Structure-function comparisons of (p)ppApp vs (p)ppGpp for Escherichia coli RNA polymerase binding sites and for rrnB P1 promoter regulatory responses in vitro

• Published in: Biochimica et biophysica acta. Gene regulatory mechanisms 2018-08, Vol.1861 (8), p.731-742
• Main Authors: Bruhn-Olszewska, Bożena, Molodtsov, Vadim, Sobala, Michał, Dylewski, Maciej, Murakami, Katsuhiko S., Cashel, Michael, Potrykus, Katarzyna
• Format: Article
• Language: English
• Subjects: (p)ppApp; (p)ppGpp; Adenine Nucleotides - chemistry; Adenine Nucleotides - metabolism; Binding Sites; DNA-Directed RNA Polymerases - chemistry; DNA-Directed RNA Polymerases - metabolism; Escherichia coli - enzymology; Escherichia coli - genetics; Escherichia coli Proteins - metabolism; Gene Expression Regulation, Bacterial; Guanosine Pentaphosphate - chemistry; Guanosine Pentaphosphate - metabolism; Models, Molecular; ppGpp; Promoter Regions, Genetic; RNAP; rrnB P1; Structure-Activity Relationship; Transcription; Transcriptional Activation
• ISSN: 1874-9399; 1876-4320
• DOI: 10.1016/j.bbagrm.2018.07.005

Precise regulation of gene expression is crucial for bacteria to respond to changing environmental conditions. In addition to protein factors affecting RNA polymerase (RNAP) activity, second messengers play an important role in transcription regulation, such as well-known effectors of the stringent response: guanosine 5′triphosphate-3′diphosphate and guanosine 3′, 5′-bis(diphosphate) [(p)ppGpp]. Although much is known about importance of the 5′ and 3′ moieties of (p)ppGpp, the role of the guanine base remains somewhat cryptic. Here, we use (p)ppGpp's adenine analogs [(p)ppApp] to investigate how the nucleobase contributes to determine its binding site and transcriptional regulation. We determined X-ray crystal structure of Escherichia coli RNAP-(p)ppApp complex, which shows the analogs bind near the active site and switch regions of RNAP. We have also explored the regulatory effects of (p)ppApp on transcription initiating from the well-studied E. coli rrnB P1 promoter to assess and compare properties of (p)ppApp with (p)ppGpp. We demonstrate that contrary to (p)ppGpp, (p)ppApp activates transcription at this promoter and DksA hinders this effect. Moreover, pppApp exerts a stronger effect than ppApp. We also show that when ppGpp and pppApp are present together, the outcome depends on which one of them was pre-incubated with RNAP first. This behavior suggests a surprising Yin-Yang like reciprocal plasticity of RNAP responses at a single promoter, occasioned simply by pre-exposure to one or the other nucleotide. Our observations underscore the importance of the (p)ppNpp's purine nucleobase for interactions with RNAP, which may lead to a better fundamental understanding of (p)ppGpp regulation of RNAP activity. •RNAP/(p)ppApp crystal structure reveals a unique binding site.•(p)ppApp activate transcription at E. coli rrnB P1; pppApp is the stronger effector.•There is competition between pppApp and ppGpp, influencing the effects they exert.