ID   RP54_PSEAE              Reviewed;         497 AA.
AC   P49988;
DT   01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT   08-DEC-2000, sequence version 2.
DT   27-MAR-2024, entry version 137.
DE   RecName: Full=RNA polymerase sigma-54 factor;
GN   Name=rpoN; OrderedLocusNames=PA4462;
OS   Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM
OS   14847 / LMG 12228 / 1C / PRS 101 / PAO1).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Pseudomonadales;
OC   Pseudomonadaceae; Pseudomonas.
OX   NCBI_TaxID=208964;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=PAK;
RX   PubMed=8113171; DOI=10.1128/jb.176.5.1316-1322.1994;
RA   Jin S., Ishimoto K., Lory S.;
RT   "Nucleotide sequence of the rpoN gene and characterization of two
RT   downstream open reading frames in Pseudomonas aeruginosa.";
RL   J. Bacteriol. 176:1316-1322(1994).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 /
RC   1C / PRS 101 / PAO1;
RX   PubMed=10984043; DOI=10.1038/35023079;
RA   Stover C.K., Pham X.-Q.T., Erwin A.L., Mizoguchi S.D., Warrener P.,
RA   Hickey M.J., Brinkman F.S.L., Hufnagle W.O., Kowalik D.J., Lagrou M.,
RA   Garber R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y.,
RA   Brody L.L., Coulter S.N., Folger K.R., Kas A., Larbig K., Lim R.M.,
RA   Smith K.A., Spencer D.H., Wong G.K.-S., Wu Z., Paulsen I.T., Reizer J.,
RA   Saier M.H. Jr., Hancock R.E.W., Lory S., Olson M.V.;
RT   "Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic
RT   pathogen.";
RL   Nature 406:959-964(2000).
RN   [3]
RP   FUNCTION IN MOTILITY, AND DISRUPTION PHENOTYPE.
RC   STRAIN=PAK;
RX   PubMed=2152909; DOI=10.1128/jb.172.1.389-396.1990;
RA   Totten P.A., Lara J.C., Lory S.;
RT   "The rpoN gene product of Pseudomonas aeruginosa is required for expression
RT   of diverse genes, including the flagellin gene.";
RL   J. Bacteriol. 172:389-396(1990).
RN   [4]
RP   FUNCTION, AND DISRUPTION PHENOTYPE.
RX   PubMed=9595661; DOI=10.1111/j.1574-6968.1998.tb12975.x;
RA   Yamano Y., Nishikawa T., Komatsu Y.;
RT   "Involvement of the RpoN protein in the transcription of the oprE gene in
RT   Pseudomonas aeruginosa.";
RL   FEMS Microbiol. Lett. 162:31-37(1998).
RN   [5]
RP   FUNCTION IN QUORUM SENSING.
RX   PubMed=12644493; DOI=10.1128/jb.185.7.2227-2235.2003;
RA   Heurlier K., Denervaud V., Pessi G., Reimmann C., Haas D.;
RT   "Negative control of quorum sensing by RpoN (sigma54) in Pseudomonas
RT   aeruginosa PAO1.";
RL   J. Bacteriol. 185:2227-2235(2003).
RN   [6]
RP   FUNCTION IN MUCOIDY.
RX   PubMed=10792721; DOI=10.1046/j.1365-2958.2000.01846.x;
RA   Boucher J.C., Schurr M.J., Deretic V.;
RT   "Dual regulation of mucoidy in Pseudomonas aeruginosa and sigma factor
RT   antagonism.";
RL   Mol. Microbiol. 36:341-351(2000).
RN   [7]
RP   FUNCTION IN QUORUM SENSING.
RX   PubMed=26633362; DOI=10.3390/ijms161226103;
RA   Cai Z., Liu Y., Chen Y., Yam J.K., Chew S.C., Chua S.L., Wang K.,
RA   Givskov M., Yang L.;
RT   "RpoN Regulates Virulence Factors of Pseudomonas aeruginosa via Modulating
RT   the PqsR Quorum Sensing Regulator.";
RL   Int. J. Mol. Sci. 16:28311-28319(2015).
RN   [8]
RP   FUNCTION IN QUORUM SENSING AND BIOFILM FORMATION, AND DISRUPTION PHENOTYPE.
RX   PubMed=29760208; DOI=10.1128/jb.00205-18;
RA   Shao X., Zhang X., Zhang Y., Zhu M., Yang P., Yuan J., Xie Y., Zhou T.,
RA   Wang W., Chen S., Liang H., Deng X.;
RT   "RpoN-Dependent Direct Regulation of Quorum Sensing and the Type VI
RT   Secretion System in Pseudomonas aeruginosa PAO1.";
RL   J. Bacteriol. 200:0-0(2018).
CC   -!- FUNCTION: Sigma factors are initiation factors that promote the
CC       attachment of RNA polymerase to specific initiation sites and are then
CC       released (PubMed:9595661). Plays a role in the regulation of many
CC       virulence factors, motility, quorum sensing, mucoidy, a general
CC       mechanism for maintaining lytic phage in populations of bacteria, and
CC       biofilm formation (PubMed:2152909, PubMed:12644493, PubMed:10792721,
CC       PubMed:26633362, PubMed:29760208). Positively controls the T6 secretion
CC       system by directly binding to the promoter regions of hcpA and hcpB
CC       genes, leading to their expression (PubMed:29760208). Thereby, allows
CC       to colonize several hosts efficiently including mammals, insects,
CC       nematodes and plants (By similarity) (PubMed:2152909, PubMed:9595661,
CC       PubMed:12644493, PubMed:10792721, PubMed:26633362, PubMed:29760208).
CC       {ECO:0000250|UniProtKB:A0A0H2ZGR9, ECO:0000269|PubMed:10792721,
CC       ECO:0000269|PubMed:12644493, ECO:0000269|PubMed:2152909,
CC       ECO:0000269|PubMed:26633362, ECO:0000269|PubMed:29760208,
CC       ECO:0000269|PubMed:9595661}.
CC   -!- DISRUPTION PHENOTYPE: Deletion mutants result in reduced production of
CC       pyocyanine, motility, and proteolytic activity. The motility defect is
CC       due to the inability of these mutants to synthesize flagellin
CC       (PubMed:2152909). Significantly decreased porin oprE expression under
CC       aerobic conditions (PubMed:9595661). Mutants also show defect in
CC       biofilm formation (PubMed:29760208). {ECO:0000269|PubMed:2152909,
CC       ECO:0000269|PubMed:29760208, ECO:0000269|PubMed:9595661}.
CC   -!- SIMILARITY: Belongs to the sigma-54 factor family. {ECO:0000305}.
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DR   EMBL; L26916; AAA19793.1; -; Unassigned_DNA.
DR   EMBL; AE004091; AAG07850.1; -; Genomic_DNA.
DR   PIR; A53373; A53373.
DR   PIR; F83087; F83087.
DR   RefSeq; NP_253152.1; NC_002516.2.
DR   RefSeq; WP_003094357.1; NZ_QZGE01000004.1.
DR   AlphaFoldDB; P49988; -.
DR   SMR; P49988; -.
DR   MINT; P49988; -.
DR   STRING; 208964.PA4462; -.
DR   PaxDb; 208964-PA4462; -.
DR   GeneID; 881022; -.
DR   KEGG; pae:PA4462; -.
DR   PATRIC; fig|208964.12.peg.4672; -.
DR   PseudoCAP; PA4462; -.
DR   HOGENOM; CLU_020569_0_1_6; -.
DR   InParanoid; P49988; -.
DR   OrthoDB; 9814402at2; -.
DR   PhylomeDB; P49988; -.
DR   BioCyc; PAER208964:G1FZ6-4551-MONOMER; -.
DR   PHI-base; PHI:7554; -.
DR   PHI-base; PHI:9213; -.
DR   Proteomes; UP000002438; Chromosome.
DR   CollecTF; EXPREG_00000ad0; -.
DR   GO; GO:0000428; C:DNA-directed RNA polymerase complex; IEA:UniProtKB-KW.
DR   GO; GO:0032993; C:protein-DNA complex; IMP:CollecTF.
DR   GO; GO:0001216; F:DNA-binding transcription activator activity; IMP:CollecTF.
DR   GO; GO:0016779; F:nucleotidyltransferase activity; IEA:UniProtKB-KW.
DR   GO; GO:0016987; F:sigma factor activity; IEA:UniProtKB-KW.
DR   GO; GO:0000976; F:transcription cis-regulatory region binding; IMP:CollecTF.
DR   GO; GO:0006352; P:DNA-templated transcription initiation; IEA:InterPro.
DR   GO; GO:1900191; P:negative regulation of single-species biofilm formation; IMP:PseudoCAP.
DR   Gene3D; 1.10.10.60; Homeodomain-like; 1.
DR   Gene3D; 1.10.10.1330; RNA polymerase sigma-54 factor, core-binding domain; 1.
DR   InterPro; IPR000394; RNA_pol_sigma_54.
DR   InterPro; IPR007046; RNA_pol_sigma_54_core-bd.
DR   InterPro; IPR007634; RNA_pol_sigma_54_DNA-bd.
DR   InterPro; IPR038709; RpoN_core-bd_sf.
DR   NCBIfam; TIGR02395; rpoN_sigma; 1.
DR   PANTHER; PTHR32248; RNA POLYMERASE SIGMA-54 FACTOR; 1.
DR   PANTHER; PTHR32248:SF4; RNA POLYMERASE SIGMA-54 FACTOR; 1.
DR   Pfam; PF00309; Sigma54_AID; 1.
DR   Pfam; PF04963; Sigma54_CBD; 1.
DR   Pfam; PF04552; Sigma54_DBD; 1.
DR   PIRSF; PIRSF000774; RpoN; 1.
DR   PRINTS; PR00045; SIGMA54FCT.
DR   PROSITE; PS00717; SIGMA54_1; 1.
DR   PROSITE; PS00718; SIGMA54_2; 1.
DR   PROSITE; PS50044; SIGMA54_3; 1.
PE   1: Evidence at protein level;
KW   DNA-binding; DNA-directed RNA polymerase; Nucleotidyltransferase;
KW   Reference proteome; Sigma factor; Transcription; Transcription regulation;
KW   Transferase.
FT   CHAIN           1..497
FT                   /note="RNA polymerase sigma-54 factor"
FT                   /id="PRO_0000205534"
FT   DNA_BIND        386..405
FT                   /note="H-T-H motif"
FT                   /evidence="ECO:0000255"
FT   REGION          42..100
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOTIF           474..482
FT                   /note="RPON box"
FT   COMPBIAS        72..89
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   CONFLICT        352
FT                   /note="S -> T (in Ref. 1; AAA19793)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   497 AA;  56054 MW;  CE1994F03FD58405 CRC64;
     MKPSLVLKMG QQLTMTPQLQ QAIRLLQLST LDLQQEIQEA LESNPMLERQ EDGDDFDNSD
     PLADGAEQAA SAPQESPLQE SATPSVESLD DDQWSERIPS ELPVDTAWED IYQTSASSLP
     SNDDDEWDFT ARTSSGESLH SHLLWQVNLA PMSDTDRMIA VTIIDSINND GYLEESLEEI
     LAAIDPELDV ELDEVEVVLR RIQQLEPAGI GARNLRECLL LQLRQLPSTT PWLNEALRLV
     SDYLDLLGGR DYSQLMRRMK LKEDELRQVI ELIQCLHPRP GSQIESSEAE YIVPDVIVRK
     DNERWLVELN QEAMPRLRVN ATYAGMVRRA DSSADNTFMR NQLQEARWFI KSLQSRNETL
     MKVATQIVEH QRGFLDYGEE AMKPLVLHDI AEAVGMHEST ISRVTTQKYM HTPRGIFELK
     YFFSSHVSTA EGGECSSTAI RAIIKKLVAA ENAKKPLSDS KIAGLLEAQG IQVARRTVAK
     YRESLGIAPS SERKRLV
//