A Perspective on the Enhancer Dependent Bacterial RNA Polymerase

Here we review recent findings and offer a perspective on how the major variant RNA polymerase of bacteria, which contains the sigma54 factor, functions for regulated gene expression. We consider what gaps exist in our understanding of its genetic, biochemical and biophysical functioning and how they might be addressed.

[1]  A. Ishihama,et al.  Mapping σ54-RNA Polymerase Interactions at the –24 Consensus Promoter Element* , 2003, Journal of Biological Chemistry.

[2]  Nan Zhang,et al.  Subunit dynamics and nucleotide-dependent asymmetry of an AAA(+) transcription complex. , 2014, Journal of molecular biology.

[3]  R. Tuma,et al.  Domain movements of the enhancer-dependent sigma factor drive DNA delivery into the RNA polymerase active site: insights from single molecule studies , 2014, Nucleic acids research.

[4]  A. Syed,et al.  Isolation and properties of enhancer‐bypass mutants of sigma 54 , 1997, Molecular microbiology.

[5]  T. Pape,et al.  Organization of an Activator-Bound RNA Polymerase Holoenzyme , 2008, Molecular cell.

[6]  Nan Zhang,et al.  Determination of the self-association residues within a homomeric and a heteromeric AAA+ enhancer binding protein. , 2014, Journal of molecular biology.

[7]  D. Kahn,et al.  Genetic regulation of biological nitrogen fixation , 2004, Nature Reviews Microbiology.

[8]  D. Szeto,et al.  Function of a bacterial activator protein that binds to transcriptional enhancers. , 1989, Science.

[9]  P. Stewart,et al.  Borrelia burgdorferi sigma54 is required for mammalian infection and vector transmission but not for tick colonization. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[10]  D. Wemmer,et al.  The C-terminal RpoN Domain of σ54 Forms an Unpredicted Helix-Turn-Helix Motif Similar to Domains of σ70* , 2005, Journal of Biological Chemistry.

[11]  R. Dixon,et al.  The Role of Bacterial Enhancer Binding Proteins as Specialized Activators of σ54-Dependent Transcription , 2012, Microbiology and Molecular Reviews.

[12]  A. Wolfe,et al.  Vibrio fischeri σ54 Controls Motility, Biofilm Formation, Luminescence, and Colonization , 2004, Applied and Environmental Microbiology.

[13]  J. Gelles,et al.  RNA polymerase approaches its promoter without long-range sliding along DNA , 2013, Proceedings of the National Academy of Sciences.

[14]  Nicolas Joly,et al.  Coupling AAA protein function to regulated gene expression. , 2012, Biochimica et biophysica acta.

[15]  G. Martin,et al.  Genomewide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factor , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Jonathan T. Wang,et al.  Abortive Cycling and the Release of Polymerase for Elongation at the σ54-dependent glnAp2 Promoter (*) , 1995, Journal of Biological Chemistry.

[17]  J. Gelles,et al.  Mechanism of Transcription Initiation at an Activator-Dependent Promoter Defined by Single-Molecule Observation , 2012, Cell.

[18]  M. Merrick.  In a class of its own--the RNA polymerase sigma factor sigma 54 (sigma N). , 1993, Molecular microbiology.

[19]  Geraint Barton,et al.  Nitrogen stress response and stringent response are coupled in Escherichia coli , 2014, Nature Communications.

[20]  Nan Zhang,et al.  A common feature from different subunits of a homomeric AAA+ protein contacts three spatially distinct transcription elements , 2012, Nucleic acids research.

[21]  M. Merrick,et al.  In a class of its own — the RNA polymerase sigma factor σ;54 (σN) , 1993 .

[22]  Nucleotide-induced asymmetry within ATPase activator ring drives σ54-RNAP interaction and ATP hydrolysis. , 2013, Genes & development.

[23]  J. Gralla,et al.  Roles for the C-terminal Region of Sigma 54 in Transcriptional Silencing and DNA Binding* , 2001, The Journal of Biological Chemistry.

[24]  M. Buck,et al.  Characterisation of holoenzyme lacking sigmaN regions I and II. , 1999, Nucleic acids research.

[25]  Akira Ishihama,et al.  Mapping sigma 54-RNA polymerase interactions at the -24 consensus promoter element. , 2003, The Journal of biological chemistry.

[26]  Richard R. Burgess,et al.  Promoter and regulon analysis of nitrogen assimilation factor, σ54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis , 2009, Nucleic acids research.

[27]  M. Buck,et al.  A prehydrolysis state of an AAA+ ATPase supports transcription activation of an enhancer-dependent RNA polymerase , 2010, Proceedings of the National Academy of Sciences.

[28]  S. Kustu,et al.  Expression of sigma 54 (ntrA)-dependent genes is probably united by a common mechanism. , 1989, Microbiological reviews.

[29]  D. Wemmer,et al.  Structural basis of DNA recognition by the alternative sigma-factor, sigma54. , 2007, Journal of molecular biology.

[30]  Lex Overmars,et al.  Comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior , 2011, BMC Genomics.

[31]  M. Buck,et al.  The biology of enhancer-dependent transcriptional regulation in bacteria: insights from genome sequences. , 2000, FEMS microbiology letters.