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础方面取得了巨大进步，但是与要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。源于少量的初步研究，基因调控概念的经典定义随着特征性启动子数量的增加而发展。结合使用新技术的发现，这些知识导致修订后的概括和原理。在本专家建议中，我们提出精确，更新的定义，以支持细菌基因调控的逻辑，一致的概念框架，并着重于转录起始。由此产生的概念可以通过本体进行形式化以用于计算建模，从而为改进的生物信息学工具奠定基础，基于知识的资源和科学交流。因此，这项工作将帮助研究人员构建具有不同形式主义的更好的预测模型，这将对工程，合成生物学，微生物学和遗传学有用。