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Escherichia coli K-12 substr. MG1655 Polypeptide: NanR DNA-binding transcriptional dual regulator



Gene: nanR Accession Numbers: G7678 (EcoCyc), b3226, ECK3215

Synonyms: yhcK

Regulation Summary Diagram: ?

Component of: NanR-NANA

Summary:
The genes regulated by NanR, "N-acetyl-neuraminic acid regulator," are involved in N-acetyl-neuraminic acid (or sialic acid) transport and metabolism [Kalivoda03] and in OFF/ON switching of type 1 fimbriation. N-acetylneuraminate (Neu5Ac), which is the most common sialic acid, induces the catabolism of sialic acids operons by directly inactivating NanR [Sohanpal04], converting the predominantly dimeric form of the repressor to an inactive monomer [Kalivoda13].

NanR is a member of the FadR/GntR family. Members of this family have two domains, an N-terminal domain with a helix-turn-helix DNA-binding motif and a C-terminal domain with dimerization and effector-binding motifs. Three-dimensional models of the N terminus of FadR and NanR show topological similarities and a ~26% sequence identity between them [Kalivoda03].

NanR regulates transcription when it binds to a region of ~30 bp that contains three conserved motifs in tandem. However, this protein can be displaced from this region by N-acetyl-neuraminic acid. Although it has been shown that NanR can form homodimers in solution, its DNA-binding stoichiometry is unknown. When this protein is repressing transcription, it overlaps the whole promoter region [Kalivoda03, Sohanpal04]. The Nan box shows affinity to a set of conserved operators with two or three exact, or nearly exact, repeats of the hexanucleotide sequence GGTATA [Kalivoda13].

The region of 30 bp that NanR binds to is close to a Dam methylation site (GATC) [Chu08, Sohanpal04] that appears to be necessary for induction of some genes of the NanR regulon [Oshima02a]. Methylation in these sites is prevented by NanR binding [Chu08, Sohanpal04].

Kalivoda et. al. (2013) have suggested that the term sialoregulon be given to genes that are directly regulated by NanR and the term sialostimulon be used for genes affected by the by-products of sialic acid metabolism [Kalivoda13].

The crystal structure of the native NanR has been solved [Kalivoda13].

Locations: cytosol

Map Position: [3,371,720 <- 3,372,511] (72.67 centisomes)
Length: 792 bp / 263 aa

Molecular Weight of Polypeptide: 29.524 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010584 , EchoBASE:EB2668 , EcoGene:EG12817 , EcoliWiki:b3226 , ModBase:P0A8W0 , OU-Microarray:b3226 , PortEco:nanR , PR:PRO_000023344 , Pride:P0A8W0 , Protein Model Portal:P0A8W0 , RefSeq:NP_417693 , RegulonDB:G7678 , SMR:P0A8W0 , String:511145.b3226 , UniProt:P0A8W0

Relationship Links: InterPro:IN-FAMILY:IPR000524 , InterPro:IN-FAMILY:IPR008920 , InterPro:IN-FAMILY:IPR011711 , InterPro:IN-FAMILY:IPR011991 , InterPro:IN-FAMILY:IPR023730 , InterPro:IN-FAMILY:IPR027376 , Pfam:IN-FAMILY:PF00392 , Pfam:IN-FAMILY:PF07729 , Prints:IN-FAMILY:PR00035 , Prosite:IN-FAMILY:PS50949 , Smart:IN-FAMILY:SM00345 , Smart:IN-FAMILY:SM00895

In Paralogous Gene Group: 38 (9 members)

In Reactions of unknown directionality:

Not in pathways:
N-acetylneuraminate + NanR = NanR-NANA

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Kalivoda03]
GO:0006355 - regulation of transcription, DNA-templated Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Kalivoda03]
GO:0045892 - negative regulation of transcription, DNA-templated Inferred by computational analysis [GOA06]
Molecular Function: GO:0003677 - DNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA06, Kalivoda03]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA06, GOA01a]
Cellular Component: GO:0032993 - protein-DNA complex Inferred from experiment [Kalivoda03]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
regulation genetic unit regulated operon
regulation type of regulation transcriptional level repressor

DNA binding site length: 6 base-pairs

Symmetry: Asymmetric

Consensus DNA Binding Sequence: GGTATA

Regulated Transcription Units (6 total): ?

Notes:

Essentiality data for nanR 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]

Credits:
Last-Curated ? 18-Mar-2008 by Gama-Castro S , UNAM


Subunit of: NanR-NANA

Synonyms: B3226, YhcK, NanR

Subunit composition of NanR-NANA = [N-acetylneuraminate][NanR]
         NanR DNA-binding transcriptional dual regulator = NanR (extended summary available)

Sequence Length: 263 AAs

Relationship Links: Pfam:IN-FAMILY:PF00392

In Reactions of unknown directionality:

Not in pathways:
N-acetylneuraminate + NanR = NanR-NANA

MultiFun Terms: information transfer RNA related Transcription related
regulation genetic unit regulated operon
regulation type of regulation transcriptional level repressor


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 30 -> 98
[UniProt09]
UniProt: HTH gntR-type;
DNA-Binding-Region 58 -> 77
[UniProt10]
UniProt: H-T-H motif; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

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

Chu08: Chu D, Roobol J, Blomfield IC (2008). "A theoretical interpretation of the transient sialic acid toxicity of a nanR mutant of Escherichia coli." J Mol Biol 375(3);875-89. PMID: 18054045

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

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

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

Kalivoda03: Kalivoda KA, Steenbergen SM, Vimr ER, Plumbridge J (2003). "Regulation of sialic acid catabolism by the DNA binding protein NanR in Escherichia coli." J Bacteriol 185(16);4806-15. PMID: 12897000

Kalivoda13: Kalivoda KA, Steenbergen SM, Vimr ER (2013). "Control of the Escherichia coli sialoregulon by transcriptional repressor NanR." J Bacteriol 195(20);4689-701. PMID: 23935044

Oshima02a: Oshima T, Wada C, Kawagoe Y, Ara T, Maeda M, Masuda Y, Hiraga S, Mori H (2002). "Genome-wide analysis of deoxyadenosine methyltransferase-mediated control of gene expression in Escherichia coli." Mol Microbiol 45(3);673-95. PMID: 12139615

Sohanpal04: Sohanpal BK, El-Labany S, Lahooti M, Plumbridge JA, Blomfield IC (2004). "Integrated regulatory responses of fimB to N-acetylneuraminic (sialic) acid and GlcNAc in Escherichia coli K-12." Proc Natl Acad Sci U S A 101(46);16322-7. PMID: 15534208

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.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."


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 Mon Nov 24, 2014, biocyc14.