期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2015
卷号：112
期号：50
页码：E6862-E6871
DOI：10.1073/pnas.1521365112
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：SignificanceThe transcription factor DksA is a critical determinant of the stringent response and is essential for virulence in many pathogenic proteobacteria. This ubiquitous transcription factor is also a model system for transcription regulation, making it essential to understand how DksA interacts with RNA polymerase (RNAP) at the molecular level. High-resolution structural information of the DksA-RNAP interaction is currently unavailable. Using genetic, biochemical, and computational approaches, we have generated a new high-quality model of the DksA-RNAP interaction that advances our understanding of DksA binding and activity and will serve as a springboard for future mechanistic investigations into DksA regulation. Sensing and responding to nutritional status is a major challenge for microbial life. In Escherichia coli, the global response to amino acid starvation is orchestrated by guanosine-3',5'-bisdiphosphate and the transcription factor DksA. DksA alters transcription by binding to RNA polymerase and allosterically modulating its activity. Using genetic analysis, photo-cross-linking, and structural modeling, we show that DksA binds and acts upon RNA polymerase through prominent features of both the nucleotide-access secondary channel and the active-site region. This work is, to our knowledge, the first demonstration of a molecular function for Sequence Insertion 1 in the {beta} subunit of RNA polymerase and significantly advances our understanding of how DksA binds to RNA polymerase and alters transcription.
