Recruitment of RNA polymerase and initiation factors to the promoter is the only known target for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation are involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Saccharolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. TEC escape is rate-limiting for transcription output during exponential growth. Oxidative stress causes changes in TEC escape that correlate with changes in the transcriptome. Our results thus establish that TEC escape contributes to the basal promoter strength and facilitates transcription regulation. Impaired TEC escape coincides with the accumulation of initiation factors at the promoter and recruitment of termination factor aCPSF1 to the early TEC. This suggests two possible mechanisms for how TEC escape limits transcription, physically blocking upstream RNA polymerases during transcription initiation and premature termination of early TECs.

RNA聚合酶和启动因子向启动子的募集是古细菌中转录激活和抑制的唯一已知目标。生产性转录延伸的任何后续步骤是否参与调节尚不清楚。我们表征了古细菌Saccharolobus solfataricus中基础转录机制如何沿着基因分布。我们发现了一个独特的早期延伸阶段，其中 RNA 聚合酶顺序招募延伸因子 Spt4/5 和 Elf1 以形成转录延伸复合物 (TEC)，然后 TEC 进入生产性转录。 TEC 逃逸是指数增长期间转录输出的速率限制。氧化应激会导致 TEC 逃逸发生变化，而这与转录组的变化相关。因此，我们的结果表明 TEC 逃逸有助于基础启动子强度并促进转录调控。 TEC 逃逸受损与启动子处起始因子的积累以及终止因子 aCPSF1 招募到早期 TEC 相一致。这表明 TEC 逃逸限制转录有两种可能的机制，即在转录起始过程中物理阻断上游 RNA 聚合酶和早期 TEC 的过早终止。