Methods in enzymology最新文献_第2页

Characterization of bacterial transporters involved in the uptake of lignin-derived aromatic compounds. 参与木质素衍生芳香族化合物摄取的细菌转运体的表征。

4区生物学

Methods in enzymology Pub Date : 2025-01-01 Epub Date: 2025-02-18 DOI: 10.1016/bs.mie.2025.01.053

Masaya Fujita, Naofumi Kamimura, Eiji Masai

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Dye-decolorising peroxidase DyP1B from Pseudomonas fluorescens: Expression, reconstitution and reaction with polymeric lignin substrates. 荧光假单胞菌染料脱色过氧化物酶DyP1B：表达、重组和与聚合木质素底物的反应。

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Methods in enzymology Pub Date : 2025-01-01 Epub Date: 2025-02-09 DOI: 10.1016/bs.mie.2025.01.049

Rahman Rahmanpour, Timothy D H Bugg

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Expression, purification, and crystallization of "humanized" Danio rerio histone deacetylase 10 "HDAC10", the eukaryotic polyamine deacetylase. 真核生物多胺脱乙酰酶“人源化”丹尼奥河组蛋白脱乙酰酶10“HDAC10”的表达、纯化和结晶。

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Methods in enzymology Pub Date : 2025-01-01 Epub Date: 2025-02-11 DOI: 10.1016/bs.mie.2025.01.074

Juana Goulart Stollmaier, Corey J Herbst-Gervasoni, David W Christianson

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Determining biosynthetic gene cluster boundaries through comparative bioinformatics. 通过比较生物信息学确定生物合成基因簇边界。

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Methods in enzymology Pub Date : 2025-01-01 Epub Date: 2025-05-16 DOI: 10.1016/bs.mie.2025.04.001

Jerry Cui, Kou-San Ju

{"title":"Determining biosynthetic gene cluster boundaries through comparative bioinformatics.","authors":"Jerry Cui, Kou-San Ju","doi":"10.1016/bs.mie.2025.04.001","DOIUrl":"https://doi.org/10.1016/bs.mie.2025.04.001","url":null,"abstract":"Modern advances in sequencing, \"-omics,\" and bioinformatics have given rise to the field of genome mining, loosely defined as the use of genomic data to guide natural product (NP) discovery. This technique applies our understanding of biosynthetic logic to predict the genes encoding for production of novel compounds. The major steps include identification of these biosynthetic gene clusters (BGCs), their classification, and prioritization for subsequent experimentation. Despite decades of effort, determination of cluster boundaries without experimental validation remains one of the greatest challenges in genome mining. Genes encoded within a BGC are the foundation for all downstream analysis. Thus, accurate determination of gene cluster content is critical for effective prioritization of BGCs and prediction of their products. Synteny, or the conservation of homologous genes and their arrangement, provides an effective solution for predicting these borders. Over evolutionary time, transfer and rearrangement of genes results in variability surrounding BGCs, such that natural breaks in conservation underlie these functional units. In this chapter, we provide a comprehensive approach for using synteny to delineate BGC boundaries.","PeriodicalId":18662,"journal":{"name":"Methods in enzymology","volume":"717 ","pages":"241-265"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144619064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Genome mining for natural products made by multinuclear iron-dependent oxidation enzymes (MNIOs). 多核铁依赖性氧化酶（MNIOs）天然产物的基因组挖掘。

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Methods in enzymology Pub Date : 2025-01-01 Epub Date: 2025-02-16 DOI: 10.1016/bs.mie.2025.01.060

Yue Yu, Wilfred A van der Donk

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Preface. 前言。

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Methods in enzymology Pub Date : 2025-01-01 DOI: 10.1016/S0076-6879(25)00184-3

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Reductive amination: Methods for cell-free and whole-cell biocatalysis. 还原胺化：无细胞和全细胞生物催化的方法。

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Methods in enzymology Pub Date : 2025-01-01 Epub Date: 2025-02-09 DOI: 10.1016/bs.mie.2025.01.002

Vasilis Tseliou, Matteo Damian, Josemarco Mendoza-Avila, Marco Rabuffetti, Francesco G Mutti

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How to engineer giant enzymes: A methodology for mutagenesis of polyketide synthases in native hosts. 如何设计巨型酶：原生宿主中聚酮合酶的诱变方法。

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Methods in enzymology Pub Date : 2025-01-01 Epub Date: 2025-03-07 DOI: 10.1016/bs.mie.2025.02.007

Susanna Kushnir, Uschi Hübner, Frank Schulz

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Defining APOBEC-induced mutation signatures and modifying activities in yeast. 在酵母中定义apobecc诱导的突变特征和修饰活性。

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Methods in enzymology Pub Date : 2025-01-01 Epub Date: 2025-04-02 DOI: 10.1016/bs.mie.2024.11.041

Tony M Mertz, Zachary W Kockler, Margo Coxon, Cameron Cordero, Atri K Raval, Alexander J Brown, Victoria Harcy, Dmitry A Gordenin, Steven A Roberts

{"title":"Defining APOBEC-induced mutation signatures and modifying activities in yeast.","authors":"Tony M Mertz, Zachary W Kockler, Margo Coxon, Cameron Cordero, Atri K Raval, Alexander J Brown, Victoria Harcy, Dmitry A Gordenin, Steven A Roberts","doi":"10.1016/bs.mie.2024.11.041","DOIUrl":"https://doi.org/10.1016/bs.mie.2024.11.041","url":null,"abstract":"APOBEC cytidine deaminases guard cells in a variety of organisms from invading viruses and foreign nucleic acids. Recently, several human APOBECs have been implicated in mutating evolving cancer genomes. Expression of APOBEC3A and APOBEC3B in yeast allowed experimental derivation of the substitution patterns they cause in dividing cells, which provided critical links to these enzymes in the etiology of the COSMIC single base substitution (SBS) signatures 2 and 13 in human tumors. Additionally, the ability to scale yeast experiments to high-throughput screens allows use of this system to also investigate cellular pathways impacting the frequency of APOBEC-induced mutation. Here, we present validated methods utilizing yeast to determine APOBEC mutation signatures, genetic interactors, and chromosomal substrate preferences. These methods can be employed to assess the potential of other human APOBECs and APOBEC orthologs in different species to contribute to cancer genome evolution as well as define the pathways that protect the nuclear genome from inadvertent APOBEC activity during viral restriction.","PeriodicalId":18662,"journal":{"name":"Methods in enzymology","volume":"713 ","pages":"115-161"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144035720","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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cP-RNA-seq for tRNA half sequencing. cP-RNA-seq用于tRNA半测序。

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Methods in enzymology Pub Date : 2025-01-01 Epub Date: 2024-12-04 DOI: 10.1016/bs.mie.2024.11.002

Megumi Shigematsu, Justin Gumas, Yohei Kirino

{"title":"cP-RNA-seq for tRNA half sequencing.","authors":"Megumi Shigematsu, Justin Gumas, Yohei Kirino","doi":"10.1016/bs.mie.2024.11.002","DOIUrl":"10.1016/bs.mie.2024.11.002","url":null,"abstract":"Although RNA-seq data are becoming more widely available for biomedical research, most datasets for short non-coding RNAs (sncRNAs) primarily focus on microRNA analysis using standard RNA-seq, which captures only sncRNAs with 5'-phosphate (5'-P) and 3'-hydroxyl (3'-OH) ends. Standard RNA-seq fails to sequence sncRNAs with different terminal phosphate states, including tRNA halves, the most abundant class of tRNA-derived sncRNAs that play diverse roles in various biological processes. tRNA halves are produced through the endoribonucleolytic cleavage of mature tRNA anticodon loops. The responsible endoribonucleases, such as Angiogenin, commonly leave a 2',3'-cyclic phosphate (cP) at the 3'-end of 5'-tRNA halves and forms a 5'-OH end of 3'-tRNA halves, making them incompatible with standard RNA-seq. We developed a method named \"cP-RNA-seq\" that selectively amplifies and sequences tRNA halves and other cP-containing sncRNAs. Here we describe a detailed and recently updated cP-RNA-seq protocol. In this method, the 3'-end of all sncRNAs, except those containing a cP, are cleaved through periodate treatment after phosphatase treatment. Consequently, adaptor ligation and cDNA amplification steps are exclusively applied to cP-containing sncRNAs. Our cP-RNA-seq only requires commercially available reagents and is broadly applicable for the global identification of tRNA halves and other cP-containing sncRNA repertoires in various transcriptomes.","PeriodicalId":18662,"journal":{"name":"Methods in enzymology","volume":"711 ","pages":"135-153"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11938272/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143425655","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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