Critical Reviews in Biochemistry and Molecular Biology最新文献_第7页

The amyloid proteome: a systematic review and proposal of a protein classification system. 淀粉样蛋白组:一种蛋白质分类系统的综述和建议。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2021-10-01 Epub Date: 2021-07-27 DOI: 10.1080/10409238.2021.1937926

Juliane Gottwald, Christoph Röcken

{"title":"The amyloid proteome: a systematic review and proposal of a protein classification system.","authors":"Juliane Gottwald, Christoph Röcken","doi":"10.1080/10409238.2021.1937926","DOIUrl":"https://doi.org/10.1080/10409238.2021.1937926","url":null,"abstract":"Amyloidosis is a disease caused by pathological fibril aggregation and deposition of proteins in different tissues and organs. Thirty-six fibril-forming proteins have been identified. So far, proteomic evaluation of amyloid focused on the detection and characterization of fibril proteins mainly for diagnostic purposes or to find novel fibril-forming proteins. However, amyloid deposits are a complex mixture of constituents that show organ-, tissue-, and amyloid-type specific patterns, that is the amyloid proteome. We carried out a comprehensive literature review on publications investigating amyloid via liquid chromatography coupled to tandem mass spectrometry, including but not limited to sample preparation by laser microdissection. Our review confirms the complexity and dynamics of the amyloid proteome, which can be divided into four functional categories: amyloid proteome-category 1 (APC1) includes exclusively fibrillary proteins found in the patient; APC2 includes potential fibril-forming proteins found in other types of amyloid; and APC3 and APC4 summarizes non-fibril proteins-some being amyloid signature proteins. Our categorization may help to systemically explore the nature and role of the amyloid proteome in the manifestation, progression, and clearance of disease. Further exploration of the amyloid proteome may form the basis for the development of novel diagnostic tools, thereby enabling the development of novel therapeutic targets.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"526-542"},"PeriodicalIF":6.5,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10409238.2021.1937926","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39224001","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}

引用次数: 7

Novel insights into the mechanism of cell cycle kinases Mec1(ATR) and Tel1(ATM). 细胞周期激酶Mec1(ATR)和Tel1(ATM)机制的新见解。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2021-10-01 Epub Date: 2021-06-20 DOI: 10.1080/10409238.2021.1925218

Elias A Tannous, Peter M Burgers

{"title":"Novel insights into the mechanism of cell cycle kinases Mec1(ATR) and Tel1(ATM).","authors":"Elias A Tannous, Peter M Burgers","doi":"10.1080/10409238.2021.1925218","DOIUrl":"https://doi.org/10.1080/10409238.2021.1925218","url":null,"abstract":"DNA replication is a highly precise process which usually functions in a perfect rhythm with cell cycle progression. However, cells are constantly faced with various kinds of obstacles such as blocks in DNA replication, lack of availability of precursors and improper chromosome alignment. When these problems are not addressed, they may lead to chromosome instability and the accumulation of mutations, and even cell death. Therefore, the cell has developed response mechanisms to keep most of these situations under control. Of the many factors that participate in this DNA damage response, members of the family of phosphatidylinositol 3-kinase-related protein kinases (PIKKs) orchestrate the response landscape. Our understanding of two members of the PIKK family, human ATR (yeast Mec1) and ATM (yeast Tel1), and their associated partner proteins, has shown substantial progress through recent biochemical and structural studies. Emerging structural information of these unique kinases show common features that reveal the mechanism of kinase activity.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"441-454"},"PeriodicalIF":6.5,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10409238.2021.1925218","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39251358","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}

引用次数: 6

Guanine quadruplexes and their roles in molecular processes. 鸟嘌呤四聚体及其在分子过程中的作用。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2021-10-01 Epub Date: 2021-06-23 DOI: 10.1080/10409238.2021.1926417

Shruti Mishra, Swathi Kota, Reema Chaudhary, H S Misra

{"title":"Guanine quadruplexes and their roles in molecular processes.","authors":"Shruti Mishra, Swathi Kota, Reema Chaudhary, H S Misra","doi":"10.1080/10409238.2021.1926417","DOIUrl":"https://doi.org/10.1080/10409238.2021.1926417","url":null,"abstract":"The role of guanine quadruplexes (G4) in fundamental biological processes like DNA replication, transcription, translation and telomere maintenance is recognized. G4 structure dynamics is regulated by G4 structure binding proteins and is thought to be crucial for the maintenance of genome integrity in both prokaryotic and eukaryotic cells. Growing research over the last decade has expanded the existing knowledge of the functional diversity of G4 (DNA and RNA) structures across the working models. The control of G4 structure dynamics using G4 binding drugs has been suggested as the putative targets in the control of cancer and bacterial pathogenesis. This review has brought forth the collections of recent information that indicate G4 (mostly G4 DNA) roles in microbial pathogenesis, DNA damaging stress response in bacteria and mammalian cells. Studies in mitochondrial gene function regulation by G4s have also been underscored. Finally, the interdependence of G4s and epigenetic modifications and their speculated medical implications through G4 interacting proteins has been discussed.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"482-499"},"PeriodicalIF":6.5,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10409238.2021.1926417","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39099502","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}

引用次数: 3

The leucine-responsive regulatory proteins/feast-famine regulatory proteins: an ancient and complex class of transcriptional regulators in bacteria and archaea. 亮氨酸反应调节蛋白/饥饿-饥饿调节蛋白:细菌和古生菌中一类古老而复杂的转录调节蛋白。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2021-08-01 Epub Date: 2021-06-20 DOI: 10.1080/10409238.2021.1925215

Christine A Ziegler, Peter L Freddolino

{"title":"The leucine-responsive regulatory proteins/feast-famine regulatory proteins: an ancient and complex class of transcriptional regulators in bacteria and archaea.","authors":"Christine A Ziegler, Peter L Freddolino","doi":"10.1080/10409238.2021.1925215","DOIUrl":"https://doi.org/10.1080/10409238.2021.1925215","url":null,"abstract":"Since the discovery of the Escherichia coli leucine-responsive regulatory protein (Lrp) almost 50 years ago, hundreds of Lrp homologs have been discovered, occurring in 45% of sequenced bacteria and almost all sequenced archaea. Lrp-like proteins are often referred to as the feast/famine regulatory proteins (FFRPs), reflecting their common regulatory roles. Acting as either global or local transcriptional regulators, FFRPs detect the environmental nutritional status by sensing small effector molecules (usually amino acids) and regulate the expression of genes involved in metabolism, virulence, motility, nutrient transport, stress tolerance, and antibiotic resistance to implement appropriate behaviors for the specific ecological niche of each organism. Despite FFRPs' complexity, a significant role in gene regulation, and prevalence throughout prokaryotes, the last comprehensive review on this family of proteins was published about a decade ago. In this review, we integrate recent notable findings regarding E. coli Lrp and other FFRPs across bacteria and archaea with previous observations to synthesize a more complete view on the mechanistic details and biological roles of this ancient class of transcription factors.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"56 4","pages":"373-400"},"PeriodicalIF":6.5,"publicationDate":"2021-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10409238.2021.1925215","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39257663","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}

引用次数: 17

Miro proteins connect mitochondrial function and intercellular transport. Miro蛋白连接线粒体功能和细胞间运输。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2021-08-01 Epub Date: 2021-06-17 DOI: 10.1080/10409238.2021.1925216

Zuzana Nahacka, Renata Zobalova, Maria Dubisova, Jakub Rohlena, Jiri Neuzil

{"title":"Miro proteins connect mitochondrial function and intercellular transport.","authors":"Zuzana Nahacka, Renata Zobalova, Maria Dubisova, Jakub Rohlena, Jiri Neuzil","doi":"10.1080/10409238.2021.1925216","DOIUrl":"https://doi.org/10.1080/10409238.2021.1925216","url":null,"abstract":"Mitochondria are organelles present in most eukaryotic cells, where they play major and multifaceted roles. The classical notion of the main mitochondrial function as the powerhouse of the cell per se has been complemented by recent discoveries pointing to mitochondria as organelles affecting a number of other auxiliary processes. They go beyond the classical energy provision via acting as a relay point of many catabolic and anabolic processes, to signaling pathways critically affecting cell growth by their implication in de novo pyrimidine synthesis. These additional roles further underscore the importance of mitochondrial homeostasis in various tissues, where its deregulation promotes a number of pathologies. While it has long been known that mitochondria can move within a cell to sites where they are needed, recent research has uncovered that mitochondria can also move between cells. While this intriguing field of research is only emerging, it is clear that mobilization of mitochondria requires a complex apparatus that critically involves mitochondrial proteins of the Miro family, whose role goes beyond the mitochondrial transfer, as will be covered in this review.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"56 4","pages":"401-425"},"PeriodicalIF":6.5,"publicationDate":"2021-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10409238.2021.1925216","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39241960","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}

引用次数: 10

ETF dehydrogenase advances in molecular genetics and impact on treatment. ETF脱氢酶的分子遗传学进展及其治疗影响。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2021-08-01 Epub Date: 2021-04-07 DOI: 10.1080/10409238.2021.1908952

Sara Missaglia, Daniela Tavian, Corrado Angelini

{"title":"ETF dehydrogenase advances in molecular genetics and impact on treatment.","authors":"Sara Missaglia, Daniela Tavian, Corrado Angelini","doi":"10.1080/10409238.2021.1908952","DOIUrl":"https://doi.org/10.1080/10409238.2021.1908952","url":null,"abstract":"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 ETFDH 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 ETFDH 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 ETFDH mutations and presenting variable degrees of clinical symptom severity.","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}

引用次数: 15

Cholesterol efflux pathways, inflammation, and atherosclerosis. 胆固醇流出途径、炎症和动脉粥样硬化。

IF 6.2 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2021-08-01 Epub Date: 2021-06-28 DOI: 10.1080/10409238.2021.1925217

Anouk G Groenen, Benedek Halmos, Alan R Tall, Marit Westerterp

{"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":"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.e. 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.","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}

引用次数: 0

How can a traffic light properly work if it is always green? The paradox of CK2 signaling. 如果交通灯一直是绿色的，它怎么能正常工作呢?CK2信号的悖论。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2021-08-01 Epub Date: 2021-04-11 DOI: 10.1080/10409238.2021.1908951

Christian Borgo, Claudio D'Amore, Luca Cesaro, Stefania Sarno, Lorenzo A Pinna, Maria Ruzzene, Mauro Salvi

引用次数: 17

The role of non-genetic information in evolutionary frameworks. 非遗传信息在进化框架中的作用。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2021-06-01 Epub Date: 2021-05-10 DOI: 10.1080/10409238.2021.1908949

Katherine L Moran, Yelyzaveta Shlyakhtina, Maximiliano M Portal

{"title":"The role of non-genetic information in evolutionary frameworks.","authors":"Katherine L Moran, Yelyzaveta Shlyakhtina, Maximiliano M Portal","doi":"10.1080/10409238.2021.1908949","DOIUrl":"https://doi.org/10.1080/10409238.2021.1908949","url":null,"abstract":"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.","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}

引用次数: 4

SMART approaches for genome-wide analyses of skeletal muscle stem and niche cells. 骨骼肌干细胞和生态位细胞全基因组分析的SMART方法。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2021-06-01 Epub Date: 2021-04-07 DOI: 10.1080/10409238.2021.1908950

Darren M Blackburn, Felicia Lazure, Vahab D Soleimani

{"title":"SMART approaches for genome-wide analyses of skeletal muscle stem and niche cells.","authors":"Darren M Blackburn, Felicia Lazure, Vahab D Soleimani","doi":"10.1080/10409238.2021.1908950","DOIUrl":"https://doi.org/10.1080/10409238.2021.1908950","url":null,"abstract":"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 in vivo 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.","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}

引用次数: 0