相关实验视频

Updated: Sep 15, 2025

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

通过基于SPECO的基因组挖掘来探索核糖体合成和翻译后修改的

Gengfan Wu¹, Longcheng Guo¹, Beibei He¹

¹Department of Chemistry, The University of Hong Kong, Hong Kong, P.R. China.

Methods in enzymology

|July 12, 2025

概括

我们开发了一种新的基因组挖掘工作流,SPECO,以发现新的核糖体合成和翻译后修饰 (RiPPs). 这种方法克服了现有工具中的偏见,使得未经探索的细菌天然产品的探索成为可能.

科学领域:

* 计算生物学和生物信息学.
* 自然产品的发现.
* 分子生物学和酶学.

背景情况:

*基因组挖掘工具识别生物合成基因集群 (BGCs) 用于自然产品 (NP) 发现.
* 由于对已知RiPP家族的偏见,现有的工具难以找到新型核糖体合成和翻译后修饰 (RiPPs).
* 需要改进的方法来探索细菌中庞大的,未被探索的RiPP多样性.

研究的目的:

* 开发一种新的基因组挖掘工作流程,SPECO (小和酶共发生),用于发现新的RiPP化学.
* 提供一个整体的基因组挖掘方法,将SPECO与其他生物信息学工具 (如AlphaFold-Multimer) 整合在一起.
*为了证明SPECO在发现尚未探索的RiPP生物合成中的实用性,以激进的S-adenosylmethionine (rSAM) 酶为例.

主要方法:

* 开发了基于前体和修饰酶在细菌基因组中的共发生和共保存的SPECO分析工作流.
*将SPECO与现有的生物信息工具集成为全面的基因组挖掘战略.
* 应用了工作流来研究涉及基修饰的激进S-adenosylmethionine (rSAM) 酶.

主要成果:

*SPECO工作流通过利用保存的生物合成逻辑有效地识别潜在的RiPP生物合成基因集群.
*综合方法成功地揭示了尚未探索的酶功能,特别是与大环化相关的rSAM酶.
* 展示了一种方法来克服当前基因组挖掘工具对RiPP发现的局限性.

结论:

*SPECO工作流提供了一种强大的新策略,用于发现新型RiPP及其相关生物合成酶.
*这种方法显著扩大了从细菌基因组中识别新天然产品的潜力.
* 该方法在未来对细菌基因组序列的探索中非常适用,以发现新的RiPP生物合成和酶学.

关键词:

生物合成酶生物合成酶生物合成基因集群生物合成基因集群基因组开采是为了挖掘基因组.的宏循环化的宏循环化这就是RiPPs.斯佩科 (SPECO) 是一个名为斯佩科的城市.

更多相关视频

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products

Published on: March 12, 2020

相关概念视频

Ribosome Profiling

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...

Leaky Scanning

Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R...

Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...

Ribosomal RNA Synthesis

Ribosomal RNA Synthesis

Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...

Ribosomes

Ribosomes

Ribosomes translate genetic information encoded by messenger RNA (mRNA) into proteins. Both prokaryotic and eukaryotic cells have ribosomes. Cells that synthesize large quantities of protein—such as secretory cells in the human pancreas—can contain millions of ribosomes.
Ribosome Structure and Assembly
Ribosomes are composed of ribosomal RNA (rRNA) and proteins. In eukaryotes, rRNA is transcribed from genes in the nucleolus—a part of the nucleus that specializes in ribosome...

Translational Regulation

Translational Regulation

Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...