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<p>Gene expression shapes phenotypes and evolution. However, studies of gene regulation focus on transcription factors, overlooking core promoters. To investigate how promoters emerge and regulate transcription, we determine the sequence–function landscapes of core elements, −35 and −10, in constitutive and transcription factor-regulated promoters in <i>Escherichia coli</i>. Characterization of in vivo transcriptional landscapes and in vitro RNA polymerase–promoter interactions shows the −10 element as essential for promoter evolution from random sequences. In contrast, the −35 element, though broadly conserved, is dispensable for promoter birth. Instead, it exerts greater impact on gene regulation via coordinated interactions with transcription activators and RNA polymerase. We further show that evolution fine-tunes the −35 and −10 sequences of transcription factor-regulated promoters to achieve near-maximal fold changes by lowering basal while elevating induced expression. A notable exception is P<sub><i>luxI</i></sub>, whose leaky expression provides a crucial baseline for initiating quorum sensing. These findings elucidate promoter design principles and underscore the interdependence and coevolution of core elements, RNA polymerase, and transcription factors.</p>

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Core elements play distinct roles in promoter birth and transcriptional regulation

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年7月17日

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  • Syue-Ting Antony Kuo,
  • Wei-Yi Shen,
  • Sheng-Wen Lai,
  • Joshua Kevin Chang,
  • Cheng-Wei Ni,
  • Chih-Chiang Chang,
  • Zoltan Palmai,
  • Lee-Wei Yang,
  • Nei-Li Chan,
  • I-Ren Lee,
  • Hsin-Hung David Chou

摘要

Gene expression shapes phenotypes and evolution. However, studies of gene regulation focus on transcription factors, overlooking core promoters. To investigate how promoters emerge and regulate transcription, we determine the sequence–function landscapes of core elements, −35 and −10, in constitutive and transcription factor-regulated promoters in Escherichia coli. Characterization of in vivo transcriptional landscapes and in vitro RNA polymerase–promoter interactions shows the −10 element as essential for promoter evolution from random sequences. In contrast, the −35 element, though broadly conserved, is dispensable for promoter birth. Instead, it exerts greater impact on gene regulation via coordinated interactions with transcription activators and RNA polymerase. We further show that evolution fine-tunes the −35 and −10 sequences of transcription factor-regulated promoters to achieve near-maximal fold changes by lowering basal while elevating induced expression. A notable exception is PluxI, whose leaky expression provides a crucial baseline for initiating quorum sensing. These findings elucidate promoter design principles and underscore the interdependence and coevolution of core elements, RNA polymerase, and transcription factors.