Unlike most transcription factors, these two molecules bind directly to the enzyme responsible for transcribing DNA into RNA, the RNA polymerase, but they do not bind to DNA.Īnother transcription factor called TraR can mimic the combined effects of ppGpp and DksA on transcription, changing the conformation of RNA polymerase in the same way. This broad response requires two transcription factors, ppGpp and DksA. When the bacterium Escherichia coli is starved for the building blocks it needs to make proteins, it changes the expression of almost one quarter of its genes within 5 minutes. The molecules that regulate when each gene is transcribed are called transcription factors. Not all genes are transcribed or expressed at the same time or the same rate, because a cell needs different proteins depending on its environment. To make a protein, a cell first needs to take the information from a gene coded in its DNA and copy it into a template made of a different molecule called RNA via a process called transcription. eLife digestĬells need to make proteins in order to survive. Using mutational approaches, we show that these structural changes, as well as effects on σ 70 region 1.1, are critical for transcription activation or inhibition, depending on the kinetic features of regulated promoters. These changes involve mobile regions of RNAP affecting promoter DNA interactions, including the βlobe, the clamp, the bridge helix, and several lineage-specific insertions. TraR binding induced RNAP conformational changes not seen in previous crystallographic analyses, and a quantitative analysis revealed TraR-induced changes in RNAP conformational heterogeneity. Here, we use cryo-electron microscopy to determine structures of Escherichia coli RNAP, with or without TraR, and of an RNAP-promoter complex. Effects of TraR mimic the combined effects of DksA and its cofactor ppGpp, but the structural basis for regulation by these factors remains unclear. TraR and its homolog DksA are bacterial proteins that regulate transcription initiation by binding directly to RNA polymerase (RNAP) rather than to promoter DNA.
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