Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México.
School of Biosciences, University of Birmingham, Birmingham, UK.
Nat Rev Genet. 2020 Nov;21(11):699-714. doi: 10.1038/s41576-020-0254-8. Epub 2020 Jul 14.
Despite enormous progress in understanding the fundamentals of bacterial gene regulation, our knowledge remains limited when compared with the number of bacterial genomes and regulatory systems to be discovered. Derived from a small number of initial studies, classic definitions for concepts of gene regulation have evolved as the number of characterized promoters has increased. Together with discoveries made using new technologies, this knowledge has led to revised generalizations and principles. In this Expert Recommendation, we suggest precise, updated definitions that support a logical, consistent conceptual framework of bacterial gene regulation, focusing on transcription initiation. The resulting concepts can be formalized by ontologies for computational modelling, laying the foundation for improved bioinformatics tools, knowledge-based resources and scientific communication. Thus, this work will help researchers construct better predictive models, with different formalisms, that will be useful in engineering, synthetic biology, microbiology and genetics.
尽管在理解细菌基因调控的基本原理方面取得了巨大进展，但与有待发现的细菌基因组和调控系统的数量相比，我们的知识仍然有限。从少数初步研究中衍生而来的经典基因调控概念，随着已鉴定启动子数量的增加而不断发展。随着新技术的发现，这些知识导致了重新概括和原则的修正。在本专家建议中，我们建议使用精确、更新的定义来支持细菌基因调控的逻辑一致的概念框架，重点关注转录起始。由此产生的概念可以通过计算模型的本体论来形式化，为改进的生物信息学工具、基于知识的资源和科学交流奠定基础。因此，这项工作将有助于研究人员构建更好的预测模型，采用不同的形式主义，这将在工程、合成生物学、微生物学和遗传学中有用。
