School of Biological Sciences, Georgia Institute of Technologygrid.213917.f, Atlanta, Georgia, USA.
Parker H. Petit Institute for Bioengineering & Bioscience, Georgia Institute of Technologygrid.213917.f, Atlanta, Georgia, USA.
mBio. 2022 Jun 28;13(3):e0042222. doi: 10.1128/mbio.00422-22. Epub 2022 May 23.
Mutations in regulatory mechanisms that control gene expression contribute to phenotypic diversity and thus facilitate the adaptation of microbes and other organisms to new niches. Comparative genomics can be used to infer rewiring of regulatory architecture based on large effect mutations like loss or acquisition of transcription factors but may be insufficient to identify small changes in noncoding, intergenic DNA sequence of regulatory elements that drive phenotypic divergence. In human-derived Vibrio cholerae, the response to distinct chemical cues triggers production of multiple transcription factors that can regulate the type VI secretion system (T6), a broadly distributed weapon for interbacterial competition. However, to date, the signaling network remains poorly understood because no regulatory element has been identified for the major T6 locus. Here we identify a conserved -acting single nucleotide polymorphism (SNP) controlling T6 transcription and activity. Sequence alignment of the T6 regulatory region from diverse V. cholerae strains revealed conservation of the SNP that we rewired to interconvert V. cholerae T6 activity between chitin-inducible and constitutive states. This study supports a model of pathogen evolution through a noncoding -regulatory mutation and preexisting, active transcription factors that confers a different fitness advantage to tightly regulated strains inside a human host and unfettered strains adapted to environmental niches. Organisms sense external cues with regulatory circuits that trigger the production of transcription factors, which bind specific DNA sequences at promoters ("" regulatory elements) to activate target genes. Mutations of transcription factors or their regulatory elements create phenotypic diversity, allowing exploitation of new niches. Waterborne pathogen Vibrio cholerae encodes the type VI secretion system "nanoweapon" to kill competitor cells when activated. Despite identification of several transcription factors, no regulatory element has been identified in the promoter of the major type VI locus, to date. Combining phenotypic, genetic, and genomic analysis of diverse V. cholerae strains, we discovered a single nucleotide polymorphism in the type VI promoter that switches its killing activity between a constitutive state beneficial outside hosts and an inducible state for constraint in a host. Our results support a role for noncoding DNA in adaptation of this pathogen.
基因突变可影响基因表达调控机制，进而导致表型多样化，使微生物和其他生物能够适应新的生态位。比较基因组学可用于推断基于转录因子的丧失或获得等大效应突变导致的调控架构重连，但可能不足以识别调控元件中非编码、基因间 DNA 序列的微小变化，而这些变化会驱动表型分化。在源自人类的霍乱弧菌中，对不同化学信号的反应会触发多种转录因子的产生，这些转录因子可以调节广泛分布的细菌间竞争武器——VI 型分泌系统（T6）。然而，迄今为止，由于尚未鉴定出主要 T6 基因座的调控元件，因此信号网络仍知之甚少。本文中，我们鉴定了一个控制 T6 转录和活性的保守 SNP。对来自不同霍乱弧菌菌株的 T6 调控区进行序列比对，发现 SNP 得以保守，我们将该 SNP 进行重连，使霍乱弧菌 T6 的活性在几丁质诱导和组成型状态之间转换。该研究支持了一种病原体进化模型，即通过非编码调控突变和预先存在的、活跃的转录因子进行，这为宿主内受到严格调控的菌株和适应环境生态位的无束缚菌株赋予了不同的适应优势。
生物体利用调控回路感知外部信号，这些回路会触发转录因子的产生，转录因子会在启动子（“调控元件”）上结合特定的 DNA 序列，以激活靶基因。转录因子或其调控元件的突变会产生表型多样性，从而允许利用新的生态位。水源性病原体霍乱弧菌在被激活时会编码 VI 型分泌系统“纳米武器”来杀死竞争细胞。尽管已经鉴定出了几种转录因子，但迄今为止，主要 VI 型基因座的启动子中尚未鉴定出调控元件。通过对不同霍乱弧菌菌株进行表型、遗传和基因组分析，我们在 VI 型启动子中发现了一个单核苷酸多态性，它可以在有利于宿主外生存的组成型状态和宿主内受限的诱导型状态之间切换其杀伤活性。我们的结果支持非编码 DNA在该病原体适应中的作用。
