Critical Reviews in Biochemistry and Molecular Biology最新文献_第4页

Overview of physiological, biochemical, and regulatory aspects of nitrogen fixation in Azotobacter vinelandii. 黄氏固氮固氮的生理、生化和调控方面综述。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2022-10-01 DOI: 10.1080/10409238.2023.2181309

Julia S Martin Del Campo, Jack Rigsbee, Marcelo Bueno Batista, Florence Mus, Luis M Rubio, Oliver Einsle, John W Peters, Ray Dixon, Dennis R Dean, Patricia C Dos Santos

引用次数: 5

2-5A-Mediated decay (2-5AMD): from antiviral defense to control of host RNA. 2-5A介导的衰变（2-5AMD）：从抗病毒防御到控制宿主RNA。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2022-10-01 Epub Date: 2023-03-20 DOI: 10.1080/10409238.2023.2181308

Eliza Prangley, Alexei Korennykh

{"title":"2-5A-Mediated decay (2-5AMD): from antiviral defense to control of host RNA.","authors":"Eliza Prangley, Alexei Korennykh","doi":"10.1080/10409238.2023.2181308","DOIUrl":"10.1080/10409238.2023.2181308","url":null,"abstract":"Mammalian cells are exquisitely sensitive to the presence of double-stranded RNA (dsRNA), a molecule that they interpret as a signal of viral presence requiring immediate attention. Upon sensing dsRNA cells activate the innate immune response, which involves transcriptional mechanisms driving inflammation and secretion of interferons (IFNs) and interferon-stimulated genes (ISGs), as well as synthesis of RNA-like signaling molecules comprised of three or more 2'-5'-linked adenylates (2-5As). 2-5As were discovered some forty years ago and described as IFN-induced inhibitors of protein synthesis. The efforts of many laboratories, aimed at elucidating the molecular mechanism and function of these mysterious RNA-like signaling oligonucleotides, revealed that 2-5A is a specific ligand for the kinase-family endonuclease RNase L. RNase L decays single-stranded RNA (ssRNA) from viruses and mRNAs (as well as other RNAs) from hosts in a process we proposed to call 2-5A-mediated decay (2-5AMD). During recent years it has become increasingly recognized that 2-5AMD is more than a blunt tool of viral RNA destruction, but a pathway deeply integrated into sensing and regulation of endogenous RNAs. Here we present an overview of recently emerged roles of 2-5AMD in host RNA regulation.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"57 5-6","pages":"477-491"},"PeriodicalIF":6.5,"publicationDate":"2022-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10576847/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9678347","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

Reversible and bidirectional signaling of notch ligands. 缺口配体的可逆和双向信号传导。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2022-08-01 DOI: 10.1080/10409238.2022.2113029

Elenaé Vázquez-Ulloa, Kai-Lan Lin, Marcela Lizano, Cecilia Sahlgren

{"title":"Reversible and bidirectional signaling of notch ligands.","authors":"Elenaé Vázquez-Ulloa, Kai-Lan Lin, Marcela Lizano, Cecilia Sahlgren","doi":"10.1080/10409238.2022.2113029","DOIUrl":"https://doi.org/10.1080/10409238.2022.2113029","url":null,"abstract":"The Notch signaling pathway is a direct cell-cell communication system involved in a wide variety of biological processes, and its disruption is observed in several pathologies. The pathway is comprised of a ligand-expressing (sender) cell and a receptor-expressing (receiver) cell. The canonical ligands are members of the Delta/Serrate/Lag-1 (DSL) family of proteins. Their binding to a Notch receptor in a neighboring cell induces a conformational change in the receptor, which will undergo regulated intramembrane proteolysis (RIP), liberating the Notch intracellular domain (NICD). The NICD is translocated to the nucleus and promotes gene transcription. It has been demonstrated that the ligands can also undergo RIP and nuclear translocation, suggesting a function for the ligands in the sender cell and possible bidirectionality of the Notch pathway. Although the complete mechanism of ligand processing is not entirely understood, and its dependence on Notch receptors has not been ruled out. Also, ligands have autonomous functions beyond Notch activation. Here we review the concepts of reverse and bidirectional signalization of DSL proteins and discuss the characteristics that make them more than just ligands of the Notch pathway.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"57 4","pages":"377-398"},"PeriodicalIF":6.5,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10613678","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: 1

Creation and resolution of non-B-DNA structural impediments during replication. 在复制过程中产生并解决非 B-DNA 结构障碍。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2022-08-01 Epub Date: 2022-09-28 DOI: 10.1080/10409238.2022.2121803

Christopher Mellor, Consuelo Perez, Julian E Sale

引用次数: 0

What makes functional amyloids work? 是什么使功能性淀粉样蛋白起作用?

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2022-08-01 DOI: 10.1080/10409238.2022.2113030

Ansgar B Siemer

引用次数: 2

Hypoxia-regulated microRNAs: the molecular drivers of tumor progression. 低氧调控的microrna:肿瘤进展的分子驱动因素。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2022-08-01 DOI: 10.1080/10409238.2022.2088684

Sakunie Sawai, Pooi-Fong Wong, Thamil Selvee Ramasamy

{"title":"Hypoxia-regulated microRNAs: the molecular drivers of tumor progression.","authors":"Sakunie Sawai, Pooi-Fong Wong, Thamil Selvee Ramasamy","doi":"10.1080/10409238.2022.2088684","DOIUrl":"https://doi.org/10.1080/10409238.2022.2088684","url":null,"abstract":"Hypoxia is a common feature of the tumor microenvironment (TME) of nearly all solid tumors, leading to therapeutic failure. The changes in stiffness of the extracellular matrix (ECM), pH gradients, and chemical balance that contribute to multiple cancer hallmarks are closely regulated by intratumoral oxygen tension via its primary mediators, hypoxia-inducible factors (HIFs). HIFs, especially HIF-1α, influence these changes in the TME by regulating vital cancer-associated signaling pathways and cellular processes including MAPK/ERK, NF-κB, STAT3, PI3K/Akt, Wnt, p53, and glycolysis. Interestingly, research has revealed the involvement of epigenetic regulation by hypoxia-regulated microRNAs (HRMs) of downstream target genes involved in these signaling. Through literature search and analysis, we identified 48 HRMs that have a functional role in the regulation of 5 key cellular processes: proliferation, metabolism, survival, invasion and migration, and immunoregulation in various cancers in hypoxic condition. Among these HRMs, 17 were identified to be directly associated with HIFs which include miR-135b, miR-145, miR-155, miR-181a, miR-182, miR-210, miR-224, miR-301a, and miR-675-5p as oncomiRNAs, and miR-100-5p, miR-138, miR-138-5p, miR-153, miR-22, miR-338-3p, miR-519d-3p, and miR-548an as tumor suppressor miRNAs. These HRMs serve as a potential lead in the development of miRNA-based targeted therapy for advanced solid tumors. Future development of combined HIF-targeted and miRNA-targeted therapy is possible, which requires comprehensive profiling of HIFs-HRMs regulatory network, and improved formula of the delivery vehicles to enhance the therapeutic kinetics of the targeted cancer therapy (TCT) moving forward.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"57 4","pages":"351-376"},"PeriodicalIF":6.5,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10668748","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: 5

Energetics, kinetics, and pathways of SNARE assembly in membrane fusion. 膜融合中SNARE组装的能量学、动力学和途径。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2022-08-01 DOI: 10.1080/10409238.2022.2121804

Yongli Zhang, Lu Ma, Huan Bao

{"title":"Energetics, kinetics, and pathways of SNARE assembly in membrane fusion.","authors":"Yongli Zhang, Lu Ma, Huan Bao","doi":"10.1080/10409238.2022.2121804","DOIUrl":"https://doi.org/10.1080/10409238.2022.2121804","url":null,"abstract":"Fusion of transmitter-containing vesicles with plasma membranes at the synaptic and neuromuscular junctions mediates neurotransmission and muscle contractions, respectively, thereby underlying all thoughts and actions. The fusion process is driven by the coupled folding and assembly of three synaptic SNARE proteins--syntaxin-1 and SNAP-25 on the target plasma membrane (t-SNAREs) and VAMP2 on the vesicular membrane (v-SNARE) into a four-helix bundle. Their assembly is chaperoned by Munc18-1 and many other proteins to achieve the speed and accuracy required for neurotransmission. However, the physiological pathway of SNARE assembly and its coupling to membrane fusion remains unclear. Here, we review recent progress in understanding SNARE assembly and membrane fusion, with a focus on results obtained by single-molecule manipulation approaches and electric recordings of single fusion pores. We describe two pathways of synaptic SNARE assembly, their associated intermediates, energetics, and kinetics. Assembly of the three SNAREs in vitro begins with the formation of a t-SNARE binary complex, on which VAMP2 folds in a stepwise zipper-like fashion. Munc18-1 significantly alters the SNARE assembly pathway: syntaxin-1 and VAMP2 first bind on the surface of Munc18-1 to form a template complex, with which SNAP-25 associates to conclude SNARE assembly and displace Munc18-1. During membrane fusion, multiple trans-SNARE complexes cooperate to open a dynamic fusion pore in a manner dependent upon their copy number and zippering states. Together, these results demonstrate that stepwise and cooperative SNARE assembly drive stagewise membrane fusion.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"57 4","pages":"443-460"},"PeriodicalIF":6.5,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9588726/pdf/nihms-1835201.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10669210","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: 9

The mechanisms of human lymphoid chromosomal translocations and their medical relevance. 人类淋巴样染色体易位的机制及其医学意义。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2022-06-01 DOI: 10.1080/10409238.2021.2004576

Di Liu, Michael R Lieber

{"title":"The mechanisms of human lymphoid chromosomal translocations and their medical relevance.","authors":"Di Liu, Michael R Lieber","doi":"10.1080/10409238.2021.2004576","DOIUrl":"https://doi.org/10.1080/10409238.2021.2004576","url":null,"abstract":"The most common human lymphoid chromosomal translocations involve concurrent failures of the recombination activating gene (RAG) complex and Activation-Induced Deaminase (AID). These are two enzymes that are normally expressed for purposes of the two site-specific DNA recombination processes: V(D)J recombination and class switch recombination (CSR). First, though it is rare, a low level of expression of AID can introduce long-lived T:G mismatch lesions at 20-600 bp fragile zones. Second, the V(D)J recombination process can occasionally fail to rejoin coding ends, and this failure may permit an opportunity for Artemis:DNA-dependent kinase catalytic subunit (DNA-PKcs) to convert the T:G mismatch sites at the fragile zones into double-strand breaks. The 20-600 bp fragile zones must be, at least transiently, in a single-stranded DNA (ssDNA) state for the first step to occur, because AID only acts on ssDNA. Here we discuss the key DNA sequence features that lead to AID action at a fragile zone, which are (a) the proximity and density of strings of cytosine nucleotides (C-strings) that cause a B/A-intermediate DNA conformation; (b) overlapping AID hotspots that contain a methyl CpG (WRCG), which AID converts to a long-lived T:G mismatch; and (c) transcription, which, though not essential, favors increased ssDNA in the fragile zone. We also summarize chromosomal features of the focal fragile zones in lymphoid malignancies and discuss the clinical relevance of understanding the translocation mechanisms. Many of the key principles covered here are also relevant to chromosomal translocations in non-lymphoid somatic cells as well.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"57 3","pages":"227-243"},"PeriodicalIF":6.5,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9632267/pdf/nihms-1845758.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9608418","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: 3

Emerging biological functions of ribonuclease 1 and angiogenin. 核糖核酸酶1和血管生成素新出现的生物学功能。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2022-06-01 DOI: 10.1080/10409238.2021.2004577

Emily R Garnett, Ronald T Raines

引用次数: 10

Structure and function of ClpXP, a AAA+ proteolytic machine powered by probabilistic ATP hydrolysis. 由概率ATP水解驱动的AAA+蛋白水解机ClpXP的结构和功能。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2022-04-01 DOI: 10.1080/10409238.2021.1979461

Robert T Sauer, Xue Fei, Tristan A Bell, Tania A Baker

引用次数: 11