rpoN

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]

RNA polymerase sigma-54 factor
Identifiers
Organism?
SymbolRpoN
UniProtP24255
Search for
StructuresSwiss-model
DomainsInterPro

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
Identifiers
SymbolSigma54_AID
PfamPF00309
InterProIPR000394
PROSITEPS50044
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary
PDB5BYH

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]

References
  1. Dong T, Yu R, Schellhorn H (January 2011). "Antagonistic regulation of motility and transcriptome expression by RpoN and RpoS in Escherichia coli". Molecular Microbiology. 79 (2): 375–86. doi:10.1111/j.1365-2958.2010.07449.x. PMID 21219458.
  2. Hunt TP, Magasanik B (December 1985). "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. Bibcode:1985PNAS...82.8453H. doi:10.1073/pnas.82.24.8453. PMC 390934. PMID 2867543.
  3. Tsang J, Hoover TR (2014). "Themes and Variations: Regulation of RpoN-Dependent Flagellar Genes across Diverse Bacterial Species". Scientifica. 2014: 681754. doi:10.1155/2014/681754. PMC 3930126. PMID 24672734.
  4. Wigneshweraraj S, Bose D, Burrows PC, Joly N, Schumacher J, Rappas M, Pape T, Zhang X, Stockley P, Severinov K, Buck M (May 2008). "Modus operandi of the bacterial RNA polymerase containing the sigma54 promoter-specificity factor". Molecular Microbiology. 68 (3): 538–46. doi:10.1111/j.1365-2958.2008.06181.x. PMID 18331472. S2CID 33750977.
  5. Gruber TM, Gross CA (2003). "Multiple sigma subunits and the partitioning of bacterial transcription space". Annual Review of Microbiology. 57: 441–66. doi:10.1146/annurev.micro.57.030502.090913. PMID 14527287.
  6. Buck M, Cannon W (July 1992). "Specific binding of the transcription factor sigma-54 to promoter DNA". Nature. 358 (6385): 422–4. Bibcode:1992Natur.358..422B. doi:10.1038/358422a0. PMID 1641025.
  7. Shingler V (May 2011). "Signal sensory systems that impact σ⁵⁴ -dependent transcription". FEMS Microbiology Reviews. 35 (3): 425–40. doi:10.1111/j.1574-6976.2010.00255.x. PMID 21054445.
  8. Bonocora RP, Smith C, Lapierre P, Wade JT (October 2015). "Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding". PLOS Genetics. 11 (10): e1005552. doi:10.1371/journal.pgen.1005552. PMC 4591121. PMID 26425847.
  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 (July 2009). "Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens". BMC Genomics. 10: 331. doi:10.1186/1471-2164-10-331. PMC 2725144. PMID 19624843.
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