Critical Reviews in Biochemistry and Molecular Biology最新文献

{"title":"ETF dehydrogenase advances in molecular genetics and impact on treatment.","authors":"Sara Missaglia,&nbsp;Daniela Tavian,&nbsp;Corrado Angelini","doi":"10.1080/10409238.2021.1908952","DOIUrl":"https://doi.org/10.1080/10409238.2021.1908952","url":null,"abstract":"<p><p>Electron transfer flavoprotein dehydrogenase, also called ETF-ubiquinone oxidoreductase (ETF-QO), is a protein localized in the inner membrane of mitochondria, playing a central role in the electron-transfer system. Indeed, ETF-QO mediates electron transport from flavoprotein dehydrogenases to the ubiquinone pool. ETF-QO mutations are often associated with riboflavin-responsive multiple acyl-CoA dehydrogenase deficiency (RR-MADD, OMIM#231680), a multisystem genetic disease characterized by various clinical manifestations with different degrees of severity. In this review, we outline the clinical features correlated with ETF-QO deficiency and the benefits obtained from different treatments, such as riboflavin, L-carnitine and/or coenzyme Q10 supplementation, and a diet poor in fat and protein. Moreover, we provide a detailed summary of molecular and bioinformatic investigations, describing the mutations identified in <i>ETFDH</i> gene and highlighting their predicted impact on enzymatic structure and activity. In addition, we report biochemical and functional analysis, performed in HEK293 cells and patient fibroblasts and muscle cells, to show the relationship between the nature of <i>ETFDH</i> mutations, the variable impairment of enzyme function, and the different degrees of RR-MADD severity. Finally, we describe in detail 5 RR-MADD patients carrying different <i>ETFDH</i> mutations and presenting variable degrees of clinical symptom severity.</p>","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"56 4","pages":"360-372"},"PeriodicalIF":6.5,"publicationDate":"2021-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10409238.2021.1908952","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25565156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cholesterol efflux pathways, inflammation, and atherosclerosis.","authors":"Anouk G Groenen, Benedek Halmos, Alan R Tall, Marit Westerterp","doi":"10.1080/10409238.2021.1925217","DOIUrl":"10.1080/10409238.2021.1925217","url":null,"abstract":"<p><p>Plasma levels of high-density lipoprotein (HDL) inversely correlate with the incidence of cardiovascular diseases (CVD). The causal relationship between plasma HDL-cholesterol levels and CVD has been called into question by Mendelian randomization studies and the majority of clinical trials not showing any benefit of plasma HDL-cholesterol raising drugs on CVD. Nonetheless, recent Mendelian randomization studies including an increased number of CVD cases compared to earlier studies have confirmed that HDL-cholesterol levels and CVD are causally linked. Moreover, several studies in large population cohorts have shown that the cholesterol efflux capacity of HDL inversely correlates with CVD. Cholesterol efflux pathways exert anti-inflammatory and anti-atherogenic effects by suppressing proliferation of hematopoietic stem and progenitor cells, and inflammation and inflammasome activation in macrophages. Cholesterol efflux pathways also suppress the accumulation of cholesteryl esters in macrophages, <i>i.e.</i> macrophage foam cell formation. Recent single-cell RNASeq studies on atherosclerotic plaques have suggested that macrophage foam cells have lower expression of inflammatory genes than non-foam cells, probably reflecting liver X receptor activation, upregulation of ATP Binding Cassette A1 and G1 cholesterol transporters and suppression of inflammation. However, when these pathways are defective lesional foam cells may become pro-inflammatory.</p>","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"56 4","pages":"426-439"},"PeriodicalIF":6.2,"publicationDate":"2021-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/f0/b4/nihms-1793347.PMC9007272.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39117763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"How can a traffic light properly work if it is always green? The paradox of CK2 signaling.","authors":"Christian Borgo,&nbsp;Claudio D'Amore,&nbsp;Luca Cesaro,&nbsp;Stefania Sarno,&nbsp;Lorenzo A Pinna,&nbsp;Maria Ruzzene,&nbsp;Mauro Salvi","doi":"10.1080/10409238.2021.1908951","DOIUrl":"https://doi.org/10.1080/10409238.2021.1908951","url":null,"abstract":"<p><p>CK2 is a constitutively active protein kinase that assuring a constant level of phosphorylation to its numerous substrates supports many of the most important biological functions. Nevertheless, its activity has to be controlled and adjusted in order to cope with the varying needs of a cell, and several examples of a fine-tune regulation of its activity have been described. More importantly, aberrant regulation of this enzyme may have pathological consequences, e.g. in cancer, chronic inflammation, neurodegeneration, and viral infection. Our review aims at summarizing our current knowledge about CK2 regulation. In the first part, we have considered the most important stimuli shown to affect protein kinase CK2 activity/expression. In the second part, we focus on the molecular mechanisms by which CK2 can be regulated, discussing controversial aspects and future perspectives.</p>","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"56 4","pages":"321-359"},"PeriodicalIF":6.5,"publicationDate":"2021-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10409238.2021.1908951","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25580842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The role of non-genetic information in evolutionary frameworks.","authors":"Katherine L Moran,&nbsp;Yelyzaveta Shlyakhtina,&nbsp;Maximiliano M Portal","doi":"10.1080/10409238.2021.1908949","DOIUrl":"https://doi.org/10.1080/10409238.2021.1908949","url":null,"abstract":"<p><p>The evolution of organisms has been a subject of paramount debate for hundreds of years and though major advances in the field have been made, the precise mechanisms underlying evolutionary processes remain fragmentary. Strikingly, the majority of the core principles accepted across the many fields of biology only consider genetic information as the major - if not exclusive - biological information carrier and thus consider it as the main evolutionary avatar. However, the real picture appears far more complex than originally anticipated, as compelling data suggest that nongenetic information steps up when highly dynamic evolutionary frameworks are explored. In light of recent evidence, we discuss herein the dynamic nature and complexity of nongenetic information carriers, and their emerging relevance in the evolutionary process. We argue that it is possible to overcome the historical arguments which dismissed these carriers, and instead consider that they are indeed core to life itself as they support a sustainable, continuous source of rapid adaptation in ever-changing environments. Ultimately, we will address the intricacies of genetic and non-genetic networks underlying evolutionary models to build a framework where both core biological information concepts are considered non-negligible and equally fundamental.</p>","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"56 3","pages":"255-283"},"PeriodicalIF":6.5,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10409238.2021.1908949","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38966321","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SMART approaches for genome-wide analyses of skeletal muscle stem and niche cells.","authors":"Darren M Blackburn,&nbsp;Felicia Lazure,&nbsp;Vahab D Soleimani","doi":"10.1080/10409238.2021.1908950","DOIUrl":"https://doi.org/10.1080/10409238.2021.1908950","url":null,"abstract":"<p><p>Muscle stem cells (MuSCs) also called satellite cells are the building blocks of skeletal muscle, the largest tissue in the human body which is formed primarily of myofibers. While MuSCs are the principal cells that directly contribute to the formation of the muscle fibers, their ability to do so depends on critical interactions with a vast array of nonmyogenic cells within their niche environment. Therefore, understanding the nature of communication between MuSCs and their niche is of key importance to understand how the skeletal muscle is maintained and regenerated after injury. MuSCs are rare and therefore difficult to study <i>in vivo</i> within the context of their niche environment. The advent of single-cell technologies, such as switching mechanism at 5' end of the RNA template (SMART) and tagmentation based technologies using hyperactive transposase, afford the unprecedented opportunity to perform whole transcriptome and epigenome studies on rare cells within their niche environment. In this review, we will delve into how single-cell technologies can be applied to the study of MuSCs and muscle-resident niche cells and the impact this can have on our understanding of MuSC biology and skeletal muscle regeneration.</p>","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"56 3","pages":"284-300"},"PeriodicalIF":6.5,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10409238.2021.1908950","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25566635","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"HIV suppressors against LINE-1: one functions as two.","authors":"Juan Du,&nbsp;Ke Zhao","doi":"10.1080/10409238.2021.1893640","DOIUrl":"https://doi.org/10.1080/10409238.2021.1893640","url":null,"abstract":"Abstract Exogenous retroviruses are RNA viruses that require reverse transcription for their replication. Among these viruses, human immunodeficiency virus (HIV) is infectious to humans and causes the development of acquired immune deficiency syndrome (AIDS). There are also endogenous retroelements that require reverse transcription for their retrotransposition, among which the type 1 long interspersed element (LINE-1) is the only type of retroelement that can replicate autonomously. It was once believed that retroviruses like HIV and retroelements like LINE-1 share similarities in processes such as reverse transcription and integration. Accordingly, many HIV suppressors are also potent LINE-1 inhibitors. However, in many cases, one suppressor uses two or more distinct mechanisms to repress HIV and LINE-1. In this review, we discuss some of these suppressors, focusing on their alternative mechanisms opposing the replication of HIV and LINE-1. Based on the differences in HIV and LINE-1 activity, the subcellular localization of these suppressors, and the impact of LINE-1 retrotransposition on human cells, we propose possible reasons for the inhibition of HIV and LINE-1 through different pathways by these suppressors, with the hope of accelerating future studies in associated research fields.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"56 3","pages":"205-220"},"PeriodicalIF":6.5,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10409238.2021.1893640","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25418981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sweet systems: technologies for glycomic analysis and their integration into systems biology.","authors":"Shuhui Chen,&nbsp;Rui Qin,&nbsp;Lara K Mahal","doi":"10.1080/10409238.2021.1908953","DOIUrl":"https://doi.org/10.1080/10409238.2021.1908953","url":null,"abstract":"<p><p>Found in virtually every organism, glycans are essential molecules that play important roles in almost every aspect of biology. The composition of glycome, the repertoire of glycans in an organism or a biological sample, is often found altered in many diseases, including cancer, infectious diseases, metabolic and developmental disorders. Understanding how glycosylation and glycomic changes enriches our knowledge of the mechanisms of disease progression and sheds light on the development of novel therapeutics. However, the inherent diversity of glycan structures imposes challenges on the experimental characterization of glycomes. Advances in high-throughput glycomic technologies enable glycomic analysis in a rapid and comprehensive manner. In this review, we discuss the analytical methods currently used in high-throughput glycomics, including mass spectrometry, liquid chromatography and lectin microarray. Concomitant with the technical advances is the integration of glycomics into systems biology in the recent years. Herein we elaborate on some representative works from this recent trend to underline the important role of glycomics in such integrated approaches to disease.</p>","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"56 3","pages":"301-320"},"PeriodicalIF":6.5,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10409238.2021.1908953","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25565016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A local regulatory network in the testis mediated by laminin and collagen fragments that supports spermatogenesis.","authors":"Linxi Li,&nbsp;Huitao Li,&nbsp;Lingling Wang,&nbsp;Tiao Bu,&nbsp;Shiwen Liu,&nbsp;Baiping Mao,&nbsp;C Yan Cheng","doi":"10.1080/10409238.2021.1901255","DOIUrl":"https://doi.org/10.1080/10409238.2021.1901255","url":null,"abstract":"<p><p>It is almost five decades since the discovery of the hypothalamic-pituitary-testicular axis. This refers to the hormonal axis that connects the hypothalamus, pituitary gland and testes, which in turn, regulates the production of spermatozoa through spermatogenesis in the seminiferous tubules, and testosterone through steroidogenesis by Leydig cells in the interstitium, of the testes. Emerging evidence has demonstrated the presence of a regulatory network across the seminiferous epithelium utilizing bioactive molecules produced locally at specific domains of the epithelium. Studies have shown that biologically active fragments are produced from structural laminin and collagen chains in the basement membrane. Additionally, bioactive peptides are also produced locally in non-basement membrane laminin chains at the Sertoli-spermatid interface known as apical ectoplasmic specialization (apical ES, a testis-specific actin-based anchoring junction type). These bioactive peptides are derived from structural laminins and/or collagens at the corresponding sites through proteolytic cleavage by matrix metalloproteinases (MMPs). They in turn serve as autocrine and/or paracrine factors to modulate and coordinate cellular events across the epithelium by linking the apical and basal compartments, the apical and basal ES, the blood-testis barrier (BTB), and the basement membrane of the tunica propria. The cellular events supported by these bioactive peptides/fragments include the release of spermatozoa at spermiation, remodeling of the immunological barrier to facilitate the transport of preleptotene spermatocytes across the BTB, and the transport of haploid spermatids across the epithelium to support spermiogenesis. In this review, we critically evaluate these findings. Our goal is to identify research areas that deserve attentions in future years. The proposed research also provides the much needed understanding on the biology of spermatogenesis supported by a local network of regulatory biomolecules.</p>","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"56 3","pages":"236-254"},"PeriodicalIF":6.5,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10409238.2021.1901255","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25512828","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Regulation of the redox metabolome and thiol proteome by hydrogen sulfide.","authors":"Roshan Kumar,&nbsp;Ruma Banerjee","doi":"10.1080/10409238.2021.1893641","DOIUrl":"https://doi.org/10.1080/10409238.2021.1893641","url":null,"abstract":"<p><p>Overproduction of reactive oxygen species and compromised antioxidant defenses perturb intracellular redox homeostasis and is associated with a myriad of human diseases as well as with the natural process of aging. Hydrogen sulfide (H₂S), which is biosynthesized by organisms ranging from bacteria to man, influences a broad range of physiological functions. A highly touted molecular mechanism by which H₂S exerts its cellular effects is via post-translational modification of the thiol redox proteome, converting cysteine thiols to persulfides, in a process referred to as protein persulfidation. The physiological relevance of this modification in the context of specific signal transmission pathways remains to be rigorously established, while a general protective role for protein persulfidation against hyper-oxidation of the cysteine proteome is better supported. A second mechanism by which H₂S modulates redox homeostasis is via remodeling the redox metabolome, targeting the electron transfer chain and perturbing the major redox nodes i.e. CoQ/CoQH₂, NAD⁺/NADH and FAD/FADH₂. The metabolic changes that result from H₂S-induced redox changes fan out from the mitochondrion to other compartments. In this review, we discuss recent developments in elucidating the roles of H₂S and its oxidation products on redox homeostasis and its role in protecting the thiol proteome.</p>","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"56 3","pages":"221-235"},"PeriodicalIF":6.5,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10409238.2021.1893641","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25480847","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Instrumental analysis of RNA modifications.","authors":"Yasemin Yoluç,&nbsp;Gregor Ammann,&nbsp;Pierre Barraud,&nbsp;Manasses Jora,&nbsp;Patrick A Limbach,&nbsp;Yuri Motorin,&nbsp;Virginie Marchand,&nbsp;Carine Tisné,&nbsp;Kayla Borland,&nbsp;Stefanie Kellner","doi":"10.1080/10409238.2021.1887807","DOIUrl":"https://doi.org/10.1080/10409238.2021.1887807","url":null,"abstract":"<p><p>Organisms from all domains of life invest a substantial amount of energy for the introduction of RNA modifications into nearly all transcripts studied to date. Instrumental analysis of RNA can focus on the modified residues and reveal the function of these epitranscriptomic marks. Here, we will review recent advances and breakthroughs achieved by NMR spectroscopy, sequencing, and mass spectrometry of the epitranscriptome.</p>","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"56 2","pages":"178-204"},"PeriodicalIF":6.5,"publicationDate":"2021-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10409238.2021.1887807","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25394775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}