Rizvi Syed M A, Densi Asha, Hakiem Owais R, McClelland Michael, Tan Ming
Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California, USA.
Department of Medicine, University of California Irvine, Irvine, California, USA.
mSystems. 2025 Jul 22;10(7):e0029225. doi: 10.1128/msystems.00292-25. Epub 2025 Jun 12.
The pathogenic bacterium reproduces via two specialized forms inside a eukaryotic host cell. The dividing form called the reticulate body (RB) must convert at late times into the infectious elementary body (EB) for spread to new host cells. Late genes are a temporal class of chlamydial genes believed to be responsible for RB-to-EB conversion, but late gene regulation is incompletely understood. In this study, we used chromatin immunoprecipitation (ChIP) to investigate two alternative sigma factors, σ and σ, that alter the promoter specificity of RNA polymerase. σ ChIP-seq identified and as the only promoters bound by σ, and binding only occurred late, around the time of RB-to-EB conversion. Overexpression of σ confirmed that these genes are transcribed in a σ-dependent manner. σ ChIP-seq showed that σ only bound and and only at late times. This σ regulon appears to be conserved as analysis identified σ promoter sequences upstream of and homologs in all spp. The genes encoding σ and σ were only transcribed at late times, but ChIP analysis with the late regulator Euo showed that Euo only controls σ expression, and late transcription of σ is regulated in an Euo-independent manner. Thus, multiple mechanisms regulate late genes, including Euo and different forms of RNA polymerase. The dedicated use of two alternative RNA polymerases to control a small subset of late genes suggests that these genes and the independent control of their temporal expression are important for RB-to-EB conversion.
In this study, we performed chromatin immunoprecipitation-seq to identify genes transcribed by alternative forms of RNA polymerases in . Under normal growth conditions, the sigma factors, σ and σ, bound only two genes each, and binding was only detected at late times. In addition, the late regulator Euo controls the expression of σ but not σ. Thus, utilizes multiple mechanisms to regulate late gene expression and uses alternative forms of RNA polymerases for specialized control of specific late genes that likely have important roles in reticulate body to elementary body conversion. This genome-wide binding approach can be applied to identify target genes of alternative sigma factors in other pathogenic bacteria.
致病细菌在真核宿主细胞内通过两种特殊形式进行繁殖。称为网状体（RB）的分裂形式必须在后期转化为具有感染性的原体（EB），以便传播到新的宿主细胞。晚期基因是衣原体基因的一个时间类别，被认为负责RB到EB的转化，但晚期基因调控尚未完全了解。在本研究中，我们使用染色质免疫沉淀（ChIP）来研究两种替代的σ因子，σ和σ，它们会改变RNA聚合酶的启动子特异性。σ ChIP-seq确定了和是仅由σ结合的启动子，并且结合仅在后期发生，大约在RB到EB转化时。σ的过表达证实这些基因以σ依赖的方式转录。σ ChIP-seq表明σ仅结合和，并且也仅在后期。这个σ调控子似乎是保守的，因为分析在所有衣原体物种中鉴定出和同源物上游的σ启动子序列。编码σ和σ的基因仅在后期转录，但用晚期调节因子Euo进行的ChIP分析表明Euo仅控制σ的表达，并且σ的晚期转录以Euo独立的方式受到调控。因此，多种机制调节晚期基因，包括Euo和不同形式的RNA聚合酶。专门使用两种替代RNA聚合酶来控制一小部分晚期基因表明这些基因及其时间表达的独立控制对于RB到EB的转化很重要。
在本研究中，我们进行了染色质免疫沉淀测序以鉴定衣原体中由替代形式的RNA聚合酶转录的基因。在正常生长条件下，σ因子σ和σ各自仅结合两个基因，并且仅在后期检测到结合。此外，晚期调节因子Euo控制σ的表达但不控制σ。因此，衣原体利用多种机制来调节晚期基因表达，并使用替代形式的RNA聚合酶对可能在网状体到原体转化中起重要作用的特定晚期基因进行专门控制。这种全基因组结合方法可用于鉴定其他致病细菌中替代σ因子的靶基因。
