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Escherichia coli K-12 substr. MG1655 Polypeptide: RNA polymerase, sigma 70 (sigma D) factor



Gene: rpoD Accession Numbers: EG10896 (EcoCyc), b3067, ECK3057

Synonyms: alt, sigma D factor, sigma 70 factor, σ70

Regulation Summary Diagram: ?

Component of: RNA polymerase sigma 70

Summary:
Sigma 70 is the primary sigma factor during exponential growth, targeting RNA polymerase sigma 70 to a wide range of promoters that are essential for normal growth. Eσ70 transcribes, in the absence of any additional transcription factor, with higher efficiency genes encoding ribosomal proteins and other protein synthesis-related genes, such as rRNA- and tRNA-encoding genes and prfB, which encodes release factor 2 [Maciag11].

Sigma 70 accounts for 60-95% of the total pool of cellular sigma factors during normal exponential growth [Jishage96]. Changes away from typical growth conditions, such as heat shock or growth into stationary phase, lead to the replacement of sigma 70 with other sigma factors in the RNA polymerase holoenzyme complex [Blaszczak95, Ozaki91, Wade04]. When this occurs, the holoenzyme no longer recognizes the same transcription targets, leading to a decline in many RNA and protein levels, including components of the protein synthesis machinery [Osawa81, Fujita87, Magnusson03].

Sigma 70 has the strongest interaction with the RNA polymerase core complex of all the known sigma factors [Maeda00]. This interaction may in fact be required for sigma 70 to bind DNA, as its amino-terminal portion normally blocks such binding in the absence of core complex [Dombroski92]. When it does bind promoter DNA, sigma 70 contacts both the -10 and -35 regions simultaneously, with a binding affinity depending on the spacing between these points [Dombroski96]. In promoters with a -35 site, sigma 70 is more effective when there is also a proximal half-site or a complete UP element, whereas the stationary phase sigma, RNA polymerase, sigma S (sigma 38) factor, has opposite selectivity [Typas05]. Both sigma 70 and RNA polymerase, sigma S (sigma 38) factor compete for available core complex during stationary phase growth [Farewell98a]. Sigma 70 also competes with NusA for binding to RNA polymerase, core enzyme, though sigma 70's affinity for the core drops off dramatically during the change from transcriptional initiation to elongation [Gill91a, Traviglia99]. Sigma 70 even competes with the nascent RNA strand for binding to RNA polymerase, core enzyme [Daube99]. The majority of early elongation complexes do appear to retain sigma 70 for a while, with this retention being promoted by promoter-like sequences in the initial transcribed region [Kapanidis05]. These sequences, bearing similarity to -10 promoters, can induce sigma 70-mediated pausing of RNA polymerase sigma 70 [Mooney03, Nickels04]. Notably, promoters recognized by sigma 70 occur in regions rife with such promoter-like sequences [Huerta03].

Sigma 70 function is blocked by the anti-sigma factor, regulator of σ70D), stationary phase protein.

Sigma 70 has undergone significant structural analysis. A crystal structure of sigma 70 has been determined to 2.6 Å resolution, revealing that residues that bind core polymerase are on one face, with DNA-binding residues on the other [Malhotra96]. Most of sigma 70 must be present to allow promoter melting [Young04]. Within sigma 70, there are conserved motifs responsible for binding to the -10 and -35 and other promoter regions [Siegele89, Gardella89, Poznanski03, Kumar93, Sanderson03]. Region 1.2 of sigma 70 is responsible for recognition of the -10-like pause regions described above, as well as recognition of the fork junction and actual promoter-proximal pausing [Zenkin07]. A region of sigma 70 that partially blocks the RNA exit channel in the holoenzyme is involved in binding the 3' initiating nucleotide in the active site and aids in promoter clearance [Kulbachinskiy06]. A crystal structure of RNA polymerase sigma 70 has been determined to 9.5 Å resolution [Finn00]. Sigma 70 undergoes conformational change when it binds to the core complex, revealing the sigma factor's DNA-binding surfaces, then undergoes another change on promoter melting [Callaci98, McMahan99, Gruber01]. RNA polymerase, α subunit interacts with sigma 70 at a subset of UP and activator-dependent promoters [Chen03g]. Interaction between RNA polymerase, β' subunit and sigma 70 promotes sigma 70 interaction with the nontemplate strand in the -10 region, while interaction between RNA polymerase, β subunit and sigma 70 acts to block extension of nascent RNA, and thus must be disrupted to allow elongation to occur [Young01, Nickels05]. The interaction of sigma 70 with activator proteins has also been addressed in detail [Kumar94].

A σ-competition model based on comparative kinetic and thermodynamic properties was developed by Ganguly and Chatterji in 2012 [Ganguly12].

Citations: [Silverstone72, Zhi03]

Gene Citations: [Burton83, Lupski83, Lupski84, Yajnik93]

Locations: cytosol

Map Position: [3,211,069 -> 3,212,910] (69.21 centisomes)
Length: 1842 bp / 613 aa

Molecular Weight of Polypeptide: 70.263 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010070 , CGSC:231 , DIP:DIP-10773N , EchoBASE:EB0889 , EcoGene:EG10896 , EcoliWiki:b3067 , Mint:MINT-1220595 , ModBase:P00579 , OU-Microarray:b3067 , PortEco:rpoD , PR:PRO_000023847 , Pride:P00579 , Protein Model Portal:P00579 , RefSeq:NP_417539 , RegulonDB:EG10896 , SMR:P00579 , String:511145.b3067 , Swiss-Model:P00579 , UniProt:P00579

Relationship Links: InterPro:IN-FAMILY:IPR000943 , InterPro:IN-FAMILY:IPR007127 , InterPro:IN-FAMILY:IPR007624 , InterPro:IN-FAMILY:IPR007627 , InterPro:IN-FAMILY:IPR007630 , InterPro:IN-FAMILY:IPR007631 , InterPro:IN-FAMILY:IPR009042 , InterPro:IN-FAMILY:IPR011991 , InterPro:IN-FAMILY:IPR012760 , InterPro:IN-FAMILY:IPR013324 , InterPro:IN-FAMILY:IPR013325 , InterPro:IN-FAMILY:IPR014284 , PDB:Structure:1SIG , PDB:Structure:1TLH , PDB:Structure:2P7V , PDB:Structure:3IYD , PDB:Structure:3T72 , PDB:Structure:4IGC , PDB:Structure:4JK1 , PDB:Structure:4JK2 , PDB:Structure:4JKR , PDB:Structure:4KMU , PDB:Structure:4KN4 , PDB:Structure:4KN7 , Pfam:IN-FAMILY:PF00140 , Pfam:IN-FAMILY:PF03979 , Pfam:IN-FAMILY:PF04539 , Pfam:IN-FAMILY:PF04542 , Pfam:IN-FAMILY:PF04545 , Pfam:IN-FAMILY:PF04546 , 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:0009408 - response to heat Inferred from experiment [Chuang93]
GO:0001123 - transcription initiation from bacterial-type RNA polymerase promoter Inferred by computational analysis [GOA06]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a]
GO:0006352 - DNA-templated transcription, initiation Inferred by computational analysis [GOA01a]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0010468 - regulation of gene expression Inferred by computational analysis [GOA06]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Yuan08a, Sharma08a, Dove01, Arifuzzaman06, Butland05, Arthur00]
GO:0016987 - sigma factor activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a, Burgess69]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]

MultiFun Terms: information transfer RNA related Transcription related
regulation genetic unit regulated stimulon
regulation type of regulation transcriptional level sigma factors, anti-sigmafactors

Essentiality data for rpoD knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Yamamoto09]

Credits:
Last-Curated ? 06-Jul-2006 by Shearer A , SRI International


Subunit of: RNA polymerase sigma 70

Synonyms: RNA polymerase sigma 70 holoenzyme, RNA polymerase sigma D

Subunit composition of RNA polymerase sigma 70 = [(RpoA)2(RpoC)(RpoB)][RpoD]
         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 70 (sigma D) factor = RpoD (extended summary available)

This protein controls transcription of 1030 transcription units (not shown).


Sequence Features

Feature Class Location Citations Comment
Protein-Segment 2 -> 80
[UniProt13]
UniProt: Sigma-70 factor domain-1; Sequence Annotation Type: region of interest.
Sequence-Conflict 149
[Burton81, UniProt, 2010]
Alternate sequence: D → N; UniProt: (in Ref. 1; AAA24601);
Acetylation-Modification 257
[Yu08]
 
Protein-Segment 379 -> 449
[UniProt13]
UniProt: Sigma-70 factor domain-2; Sequence Annotation Type: region of interest.
Protein-Segment 403 -> 406
[UniProt13]
UniProt: Interaction with polymerase core subunit RpoC; Sequence Annotation Type: short sequence motif.
Protein-Segment 458 -> 534
[UniProt13]
UniProt: Sigma-70 factor domain-3; Sequence Annotation Type: region of interest.
Protein-Segment 547 -> 600
[UniProt13]
UniProt: Sigma-70 factor domain-4; Sequence Annotation Type: region of interest.
Amino-Acid-Site 562
[UniProt13]
UniProt: Interaction with anti-sigma factors; Sequence Annotation Type: site.
DNA-Binding-Region 573 -> 592
[Blanco11, Dombroski92, Hudson09, UniProt13]
UniProt: H-T-H motif.
Protein-Segment 584 -> 599
[UniProt13]
UniProt: Interaction with anti-sigma factors; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 596
[Rhodius00, UniProt14]
Alternate sequence: R → E; UniProt: 2-fold reduction in activation of class II Crp-dependent promoters.
Alternate sequence: R → D; UniProt: 2-fold reduction in activation of class II Crp-dependent promoters.


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3067 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10896; 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

Arthur00: Arthur TM, Anthony LC, Burgess RR (2000). "Mutational analysis of beta '260-309, a sigma 70 binding site located on Escherichia coli core RNA polymerase." J Biol Chem 275(30);23113-9. PMID: 10764785

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

Blanco11: Blanco AG, Canals A, Bernues J, Sola M, Coll M (2011). "The structure of a transcription activation subcomplex reveals how σ(70) is recruited to PhoB promoters." EMBO J 30(18);3776-85. PMID: 21829166

Blaszczak95: Blaszczak A, Zylicz M, Georgopoulos C, Liberek K (1995). "Both ambient temperature and the DnaK chaperone machine modulate the heat shock response in Escherichia coli by regulating the switch between sigma 70 and sigma 32 factors assembled with RNA polymerase." EMBO J 14(20);5085-93. PMID: 7588636

Burgess69: Burgess RR, Travers AA, Dunn JJ, Bautz EK (1969). "Factor stimulating transcription by RNA polymerase." Nature 221(5175);43-6. PMID: 4882047

Burton81: Burton Z, Burgess RR, Lin J, Moore D, Holder S, Gross CA (1981). "The nucleotide sequence of the cloned rpoD gene for the RNA polymerase sigma subunit from E coli K12." Nucleic Acids Res 1981;9(12);2889-903. PMID: 6269063

Burton83: Burton ZF, Gross CA, Watanabe KK, Burgess RR (1983). "The operon that encodes the sigma subunit of RNA polymerase also encodes ribosomal protein S21 and DNA primase in E. coli K12." Cell 1983;32(2);335-49. PMID: 6186393

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

Callaci98: Callaci S, Heyduk E, Heyduk T (1998). "Conformational changes of Escherichia coli RNA polymerase sigma70 factor induced by binding to the core enzyme." J Biol Chem 273(49);32995-3001. PMID: 9830052

Chen03g: Chen H, Tang H, Ebright RH (2003). "Functional interaction between RNA polymerase alpha subunit C-terminal domain and sigma70 in UP-element- and activator-dependent transcription." Mol Cell 11(6);1621-33. PMID: 12820974

Chuang93: Chuang SE, Blattner FR (1993). "Characterization of twenty-six new heat shock genes of Escherichia coli." J Bacteriol 175(16);5242-52. PMID: 8349564

Daube99: Daube SS, von Hippel PH (1999). "Interactions of Escherichia coli sigma(70) within the transcription elongation complex." Proc Natl Acad Sci U S A 96(15);8390-5. PMID: 10411885

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

Dombroski92: Dombroski AJ, Walter WA, Record MT, Siegele DA, Gross CA (1992). "Polypeptides containing highly conserved regions of transcription initiation factor sigma 70 exhibit specificity of binding to promoter DNA." Cell 70(3);501-12. PMID: 1643661

Dombroski96: Dombroski AJ, Johnson BD, Lonetto M, Gross CA (1996). "The sigma subunit of Escherichia coli RNA polymerase senses promoter spacing." Proc Natl Acad Sci U S A 93(17);8858-62. PMID: 8799117

Dove01: Dove SL, Hochschild A (2001). "Bacterial two-hybrid analysis of interactions between region 4 of the sigma(70) subunit of RNA polymerase and the transcriptional regulators Rsd from Escherichia coli and AlgQ from Pseudomonas aeruginosa." J Bacteriol 183(21);6413-21. PMID: 11591686

Farewell98a: Farewell A, Kvint K, Nystrom T (1998). "Negative regulation by RpoS: a case of sigma factor competition." Mol Microbiol 29(4);1039-51. PMID: 9767572

Finn00: Finn RD, Orlova EV, Gowen B, Buck M, van Heel M (2000). "Escherichia coli RNA polymerase core and holoenzyme structures." EMBO J 19(24);6833-44. PMID: 11118218

Fujita87: Fujita N, Nomura T, Ishihama A (1987). "Promoter selectivity of Escherichia coli RNA polymerase. Purification and properties of holoenzyme containing the heat-shock sigma subunit." J Biol Chem 262(4);1855-9. PMID: 3543015

Ganguly12: Ganguly A, Chatterji D (2012). "A comparative kinetic and thermodynamic perspective of the σ-competition model in Escherichia coli." Biophys J 103(6);1325-33. PMID: 22995505

Gardella89: Gardella T, Moyle H, Susskind MM (1989). "A mutant Escherichia coli sigma 70 subunit of RNA polymerase with altered promoter specificity." J Mol Biol 206(4);579-90. PMID: 2661827

Gill91a: Gill SC, Yager TD, von Hippel PH (1991). "Escherichia coli sigma 70 and NusA proteins. II. Physical properties and self-association states." J Mol Biol 220(2);325-33. PMID: 1856862

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."

Gruber01: Gruber TM, Markov D, Sharp MM, Young BA, Lu CZ, Zhong HJ, Artsimovitch I, Geszvain KM, Arthur TM, Burgess RR, Landick R, Severinov K, Gross CA (2001). "Binding of the initiation factor sigma(70) to core RNA polymerase is a multistep process." Mol Cell 8(1);21-31. PMID: 11511357

Hudson09: Hudson BP, Quispe J, Lara-Gonzalez S, Kim Y, Berman HM, Arnold E, Ebright RH, Lawson CL (2009). "Three-dimensional EM structure of an intact activator-dependent transcription initiation complex." Proc Natl Acad Sci U S A 106(47);19830-5. PMID: 19903881

Huerta03: Huerta AM, Collado-Vides J (2003). "Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals." J Mol Biol 333(2);261-78. PMID: 14529615

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Kapanidis05: Kapanidis AN, Margeat E, Laurence TA, Doose S, Ho SO, Mukhopadhyay J, Kortkhonjia E, Mekler V, Ebright RH, Weiss S (2005). "Retention of transcription initiation factor sigma70 in transcription elongation: single-molecule analysis." Mol Cell 20(3);347-56. PMID: 16285917

Kulbachinskiy06: Kulbachinskiy A, Mustaev A (2006). "Region 3.2 of the sigma subunit contributes to the binding of the 3'-initiating nucleotide in the RNA polymerase active center and facilitates promoter clearance during initiation." J Biol Chem 281(27);18273-6. PMID: 16690607

Kumar93: Kumar A, Malloch RA, Fujita N, Smillie DA, Ishihama A, Hayward RS (1993). "The minus 35-recognition region of Escherichia coli sigma 70 is inessential for initiation of transcription at an "extended minus 10" promoter." J Mol Biol 232(2);406-18. PMID: 8345519

Kumar94: Kumar A, Grimes B, Fujita N, Makino K, Malloch RA, Hayward RS, Ishihama A (1994). "Role of the sigma 70 subunit of Escherichia coli RNA polymerase in transcription activation." J Mol Biol 235(2);405-13. PMID: 8289270

Lupski83: Lupski JR, Smiley BL, Godson GN (1983). "Regulation of the rpsU-dnaG-rpoD macromolecular synthesis operon and the initiation of DNA replication in Escherichia coli K-12." Mol Gen Genet 1983;189(1);48-57. PMID: 6222240

Lupski84: Lupski JR, Ruiz AA, Godson GN (1984). "Promotion, termination, and anti-termination in the rpsU-dnaG-rpoD macromolecular synthesis operon of E. coli K-12." Mol Gen Genet 1984;195(3);391-401. PMID: 6206376

Maciag11: Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P (2011). "In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements." Nucleic Acids Res 39(13);5338-55. PMID: 21398637

Maeda00: Maeda H, Fujita N, Ishihama A (2000). "Competition among seven Escherichia coli sigma subunits: relative binding affinities to the core RNA polymerase." Nucleic Acids Res 28(18);3497-503. PMID: 10982868

Magnusson03: Magnusson LU, Nystrom T, Farewell A (2003). "Underproduction of sigma 70 mimics a stringent response. A proteome approach." J Biol Chem 278(2);968-73. PMID: 12421813

Malhotra96: Malhotra A, Severinova E, Darst SA (1996). "Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase." Cell 87(1);127-36. PMID: 8858155

McMahan99: McMahan SA, Burgess RR (1999). "Mapping protease susceptibility sites on the Escherichia coli transcription factor sigma70." Biochemistry 38(38);12424-31. PMID: 10493811

Mooney03: Mooney RA, Landick R (2003). "Tethering sigma70 to RNA polymerase reveals high in vivo activity of sigma factors and sigma70-dependent pausing at promoter-distal locations." Genes Dev 17(22);2839-51. PMID: 14630944

Nickels04: Nickels BE, Mukhopadhyay J, Garrity SJ, Ebright RH, Hochschild A (2004). "The sigma 70 subunit of RNA polymerase mediates a promoter-proximal pause at the lac promoter." Nat Struct Mol Biol 11(6);544-50. PMID: 15122345

Nickels05: Nickels BE, Garrity SJ, Mekler V, Minakhin L, Severinov K, Ebright RH, Hochschild A (2005). "The interaction between sigma70 and the beta-flap of Escherichia coli RNA polymerase inhibits extension of nascent RNA during early elongation." Proc Natl Acad Sci U S A 102(12);4488-93. PMID: 15761057

Osawa81: Osawa T, Yura T (1981). "Effects of reduced amount of RNA polymerase sigma factor on gene expression and growth of Escherichia coli: studies of the rpoD450 (amber) mutation." Mol Gen Genet 184(2);166-73. PMID: 7035833

Ozaki91: Ozaki M, Wada A, Fujita N, Ishihama A (1991). "Growth phase-dependent modification of RNA polymerase in Escherichia coli." Mol Gen Genet 230(1-2);17-23. PMID: 1745227

Poznanski03: Poznanski J, Bolewska K, Zhukov I, Wierzchowski KL (2003). "Characterization of the low pH solution structure and dynamics of the region 4 of Escherichia coli RNA polymerase sigma70 subunit." Biochemistry 42(46);13438-48. PMID: 14621989

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

Rhodius00: Rhodius VA, Busby SJ (2000). "Interactions between activating region 3 of the Escherichia coli cyclic AMP receptor protein and region 4 of the RNA polymerase sigma(70) subunit: application of suppression genetics." J Mol Biol 299(2);311-24. PMID: 10860740

Sanderson03: Sanderson A, Mitchell JE, Minchin SD, Busby SJ (2003). "Substitutions in the Escherichia coli RNA polymerase sigma70 factor that affect recognition of extended -10 elements at promoters." FEBS Lett 544(1-3);199-205. PMID: 12782316

Sharma08a: Sharma UK, Chatterji D (2008). "Differential mechanisms of binding of anti-sigma factors Escherichia coli Rsd and bacteriophage T4 AsiA to E. coli RNA polymerase lead to diverse physiological consequences." J Bacteriol 190(10);3434-43. PMID: 18359804

Siegele89: Siegele DA, Hu JC, Walter WA, Gross CA (1989). "Altered promoter recognition by mutant forms of the sigma 70 subunit of Escherichia coli RNA polymerase." J Mol Biol 206(4);591-603. PMID: 2661828

Silverstone72: Silverstone AE, Goman M, Scaife JG (1972). "ALT: a new factor involved in the synthesis of RNA by Escherichia coli." Mol Gen Genet 118(3);223-34. PMID: 4343249

Traviglia99: Traviglia SL, Datwyler SA, Yan D, Ishihama A, Meares CF (1999). "Targeted protein footprinting: where different transcription factors bind to RNA polymerase." Biochemistry 38(48);15774-8. PMID: 10625443

Typas05: Typas A, Hengge R (2005). "Differential ability of sigma(s) and sigma70 of Escherichia coli to utilize promoters containing half or full UP-element sites." Mol Microbiol 55(1);250-60. PMID: 15612932

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

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

UniProt14: UniProt Consortium (2014). "UniProt version 2014-01 released on 2014-01-01 00:00:00." Database.

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

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

Wade04: Wade JT, Struhl K (2004). "Association of RNA polymerase with transcribed regions in Escherichia coli." Proc Natl Acad Sci U S A 101(51);17777-82. PMID: 15596728

Yajnik93: Yajnik V, Godson GN (1993). "Selective decay of Escherichia coli dnaG messenger RNA is initiated by RNase E." J Biol Chem 1993;268(18);13253-60. PMID: 7685758

Yamamoto09: Yamamoto N, Nakahigashi K, Nakamichi T, Yoshino M, Takai Y, Touda Y, Furubayashi A, Kinjyo S, Dose H, Hasegawa M, Datsenko KA, Nakayashiki T, Tomita M, Wanner BL, Mori H (2009). "Update on the Keio collection of Escherichia coli single-gene deletion mutants." Mol Syst Biol 5;335. PMID: 20029369

Young01: Young BA, Anthony LC, Gruber TM, Arthur TM, Heyduk E, Lu CZ, Sharp MM, Heyduk T, Burgess RR, Gross CA (2001). "A coiled-coil from the RNA polymerase beta' subunit allosterically induces selective nontemplate strand binding by sigma(70)." Cell 105(7);935-44. PMID: 11439189

Young04: Young BA, Gruber TM, Gross CA (2004). "Minimal machinery of RNA polymerase holoenzyme sufficient for promoter melting." Science 303(5662);1382-4. PMID: 14988563

Yu08: Yu BJ, Kim JA, Moon JH, Ryu SE, Pan JG (2008). "The diversity of lysine-acetylated proteins in Escherichia coli." J Microbiol Biotechnol 18(9);1529-36. PMID: 18852508

Yuan08a: Yuan AH, Gregory BD, Sharp JS, McCleary KD, Dove SL, Hochschild A (2008). "Rsd family proteins make simultaneous interactions with regions 2 and 4 of the primary sigma factor." Mol Microbiol 70(5);1136-51. PMID: 18826409

Zenkin07: Zenkin N, Kulbachinskiy A, Yuzenkova Y, Mustaev A, Bass I, Severinov K, Brodolin K (2007). "Region 1.2 of the RNA polymerase sigma subunit controls recognition of the -10 promoter element." EMBO J 26(4);955-64. PMID: 17268549

Zhi03: Zhi H, Jin DJ (2003). "Purification of highly-active and soluble Escherichia coli sigma 70 polypeptide overproduced at low temperature." Methods Enzymol 370;174-80. PMID: 14712643

Other References Related to Gene Regulation

Dartigalongue01: Dartigalongue C, Missiakas D, Raina S (2001). "Characterization of the Escherichia coli sigma E regulon." J Biol Chem 276(24);20866-75. PMID: 11274153

Lemke11: Lemke JJ, Sanchez-Vazquez P, Burgos HL, Hedberg G, Ross W, Gourse RL (2011). "Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA." Proc Natl Acad Sci U S A 108(14);5712-7. PMID: 21402902

Marzan13: Marzan LW, Hasan CM, Shimizu K (2013). "Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant." Arch Microbiol 195(3);161-71. PMID: 23274360

Nesin88: Nesin M, Lupski JR, Godson GN (1988). "Role of the 5' upstream sequence and tandem promoters in regulation of the rpsU-dnaG-rpoD macromolecular synthesis operon." J Bacteriol 170(12);5759-64. PMID: 2848013

Taylor84: Taylor WE, Straus DB, Grossman AD, Burton ZF, Gross CA, Burgess RR (1984). "Transcription from a heat-inducible promoter causes heat shock regulation of the sigma subunit of E. coli RNA polymerase." Cell 1984;38(2);371-81. PMID: 6380764

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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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