A non-canonical promoter element drives spurious transcription of horizontally acquired bacterial genes

• Published in: Nucleic acids research Vol. 48; no. 9; pp. 4891 - 4901
• Main Authors: Warman, Emily A, Singh, Shivani S, Gubieda, Alicia G, Grainger, David C
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 21.05.2020
• Subjects: AT Rich Sequence; Bacterial Proteins - metabolism; DNA - chemistry; DNA-Binding Proteins - metabolism; DNA-Directed RNA Polymerases - chemistry; DNA-Directed RNA Polymerases - metabolism; Gene regulation, Chromatin and Epigenetics; Gene Transfer, Horizontal; Genes, Bacterial; Promoter Regions, Genetic; Sigma Factor - chemistry; Sigma Factor - metabolism; Transcription, Genetic; Transcriptional Activation
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkaa244

Abstract RNA polymerases initiate transcription at DNA sequences called promoters. In bacteria, the best conserved promoter feature is the AT-rich -10 element; a sequence essential for DNA unwinding. Further elements, and gene regulatory proteins, are needed to recruit RNA polymerase to the -10 sequence. Hence, -10 elements cannot function in isolation. Many horizontally acquired genes also have a high AT-content. Consequently, sequences that resemble the -10 element occur frequently. As a result, foreign genes are predisposed to spurious transcription. However, it is not clear how RNA polymerase initially recognizes such sequences. Here, we identify a non-canonical promoter element that plays a key role. The sequence, itself a short AT-tract, resides 5 base pairs upstream of otherwise cryptic -10 elements. The AT-tract alters DNA conformation and enhances contacts between the DNA backbone and RNA polymerase.