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Escherichia coli K-12 substr. MG1655 Polypeptide: RNA polymerase, sigma 54 (sigma N) factor

Gene: rpoN Accession Numbers: EG10898 (EcoCyc), b3202, ECK3191

Synonyms: glnF, ntrA, sigma N factor, sigma 54 factor, sigma N, σ54

Regulation Summary Diagram: ?

Component of: RNA polymerase sigma 54

Sigma 54 controls expression of nitrogen-related genes, directing RNA polymerase sigma 54 to the consensus nitrogen promoter.

Sigma 54 is the sigma factor controlling nitrogen-regulated and other nitrogen-related promoters [Hunt85, Reitzer87]. It copurifies with the RNA polymerase core enzyme and binds to the consensus nitrogen promoter [Hirschman85, Hunt85]. It is also involved in the nitric oxide stress response [Gardner03]. During typical exponential and stationary phase growth, the amount of sigma 54 present in the cell is one tenth that of the amount of sigma 70 [Jishage96]. The metabolic context of genes dependent on sigma54 for transcription is reviewed in [Reitzer01].

Sigma 54 activity is activator dependent, requiring NtrC-Phosphorylated DNA-binding transcriptional dual regulator to initiate transcription.

In some sigma 54-dependent promoters, DNA bending occurs, allowing NtrC-Phosphorylated DNA-binding transcriptional dual regulator to reach the translational start site [Carmona96]. It has been suggested, however, that DNA bending related to sigma 54 is not as extreme as originally reported [Schulz98]. Sigma 54 has also been alternately reported to remain bound to the promoter after RNA polymerase departs during transcript elongation, or to separate from the promoter between each round of transcription [Tintut95, Bondarenko02].

The binding affinity of RNA polymerase sigma 54 for several target promoters has been evaluated [Vogel02].

Sigma 54 has a number of structural features that affect its activity. It has a pair of leucine zipper motifs that are involved in promoter melting, as well as an acidic region that has a role in the same process and a carboxy-terminal helix-turn-helix motif that is required for promoter recognition [SasseDwight90, Wong92a, Wong94]. A strongly acidic hydrophic repeat region is required for binding to RNA core polymerase [Tintut94, Hsieh94]. Four leucines in the amino-terminal region are required for NtrC-Phosphorylated DNA-binding transcriptional dual regulator regulation of sigma 54 activity [Wang95b, Syed97]. Sigma 54 binds to the core polymerase via a region that is very similar to sigma70 [Tintut95a, Oguiza97].

The structure of sigma 54 has been evaluated via scanning force microscopy [Rippe97]. Additional examination via x-ray scattering microscopy shows that sigma 54 and sigma 70 share broad structural similarity [Svergun00]. A 24 Å cryo-electron structure of sigma 54 holoenzyme reveals major conformational changes during DNA binding [Ray05].

A global antagonistic effect on gene expression was perceived between σS, σ54, and σ28, based on transcriptome expression analysis, and this resulted in many physiological traits, including flagellum-mediated motility and utilization of nitrogen sources; as many as 60% of genes in the RpoN regulon are under reciprocal RpoS control [Dong11]. In addition, there is a complex regulatory interaction of the three σ factors: σS, σ54, and σ28 [Dong11].

Gene Citations: [Rhodius05, Jones94]

Locations: cytosol

Map Position: [3,342,739 -> 3,344,172] (72.05 centisomes)
Length: 1434 bp / 477 aa

Molecular Weight of Polypeptide: 53.99 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010514 , CGSC:17926 , DIP:DIP-10776N , EchoBASE:EB0891 , EcoGene:EG10898 , EcoliWiki:b3202 , Mint:MINT-1224654 , OU-Microarray:b3202 , PortEco:rpoN , PR:PRO_000023850 , Pride:P24255 , Protein Model Portal:P24255 , RefSeq:NP_417669 , RegulonDB:EG10898 , SMR:P24255 , String:511145.b3202 , UniProt:P24255

Relationship Links: InterPro:IN-FAMILY:IPR000394 , InterPro:IN-FAMILY:IPR007046 , InterPro:IN-FAMILY:IPR007634 , Pfam:IN-FAMILY:PF00309 , Pfam:IN-FAMILY:PF04552 , Pfam:IN-FAMILY:PF04963 , Prints:IN-FAMILY:PR00045 , Prosite:IN-FAMILY:PS00717 , Prosite:IN-FAMILY:PS00718 , Prosite:IN-FAMILY:PS50044

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006352 - DNA-templated transcription, initiation Inferred by computational analysis [GOA01]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0006525 - arginine metabolic process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01]
GO:0003899 - DNA-directed RNA polymerase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0016779 - nucleotidyltransferase activity Inferred by computational analysis [UniProtGOA11]
GO:0016987 - sigma factor activity Inferred by computational analysis [UniProtGOA11, GOA01]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: extrachromosomal prophage genes and phage related functions
information transfer RNA related Transcription related
metabolism metabolism of other compounds nitrogen metabolism
regulation genetic unit regulated stimulon
regulation type of regulation transcriptional level sigma factors, anti-sigmafactors

Essentiality data for rpoN knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Last-Curated ? 25-Jul-2006 by Shearer A , SRI International

Subunit of: RNA polymerase sigma 54

Synonyms: RNA polymerase sigma 54 holoenzyme, RNA polymerase sigmaN

Subunit composition of RNA polymerase sigma 54 = [(RpoA)2(RpoC)(RpoB)][RpoN]
         RNA polymerase, core enzyme = (RpoA)2(RpoC)(RpoB) (extended summary available)
                 RNA polymerase, α subunit = RpoA (extended summary available)
                 RNA polymerase, β' subunit = RpoC (extended summary available)
                 RNA polymerase, β subunit = RpoB (summary available)
         RNA polymerase, sigma 54 (sigma N) factor = RpoN (extended summary available)

Controlled Transcription Units (49 total): ?


Sequence Features

Feature Class Location Citations Comment
Protein-Segment 3 -> 39
UniProt: Gln-rich; Sequence Annotation Type: compositionally biased region;
Sequence-Conflict 99 -> 103
[SasseDwight90, Imaishi93, UniProt10a]
Alternate sequence: GTSGD → APAVT; UniProt: (in Ref. 1 and 2);
DNA-Binding-Region 366 -> 385
UniProt: H-T-H motif; Non-Experimental Qualifier: by similarity;
Protein-Segment 454 -> 462
UniProt: RPON box; Sequence Annotation Type: short sequence motif;

Gene Local Context (not to scale): ?

Transcription Units:


10/20/97 Gene b3202 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10898; confirmed by SwissProt match.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bondarenko02: Bondarenko V, Liu Y, Ninfa A, Studitsky VM (2002). "Action of prokaryotic enhancer over a distance does not require continued presence of promoter-bound sigma54 subunit." Nucleic Acids Res 30(3);636-42. PMID: 11809874

Carmona96: Carmona M, Magasanik B (1996). "Activation of transcription at sigma 54-dependent promoters on linear templates requires intrinsic or induced bending of the DNA." J Mol Biol 261(3);348-56. PMID: 8780778

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Dong11: Dong T, Yu R, Schellhorn H (2011). "Antagonistic regulation of motility and transcriptome expression by RpoN and RpoS in Escherichia coli." Mol Microbiol 79(2);375-86. PMID: 21219458

Gardner03: Gardner AM, Gessner CR, Gardner PR (2003). "Regulation of the nitric oxide reduction operon (norRVW) in Escherichia coli. Role of NorR and sigma54 in the nitric oxide stress response." J Biol Chem 278(12);10081-6. PMID: 12529359

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Hirschman85: Hirschman J, Wong PK, Sei K, Keener J, Kustu S (1985). "Products of nitrogen regulatory genes ntrA and ntrC of enteric bacteria activate glnA transcription in vitro: evidence that the ntrA product is a sigma factor." Proc Natl Acad Sci U S A 82(22);7525-9. PMID: 2999766

Hsieh94: Hsieh M, Gralla JD (1994). "Analysis of the N-terminal leucine heptad and hexad repeats of sigma 54." J Mol Biol 239(1);15-24. PMID: 8196043

Hunt85: Hunt TP, Magasanik B (1985). "Transcription of glnA by purified Escherichia coli components: core RNA polymerase and the products of glnF, glnG, and glnL." Proc Natl Acad Sci U S A 82(24);8453-7. PMID: 2867543

Imaishi93: Imaishi H, Gomada M, Inouye S, Nakazawa A (1993). "Physical map location of the rpoN gene of Escherichia coli." J Bacteriol 175(5);1550-1. PMID: 8444818

Jishage96: Jishage M, Iwata A, Ueda S, Ishihama A (1996). "Regulation of RNA polymerase sigma subunit synthesis in Escherichia coli: intracellular levels of four species of sigma subunit under various growth conditions." J Bacteriol 178(18);5447-51. PMID: 8808934

Jones94: Jones DH, Franklin FC, Thomas CM (1994). "Molecular analysis of the operon which encodes the RNA polymerase sigma factor sigma 54 of Escherichia coli." Microbiology 1994;140 ( Pt 5);1035-43. PMID: 8025669

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Oguiza97: Oguiza JA, Buck M (1997). "DNA-binding domain mutants of sigma-N (sigmaN, sigma54) defective between closed and stable open promoter complex formation." Mol Microbiol 26(4);655-64. PMID: 9427396

Ray05: Ray P, Hall RJ, Finn RD, Chen S, Patwardhan A, Buck M, van Heel M (2005). "Conformational changes of Escherichia coli sigma54-RNA-polymerase upon closed-promoter complex formation." J Mol Biol 354(2);201-5. PMID: 16246367

Reitzer01: Reitzer L, Schneider BL (2001). "Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli." Microbiol Mol Biol Rev 65(3);422-44, table of contents. PMID: 11528004

Reitzer87: Reitzer LJ, Bueno R, Cheng WD, Abrams SA, Rothstein DM, Hunt TP, Tyler B, Magasanik B (1987). "Mutations that create new promoters suppress the sigma 54 dependence of glnA transcription in Escherichia coli." J Bacteriol 169(9);4279-84. PMID: 2887548

Rhodius05: Rhodius VA, Suh WC, Nonaka G, West J, Gross CA (2005). "Conserved and variable functions of the sigmaE stress response in related genomes." PLoS Biol 4(1);e2. PMID: 16336047

Rippe97: Rippe K, Guthold M, von Hippel PH, Bustamante C (1997). "Transcriptional activation via DNA-looping: visualization of intermediates in the activation pathway of E. coli RNA polymerase x sigma 54 holoenzyme by scanning force microscopy." J Mol Biol 270(2);125-38. PMID: 9236116

SasseDwight90: Sasse-Dwight S, Gralla JD (1990). "Role of eukaryotic-type functional domains found in the prokaryotic enhancer receptor factor sigma 54." Cell 62(5);945-54. PMID: 2203540

Schulz98: Schulz A, Mucke N, Langowski J, Rippe K (1998). "Scanning force microscopy of Escherichia coli RNA polymerase.sigma54 holoenzyme complexes with DNA in buffer and in air." J Mol Biol 283(4);821-36. PMID: 9790843

Svergun00: Svergun DI, Malfois M, Koch MH, Wigneshweraraj SR, Buck M (2000). "Low resolution structure of the sigma54 transcription factor revealed by X-ray solution scattering." J Biol Chem 275(6);4210-4. PMID: 10660585

Syed97: Syed A, Gralla JD (1997). "Isolation and properties of enhancer-bypass mutants of sigma 54." Mol Microbiol 23(5);987-95. PMID: 9076735

Tintut94: Tintut Y, Wong C, Jiang Y, Hsieh M, Gralla JD (1994). "RNA polymerase binding using a strongly acidic hydrophobic-repeat region of sigma 54." Proc Natl Acad Sci U S A 91(6);2120-4. PMID: 8134358

Tintut95: Tintut Y, Wang JT, Gralla JD (1995). "A novel bacterial transcription cycle involving sigma 54." Genes Dev 9(18);2305-13. PMID: 7557383

Tintut95a: Tintut Y, Gralla JD (1995). "PCR mutagenesis identifies a polymerase-binding sequence of sigma 54 that includes a sigma 70 homology region." J Bacteriol 177(20);5818-25. PMID: 7592329

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Vogel02: Vogel SK, Schulz A, Rippe K (2002). "Binding affinity of Escherichia coli RNA polymerase*sigma54 holoenzyme for the glnAp2, nifH and nifL promoters." Nucleic Acids Res 30(18);4094-101. PMID: 12235394

Wang95b: Wang JT, Syed A, Hsieh M, Gralla JD (1995). "Converting Escherichia coli RNA polymerase into an enhancer-responsive enzyme: role of an NH2-terminal leucine patch in sigma 54." Science 270(5238);992-4. PMID: 7481805

Wong92a: Wong C, Gralla JD (1992). "A role for the acidic trimer repeat region of transcription factor sigma 54 in setting the rate and temperature dependence of promoter melting in vivo." J Biol Chem 267(34);24762-8. PMID: 1447214

Wong94: Wong C, Tintut Y, Gralla JD (1994). "The domain structure of sigma 54 as determined by analysis of a set of deletion mutants." J Mol Biol 236(1);81-90. PMID: 8107127

Other References Related to Gene Regulation

Kumar11: Kumar R, Shimizu K (2011). "Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures." Microb Cell Fact 10;3. PMID: 21272324

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Fri Mar 6, 2015, BIOCYC14A.