The evolutionary impact of intragenic FliA promoters in proteobacteria

Molecular Microbiology
Devon M FitzgeraldJoseph T Wade

Abstract

In Escherichia coli, one sigma factor recognizes the majority of promoters, and six 'alternative' sigma factors recognize specific subsets of promoters. The alternative sigma factor FliA (σ28 ) recognizes promoters upstream of many flagellar genes. We previously showed that most E. coli FliA binding sites are located inside genes. However, it was unclear whether these intragenic binding sites represent active promoters. Here, we construct and assay transcriptional promoter-lacZ fusions for all 52 putative FliA promoters previously identified by ChIP-seq. These experiments, coupled with integrative analysis of published genome-scale transcriptional datasets, strongly suggest that most intragenic FliA binding sites are active promoters that transcribe highly unstable RNAs. Additionally, we show that widespread intragenic FliA-dependent transcription may be a conserved phenomenon, but that specific promoters are not themselves conserved. We conclude that intragenic FliA-dependent promoters and the resulting RNAs are unlikely to have important regulatory functions. Nonetheless, one intragenic FliA promoter is broadly conserved and constrains evolution of the overlapping protein-coding gene. Thus, our data indicate that intragenic r...Continue Reading

References

Jun 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·Y F Chen, J D Helmann
Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Nov 18, 2003·Molecular Microbiology·Hilda Hiu Yin Yu, Ming Tan
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Dec 13, 2005·Journal of Molecular Biology·Shuying WangDavid B McKay
May 13, 2006·FEMS Microbiology Ecology·Milagros ZaballosFrancisco Rodríguez-Valera
Jul 15, 2006·Nucleic Acids Research·Irma Lozada-ChávezJulio Collado-Vides
Aug 8, 2006·Nature Structural & Molecular Biology·Joseph T WadeEvgeny Nudler
Jul 28, 2009·Cell·J Christian Perez, Eduardo A Groisman
Oct 10, 2009·Trends in Genetics : TIG·Zeba Wunderlich, Leonid A Mirny
Jan 21, 2011·Nature·L Stirling Churchman, Jonathan S Weissman
Feb 7, 2012·Journal of Bacteriology·Ruben C HartkoornStewart T Cole
Dec 1, 2012·Nucleic Acids Research·Jindan Zhou, Kenneth E Rudd
Dec 5, 2012·Genes & Development·Jason M PetersRobert Landick
Jan 18, 2013·RNA Biology·Arthur BeauregardJoseph T Wade
Apr 16, 2013·Journal of Bacteriology·Evgeny N GordienkoMikhail S Gelfand
Apr 17, 2013·BMC Genomics·Richard P BonocoraJoseph T Wade
May 30, 2013·Nucleic Acids Research·Ryan McClureBrian Tjaden
Jul 5, 2013·Nature·James E GalaganGary K Schoolnik
Dec 18, 2013·Science·Andrew B StergachisJohn A Stamatoyannopoulos
Jan 23, 2014·Genes & Development·Shivani S SinghDavid C Grainger
Jul 9, 2014·Annual Review of Microbiology·Andrey FeklístovCarol A Gross
Jul 16, 2014·Current Opinion in Microbiology·Cynthia M Sharma, Jörg Vogel
Jul 30, 2014·Nature Reviews. Microbiology·Joseph T Wade, David C Grainger
Oct 3, 2014·PLoS Genetics·Devon M FitzgeraldJoseph T Wade
Dec 9, 2014·Transcription·Meghan LybeckerRahul Raghavan
Jan 15, 2015·Molecular Biology and Evolution·Ke Xing, Xionglei He
Apr 24, 2015·Nucleic Acids Research·Alejandra Medina-RiveraJacques van Helden

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