biochemical communities abroad, especially in Ukraine, which owes as much to Prof. Parnas as Poland does.","PeriodicalId":20341,"journal":{"name":"Postępy Biochemii","volume":"7 1-2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140250080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MicroRNAs are small RNAs that enable parts of the genome to regulate the other parts of the genome by RNA::RNA complementarity. Genes that encode microRNAs function as trans-acting regulators of hundreds of other genes, primarily by inhibiting the production of protein from mRNAs to which the microRNAs can bind by base pairing. MicroRNAs and their Argonaute partner proteins constitute a regulatory complex (the miRISC) that exhibits astonishing regulatory versatility. microRNAs have been shown to perform diverse roles in genetic regulatory networks (GRNs) – to control developmental switches, to dampen gene expression noise, to coordinate multigene functional modules, and more broadly, to confer robustness and resilience to developmental and homeostatic processes. Genetic analysis reveals that the function of particular microRNAs can be conditional, such that the microRNA is required under particular environmental or physiological conditions, but relatively dispensable under other conditions. The diversity and versatility of microRNA function in animal systems reflects the many ways that miRISC can be regulated by cellular signaling pathways, and the structure-function interplay among microRNA, target, and Argonaute.
{"title":"MicroRNA-mediated gene regulation and the resilience of multicellular animals","authors":"Victor Ambros","doi":"10.18388/pb.2021_515","DOIUrl":"https://doi.org/10.18388/pb.2021_515","url":null,"abstract":"MicroRNAs are small RNAs that enable parts of the genome to regulate the other parts of the genome by RNA::RNA complementarity. Genes that encode microRNAs function as trans-acting regulators of hundreds of other genes, primarily by inhibiting the production of protein from mRNAs to which the microRNAs can bind by base pairing. MicroRNAs and their Argonaute partner proteins constitute a regulatory complex (the miRISC) that exhibits astonishing regulatory versatility. microRNAs have been shown to perform diverse roles in genetic regulatory networks (GRNs) – to control developmental switches, to dampen gene expression noise, to coordinate multigene functional modules, and more broadly, to confer robustness and resilience to developmental and homeostatic processes. Genetic analysis reveals that the function of particular microRNAs can be conditional, such that the microRNA is required under particular environmental or physiological conditions, but relatively dispensable under other conditions. The diversity and versatility of microRNA function in animal systems reflects the many ways that miRISC can be regulated by cellular signaling pathways, and the structure-function interplay among microRNA, target, and Argonaute. ","PeriodicalId":20341,"journal":{"name":"Postępy Biochemii","volume":"21 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140422292","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The p53 tumor suppressor protein is best known as an activator of cell cycle arrest and apoptosis. Only a fraction of p53-activated genes encode proteins affecting cellular replication and various forms of cell death (apoptosis, ferroptosis, autophagy). The p53-regulated genes can be divided into so-called the core transcriptional program, which comprises genes activated in most cell types by most activators, and into the group of genes activated in in cell- or stress-specific manner. Activation of p53 occurs via the extensive set of posttranslational modifications, which adjust its stability, interaction with other transcription regulators, and its ability to form a tetramer. Surprisingly, in mouse models, the activation of the best-studied p53 target genes encoding the inhibitor of the cell cycle (CDKN1A) or the inducers of apoptosis (e.g. NOXA, PUMA) is dispensable for protection against cancers. Thus, the non-classical functions of p53 must be studied to better understand its tumor suppressive mechanisms.
{"title":"The p53 protein – not only the guardian of the genome","authors":"M. Rusin","doi":"10.18388/pb.2021_518","DOIUrl":"https://doi.org/10.18388/pb.2021_518","url":null,"abstract":"The p53 tumor suppressor protein is best known as an activator of cell cycle arrest and apoptosis. Only a fraction of p53-activated genes encode proteins affecting cellular replication and various forms of cell death (apoptosis, ferroptosis, autophagy). The p53-regulated genes can be divided into so-called the core transcriptional program, which comprises genes activated in most cell types by most activators, and into the group of genes activated in in cell- or stress-specific manner. Activation of p53 occurs via the extensive set of posttranslational modifications, which adjust its stability, interaction with other transcription regulators, and its ability to form a tetramer. Surprisingly, in mouse models, the activation of the best-studied p53 target genes encoding the inhibitor of the cell cycle (CDKN1A) or the inducers of apoptosis (e.g. NOXA, PUMA) is dispensable for protection against cancers. Thus, the non-classical functions of p53 must be studied to better understand its tumor suppressive mechanisms.","PeriodicalId":20341,"journal":{"name":"Postępy Biochemii","volume":"135 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140417691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The article has been written for the occasion of 25 Anniversary of Gliwice Scientific Meetings (GSN). For this reason, I am going to present scientific contacts of the Institute of Oncology at Gliwice with the Institute of Human Genetics of the Polish Academy of Sciences at Poznań not only at conference occasions but also in regular research manner.
{"title":"Gliwice Scientific Meetings as a forum for discussion of research projects.Personal impressions","authors":"Krzysztof Szyfter","doi":"10.18388/pb.2021_516","DOIUrl":"https://doi.org/10.18388/pb.2021_516","url":null,"abstract":"The article has been written for the occasion of 25 Anniversary of Gliwice Scientific Meetings (GSN). For this reason, I am going to present scientific contacts of the Institute of Oncology at Gliwice with the Institute of Human Genetics of the Polish Academy of Sciences at Poznań not only at conference occasions but also in regular research manner.","PeriodicalId":20341,"journal":{"name":"Postępy Biochemii","volume":"9 S1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140443258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sylwia Machcińska-Zielińska, Barbara Gawrońska-Kozak
The skin, as the largest organ of the body, is constantly exposed to environmental threats, including: injuries and oxidative stress. The thioredoxin system is one of the skin antioxidant systems , which protects cells against oxidative stress, regulates cell migration, proliferation and apoptosis, and also participates in signal transmission by regulating the activity of transcription factors. Recent studies have shown a correlation between the epidermal transcription factor Foxn1 and the thioredoxin system in mouse skin. Mass spectrometry analysis, followed by in vitro and in vivo experiments, showed that Foxn1 in keratinocytes regulates elements of the electron transport chain as well as the thioredoxin system (Txn2, Txnrd3), especially under hypoxic condition. High levels of Txnrd3 mRNA were detected for the first time in the injured skin of Foxn1+/+ mice compared to Foxn1-/- mice, and also showed that Foxn1 in keratinocytes upregulates Txnrd3 protein expression. Moreover, in silico analyzes indicated possible binding sites of the transcription factor Foxn1 in the Txn system. In conclusion, the data presented in this review identify Foxn1 as a novel component of the skin antioxidant system.
{"title":"Epidermal factor Foxn1 as a regulator of antioxidant defense in the skin","authors":"Sylwia Machcińska-Zielińska, Barbara Gawrońska-Kozak","doi":"10.18388/pb.2021_503","DOIUrl":"https://doi.org/10.18388/pb.2021_503","url":null,"abstract":"The skin, as the largest organ of the body, is constantly exposed to environmental threats, including: injuries and oxidative stress. The thioredoxin system is one of the skin antioxidant systems , which protects cells against oxidative stress, regulates cell migration, proliferation and apoptosis, and also participates in signal transmission by regulating the activity of transcription factors. Recent studies have shown a correlation between the epidermal transcription factor Foxn1 and the thioredoxin system in mouse skin. Mass spectrometry analysis, followed by in vitro and in vivo experiments, showed that Foxn1 in keratinocytes regulates elements of the electron transport chain as well as the thioredoxin system (Txn2, Txnrd3), especially under hypoxic condition. High levels of Txnrd3 mRNA were detected for the first time in the injured skin of Foxn1+/+ mice compared to Foxn1-/- mice, and also showed that Foxn1 in keratinocytes upregulates Txnrd3 protein expression. Moreover, in silico analyzes indicated possible binding sites of the transcription factor Foxn1 in the Txn system. In conclusion, the data presented in this review identify Foxn1 as a novel component of the skin antioxidant system.","PeriodicalId":20341,"journal":{"name":"Postępy Biochemii","volume":"95 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140482256","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dariusz Górka, Krzysztof Suszyński, Natalia Białoń, Mikołaj Górka, Michał Trzęsicki, Kacper Zając, A. Dolińska, Filip Tomsia
The problem of regeneration of damaged peripheral nerves is an ongoing topic and has long been the subject of intensive research worldwide. This study examined the morphological and functional evaluation of the regeneration process within the damaged sciatic nerve, a mouse animal model. The effect of impaired expression of the TSC-1 gene on the process of nerve regeneration was evaluated, depending on the mode of damage. The research object consisted of 48, 2-month-old male TSC lines. The test group consisted of animals that underwent damage to the sciatic nerve by crushing, freezing and electrocoagulation, while the control group includes mice whose sciatic nerve was not damaged. Behavioral tests were conducted to evaluate the functional return of the limb, after 3,5,7 and 14 days. The first changes in the regeneration process of the damaged neurite are observed as early as day 3 after the injury, while on day 14 after the injury the functional return of the damaged limb was noted.
{"title":"Evaluation of the regeneration process of the sciatic nerve of a mouse animal model after application of freezing, crushing or electrocoagulation damage","authors":"Dariusz Górka, Krzysztof Suszyński, Natalia Białoń, Mikołaj Górka, Michał Trzęsicki, Kacper Zając, A. Dolińska, Filip Tomsia","doi":"10.18388/pb.2021_504","DOIUrl":"https://doi.org/10.18388/pb.2021_504","url":null,"abstract":"The problem of regeneration of damaged peripheral nerves is an ongoing topic and has long been the subject of intensive research worldwide. This study examined the morphological and functional evaluation of the regeneration process within the damaged sciatic nerve, a mouse animal model. The effect of impaired expression of the TSC-1 gene on the process of nerve regeneration was evaluated, depending on the mode of damage. The research object consisted of 48, 2-month-old male TSC lines. The test group consisted of animals that underwent damage to the sciatic nerve by crushing, freezing and electrocoagulation, while the control group includes mice whose sciatic nerve was not damaged. Behavioral tests were conducted to evaluate the functional return of the limb, after 3,5,7 and 14 days. The first changes in the regeneration process of the damaged neurite are observed as early as day 3 after the injury, while on day 14 after the injury the functional return of the damaged limb was noted.","PeriodicalId":20341,"journal":{"name":"Postępy Biochemii","volume":"152 17","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140484512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Epigenetics is a term that refers to the changes in gene expression that are heritable and induced by DNA methylation, histones post-translational modifications, or sncRNA, not resulting from the DNA sequence rearrangements. Epigenetic modifications influence gene expression, and thus, the plasticity of plants' development and phenotype in response to external and internal factors. Until recently, the only known epigenetic modification of the DNA in eukaryotic organisms was 5-methylcytosine. The growing interest in epigenetics and the development of sensitive detection methods enabled the discovery of other modifications of the DNA nitrogenous bases, i.e., 4-methylcytosine and 6-methyladenine. However, whilst research on the 5mC distribution and role in eukaryotic organisms is widespread, analyses regarding 6mA are scarced. Nevertheless, there are indications of a potential epigenetic role of 6-methyladenine in eukaryotic genomes. Understanding epigenetic mechanisms, which are triggered in response to environmental changes, is crucial for agriculture. This review shows epigenetic mechanisms, with particular emphasis on adenine methylation in plants, as well as the role of epigenetic variation in epibreeding, affecting the improvement of agronomic traits.
表观遗传学（Epigenetics）是一个术语，指基因表达的变化是可遗传的，是由 DNA 甲基化、组蛋白翻译后修饰或 sncRNA 诱导的，而不是由 DNA 序列重排引起的。表观遗传修饰影响基因表达，进而影响植物发育和表型对内外因素的可塑性。直到最近，真核生物中唯一已知的 DNA 表观遗传修饰是 5-甲基胞嘧啶。随着人们对表观遗传学的兴趣日益浓厚以及灵敏检测方法的发展，人们发现了 DNA 含氮碱基的其他修饰，即 4-甲基胞嘧啶和 6-甲基腺嘌呤。然而，尽管有关 5mC 在真核生物体内的分布和作用的研究非常广泛，但有关 6mA 的分析却很少。不过，有迹象表明 6-甲基腺嘌呤在真核生物基因组中具有潜在的表观遗传作用。了解随环境变化而触发的表观遗传机制对农业至关重要。本综述介绍了表观遗传机制，特别强调了植物中的腺嘌呤甲基化，以及表观遗传变异在表观育种中的作用，它影响着农艺性状的改良。
{"title":"Epigenetics and the improvement of crop plants","authors":"Klaudia Bernacka, M. Achrem, A. Kalinka","doi":"10.18388/pb.2021_514","DOIUrl":"https://doi.org/10.18388/pb.2021_514","url":null,"abstract":"Epigenetics is a term that refers to the changes in gene expression that are heritable and induced by DNA methylation, histones post-translational modifications, or sncRNA, not resulting from the DNA sequence rearrangements. Epigenetic modifications influence gene expression, and thus, the plasticity of plants' development and phenotype in response to external and internal factors. Until recently, the only known epigenetic modification of the DNA in eukaryotic organisms was 5-methylcytosine. The growing interest in epigenetics and the development of sensitive detection methods enabled the discovery of other modifications of the DNA nitrogenous bases, i.e., 4-methylcytosine and 6-methyladenine. However, whilst research on the 5mC distribution and role in eukaryotic organisms is widespread, analyses regarding 6mA are scarced. Nevertheless, there are indications of a potential epigenetic role of 6-methyladenine in eukaryotic genomes. Understanding epigenetic mechanisms, which are triggered in response to environmental changes, is crucial for agriculture. This review shows epigenetic mechanisms, with particular emphasis on adenine methylation in plants, as well as the role of epigenetic variation in epibreeding, affecting the improvement of agronomic traits.","PeriodicalId":20341,"journal":{"name":"Postępy Biochemii","volume":" 12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139623008","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The review analyzes the role of physicochemical processes in the formation of the function-dependent architecture of the cell nucleus, built on the platform of a folded genome. The main attention is paid to various forms of the phase separation process, primarily the processes of liquid-liquid phase separation and polymer-polymer phase separation. The role of these processes in the formation of chromatin compartments and maintenance of three-dimensional genome architecture is discussed in detail. The relationship between genome activity and the creation of functional compartments in the cell nucleus is also analyzed.
{"title":"The role of physicochemical processes in the formation of the 3D genome and compartmentalization of the cell nucleus","authors":"Sergey V. Razin","doi":"10.18388/pb.2021_512","DOIUrl":"https://doi.org/10.18388/pb.2021_512","url":null,"abstract":"The review analyzes the role of physicochemical processes in the formation of the function-dependent architecture of the cell nucleus, built on the platform of a folded genome. The main attention is paid to various forms of the phase separation process, primarily the processes of liquid-liquid phase separation and polymer-polymer phase separation. The role of these processes in the formation of chromatin compartments and maintenance of three-dimensional genome architecture is discussed in detail. The relationship between genome activity and the creation of functional compartments in the cell nucleus is also analyzed.","PeriodicalId":20341,"journal":{"name":"Postępy Biochemii","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139530048","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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