It is commonly understood that RNA-binding proteins crucially determine the fate of their target RNAs. Vice versa, RNAs are becoming increasingly recognized for their functions in protein regulation and the dynamics of RNA-protein complexes. Long non-coding RNAs are emerging as potent regulators of proteins that exert unknown RNA-binding properties and moonlighting functions. A vast array of RNA- and protein-centric techniques have been developed for the identification of protein and RNA targets, respectively, including unbiased protein mass spectrometry and next-generation RNA sequencing as readout. Determining true physiological RNA and protein targets is challenging as RNA–protein interaction is highly dynamic, tissue- and cell-type-specific, and changes with the environment. Here I review current techniques for the analysis of RNA–protein interactions in living cells and in vitro. RNA-centric techniques are presented on the basis of cross-linking or the use of alternative approaches. Protein-centric approaches are discussed in combination with high-throughput sequencing. Finally, the impact of mutations in RNA–protein complexes on human disease is highlighted.
{"title":"Current Technical Approaches to Study RNA–Protein Interactions in mRNAs and Long Non-Coding RNAs","authors":"Johanna Mattay","doi":"10.3390/biochem3010001","DOIUrl":"https://doi.org/10.3390/biochem3010001","url":null,"abstract":"It is commonly understood that RNA-binding proteins crucially determine the fate of their target RNAs. Vice versa, RNAs are becoming increasingly recognized for their functions in protein regulation and the dynamics of RNA-protein complexes. Long non-coding RNAs are emerging as potent regulators of proteins that exert unknown RNA-binding properties and moonlighting functions. A vast array of RNA- and protein-centric techniques have been developed for the identification of protein and RNA targets, respectively, including unbiased protein mass spectrometry and next-generation RNA sequencing as readout. Determining true physiological RNA and protein targets is challenging as RNA–protein interaction is highly dynamic, tissue- and cell-type-specific, and changes with the environment. Here I review current techniques for the analysis of RNA–protein interactions in living cells and in vitro. RNA-centric techniques are presented on the basis of cross-linking or the use of alternative approaches. Protein-centric approaches are discussed in combination with high-throughput sequencing. Finally, the impact of mutations in RNA–protein complexes on human disease is highlighted.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78169878","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}
E. Oliveira, S. A. Vieira, F. A. G. da Silva, M. M. da Costa, A. Gomes, H. P. Oliveira
The development of composites with antibacterial activity represents an important strategy to avoid side effects such as increasing bacterial resistance to antibiotics. In particular, the green synthesis of metal nanoparticles avoids the use of hazardous chemical compounds and introduces the intrinsic beneficial properties of plant-derived compounds. Herein, the reduction of gold salt into metal nanoparticles was provided by the action of a cationic polymer derived from tannin (Tanfloc®). Comparative activity of antibacterial agents (pure Tanfloc and Au NPs—Tanfloc) at different concentrations were evaluated in terms of the antibiofilm activity, kill-time assays and inhibition haloes confirming the antibacterial activity of the Tanfloc that is reinforced by the incorporation of reduced gold nanoparticles, resulting in the complete elimination of S. aureus from an initial concentration of 108 CFU/mL after 120 min of reaction of Au NPs + Tanfloc solution in association with strong inhibition of the biofilm formation attributed to the Tanfloc.
{"title":"Synergistic Antibacterial Activity of Green Gold Nanoparticles and Tannin-Based Derivatives","authors":"E. Oliveira, S. A. Vieira, F. A. G. da Silva, M. M. da Costa, A. Gomes, H. P. Oliveira","doi":"10.3390/biochem2040019","DOIUrl":"https://doi.org/10.3390/biochem2040019","url":null,"abstract":"The development of composites with antibacterial activity represents an important strategy to avoid side effects such as increasing bacterial resistance to antibiotics. In particular, the green synthesis of metal nanoparticles avoids the use of hazardous chemical compounds and introduces the intrinsic beneficial properties of plant-derived compounds. Herein, the reduction of gold salt into metal nanoparticles was provided by the action of a cationic polymer derived from tannin (Tanfloc®). Comparative activity of antibacterial agents (pure Tanfloc and Au NPs—Tanfloc) at different concentrations were evaluated in terms of the antibiofilm activity, kill-time assays and inhibition haloes confirming the antibacterial activity of the Tanfloc that is reinforced by the incorporation of reduced gold nanoparticles, resulting in the complete elimination of S. aureus from an initial concentration of 108 CFU/mL after 120 min of reaction of Au NPs + Tanfloc solution in association with strong inhibition of the biofilm formation attributed to the Tanfloc.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":"23 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84724022","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}
M. O. S. D. Santos, Mariana Nepomuceno, J. Gonçalves, Ana Catarina Leite Véras Medeiros, Rafaella Miranda Machado, Caroline P S Santos, M. J. C. F. Alves, Aline do Monte Gurgel, I. G. D. Gurgel
The 2019 oil spill was considered the largest environmental disaster in the Brazilian Northeastern coast. It was associated with mostly ineffective government actions, thus intensifying historical vulnerabilities faced by local populations. We aimed to analyze the environmental conflicts and injustices and the socio-environmental, economic, and health vulnerabilities arising from the oil spill, considering the COVID-19 pandemic, impacting artisanal fishing communities of the Northeastern coast. A document-based, qualitative, cross-sectional research was carried out between September 2019 and October 2022, in open access secondary databases, and using field diaries from research of the Environmental Health and Work Laboratory (LASAT) of the Aggeu Magalhães Institute of the Oswaldo Cruz Foundation. The disaster caused situations of injustice and environmental conflicts that had negative repercussions in the territories with socioeconomic impacts, on the environment, and on the health of the population. The entire marine environment was affected, resulting in physical and chemical alterations. The health vulnerabilities faced by local people were intensified, influencing the social determination of the health–disease process. The local economy was extremely affected, generating job insecurity and several socio-cultural problems. It is essential to build environmental and health diagnoses for remedial measures in disasters such as the oil spill.
{"title":"Oil Spill in Brazil—Analysis of Vulnerabilities and Socio-Environmental Conflicts","authors":"M. O. S. D. Santos, Mariana Nepomuceno, J. Gonçalves, Ana Catarina Leite Véras Medeiros, Rafaella Miranda Machado, Caroline P S Santos, M. J. C. F. Alves, Aline do Monte Gurgel, I. G. D. Gurgel","doi":"10.3390/biochem2040018","DOIUrl":"https://doi.org/10.3390/biochem2040018","url":null,"abstract":"The 2019 oil spill was considered the largest environmental disaster in the Brazilian Northeastern coast. It was associated with mostly ineffective government actions, thus intensifying historical vulnerabilities faced by local populations. We aimed to analyze the environmental conflicts and injustices and the socio-environmental, economic, and health vulnerabilities arising from the oil spill, considering the COVID-19 pandemic, impacting artisanal fishing communities of the Northeastern coast. A document-based, qualitative, cross-sectional research was carried out between September 2019 and October 2022, in open access secondary databases, and using field diaries from research of the Environmental Health and Work Laboratory (LASAT) of the Aggeu Magalhães Institute of the Oswaldo Cruz Foundation. The disaster caused situations of injustice and environmental conflicts that had negative repercussions in the territories with socioeconomic impacts, on the environment, and on the health of the population. The entire marine environment was affected, resulting in physical and chemical alterations. The health vulnerabilities faced by local people were intensified, influencing the social determination of the health–disease process. The local economy was extremely affected, generating job insecurity and several socio-cultural problems. It is essential to build environmental and health diagnoses for remedial measures in disasters such as the oil spill.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81960109","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}
Elżbieta Wanowska, Alexis McFeely, Joanna Sztuba-Solinska
Epitranscriptome refers to post-transcriptional modifications to RNA and their associated regulatory factors that can govern changes in an organism’s cells in response to various environmental stimuli. Recent studies have recognized over 170 distinct chemical signatures in RNA, and the list keeps expanding. These modifications are hypothesized to have roles beyond simply fine-tuning the structure and function of RNA, as studies have linked them to various infectious and noninfectious diseases in humans. Dedicated cellular machinery comprising of RNA-binding proteins (RBPs) that can write, erase, and read these modifications drives the regulation of the epitranscriptomic code, and as such influences RNA metabolism and homeostasis. Equally, perturbations in the function of RBPs may disrupt RNA processing, further implicating them in pathogenesis. As such, the mechanisms underlying RNA modifications and their association with RBPs are emerging areas of interest within the field of biomedicine. This review focuses on understanding epitranscriptomic modifications, their effects on RNA–RBPs interactions, and their influence on cellular processes.
{"title":"The Role of Epitranscriptomic Modifications in the Regulation of RNA–Protein Interactions","authors":"Elżbieta Wanowska, Alexis McFeely, Joanna Sztuba-Solinska","doi":"10.3390/biochem2040017","DOIUrl":"https://doi.org/10.3390/biochem2040017","url":null,"abstract":"Epitranscriptome refers to post-transcriptional modifications to RNA and their associated regulatory factors that can govern changes in an organism’s cells in response to various environmental stimuli. Recent studies have recognized over 170 distinct chemical signatures in RNA, and the list keeps expanding. These modifications are hypothesized to have roles beyond simply fine-tuning the structure and function of RNA, as studies have linked them to various infectious and noninfectious diseases in humans. Dedicated cellular machinery comprising of RNA-binding proteins (RBPs) that can write, erase, and read these modifications drives the regulation of the epitranscriptomic code, and as such influences RNA metabolism and homeostasis. Equally, perturbations in the function of RBPs may disrupt RNA processing, further implicating them in pathogenesis. As such, the mechanisms underlying RNA modifications and their association with RBPs are emerging areas of interest within the field of biomedicine. This review focuses on understanding epitranscriptomic modifications, their effects on RNA–RBPs interactions, and their influence on cellular processes.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87414112","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 bilayer’s formations of amphiphilic molecules or polyions of different ionogenity comprise the basic building units of most organic biological and non-biological systems. A theory has evolved to explain their behaviour during the creation of those organized structures, such as anisotropic liquid crystal (LC) in lyotropic (especially hydrotropic) systems and polyelectrolyte multilayer (PEM) assemblies. Particular attention has been paid to the temperature and the important role of water in the formation and behaviour of the bilayers. A novel insight into the formation of hydrotropic liquid LC systems and their thermotropic behaviour is presented. In this context, the systems PEM assemblies are also discussed. Essentially, a structuralised form of water fills out continuous and discontinuous, i.e., confined, nano-spaces among hydrophilic interfaces of bilayers, controlling their supramolecular structure through a system of attractive and repulsive hydration forces. The character of those sophisticated bonding hydration systems is predestined by the composition and type of these hydrophilic interface groups. The miscellaneous complexity of the bilayer’s aqueous systems suggests the need to study these examples in greater detail. Therefore, the bilayer’s processes connected with disruption as far as destruction of bilayers are mentioned, i.e., the processes with the highest potential to combat bacteria, fungi, and viruses, such as in a situation where a person exhales a breath of micro-droplets containing virus nanoparticles (e.g., the COVID-19 virus).
{"title":"Bilayers as Basic Formation of Epimolecular Structure of Mostly Lyotropic (Hydrotropic) Structuralized Liquid Systems Being Influenced Predominantly by the Temperature","authors":"M. Milichovský","doi":"10.3390/biochem2040016","DOIUrl":"https://doi.org/10.3390/biochem2040016","url":null,"abstract":"The bilayer’s formations of amphiphilic molecules or polyions of different ionogenity comprise the basic building units of most organic biological and non-biological systems. A theory has evolved to explain their behaviour during the creation of those organized structures, such as anisotropic liquid crystal (LC) in lyotropic (especially hydrotropic) systems and polyelectrolyte multilayer (PEM) assemblies. Particular attention has been paid to the temperature and the important role of water in the formation and behaviour of the bilayers. A novel insight into the formation of hydrotropic liquid LC systems and their thermotropic behaviour is presented. In this context, the systems PEM assemblies are also discussed. Essentially, a structuralised form of water fills out continuous and discontinuous, i.e., confined, nano-spaces among hydrophilic interfaces of bilayers, controlling their supramolecular structure through a system of attractive and repulsive hydration forces. The character of those sophisticated bonding hydration systems is predestined by the composition and type of these hydrophilic interface groups. The miscellaneous complexity of the bilayer’s aqueous systems suggests the need to study these examples in greater detail. Therefore, the bilayer’s processes connected with disruption as far as destruction of bilayers are mentioned, i.e., the processes with the highest potential to combat bacteria, fungi, and viruses, such as in a situation where a person exhales a breath of micro-droplets containing virus nanoparticles (e.g., the COVID-19 virus).","PeriodicalId":72357,"journal":{"name":"BioChem","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81879928","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}
Mariana Marques, João Nunes, Bárbara Ustymenko, L. Fialho, Luís Martins, A. Burke, Cesar Filho, Alexandre C. Craveiro, Ana R. Costa, S. Branco, C. Antunes
Skin is one of the organs most tested for toxicity and safety evaluation during the process of drug research and development and in the past has usually been performed in vivo using animals. Over the last few years, non-animal alternatives have been developed and validated epidermis models for human and rat skin are already available. Our goal was to develop a histotypical canine skin analog, suitable for non-animal biocompatibility and biosafety assessment. Canine keratinocytes were seeded in an air-lift culture using an adapted version of the CELLnTEC protocol. Corrosion and irritation protocols were adapted from human EpiSkinTM. For histological analysis, sample biopsies were fixed in neutral-buffered formalin, and paraffin slices were routinely processed and stained with hematoxylin and eosin. A canine multilayer and stratified epidermal-like tissue (cEpiderm), confirmed by histological analysis, was obtained. The cEpiderm tissue exhibited normal morphological and functional characteristics of epidermis, namely impermeability and an adequate response to stressors. The cEpiderm is a promising canine skin model for non-animal safety testing of veterinary pharmaceuticals and/or cosmetics, significantly contributing to reducing undesirable in vivo approaches. cEpiderm is therefore a valid canine skin model and may be made commercially available either as a service or as a product.
{"title":"cEpiderm, a Canine Skin Analog Suitable for In Vivo Testing Replacement","authors":"Mariana Marques, João Nunes, Bárbara Ustymenko, L. Fialho, Luís Martins, A. Burke, Cesar Filho, Alexandre C. Craveiro, Ana R. Costa, S. Branco, C. Antunes","doi":"10.3390/biochem2040015","DOIUrl":"https://doi.org/10.3390/biochem2040015","url":null,"abstract":"Skin is one of the organs most tested for toxicity and safety evaluation during the process of drug research and development and in the past has usually been performed in vivo using animals. Over the last few years, non-animal alternatives have been developed and validated epidermis models for human and rat skin are already available. Our goal was to develop a histotypical canine skin analog, suitable for non-animal biocompatibility and biosafety assessment. Canine keratinocytes were seeded in an air-lift culture using an adapted version of the CELLnTEC protocol. Corrosion and irritation protocols were adapted from human EpiSkinTM. For histological analysis, sample biopsies were fixed in neutral-buffered formalin, and paraffin slices were routinely processed and stained with hematoxylin and eosin. A canine multilayer and stratified epidermal-like tissue (cEpiderm), confirmed by histological analysis, was obtained. The cEpiderm tissue exhibited normal morphological and functional characteristics of epidermis, namely impermeability and an adequate response to stressors. The cEpiderm is a promising canine skin model for non-animal safety testing of veterinary pharmaceuticals and/or cosmetics, significantly contributing to reducing undesirable in vivo approaches. cEpiderm is therefore a valid canine skin model and may be made commercially available either as a service or as a product.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":"41 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85174094","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}
Ricardo Silva, D. Carrageta, M. Alves, P. Oliveira
The incidence of male infertility has been increasing over the years and is now becoming a serious health problem. This trend has been followed by an increase in metabolic diseases, which are known to induce clear alterations in testicular metabolism, although the underlying mechanismremain unclear. Testicular metabolism displays several unique features, with testicular somatic cells being central in providing the conditions needed for spermatogenesis, including its nutritional and hormonal support. In addition to glucose and lactate, the two main energy sources used by the testis, glycogen is also present in testicular cells. Glycogen metabolism is a potential source of glucose to both testicular somatic (namely Sertoli and Leydig cells) and germ cells. Many of the enzymes involved in the pathways of the synthesis and degradation of glycogen were identified in these cells, emphasising the relevance of this complex carbohydrate. Glycogen, however, has other non-canonical functions in testicular cells; besides its role as a source of energy, it is also associated with events such as cellular differentiation and apoptosis. In this review, we address the relevance of testicular glycogen metabolism, focusing on its role in Sertoli and Leydig cells and spermatogenesis. In addition, all the available information on the role of glycogen and related pathways in male infertility cases is discussed. Our discussion highlights that glycogen metabolism has been somewhat overlooked in testis and its contribution to spermatogenesis may be underestimated.
{"title":"Testicular Glycogen Metabolism: An Overlooked Source of Energy for Spermatogenesis?","authors":"Ricardo Silva, D. Carrageta, M. Alves, P. Oliveira","doi":"10.3390/biochem2030014","DOIUrl":"https://doi.org/10.3390/biochem2030014","url":null,"abstract":"The incidence of male infertility has been increasing over the years and is now becoming a serious health problem. This trend has been followed by an increase in metabolic diseases, which are known to induce clear alterations in testicular metabolism, although the underlying mechanismremain unclear. Testicular metabolism displays several unique features, with testicular somatic cells being central in providing the conditions needed for spermatogenesis, including its nutritional and hormonal support. In addition to glucose and lactate, the two main energy sources used by the testis, glycogen is also present in testicular cells. Glycogen metabolism is a potential source of glucose to both testicular somatic (namely Sertoli and Leydig cells) and germ cells. Many of the enzymes involved in the pathways of the synthesis and degradation of glycogen were identified in these cells, emphasising the relevance of this complex carbohydrate. Glycogen, however, has other non-canonical functions in testicular cells; besides its role as a source of energy, it is also associated with events such as cellular differentiation and apoptosis. In this review, we address the relevance of testicular glycogen metabolism, focusing on its role in Sertoli and Leydig cells and spermatogenesis. In addition, all the available information on the role of glycogen and related pathways in male infertility cases is discussed. Our discussion highlights that glycogen metabolism has been somewhat overlooked in testis and its contribution to spermatogenesis may be underestimated.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90933574","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}
Metalloenzymes are the most proficient nature catalysts that are responsible for diverse biochemical transformations introducing excellent selectivity and performing at high rates, using intricate mutual relationships between metal ions and proteins. Inspired by nature, chemists started using naturally occurring proteins as templates to harbor non-native metal catalysts for the sustainable synthesis of molecules for pharmaceutical, biotechnological and industrial purposes. Therefore, metalloenzymes are the relevant targets for the design of artificial biocatalysts. The search and development of new scaffolds capable of hosting metals with high levels of selectivity could significantly expand the scope of bio-catalysis. To meet this challenge, herein, three native scaffolds: [1Fe-4Cys] (rubredoxin), [3Fe-4S] (ferredoxin), and [S2MoS2CuS2MoS2]-ORP (orange protein) protein scaffolds are case studies describing templates for the synthesis of non-native monomeric to mixed metal–sulfur clusters, which mimic native Ni containing metalloenzymes including [Ni-Fe] Hydrogenase and [Ni-Fe] CO Dehydrogenase. The non-native metal-substituted metalloproteins are not only useful for catalysis but also as spectroscopic probes.
{"title":"Native Protein Template Assisted Synthesis of Non-Native Metal-Sulfur Clusters","authors":"B. Maiti, J. Moura","doi":"10.3390/biochem2030013","DOIUrl":"https://doi.org/10.3390/biochem2030013","url":null,"abstract":"Metalloenzymes are the most proficient nature catalysts that are responsible for diverse biochemical transformations introducing excellent selectivity and performing at high rates, using intricate mutual relationships between metal ions and proteins. Inspired by nature, chemists started using naturally occurring proteins as templates to harbor non-native metal catalysts for the sustainable synthesis of molecules for pharmaceutical, biotechnological and industrial purposes. Therefore, metalloenzymes are the relevant targets for the design of artificial biocatalysts. The search and development of new scaffolds capable of hosting metals with high levels of selectivity could significantly expand the scope of bio-catalysis. To meet this challenge, herein, three native scaffolds: [1Fe-4Cys] (rubredoxin), [3Fe-4S] (ferredoxin), and [S2MoS2CuS2MoS2]-ORP (orange protein) protein scaffolds are case studies describing templates for the synthesis of non-native monomeric to mixed metal–sulfur clusters, which mimic native Ni containing metalloenzymes including [Ni-Fe] Hydrogenase and [Ni-Fe] CO Dehydrogenase. The non-native metal-substituted metalloproteins are not only useful for catalysis but also as spectroscopic probes.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":"37 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87316691","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}
Three forms of methylated cytosines are present in the eukaryotic genome: 3-methylcytosine, 4-methylcytosine and 5-methylcytosine. 3-methylcytosines create methyl lesions, which impair local DNA function and flexibility, resulting in replication and transcription error. On the other hand, 5-methylcytosine is usually present at the gene promoter which blocks transcription and translation. Fe(II)/2OG-dependent nucleic acid-modifying enzymes are the class of enzymes responsible for the demethylation of these modified cytosines. ALKBH2 and 3 remove 3-methylcytosine via a one-step direct demethylation process. On the other hand, active demethylation of 5mC is initiated by Ten-Eleven Translocation (TET)-family dioxygenases. Via oxidative demethylation, TET1-3 converts 5mC into 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine. Remarkably, recent findings demonstrate that ALKBH2,3 possess oxidative demethylation properties, along with direct demethylation. On the other hand, the TET family of enzymes possess direct demethylation properties along with oxidative demethylation. Here we review the importance of methylated cytosines in human DNA, their origin, function and removal. In addition, we discuss the recent findings of extraordinary flexibility of Fe(II)/2OG-dependent nucleic acid-modifying enzymes ALKBH2,3 and TET family of enzymes in cytosine demethylation, as well as their impact on epigenetics.
{"title":"Bifunctional Role of Fe(II)/2OG-Dependent TET Family 5-Methylcytosine Dioxygenases and ALKBH2,3 in Modified Cytosine Demethylation","authors":"Aninda Sundar Dey","doi":"10.3390/biochem2030012","DOIUrl":"https://doi.org/10.3390/biochem2030012","url":null,"abstract":"Three forms of methylated cytosines are present in the eukaryotic genome: 3-methylcytosine, 4-methylcytosine and 5-methylcytosine. 3-methylcytosines create methyl lesions, which impair local DNA function and flexibility, resulting in replication and transcription error. On the other hand, 5-methylcytosine is usually present at the gene promoter which blocks transcription and translation. Fe(II)/2OG-dependent nucleic acid-modifying enzymes are the class of enzymes responsible for the demethylation of these modified cytosines. ALKBH2 and 3 remove 3-methylcytosine via a one-step direct demethylation process. On the other hand, active demethylation of 5mC is initiated by Ten-Eleven Translocation (TET)-family dioxygenases. Via oxidative demethylation, TET1-3 converts 5mC into 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine. Remarkably, recent findings demonstrate that ALKBH2,3 possess oxidative demethylation properties, along with direct demethylation. On the other hand, the TET family of enzymes possess direct demethylation properties along with oxidative demethylation. Here we review the importance of methylated cytosines in human DNA, their origin, function and removal. In addition, we discuss the recent findings of extraordinary flexibility of Fe(II)/2OG-dependent nucleic acid-modifying enzymes ALKBH2,3 and TET family of enzymes in cytosine demethylation, as well as their impact on epigenetics.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":"41 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86261313","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}
Márcio Simão, N. Conceição, Susana Imaginário, J. Amaro, M. Cancela
The Molecular Genetics Mobile Lab or “Laboratório itinerante de Genética Molecular” (Lab-it) was funded in 2008 by Leonor Cancela to promote the learning of molecular genetics which had been introduced at that time into high school biology programms. The project aimed to introduce hands-on laboratory activities in molecular genetics to complement the theoretical concepts taught in school. These included the development of experimental protocols based on theoretical scenarios focusing on themes of forensics sciences, biomedical applications, diagnostic methods, and ecological research using basic molecular biology techniques, such as DNA extraction, polymerase chain reaction (PCR), electrophoresis, and restriction enzyme application. In these scenarios, the students execute all the procedures with the help of the Lab-it instructor and using the Lab-it equipment, followed by a discussion of the results with all the participants and the school teacher. These approaches help the students to consolidate the concepts of molecular biology and simultaneously promote discussions on new advances in the area and choices for university careers. In addition to practical sessions, Lab-it also promotes seminars on topics of interest to the students and teachers. Since 2008, 18 high schools have participated in the region of Algarve, averaging each year about 400 students participating in practical activities. In 2021, despite the COVID pandemic, 9 schools and 379 students were involved in Lab-it practical sessions and 99% of them considered the activity to contribute to better understanding the molecular biology methods approached in theoretical classes and expressed high interest in those sessions.
分子遗传学移动实验室，或称“Laboratório itinerante de gen诈骗学分子实验室”(Lab-it)是由Leonor Cancela于2008年资助的，目的是促进分子遗传学的学习，当时分子遗传学已被引入高中生物课程。该项目旨在引入分子遗传学的动手实验活动，以补充学校教授的理论概念。其中包括基于法医学、生物医学应用、诊断方法和使用基本分子生物学技术(如DNA提取、聚合酶链反应(PCR)、电泳和限制性内切酶应用)的生态研究等主题的理论场景的实验方案的开发。在这些场景中，学生们在Lab-it指导老师的帮助下使用Lab-it设备执行所有程序，然后与所有参与者和学校老师讨论结果。这些方法有助于学生巩固分子生物学的概念，同时促进对该领域新进展的讨论和对大学职业的选择。除了实践课程，Lab-it还举办学生和教师感兴趣的主题研讨会。自2008年以来，18所高中参加了阿尔加维地区的实践活动，平均每年约有400名学生参加实践活动。2021年，尽管发生了新冠肺炎疫情，但仍有9所学校和379名学生参与了Lab-it实践课程，其中99%的学生认为该活动有助于更好地理解理论课中使用的分子生物学方法，并对这些课程表达了浓厚的兴趣。
{"title":"Lab-It Is Taking Molecular Genetics to School","authors":"Márcio Simão, N. Conceição, Susana Imaginário, J. Amaro, M. Cancela","doi":"10.3390/biochem2020011","DOIUrl":"https://doi.org/10.3390/biochem2020011","url":null,"abstract":"The Molecular Genetics Mobile Lab or “Laboratório itinerante de Genética Molecular” (Lab-it) was funded in 2008 by Leonor Cancela to promote the learning of molecular genetics which had been introduced at that time into high school biology programms. The project aimed to introduce hands-on laboratory activities in molecular genetics to complement the theoretical concepts taught in school. These included the development of experimental protocols based on theoretical scenarios focusing on themes of forensics sciences, biomedical applications, diagnostic methods, and ecological research using basic molecular biology techniques, such as DNA extraction, polymerase chain reaction (PCR), electrophoresis, and restriction enzyme application. In these scenarios, the students execute all the procedures with the help of the Lab-it instructor and using the Lab-it equipment, followed by a discussion of the results with all the participants and the school teacher. These approaches help the students to consolidate the concepts of molecular biology and simultaneously promote discussions on new advances in the area and choices for university careers. In addition to practical sessions, Lab-it also promotes seminars on topics of interest to the students and teachers. Since 2008, 18 high schools have participated in the region of Algarve, averaging each year about 400 students participating in practical activities. In 2021, despite the COVID pandemic, 9 schools and 379 students were involved in Lab-it practical sessions and 99% of them considered the activity to contribute to better understanding the molecular biology methods approached in theoretical classes and expressed high interest in those sessions.","PeriodicalId":72357,"journal":{"name":"BioChem","volume":"18 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85663233","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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