Bacterial genomes are now recognized as interacting intimately with cellular processes. Uncovering organizational mechanisms of bacterial genomes has been a primary focus of researchers to reveal the potential cellular activities. The advances in both experimental techniques and computational models provide a tremendous opportunity for understanding these mechanisms, and various studies have been proposed to explore the organization rules of bacterial genomes associated with functions recently. This review focuses mainly on the principles that shape the organization of bacterial genomes, both locally and globally. We first illustrate local structures as operons/transcription units for facilitating co-transcription and horizontal transfer of genes. We then clarify the constraints that globally shape bacterial genomes, such as metabolism, transcription and replication. Finally, we highlight challenges and opportunities to advance bacterial genomic studies and provide application perspectives of genome organization, including pathway hole assignment and genome assembly and understanding disease mechanisms.

中文翻译：

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细菌基因组组织中的功能决定因素。

细菌基因组现在被认为与细胞过程密切相关。发现细菌基因组的组织机制一直是研究人员揭示潜在细胞活动的主要焦点。实验技术和计算模型的进步为理解这些机制提供了巨大的机会，并且最近提出了各种研究来探索与功能相关的细菌基因组的组织规则。本综述主要关注在局部和全球范围内塑造细菌基因组组织的原则。我们首先将局部结构说明为操纵子/转录单位，以促进基因的共转录和水平转移。然后我们阐明了全局塑造细菌基因组的限制，例如新陈代谢，转录和复制。最后，我们强调推进细菌基因组研究的挑战和机遇，并提供基因组组织的应用前景，包括通路孔分配和基因组组装以及了解疾病机制。