解码质粒复制动力学:预测cole1样质粒拷贝数的计算方法。

IF 3.5 2区 综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES
Journal of The Royal Society Interface Pub Date : 2025-07-01 Epub Date: 2025-07-16 DOI:10.1098/rsif.2024.0783
Rinat Saban, Ofri Tfilin, David Haggiag, Yam Tawachi, Matan Arbel, Tamir Tuller
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引用次数: 0

摘要

质粒是合成生物学的关键工具,为各种研究和工业企业提供了一个通用的框架。质粒功能的一个基本决定因素是它的拷贝数,影响蛋白质的产生速率和宿主细胞的代谢负担。然而,目前还没有一种模型可以从质粒的复制起始序列(ORI)计算预测质粒的拷贝数。我们提出了一种新颖的软件解决方案,旨在简化质粒拷贝数设计,重新定义质粒工程工作流程。我们的工具的核心是一个全面的机器学习模型,该模型由从ORI中提取的许多特征提供信息。该计算模型强调了启动子强度和ORI中调控元件的RNA折叠动力学的重要性。此外,我们详细介绍了一个强大的协议,用于有效地操作质粒ori,以验证我们模型的预测能力。这一创新代表了以质粒为中心的方法的范式转变,为合成生物学研究和工业应用的进步提供了前所未有的途径。该软件可在https://pcn-gradient.vercel.app/上获得。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Deciphering plasmid replication dynamics: a computational approach to predict ColE1-like plasmid copy number.

Plasmids constitute a key tool in synthetic biology, providing a versatile framework for various research and industrial ventures. An essential determinant of plasmid functionality is its copy number, impacting both protein production rates and host cell metabolic burden. However, currently there is no model that can computationally predict the plasmid copy number from the sequence of its origin of replication (ORI). We present a novel software solution tailored to simplify plasmid copy number design, poised to redefine plasmid engineering workflows. At the heart of our tool lies a comprehensive machine learning model, informed by numerous features extracted from the ORI. This computational model emphasizes the importance of promoter strength and the RNA folding dynamics of regulatory elements within the ORI. Additionally, we detail a robust protocol for the efficient manipulation of plasmid ORIs used to validate our model's predictive capabilities. This innovation represents a paradigm shift in plasmid-centric methodologies, offering unprecedented avenues for advancement in synthetic biology research and industrial applications. The software is available at: https://pcn-gradient.vercel.app/.

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来源期刊
Journal of The Royal Society Interface
Journal of The Royal Society Interface 综合性期刊-综合性期刊
CiteScore
7.10
自引率
2.60%
发文量
234
审稿时长
2.5 months
期刊介绍: J. R. Soc. Interface welcomes articles of high quality research at the interface of the physical and life sciences. It provides a high-quality forum to publish rapidly and interact across this boundary in two main ways: J. R. Soc. Interface publishes research applying chemistry, engineering, materials science, mathematics and physics to the biological and medical sciences; it also highlights discoveries in the life sciences of relevance to the physical sciences. Both sides of the interface are considered equally and it is one of the only journals to cover this exciting new territory. J. R. Soc. Interface welcomes contributions on a diverse range of topics, including but not limited to; biocomplexity, bioengineering, bioinformatics, biomaterials, biomechanics, bionanoscience, biophysics, chemical biology, computer science (as applied to the life sciences), medical physics, synthetic biology, systems biology, theoretical biology and tissue engineering.
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