RpoN explained

RNA polymerase sigma-54 factor
Symbol:	RpoN
Uniprot:	P24255

The gene rpoN (RNA polymerase, nitrogen-limitation N) encodes the sigma factor sigma-54 (σ54, sigma N, or RpoN), a protein in Escherichia coli and other species of bacteria. RpoN antagonizes RpoS sigma factors.^[1]

Biological role

Originally identified as a regulator of genes involved in nitrogen metabolism and assimilation under nitrogen limiting conditions,^[2] E. coli σ54 has since been shown to play important regulatory roles in a variety of other cellular processes. Similarly, σ54 homologues in other species regulate a wide range of processes, including flagellar synthesis and virulence.^[3]

Sequence specificity and mechanism of action

Sigma-54 factor, Activator interacting domain
Symbol:	Sigma54_AID
Pfam:	PF00309
Pdb:	5BYH
Interpro:	IPR000394
Prosite:	PS50044

σ54 promoter elements consist of conserved nucleotides located at −12 and −24 with respect to the transcription start site.^[4] This contrasts with members of the σ70 family, which recognize conserved promoter elements located at roughly −10 and −35 with respect to the transcription start site.^[5] Unlike the members of the σ70 family, σ54 proteins have been shown to bind promoter DNA independent of core RNAPin vitro.^[6] Another distinguishing characteristic of σ54 proteins is their absolute requirement for activator proteins, known as bacterial enhancer binding proteins (bEBPs), to initiate transcription.^{[4] [7]} Thus, both active and inactive forms of RNAP:σ54 are bound at promoters.^[8]

The RpoN-regulated promoter elements have the consensus sequence as follows: TTGGCACGGTTTTTGCT.^[9]

Notes and References

1. Dong T, Yu R, Schellhorn H . Antagonistic regulation of motility and transcriptome expression by RpoN and RpoS in Escherichia coli . Molecular Microbiology . 79 . 2 . 375–86 . January 2011 . 21219458 . 10.1111/j.1365-2958.2010.07449.x . free .
2. Hunt TP, Magasanik B . Transcription of glnA by purified Escherichia coli components: core RNA polymerase and the products of glnF, glnG, and glnL . Proceedings of the National Academy of Sciences of the United States of America . 82 . 24 . 8453–7 . December 1985 . 2867543 . 390934 . 10.1073/pnas.82.24.8453 . 1985PNAS...82.8453H . free .
3. Tsang J, Hoover TR . Themes and Variations: Regulation of RpoN-Dependent Flagellar Genes across Diverse Bacterial Species . Scientifica . 2014 . 681754 . 2014 . 24672734 . 3930126 . 10.1155/2014/681754 . free .
4. Wigneshweraraj S, Bose D, Burrows PC, Joly N, Schumacher J, Rappas M, Pape T, Zhang X, Stockley P, Severinov K, Buck M . Modus operandi of the bacterial RNA polymerase containing the sigma54 promoter-specificity factor . Molecular Microbiology . 68 . 3 . 538–46 . May 2008 . 18331472 . 10.1111/j.1365-2958.2008.06181.x . 33750977 . free .
5. Gruber TM, Gross CA . Multiple sigma subunits and the partitioning of bacterial transcription space . Annual Review of Microbiology . 57 . 441–66 . 2003 . 14527287 . 10.1146/annurev.micro.57.030502.090913 .
6. Buck M, Cannon W . Specific binding of the transcription factor sigma-54 to promoter DNA . Nature . 358 . 6385 . 422–4 . July 1992 . 1641025 . 10.1038/358422a0 . 1992Natur.358..422B . free .
7. Shingler V . Signal sensory systems that impact σ⁵⁴ -dependent transcription . FEMS Microbiology Reviews . 35 . 3 . 425–40 . May 2011 . 21054445 . 10.1111/j.1574-6976.2010.00255.x . free .
8. Bonocora RP, Smith C, Lapierre P, Wade JT . Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding . PLOS Genetics . 11 . 10 . e1005552 . October 2015 . 26425847 . 10.1371/journal.pgen.1005552 . 4591121 . free .
9. Leang C, Krushkal J, Ueki T, Puljic M, Sun J, Juárez K, Núñez C, Reguera G, DiDonato R, Postier B, Adkins RM, Lovley DR . Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens . BMC Genomics . 10 . 331 . July 2009 . 19624843 . 2725144 . 10.1186/1471-2164-10-331 . free .