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Escherichia coli K-12 substr. MG1655 Polypeptide: RNA polymerase, sigma 28 (sigma F) factor



Gene: fliA Accession Numbers: EG11355 (EcoCyc), b1922, ECK1921

Synonyms: rpoF, flaD, sigma F factor, sigma 28 factor, σ28

Regulation Summary Diagram: ?

Component of: RNA polymerase sigma 28

Summary:
σ28 is a minor sigma factor that is responsible for initiation of transcription of a number of genes involved in motility and flagellar synthesis [Komeda86, Arnosti89, Liu95, Liu96b]. σ28 competes with σ70 for RNA polymerase, core enzyme, binding to it more tightly than σ70 [Kundu97].

A distinguishing feature of σ28 promoters is a long -10 region (GCCGATAA); in addition, its upstream GC is highly conserved [Koo09]. Thus, σ28 not only uses extended -10 recognition but also requires three recognition regions, -35, extended -10, and -10, for successful utilization of the core σ28 promoter [Koo09].

Both GC and the CG motifs are functionally important in the -10 region of σ28, and this is a composite element. Based on mutational and biochemical analyses, it was shown that the upstream GC constitutes an extended -10 motif and is recognized by R91 (which recognizes both 14G and 13C), a residue in domain 3 of σ28. The downstream CG is the upstream edge of the -10 region of the promoter; two residues in region 2.4 of domain 2, D81 (which recognizes 11G) and R84 (which recognizes 12C), participate in its recognition [Koo09].

R91, D81, and R84 are universally conserved in σ28 orthologues [Koo09].

The dependence of σ28 on promoter sequence has been tested using the Chlamydia trachomatis hctB promoter [Yu06b].

σ28 is required for flagellin production [Komeda80, Komeda84]. The structural consequences of fliA mutation have been examined via electron microscopy [Suzuki81].

σ28 is half as abundant as σ70 under most growth conditions, but drops in abundance following heat shock [Jishage96].

Biofilm formation depends on the level of fliA expression [Barrios06, Wood06].

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].

Review: [Koo09].

Gene Citations: [Mytelka96, Bertin94]

Locations: cytosol

Map Position: [1,999,094 <- 1,999,813] (43.09 centisomes)
Length: 720 bp / 239 aa

Molecular Weight of Polypeptide: 27.521 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0006396 , CGSC:771 , DIP:DIP-47959N , EchoBASE:EB1330 , EcoGene:EG11355 , EcoliWiki:b1922 , Mint:MINT-1250982 , ModBase:P0AEM6 , OU-Microarray:b1922 , PortEco:fliA , PR:PRO_000022654 , Pride:P0AEM6 , Protein Model Portal:P0AEM6 , RefSeq:NP_416432 , RegulonDB:EG11355 , SMR:P0AEM6 , String:511145.b1922 , UniProt:P0AEM6

Relationship Links: InterPro:IN-FAMILY:IPR000943 , InterPro:IN-FAMILY:IPR007624 , InterPro:IN-FAMILY:IPR007627 , InterPro:IN-FAMILY:IPR007630 , InterPro:IN-FAMILY:IPR011991 , InterPro:IN-FAMILY:IPR012845 , InterPro:IN-FAMILY:IPR013324 , InterPro:IN-FAMILY:IPR013325 , InterPro:IN-FAMILY:IPR014284 , Pfam:IN-FAMILY:PF04539 , Pfam:IN-FAMILY:PF04542 , Pfam:IN-FAMILY:PF04545 , Prints:IN-FAMILY:PR00046 , Prosite:IN-FAMILY:PS00715 , Prosite:IN-FAMILY:PS00716

In Paralogous Gene Group: 363 (4 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0001123 - transcription initiation from bacterial-type RNA polymerase promoter Inferred by computational analysis [GOA06]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
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:0010468 - regulation of gene expression Inferred by computational analysis [GOA06]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Arifuzzaman06, Rajagopala09]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11, GOA06, 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 [GOA01]
GO:0016987 - sigma factor activity Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, LopezCampistrou05]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06]

MultiFun Terms: cell processes motility, chemotaxis, energytaxis (aerotaxis, redoxtaxis etc)
cell structure flagella
information transfer RNA related Transcription related
regulation genetic unit regulated stimulon
regulation type of regulation transcriptional level sigma factors, anti-sigmafactors

Essentiality data for fliA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Subunit of: RNA polymerase sigma 28

Synonyms: RNA polymerase sigma 28 holoenzyme, RNA polymerase sigma F

Subunit composition of RNA polymerase sigma 28 = [FliA][(RpoA)2(RpoC)(RpoB)]
         RNA polymerase, sigma 28 (sigma F) factor = FliA (extended summary available)
         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)

Controlled Transcription Units (34 total): ?

Notes:


Sequence Features

Feature Class Location Citations Comment
Protein-Segment 16 -> 88
[UniProt13]
UniProt: Sigma-70 factor domain-2; Sequence Annotation Type: region of interest.
Protein-Segment 43 -> 46
[UniProt13]
UniProt: Interaction with polymerase core subunit RpoC; Sequence Annotation Type: short sequence motif.
Mutagenesis-Variant 73
[Koo09, UniProt13]
Alternate sequence: Q → A; UniProt: No change in activity.
Mutagenesis-Variant 74
[Koo09, UniProt13]
Alternate sequence: R → W; UniProt: Decrease in activity.
Alternate sequence: R → A; UniProt: Decrease in activity.
Mutagenesis-Variant 78
[Koo09, UniProt13]
Alternate sequence: A → E; UniProt: Decrease in activity.
Mutagenesis-Variant 81
[Koo09, UniProt13]
Alternate sequence: D → A; UniProt: Loss of activity.
Mutagenesis-Variant 84
[Koo09, UniProt13]
Alternate sequence: R → A; UniProt: Loss of activity.
Mutagenesis-Variant 91
[Koo09, UniProt13]
Alternate sequence: R → A; UniProt: Loss of activity.
Mutagenesis-Variant 92
[Koo09, UniProt13]
Alternate sequence: S → A; UniProt: No change in activity.
Mutagenesis-Variant 94
[Koo09, UniProt13]
Alternate sequence: R → A; UniProt: Decrease in activity.
Mutagenesis-Variant 95
[Koo09, UniProt13]
Alternate sequence: R → A; UniProt: No change in activity.
Mutagenesis-Variant 96
[Koo09, UniProt13]
Alternate sequence: N → A; UniProt: No change in activity.
Protein-Segment 96 -> 166
[UniProt13]
UniProt: Sigma-70 factor domain-3; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 98
[Koo09, UniProt13]
Alternate sequence: R → A; UniProt: Strong decrease in activity.
Protein-Segment 185 -> 233
[UniProt13]
UniProt: Sigma-70 factor domain-4; Sequence Annotation Type: region of interest.
DNA-Binding-Region 207 -> 226
[UniProt10]
UniProt: H-T-H motif; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b1922 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11355; confirmed by SwissProt match.


References

Arifuzzaman06: Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H (2006). "Large-scale identification of protein-protein interaction of Escherichia coli K-12." Genome Res 16(5);686-91. PMID: 16606699

Arnosti89: Arnosti DN, Chamberlin MJ (1989). "Secondary sigma factor controls transcription of flagellar and chemotaxis genes in Escherichia coli." Proc Natl Acad Sci U S A 86(3);830-4. PMID: 2644646

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

Barrios06: Barrios AF, Zuo R, Ren D, Wood TK (2006). "Hha, YbaJ, and OmpA regulate Escherichia coli K12 biofilm formation and conjugation plasmids abolish motility." Biotechnol Bioeng 93(1);188-200. PMID: 16317765

Bertin94: Bertin P, Terao E, Lee EH, Lejeune P, Colson C, Danchin A, Collatz E (1994). "The H-NS protein is involved in the biogenesis of flagella in Escherichia coli." J Bacteriol 1994;176(17);5537-40. PMID: 8071234

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

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: 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."

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

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

Komeda80: Komeda Y, Kutsukake K, Iino T (1980). "Definition of additional flagellar genes in Escherichia coli K12." Genetics 94(2);277-90. PMID: 6993282

Komeda84: Komeda Y, Ono N, Kagawa H (1984). "Synthesis of flagellin and hook subunit protein in flagellar mutants of Escherichia coli K12." Mol Gen Genet 194(1-2);49-51. PMID: 6374380

Komeda86: Komeda Y (1986). "Transcriptional control of flagellar genes in Escherichia coli K-12." J Bacteriol 168(3);1315-8. PMID: 3536871

Koo09: Koo BM, Rhodius VA, Campbell EA, Gross CA (2009). "Mutational analysis of Escherichia coli sigma28 and its target promoters reveals recognition of a composite -10 region, comprised of an 'extended -10' motif and a core -10 element." Mol Microbiol 72(4);830-43. PMID: 19400790

Kundu97: Kundu TK, Kusano S, Ishihama A (1997). "Promoter selectivity of Escherichia coli RNA polymerase sigmaF holoenzyme involved in transcription of flagellar and chemotaxis genes." J Bacteriol 179(13);4264-9. PMID: 9209042

Liu95: Liu X, Matsumura P (1995). "An alternative sigma factor controls transcription of flagellar class-III operons in Escherichia coli: gene sequence, overproduction, purification and characterization." Gene 164(1);81-4. PMID: 7590326

Liu96b: Liu X, Matsumura P (1996). "Differential regulation of multiple overlapping promoters in flagellar class II operons in Escherichia coli." Mol Microbiol 21(3);613-20. PMID: 8866483

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Mytelka96: Mytelka DS, Chamberlin MJ (1996). "Escherichia coli fliAZY operon." J Bacteriol 1996;178(1);24-34. PMID: 8550423

Rajagopala09: Rajagopala SV, Hughes KT, Uetz P (2009). "Benchmarking yeast two-hybrid systems using the interactions of bacterial motility proteins." Proteomics 9(23);5296-302. PMID: 19834901

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Suzuki81: Suzuki T, Komeda Y (1981). "Incomplete flagellar structures in Escherichia coli mutants." J Bacteriol 145(2);1036-41. PMID: 7007337

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

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 00:00:00." Database.

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

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

Wood06: Wood TK, Gonzalez Barrios AF, Herzberg M, Lee J (2006). "Motility influences biofilm architecture in Escherichia coli." Appl Microbiol Biotechnol 72(2);361-7. PMID: 16397770

Yu06b: Yu HH, Di Russo EG, Rounds MA, Tan M (2006). "Mutational analysis of the promoter recognized by Chlamydia and Escherichia coli sigma(28) RNA polymerase." J Bacteriol 188(15);5524-31. PMID: 16855242

Other References Related to Gene Regulation

Dudin14: Dudin O, Geiselmann J, Ogasawara H, Ishihama A, Lacour S (2014). "Repression of flagellar genes in exponential phase by CsgD and CpxR, two crucial modulators of Escherichia coli biofilm formation." J Bacteriol 196(3);707-15. PMID: 24272779

Ide99: Ide N, Ikebe T, Kutsukake K (1999). "Reevaluation of the promoter structure of the class 3 flagellar operons of Escherichia coli and Salmonella." Genes Genet Syst 74(3);113-6. PMID: 10586520

Ikebe99: Ikebe T, Iyoda S, Kutsukake K (1999). "Promoter analysis of the class 2 flagellar operons of Salmonella." Genes Genet Syst 74(4);179-83. PMID: 10650844

Lee11: Lee YY, Barker CS, Matsumura P, Belas R (2011). "Refining the Binding of the Escherichia coli Flagellar Master Regulator, FlhD4C2, on a Base-Specific Level." J Bacteriol 193(16);4057-68. PMID: 21685294

Lehti12: Lehti TA, Bauchart P, Dobrindt U, Korhonen TK, Westerlund-Wikstrom B (2012). "The fimbriae activator MatA switches off motility in Escherichia coli by repression of the flagellar master operon flhDC." Microbiology 158(Pt 6);1444-55. PMID: 22422754

Liu94: Liu X, Matsumura P (1994). "The FlhD/FlhC complex, a transcriptional activator of the Escherichia coli flagellar class II operons." J Bacteriol 176(23);7345-51. PMID: 7961507

Park01: Park K, Choi S, Ko M, Park C (2001). "Novel sigmaF-dependent genes of Escherichia coli found using a specified promoter consensus." FEMS Microbiol Lett 2001;202(2);243-50. PMID: 11520622

Partridge09: Partridge JD, Bodenmiller DM, Humphrys MS, Spiro S (2009). "NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility." Mol Microbiol 73(4);680-94. PMID: 19656291

Stafford05: Stafford GP, Ogi T, Hughes C (2005). "Binding and transcriptional activation of non-flagellar genes by the Escherichia coli flagellar master regulator FlhD2C2." Microbiology 151(Pt 6);1779-88. PMID: 15941987

Theodorou12: Theodorou MC, Theodorou EC, Kyriakidis DA (2012). "Involvement of AtoSC two-component system in Escherichia coli flagellar regulon." Amino Acids 43(2);833-44. PMID: 22083893

Typas07a: Typas A, Stella S, Johnson RC, Hengge R (2007). "The -35 sequence location and the Fis-sigma factor interface determine sigmas selectivity of the proP (P2) promoter in Escherichia coli." Mol Microbiol 63(3);780-96. PMID: 17302803


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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