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Escherichia coli K-12 substr. MG1655 Polypeptide: RNA polymerase, β subunit



Gene: rpoB Accession Numbers: EG10894 (EcoCyc), b3987, ECK3978

Synonyms: sdgB, tabD, stv, stl, ftsR, groN, nitB, rif, ron

Regulation Summary Diagram: ?

Component of:
RNA polymerase, core enzyme (extended summary available)
RNA polymerase sigma 24
RNA polymerase sigma 19 (summary available)
RNA polymerase sigma 28
RNA polymerase sigma S
RNA polymerase sigma 32
RNA polymerase sigma 54
RNA polymerase sigma 70

Summary:
Along with its β' partner, the β subunit of is integrally involved in the enzymatic function of RNA polymerase.

Both the β and β' subunits interact with DNA and may contribute to the polymerase active site [Chenchik82, Simpson79, Ross93, Kashlev90, Landick90]. Two conserved areas near the carboxy-terminus of RpoB are required for RNA polymerase assembly [Wang97b].

RpoB has a "flexible flap" element that contacts sigma factors and is either involved in or required for transcription by various RNA polymerase holoenzyme complexes [Kuznedelov02, Wigneshweraraj03]. These interactions are mediated via a hydrophic patch on the flap element [Geszvain04].

Gene Citations: [Steward91, Fukuda83, Barry80]

Locations: cytosol, membrane

Map Position: [4,179,268 -> 4,183,296] (90.08 centisomes)
Length: 4029 bp / 1342 aa

Molecular Weight of Polypeptide: 150.63 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013041 , CGSC:233 , DIP:DIP-35777N , EchoBASE:EB0887 , EcoGene:EG10894 , EcoliWiki:b3987 , Mint:MINT-1222430 , ModBase:P0A8V2 , OU-Microarray:b3987 , PortEco:rpoB , PR:PRO_000023845 , Pride:P0A8V2 , Protein Model Portal:P0A8V2 , RefSeq:NP_418414 , RegulonDB:EG10894 , SMR:P0A8V2 , String:511145.b3987 , Swiss-Model:P0A8V2 , UniProt:P0A8V2

Relationship Links: InterPro:IN-FAMILY:IPR007120 , InterPro:IN-FAMILY:IPR007121 , InterPro:IN-FAMILY:IPR007641 , InterPro:IN-FAMILY:IPR007642 , InterPro:IN-FAMILY:IPR007644 , InterPro:IN-FAMILY:IPR007645 , InterPro:IN-FAMILY:IPR010243 , InterPro:IN-FAMILY:IPR014724 , InterPro:IN-FAMILY:IPR015712 , InterPro:IN-FAMILY:IPR019462 , Panther:IN-FAMILY:PTHR20856 , Panther:IN-FAMILY:PTHR20856:SF3 , PDB:Structure:3IYD , PDB:Structure:3LTI , PDB:Structure:3LU0 , PDB:Structure:3T72 , PDB:Structure:3TBI , PDB:Structure:4IGC , PDB:Structure:4JK1 , PDB:Structure:4JK2 , PDB:Structure:4KMU , PDB:Structure:4KN4 , PDB:Structure:4KN7 , Pfam:IN-FAMILY:PF00562 , Pfam:IN-FAMILY:PF04560 , Pfam:IN-FAMILY:PF04561 , Pfam:IN-FAMILY:PF04563 , Pfam:IN-FAMILY:PF04565 , Pfam:IN-FAMILY:PF10385 , Prosite:IN-FAMILY:PS01166

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Arifuzzaman06, Butland05, Weerasekera07]
GO:0003677 - DNA binding Inferred by computational analysis [GOA06, GOA01]
GO:0003899 - DNA-directed RNA polymerase activity Inferred by computational analysis [UniProtGOA11, GOA06, GOA01a, GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0016779 - nucleotidyltransferase activity Inferred by computational analysis [UniProtGOA11]
GO:0032549 - ribonucleoside binding Inferred by computational analysis [GOA01]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Lasserre06]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0016020 - membrane Inferred from experiment [Lasserre06]

MultiFun Terms: information transfer RNA related Transcription related

Essentiality data for rpoB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Credits:
Last-Curated ? 03-Jul-2006 by Shearer A , SRI International


Subunit of: RNA polymerase, core enzyme

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

Component of:
RNA polymerase sigma 24
RNA polymerase sigma 19 (summary available)
RNA polymerase sigma 28
RNA polymerase sigma S
RNA polymerase sigma 32
RNA polymerase sigma 54
RNA polymerase sigma 70

Summary:
RNA polymerase carries out DNA-dependent RNA synthesis, transcribing genes into RNAs. The core polymerase, consisting of two alpha, one beta and one beta' subunit, binds to one of several sigma factors to form an RNA polymerase holoenzyme that can then initiate transcription at a target promoter. Following initiation, the sigma factor is discarded and the core polymerase transcribes RNA in a step called elongation, which ceases when it reaches a transcription termination site.

Initiation of RNA synthesis requires the RNA polymerase core enzyme, an associated sigma factor and a promoter site. RNA polymerase moves along the DNA during its promoter search, stopping to bind initially at one of a number of possible positions in the -55 to -5 position relative to the transcription start site [SakataSogawa04, Bokal95, Cowing89, Hofer82, Kovacic87, Mecsas91, Schickor90, Hawley83]. When a -35 sequence is present, the sigma factor makes first contact contact there [Buckle99]. Following initial contact, the binding interaction spreads to the +20 position and involves the sigma, beta and beta' subunits [Cowing89, Hofer85, Mecsas91, Schickor90, Brodolin93, Buckle91, Gardella89, Harrison82, Park80, Simpson79]. Binding appears to involve contact between RNA polymerase and both helix faces as the DNA is wrapped around the protein [Mecsas91, Schickor90, Darst89, Rees93, Garland99, Rivetti99]. Once binding is complete, the DNA helix is opened starting at the -12 to -10 positions and proceeding to around the +2 position [DuvalValentin86, Kirkegaard83, SasseDwight89, Siebenlist79, Suh93, Tsujikawa02].

Several factors modulate the strength of a promoter. Promoter sequence can affect initiation time and the amount of transcript produced [Kobayashi90, Malan84]. Both the sequences of the -10 and -35 sites and the distance between them play into activity at a given promoter [Harley87, Lisser93, Ayers89, Hawley83, Mulligan85, Stefano82, Szoke87, Miksch05]. The -10 sequence alone is important for helix unwinding [NiedzielaMajka05]. For one class of promoters lacking a -10 sequence, activity depends on the presence of a -35 site and an extended TGn motif [HookBarnard06]. In addition to the sequence near the start site, upstream promoter elements (UPs) that occur from in the -40 to -60 region are very important for transcription from some promoters and can stimulate transcription even in the absence of sigma factors [Leirmo91, Newlands91, Rao94, Ross93, Strainic98, Fredrick97]. The carboxy-terminus of the alpha subunit binds UPs in the minor groove, though no conformational change occurs in the UP DNA [Blatter94, Ross93, Ross01, Heyduk01]. Generally, the effectiveness of a UP depends on its similarity to the consensus UP sequence of alternating A and T tracts and on its distance from the -35 site [Ross98, Tagami99]. The two alpha subunits of RNA polymerase bind in tandem to two helix turns of a typical UP [Murakami97]. Modifications that alter UP-promoter spacing by half a turn or one or two full turns abolish transcription [Meng01]. Finally, even for a promoter without a UP, the simple presence of upstream DNA strongly enhances transcription initiation [Davis05a].

Targeting to a specific promoter depends on the appropriate sigma factor [Burgess69, Hinkle72]. For more information, see each sigma factor holoenzyme complex.

Promoter clearance involves release of the promoter and loss of the sigma subunit, both usually occuring after 7-12 nucleotides of RNA transcript have been synthesized [Carpousis85, Hansen80, Krummel92, Straney87, Michalke69]. There may be several abortive attempts at elongation from a promoter before elongation proceeds [Carpousis80, Grachev80, Krummel89, Munson81, Straney87]. RNA polymerase can also slip when faced with an initial AT tract, leading to an extended UA tract in the transcript [Gulland92, Xiong93].

During elongation of the RNA transcript, one strand of DNA is transcribed without permanent disruption of the double helix [Geiduschek61]. Throughout elongation, about 18 bps of double helix are unwound, with about 30-40 bps of total DNA sequence in contact with the polymerase, rather than the 75 bps or more of contact seen during initiation [Gamper82, SasseDwight89, Lee92, Krummel92a, Simpson79]. DNA continues to be bent by RNA polymerase during transcription [Schulz98a, Zaychikov99]. Though one study indicates as few as 3 bp of stable DNA-RNA hybrid may exist during transcription, most results point to a hybrid of 8-10 bps being required to keep RNA polymerase attached to substrate DNA [Milan99, Lee92, Komissarova98, Sidorenkov98]. This may serve as a proofreading mechanism for the polymerase, as a single mismatch forces it to slide backwards from the point of the mismatch to regain a stable hybrid [Nudler97]. Following this slide, transcription elongation factor GreA and transcription elongation factor GreB induce cleavage near the 3' end of the transcript to clear the mismatch [Borukhov92, Borukhov93].

Transcription elongation is enhanced by transcription termination factor NusG.

Measured elongation rates for individual RNA polymerases and for transcription in general vary widely, from 0.5-50 nucleotides per second [Mosteller70, Morgan83, Vogel94, Kasas97, Davenport00]. rRNA can be synthesized at up to 90 nucleotides per second [Vogel94]. At the molecular level, RNA polymerase progresses one bp per nucleotide added to its transcript, though this movement appears to be by Brownian ratchet rather than force generated by nucleotide addition itself [Wang98d, Abbondanzieri05]. At larger scales, the heterogeneity of translation rates appears to be due to variation in the frequency and duration of transcriptional pausing, which can vary for each polymerase [Adelman02, TolicNorrelykke04]. Notably, although many in vitro measurements of polymerase rate are done with single molecules, when multiple polymerases are transcribing the same DNA, the trailing proteins push the leader through pauses and blocks, increasing the overall transcription rate [Epshtein03, Epshtein03a]. Additionally, should two polymerases transcribing in opposing directions ever collide, one will typically shove the other backwards along the DNA until both complexes stall [Crampton06].

Though RNA polymerase generally proceeds as a unit, sometimes it appears to undergo inchworm motion as it approaches pause and termination points, with its carboxy-terminus advancing as the amino-terminus remains still [Nudler94, Wang95a, Nudler95]. RNA polymerase appears to backtrack up to 5 bp at pause sites, taking from 20 seconds to more than half an hour to restart transcription, though at least one study suggests that no backtracking occurs [Komissarova97, Shaevitz03, Neuman03]. Transcriptional pause sites typically occur shortly after a stretch of sequence that can generate an RNA hairpin or duplex once it is transcribed [Levin87, Artsimovitch98]. Such hairpins may stall RNA polymerase via electrostatic interaction with part of the polymerase, as well as via the action of transcription termination/antitermination L factor [Chan93, Toulokhonov01]. The interplay between exit channel duplexes and nucleotide addition in the active site is mediated through the polymerase clamp conformation [Hein14].

Pausing not associated with RNA hairpin elements also occurs at pause elements (PE) which disfavor translocation of the elongating polymerase from the pre- to the posttranslocated state. The PE consensus sequence was identified by native elongating transcript sequencing (NET-seq) [Larson14, Vvedenskaya14, Churchman11] (comment by [Roberts14] .

Transcription termination may depend on transcription termination factor Rho or be Rho-independent. Rho-independent termination appears to depend on a GC-rich stretch of sequence that yields a stem-loop after transcription, followed by an A-rich segment on the template strand [Brendel86, dAubenton90, Cheng91, Mahadevan87, Ryan83, Yang89]. This A-rich tract may aid release by creating weak hybridization with the U-tract generated in the transcript [Martin80]. Rho-independent termination has also been identified in the absence of stem-loop formation [Yarnell99].

Termination can, in turn, be prevented by such proteins as BglG transcriptional antiterminator and transcription antitermination protein NusB, as well as the presence of a boxA element (TGCTCTTTAACA) downstream from the promoter [NussbaumShochat99, Houman90, Mahadevan87, Squires93, Berg89, Li84].

The RNA polymerase core is assembled via dimerization of its alpha subunit, followed by addition of beta and then beta' [Ishihama81]. Extensive examination of the core and holoenzymes via cryo-electron microscopy and small-angle X-ray scattering show that the enzyme is structurally flexible and undergoes conformational change on interacting with sigma and on binding DNA [Darst89, Darst98, Darst02, Finn00, Ray05]. The enzyme has a "lid" element that is required for initiation, as well as a loop region that is involved in promoter clearance and interaction with the nascent strand [Toulokhonov06, Kulbachinskiy06]. Mutational analysis has been used to develop a model of nucleotide discrimination by the core enzyme [Holmes06].

Credits:
Last-Curated ? 03-Jul-2006 by Shearer A , SRI International


Enzymatic reaction of: RNA polymerase

EC Number: 2.7.7.6

a nucleoside triphosphate + RNA(n) <=> RNA(n+1) + diphosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

Reversibility of this reaction is unspecified.


Subunit of: RNA polymerase sigma 24

Synonyms: RNA polymerase sigma E, RNA polymerase sigma 24 holoenzyme

Subunit composition of RNA polymerase sigma 24 = [(RpoA)2(RpoC)(RpoB)][RpoE]
         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 24 (sigma E) factor = RpoE (extended summary available)

Controlled Transcription Units (82 total): ?

Notes:


Subunit of: RNA polymerase sigma 19

Synonyms: sigma fecI

Subunit composition of RNA polymerase sigma 19 = [(RpoA)2(RpoC)(RpoB)][FecI]
         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 19 factor = FecI (extended summary available)

Summary:

Symmetry: Inverted Repeat

Controlled Transcription Units (1 total): ?

Notes:


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:


Subunit of: RNA polymerase sigma S

Synonyms: RNA polymerase sigma 38, RNA polymerase sigma 38 holoenzyme

Subunit composition of RNA polymerase sigma S = [(RpoA)2(RpoC)(RpoB)][RpoS]
         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 S (sigma 38) factor = RpoS (extended summary available)

Controlled Transcription Units (206 total): ?

Notes:


Subunit of: RNA polymerase sigma 32

Synonyms: RNA polymerase sigma 32 holoenzyme, RNA polymerase sigma H

Subunit composition of RNA polymerase sigma 32 = [(RpoA)2(RpoC)(RpoB)][RpoH]
         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 32 (sigma H) factor = RpoH (extended summary available)

Controlled Transcription Units (97 total): ?

Notes:


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): ?

Notes:


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 Homology Motif Citations Comment
Sequence-Conflict 4  
[Fujiki75, UniProt14]
Alternate sequence: S → R; UniProt: (in Ref. 10; AA sequence).
Sequence-Conflict 106 -> 107  
[Delcuve80, UniProt10a]
Alternate sequence: ER → G; UniProt: (in Ref. 6; CAA23629);
Sequence-Conflict 384 -> 391  
[Delcuve80, UniProt10a]
Alternate sequence: LFENLFFS → CSRTCSSPT; UniProt: (in Ref. 6);
Sequence-Conflict 516  
[Ovchinnikov80, Ovchinnikov81, UniProt11]
Alternate sequence: D → V; UniProt: (in Ref. 1 and 10).
Mutagenesis-Variant 813  
[Lee91a, UniProt11]
Alternate sequence: E → K; UniProt: Disrupts the enzyme's active center.
Acetylation-Modification 1022  
[Zhang09a, UniProt11]
UniProt: N6-acetyllysine.
Conserved-Region 1104 -> 1107 PSRM
[Polyakov99]
Substrate binding is negatively impacted by mutations in this conserved motif.
Acetylation-Modification 1200  
[Zhang09a, UniProt11]
UniProt: N6-acetyllysine.
Conserved-Region 1269 -> 1274 RFGEME
[Polyakov99]
Mutations in this conserved motif negatively impact substrate binding.


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3987 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10894; confirmed by SwissProt match.


References

Abbondanzieri05: Abbondanzieri EA, Greenleaf WJ, Shaevitz JW, Landick R, Block SM (2005). "Direct observation of base-pair stepping by RNA polymerase." Nature 438(7067);460-5. PMID: 16284617

Adelman02: Adelman K, La Porta A, Santangelo TJ, Lis JT, Roberts JW, Wang MD (2002). "Single molecule analysis of RNA polymerase elongation reveals uniform kinetic behavior." Proc Natl Acad Sci U S A 99(21);13538-43. PMID: 12370445

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

Artsimovitch98: Artsimovitch I, Landick R (1998). "Interaction of a nascent RNA structure with RNA polymerase is required for hairpin-dependent transcriptional pausing but not for transcript release." Genes Dev 12(19);3110-22. PMID: 9765211

Ayers89: Ayers DG, Auble DT, deHaseth PL (1989). "Promoter recognition by Escherichia coli RNA polymerase. Role of the spacer DNA in functional complex formation." J Mol Biol 207(4);749-56. PMID: 2668539

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

Barry80: Barry G, Squires C, Squires CL (1980). "Attenuation and processing of RNA from the rplJL--rpoBC transcription unit of Escherichia coli." Proc Natl Acad Sci U S A 77(6);3331-5. PMID: 6158044

Berg89: Berg KL, Squires C, Squires CL (1989). "Ribosomal RNA operon anti-termination. Function of leader and spacer region box B-box A sequences and their conservation in diverse micro-organisms." J Mol Biol 209(3);345-58. PMID: 2479752

Blatter94: Blatter EE, Ross W, Tang H, Gourse RL, Ebright RH (1994). "Domain organization of RNA polymerase alpha subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding." Cell 78(5);889-96. PMID: 8087855

Bokal95: Bokal AJ, Ross W, Gourse RL (1995). "The transcriptional activator protein FIS: DNA interactions and cooperative interactions with RNA polymerase at the Escherichia coli rrnB P1 promoter." J Mol Biol 245(3);197-207. PMID: 7844812

Borukhov92: Borukhov S, Polyakov A, Nikiforov V, Goldfarb A (1992). "GreA protein: a transcription elongation factor from Escherichia coli." Proc Natl Acad Sci U S A 89(19);8899-902. PMID: 1384037

Borukhov93: Borukhov S, Sagitov V, Goldfarb A (1993). "Transcript cleavage factors from E. coli." Cell 72(3);459-66. PMID: 8431948

Brendel86: Brendel V, Hamm GH, Trifonov EN (1986). "Terminators of transcription with RNA polymerase from Escherichia coli: what they look like and how to find them." J Biomol Struct Dyn 3(4);705-23. PMID: 3078109

Brodolin93: Brodolin KL, Studitsky VM, Mirzabekov AD (1993). "Conformational changes in E. coli RNA polymerase during promoter recognition." Nucleic Acids Res 21(24);5748-53. PMID: 8284224

Buckle91: Buckle M, Geiselmann J, Kolb A, Buc H (1991). "Protein-DNA cross-linking at the lac promoter." Nucleic Acids Res 19(4);833-40. PMID: 2017366

Buckle99: Buckle M, Pemberton IK, Jacquet MA, Buc H (1999). "The kinetics of sigma subunit directed promoter recognition by E. coli RNA polymerase." J Mol Biol 285(3);955-64. PMID: 9918716

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

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

Carpousis80: Carpousis AJ, Gralla JD (1980). "Cycling of ribonucleic acid polymerase to produce oligonucleotides during initiation in vitro at the lac UV5 promoter." Biochemistry 19(14);3245-53. PMID: 6996702

Carpousis85: Carpousis AJ, Gralla JD (1985). "Interaction of RNA polymerase with lacUV5 promoter DNA during mRNA initiation and elongation. Footprinting, methylation, and rifampicin-sensitivity changes accompanying transcription initiation." J Mol Biol 183(2);165-77. PMID: 2409292

Chan93: Chan CL, Landick R (1993). "Dissection of the his leader pause site by base substitution reveals a multipartite signal that includes a pause RNA hairpin." J Mol Biol 233(1);25-42. PMID: 8377190

Chenchik82: Chenchik AA, Bibilashvili RSh, Mirzabekov AD, Shik VV (1982). "[Contacts of Escherichia coli RNA polymerase subunits with nucleotides of lacUV5 promoter]." Mol Biol (Mosk) 16(1);35-46. PMID: 7040939

Cheng91: Cheng SW, Lynch EC, Leason KR, Court DL, Shapiro BA, Friedman DI (1991). "Functional importance of sequence in the stem-loop of a transcription terminator." Science 254(5035);1205-7. PMID: 1835546

Churchman11: Churchman LS, Weissman JS (2011). "Nascent transcript sequencing visualizes transcription at nucleotide resolution." Nature 469(7330);368-73. PMID: 21248844

Cowing89: Cowing DW, Mecsas J, Record MT, Gross CA (1989). "Intermediates in the formation of the open complex by RNA polymerase holoenzyme containing the sigma factor sigma 32 at the groE promoter." J Mol Biol 210(3);521-30. PMID: 2693737

Crampton06: Crampton N, Bonass WA, Kirkham J, Rivetti C, Thomson NH (2006). "Collision events between RNA polymerases in convergent transcription studied by atomic force microscopy." Nucleic Acids Res 34(19);5416-25. PMID: 17012275

Darst02: Darst SA, Opalka N, Chacon P, Polyakov A, Richter C, Zhang G, Wriggers W (2002). "Conformational flexibility of bacterial RNA polymerase." Proc Natl Acad Sci U S A 99(7);4296-301. PMID: 11904365

Darst89: Darst SA, Kubalek EW, Kornberg RD (1989). "Three-dimensional structure of Escherichia coli RNA polymerase holoenzyme determined by electron crystallography." Nature 340(6236);730-2. PMID: 2671751

Darst98: Darst SA, Polyakov A, Richter C, Zhang G (1998). "Insights into Escherichia coli RNA polymerase structure from a combination of x-ray and electron crystallography." J Struct Biol 124(2-3);115-22. PMID: 10049799

dAubenton90: d'Aubenton Carafa Y, Brody E, Thermes C (1990). "Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures." J Mol Biol 216(4);835-58. PMID: 1702475

Davenport00: Davenport RJ, Wuite GJ, Landick R, Bustamante C (2000). "Single-molecule study of transcriptional pausing and arrest by E. coli RNA polymerase." Science 287(5462);2497-500. PMID: 10741971

Davis05a: Davis CA, Capp MW, Record MT, Saecker RM (2005). "The effects of upstream DNA on open complex formation by Escherichia coli RNA polymerase." Proc Natl Acad Sci U S A 102(2);285-90. PMID: 15626761

Delcuve80: Delcuve G, Downing W, Lewis H, Dennis PP (1980). "Nucleotide sequence of the proximal portion of the RNA polymerase beta subunit gene of Escherichia coli." Gene 11(3-4);367-73. PMID: 7011900

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

DuvalValentin86: Duval-Valentin G, Ehrlich R (1986). "Interaction between E. coli RNA polymerase and the tetR promoter from pSC101: homologies and differences with other E. coli promoter systems from close contact point studies." Nucleic Acids Res 14(5);1967-83. PMID: 3960716

Epshtein03: Epshtein V, Toulme F, Rahmouni AR, Borukhov S, Nudler E (2003). "Transcription through the roadblocks: the role of RNA polymerase cooperation." EMBO J 22(18);4719-27. PMID: 12970184

Epshtein03a: Epshtein V, Nudler E (2003). "Cooperation between RNA polymerase molecules in transcription elongation." Science 300(5620);801-5. PMID: 12730602

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Other References Related to Gene Regulation

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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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