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New reactions by pyridoxal phosphate-dependent enzymes 依赖磷酸吡哆醛的酶的新反应
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2024-05-29 DOI: 10.1016/j.cbpa.2024.102472
Phillip Daniel-Ivad, Katherine S. Ryan
{"title":"New reactions by pyridoxal phosphate-dependent enzymes","authors":"Phillip Daniel-Ivad,&nbsp;Katherine S. Ryan","doi":"10.1016/j.cbpa.2024.102472","DOIUrl":"10.1016/j.cbpa.2024.102472","url":null,"abstract":"<div><p>Pyridoxal phosphate (PLP) is a cofactor that is widely employed in enzymology. This pyridine-containing cofactor can be used for reactions ranging from transaminations to oxidations. The catalytic versatility can be understood by considering the chemical features of this cofactor. In recent years, exciting new reactions involving PLP have been discovered in natural products biosynthesis, upending our understanding of what this cofactor is capable of. Here we review some of the most exciting PLP-dependent reactions from the last five years.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"81 ","pages":"Article 102472"},"PeriodicalIF":7.8,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1367593124000486/pdfft?md5=90c95973227f092b2660e8c5a58d3bd9&pid=1-s2.0-S1367593124000486-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141178450","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
Specific signaling by nicotinamide adenine dinucleotide oxidases – Role of their site of action 烟酰胺腺嘌呤二核苷酸氧化酶的特异性信号传递--其作用部位的作用。
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2024-05-28 DOI: 10.1016/j.cbpa.2024.102461
Katrin Schröder
{"title":"Specific signaling by nicotinamide adenine dinucleotide oxidases – Role of their site of action","authors":"Katrin Schröder","doi":"10.1016/j.cbpa.2024.102461","DOIUrl":"10.1016/j.cbpa.2024.102461","url":null,"abstract":"<div><p>Nicotinamide adenine dinucleotide (NADPH) oxidases, known for their role in generating reactive oxygen species (ROS) have emerged as key regulators of specific cellular signaling pathways. While their primary function is ROS production, recent research has highlighted the significance of their site-specific activity in governing distinct cellular signaling events.</p><p>NADPH oxidases (Nox) are found in various cell types, and both their expression and activities are tightly regulated. The generated ROS, such as superoxide anions and hydrogen peroxide, function as secondary messengers that modulate various signaling molecules, including protein kinases, transcription factors, and phosphatases.</p><p>The site-specific action of NADPH oxidases in different cellular compartments, such as the plasma membrane, endosomes, and endoplasmic reticulum, allows for precise control over specific signaling pathways. Understanding the complex interplay of NADPH oxidases in cellular signaling is essential for deciphering their roles in health and disease. Dysregulation of these enzymes can lead to oxidative stress and inflammation, making them potential therapeutic targets in various pathological conditions. Ongoing research into NADPH oxidase activation and site-specific signaling promises to unveil new insights into cellular physiology and potential treatment strategies.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"81 ","pages":"Article 102461"},"PeriodicalIF":7.8,"publicationDate":"2024-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141173631","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
Biosynthesis of isonitrile lipopeptides 异腈脂肽的生物合成
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2024-05-23 DOI: 10.1016/j.cbpa.2024.102470
Kaimin Jia , Helen Sun , Yiyan Zhou , Wenjun Zhang
{"title":"Biosynthesis of isonitrile lipopeptides","authors":"Kaimin Jia ,&nbsp;Helen Sun ,&nbsp;Yiyan Zhou ,&nbsp;Wenjun Zhang","doi":"10.1016/j.cbpa.2024.102470","DOIUrl":"https://doi.org/10.1016/j.cbpa.2024.102470","url":null,"abstract":"<div><p>Isonitrile lipopeptides discovered from Actinobacteria have attracted wide attention due to their fascinating biosynthetic pathways and relevance to the virulence of many human pathogens including <em>Mycobacterium tuberculosis</em>. Specifically, the identification of the new class of isonitrile-forming enzymes that belong to non-heme iron (II) and α-ketoglutarate dependent dioxygenases has intrigued several research groups to investigate their catalytic mechanism. Here we summarize the recent studies on the biosynthesis of isonitrile lipopeptides from <em>Streptomyces</em> and <em>Mycobacterium</em>. The latest research on the core and tailoring enzymes involved in the pathway as well as the isonitrile metabolic enzymes are discussed in this review.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"81 ","pages":"Article 102470"},"PeriodicalIF":7.8,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141090176","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
Lanthanide-dye hybrid luminophores for advanced NIR-II bioimaging 用于先进近红外-II 生物成像的镧系元素-染料混合发光体
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2024-05-21 DOI: 10.1016/j.cbpa.2024.102469
Mei Mei, Bin Wu, Shangfeng Wang, Fan Zhang
{"title":"Lanthanide-dye hybrid luminophores for advanced NIR-II bioimaging","authors":"Mei Mei,&nbsp;Bin Wu,&nbsp;Shangfeng Wang,&nbsp;Fan Zhang","doi":"10.1016/j.cbpa.2024.102469","DOIUrl":"https://doi.org/10.1016/j.cbpa.2024.102469","url":null,"abstract":"<div><p>In vivo luminescence imaging in the second near-infrared window (NIR-II, 1000–2000 nm) is a potent technique for observing deep-tissue life activities, leveraging reduced light scattering, minimized autofluorescence, and moderate absorption attenuation to substantially enhance image contrast. Pushing the frontiers of NIR-II luminescence imaging forward, moving from static to dynamic event visualization, monochromatic to multicolor images, and fundamental research to clinical applications, necessitates the development of novel luminophores featuring bright emission, extendable wavelength, and optimal biocompatibility. Recently, lanthanide-dye hybrid luminophores (LDHLs) are gaining increasing attention for their wavelength extensibility, molecular size, narrowband emission, mega stokes shift, long lifetime, and high photostability. In this review, we will summarize the recent advances of NIR-II LDHLs and their applications in imaging and analysis of living mammals, and discuss future challenges in designing new LDHLs for deep-tissue imaging.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"80 ","pages":"Article 102469"},"PeriodicalIF":7.8,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141072927","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
F420-dependent transformations in biosynthesis of secondary metabolites 次生代谢物生物合成中依赖 F420 的转化
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2024-05-21 DOI: 10.1016/j.cbpa.2024.102468
Ghader Bashiri
{"title":"F420-dependent transformations in biosynthesis of secondary metabolites","authors":"Ghader Bashiri","doi":"10.1016/j.cbpa.2024.102468","DOIUrl":"https://doi.org/10.1016/j.cbpa.2024.102468","url":null,"abstract":"<div><p>Cofactor F<sub>420</sub> has been historically known as the “methanogenic redox cofactor”. It is now recognised that F<sub>420</sub> has essential roles in the primary and secondary metabolism of archaea and bacteria. Recent discoveries highlight the role of F<sub>420</sub> as a redox cofactor in the biosynthesis of various natural products, including ribosomally synthesised and post-translationally modified peptides, and a new class of nicotinamide adenine dinucleotide-based secondary metabolites. With the vast availability of (meta)genomic data, the identification of uncharacterised F<sub>420</sub>-dependent enzymes offers the potential for discovering novel secondary metabolites, presenting valuable prospects for clinical and biotechnological applications.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"80 ","pages":"Article 102468"},"PeriodicalIF":7.8,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1367593124000449/pdfft?md5=ecc1a03e1981ca1f49df232c88201ce5&pid=1-s2.0-S1367593124000449-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141072926","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
Multinuclear non-heme iron dependent oxidative enzymes (MNIOs) involved in unusual peptide modifications 参与异常肽修饰的多核非血红素铁依赖性氧化酶（MNIOs）
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2024-05-20 DOI: 10.1016/j.cbpa.2024.102467
Jeff Y. Chen, Wilfred A. van der Donk
{"title":"Multinuclear non-heme iron dependent oxidative enzymes (MNIOs) involved in unusual peptide modifications","authors":"Jeff Y. Chen,&nbsp;Wilfred A. van der Donk","doi":"10.1016/j.cbpa.2024.102467","DOIUrl":"https://doi.org/10.1016/j.cbpa.2024.102467","url":null,"abstract":"<div><p>Multinuclear non-heme iron dependent oxidative enzymes (MNIOs), formerly known as domain of unknown function 692 (DUF692), are involved in the post-translational modification of peptides during the biosynthesis of peptide-based natural products. These enzymes catalyze highly unusual and diverse chemical modifications. Several class-defining features of this large family (&gt;14 000 members) are beginning to emerge. Structurally, the enzymes are characterized by a TIM-barrel fold and a set of conserved residues for a di- or tri–iron binding site. They use molecular oxygen to modify peptide substrates, often in a four-electron oxidation taking place at a cysteine residue. This review summarizes the current understanding of MNIOs. Four modifications are discussed in detail: oxazolone-thioamide formation, β-carbon excision, hydantoin-macrocycle formation, and 5-thiooxazole formation. Briefly discussed are two other reactions that do not take place on Cys residues.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"80 ","pages":"Article 102467"},"PeriodicalIF":7.8,"publicationDate":"2024-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1367593124000437/pdfft?md5=ff0d2067bb16ebe523993dbaeab8b350&pid=1-s2.0-S1367593124000437-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141072924","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
New analytical methods focusing on polar metabolite analysis in mass spectrometry and NMR-based metabolomics 以质谱和核磁共振为基础的代谢组学中极性代谢物分析为重点的新分析方法
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2024-05-20 DOI: 10.1016/j.cbpa.2024.102466
James McCullagh, Fay Probert
{"title":"New analytical methods focusing on polar metabolite analysis in mass spectrometry and NMR-based metabolomics","authors":"James McCullagh,&nbsp;Fay Probert","doi":"10.1016/j.cbpa.2024.102466","DOIUrl":"https://doi.org/10.1016/j.cbpa.2024.102466","url":null,"abstract":"<div><p>Following in the footsteps of genomics and proteomics, metabolomics has revolutionised the way we investigate and understand biological systems. Rapid development in the last 25 years has been driven largely by technical innovations in mass spectrometry and nuclear magnetic resonance spectroscopy. However, despite the modest size of metabolomes relative to proteomes and genomes, methodological capabilities for robust, comprehensive metabolite analysis remain a major challenge. Therefore, development of new methods and techniques remains vital for progress in the field. Here, we review developments in LC-MS, GC–MS and NMR methods in the last few years that have enhanced quantitative and comprehensive metabolome coverage, highlighting the techniques involved, their technical capabilities, relative performance, and potential impact.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"80 ","pages":"Article 102466"},"PeriodicalIF":7.8,"publicationDate":"2024-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1367593124000425/pdfft?md5=25040f8c102ce990a0b903886e423e0e&pid=1-s2.0-S1367593124000425-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141072925","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
Penicillin-binding protein-type thioesterases: An emerging family of non-ribosomal peptide cyclases with biocatalytic potentials 青霉素结合蛋白型硫酯酶：具有生物催化潜力的新兴非核糖体肽环酶家族
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2024-05-17 DOI: 10.1016/j.cbpa.2024.102465
Kenichi Matsuda, Toshiyuki Wakimoto
{"title":"Penicillin-binding protein-type thioesterases: An emerging family of non-ribosomal peptide cyclases with biocatalytic potentials","authors":"Kenichi Matsuda,&nbsp;Toshiyuki Wakimoto","doi":"10.1016/j.cbpa.2024.102465","DOIUrl":"https://doi.org/10.1016/j.cbpa.2024.102465","url":null,"abstract":"<div><p>Macrocyclization of peptides reduces conformational flexibilities, potentially leading to improved drug-like properties, such as target specificities and metabolic stabilities. As chemical methodologies often allow side reactions like epimerization and oligomerization, keen attention has been directed toward enzymatic peptide cyclization using peptide cyclases from specialized metabolic pathways. Penicillin-binding protein-type thioesterases (PBP-type TEs) are a recently identified family of peptide cyclases involved in the biosynthesis of non-ribosomal peptides in actinobacteria. PBP-type TEs have undergone intensive investigation due to their outstanding potential as biocatalysts. This review summarizes the rapidly growing knowledge on PBP-type TEs, with special emphasis on their functions, scopes, and structures, and efforts towards their biocatalytic applications.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"80 ","pages":"Article 102465"},"PeriodicalIF":7.8,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1367593124000413/pdfft?md5=fde71fc72bbc60c147987a83d6920144&pid=1-s2.0-S1367593124000413-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140951749","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
Oxygen-transfer reactions by enzymatic flavin-N5 oxygen adducts—Oxidation is not a must 酶促黄素-N5 氧加合物的氧转移反应--氧化并非必要条件
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2024-05-12 DOI: 10.1016/j.cbpa.2024.102464
Robin Teufel
{"title":"Oxygen-transfer reactions by enzymatic flavin-N5 oxygen adducts—Oxidation is not a must","authors":"Robin Teufel","doi":"10.1016/j.cbpa.2024.102464","DOIUrl":"https://doi.org/10.1016/j.cbpa.2024.102464","url":null,"abstract":"<div><p>Flavoenzymes catalyze numerous redox reactions including the transfer of an O<sub>2</sub>-derived oxygen atom to organic substrates, while the other one is reduced to water. Investigation of some of these monooxygenases led to a detailed understanding of their catalytic cycle, which involves the flavin-C<sub>4α</sub>-(hydro)peroxide as hallmark oxygenating species, and newly discovered flavoprotein monooxygenases were generally assumed to operate similarly. However, discoveries in recent years revealed a broader mechanistic versatility, including enzymes that utilize flavin-N<sub>5</sub> oxygen adducts for catalysis in the form of the flavin-N<sub>5</sub>-(hydro)peroxide and the flavin-N<sub>5</sub>-oxide species. In this review, I will highlight recent developments in that area, including noncanonical flavoenzymes from natural product biosynthesis and sulfur metabolism that provide first insights into the chemical properties of these species. Remarkably, some enzymes may even combine the flavin-N<sub>5</sub>-peroxide and the flavin-N<sub>5</sub>-oxide species for consecutive oxygen-transfers to the same substrate and thereby in essence operate as dioxygenases.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"80 ","pages":"Article 102464"},"PeriodicalIF":7.8,"publicationDate":"2024-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1367593124000401/pdfft?md5=8da170b60e8a1b645e526e1bec5a4df5&pid=1-s2.0-S1367593124000401-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140913872","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
Novel types of RiPP-modifying enzymes 新型 RiPP 改性酶
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2024-05-09 DOI: 10.1016/j.cbpa.2024.102463
Daniel Richter, Jörn Piel
{"title":"Novel types of RiPP-modifying enzymes","authors":"Daniel Richter,&nbsp;Jörn Piel","doi":"10.1016/j.cbpa.2024.102463","DOIUrl":"https://doi.org/10.1016/j.cbpa.2024.102463","url":null,"abstract":"<div><p>Novel discoveries in natural product biosynthesis reveal hidden bioactive compounds and expand our knowledge in enzymology. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a rapidly growing class of natural products featuring diverse non-canonical amino acids introduced by maturation enzymes as a class-defining characteristic. Underexplored RiPP sources, such as the human microbiome, the oceans, uncultured microorganisms, and plants are rich hunting grounds for novel enzymology. Unusual α- and β-amino acids, peptide cleavages, lipidations, diverse macrocyclizations, and other features expand the range of chemical groups that are installed in RiPPs by often promiscuous enzymes. This review highlights the search for novelty in RiPP enzymology in the past two years, with respect to the discovery of new biochemical modifications but also towards novel applications.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"80 ","pages":"Article 102463"},"PeriodicalIF":7.8,"publicationDate":"2024-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1367593124000395/pdfft?md5=7cda049b2f007dbdc70542ed0bb0736b&pid=1-s2.0-S1367593124000395-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140902336","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
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