Escherichia coli K-12 substr. MG1655 Protein: RNA polymerase sigma 70
Inferred from experiment

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

Superclasses: an RNA polymerase

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)

Gene-Reaction Schematic

Gene-Reaction Schematic

This protein controls transcription of 1054 transcription units (not shown).

Component enzyme of RNA polymerase sigma 70 : RNA polymerase, core enzyme

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

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 [Davis05].

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, Lee92a, Krummel92a, Simpson79]. DNA continues to be bent by RNA polymerase during transcription [Schulz98, 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, Lee92a, 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 [Wang98e, 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, Yang89a]. 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].

Subunit of RNA polymerase, core enzyme: RNA polymerase, α subunit

Synonyms: Sez, Phs, Pez, RpoA

Gene: rpoA Accession Numbers: EG10893 (EcoCyc), b3295, ECK3282

Locations: cytosol, membrane

Sequence Length: 329 AAs

Molecular Weight: 36.512 kD (from nucleotide sequence)

GO Terms:
Biological Process:
Inferred by computational analysisGO:0006351 - transcription, DNA-templated [GOA06, GOA01a]
Molecular Function:
Inferred from experimentGO:0005515 - protein binding [Rippa10, Arifuzzaman06, Butland05]
Inferred from experimentGO:0008270 - zinc ion binding [Groomes91]
Inferred by computational analysisGO:0003677 - DNA binding [GOA06, GOA01a]
Inferred by computational analysisGO:0003899 - DNA-directed RNA polymerase activity [UniProtGOA11a, GOA06, GOA01, GOA01a]
Inferred by computational analysisGO:0016740 - transferase activity [UniProtGOA11a]
Inferred by computational analysisGO:0016779 - nucleotidyltransferase activity [UniProtGOA11a]
Inferred by computational analysisGO:0046983 - protein dimerization activity [GOA01a]
Cellular Component:
Inferred from experimentGO:0005737 - cytoplasm [Lasserre06]
Inferred from experimentInferred by computational analysisGO:0005829 - cytosol [DiazMejia09, Ishihama08, LopezCampistrou05]
Inferred from experimentGO:0016020 - membrane [Lasserre06]

MultiFun Terms: information transferRNA relatedTranscription related

Unification Links: DIP:DIP-35879N, EcoliWiki:b3295, Mint:MINT-6478247, ModBase:P0A7Z4, PR:PRO_000023844, Pride:P0A7Z4, Protein Model Portal:P0A7Z4, RefSeq:NP_417754, SMR:P0A7Z4, UniProt:P0A7Z4

Relationship Links: InterPro:IN-FAMILY:IPR009025, InterPro:IN-FAMILY:IPR011260, InterPro:IN-FAMILY:IPR011262, InterPro:IN-FAMILY:IPR011263, InterPro:IN-FAMILY:IPR011773, PDB:Structure:1BDF, PDB:Structure:1COO, PDB:Structure:1LB2, PDB:Structure:1XS9, PDB:Structure:3IYD, PDB:Structure:3K4G, PDB:Structure:3LU0, PDB:Structure:3N4M, PDB:Structure:3N97, PDB:Structure:4JK1, PDB:Structure:4JK2, PDB:Structure:4KMU, PDB:Structure:4KN4, PDB:Structure:4KN7, PDB:Structure:4MEX, PDB:Structure:4MEY, PDB:Structure:4YG2, PDB:Structure:4YLN, PDB:Structure:4YLO, PDB:Structure:4YLP, Pfam:IN-FAMILY:PF01000, Pfam:IN-FAMILY:PF01193, Pfam:IN-FAMILY:PF03118, ProDom:IN-FAMILY:PD001179, Smart:IN-FAMILY:SM00662

RpoA is the α subunit of the RNA polymerase core enzyme. It consists of two domains connected by a flexible linker.

The RpoA amino-terminus is both necessary and sufficient for dimerization of RpoA and subsequent assembly of the RNA polymerase core complex [Zhang98c]. The amino-terminus has been analyzed both by NMR and via a 2.5 Å resolution cystral structure [Otomo00, Zhang98c].

The amino-terminal and carboxy-terminal domains of RpoA are connected by a flexible linker, which has been shown to affect transcription in a promoter-dependent fashion [Jeon97, Fujita00, Meng00].

The carboxy-terminal domain of RpoA is involved in antitermination, rho-dependent termination, and is a target for interactions with transcription termination/antitermination L factor that control termination and pausing [Schauer96, Kainz98]. Interaction with the RpoA carboxy-terminal domain activates RNA binding by transcription termination/antitermination L factor [Mah00]. The RpoA carboxy-terminal domain is also required for some kinds of transcriptional activation and plays a role in some transcriptional initiation [Zou97, Burns99].

Essentiality data for rpoA knockouts:

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

Subunit of RNA polymerase, core enzyme: RNA polymerase, β' subunit

Synonyms: TabB, RpoC

Gene: rpoC Accession Numbers: EG10895 (EcoCyc), b3988, ECK3979

Locations: cytosol, membrane

Sequence Length: 1407 AAs

Molecular Weight: 155.16 kD (from nucleotide sequence)

GO Terms:
Biological Process:
Inferred by computational analysisGO:0006351 - transcription, DNA-templated [GOA06, GOA01a]
Molecular Function:
Inferred from experimentGO:0005515 - protein binding [Arifuzzaman06, Weerasekera07, Arthur00, Butland05]
Inferred by computational analysisGO:0003677 - DNA binding [GOA06, GOA01a]
Inferred by computational analysisGO:0003899 - DNA-directed RNA polymerase activity [UniProtGOA11a, GOA06, GOA01, GOA01a]
Inferred by computational analysisGO:0016740 - transferase activity [UniProtGOA11a]
Inferred by computational analysisGO:0016779 - nucleotidyltransferase activity [UniProtGOA11a]
Cellular Component:
Inferred from experimentGO:0005737 - cytoplasm [Lasserre06]
Inferred from experimentInferred by computational analysisGO:0005829 - cytosol [DiazMejia09, Ishihama08]
Inferred from experimentGO:0016020 - membrane [Lasserre06]
Inferred by computational analysisGO:0000428 - DNA-directed RNA polymerase complex [Gaudet10]

MultiFun Terms: information transferRNA relatedTranscription related

Unification Links: DIP:DIP-35803N, EcoliWiki:b3988, Mint:MINT-1220667, ModBase:P0A8T7, PR:PRO_000023846, Pride:P0A8T7, Protein Model Portal:P0A8T7, RefSeq:NP_418415, SMR:P0A8T7, Swiss-Model:P0A8T7, UniProt:P0A8T7

Relationship Links: InterPro:IN-FAMILY:IPR000722, InterPro:IN-FAMILY:IPR006592, InterPro:IN-FAMILY:IPR007066, InterPro:IN-FAMILY:IPR007080, InterPro:IN-FAMILY:IPR007081, InterPro:IN-FAMILY:IPR007083, InterPro:IN-FAMILY:IPR012754, PDB:Structure:2AUK, PDB:Structure:2LMC, PDB:Structure:3IYD, PDB:Structure:3LU0, PDB:Structure:4IQZ, PDB:Structure:4JK1, PDB:Structure:4JK2, PDB:Structure:4KMU, PDB:Structure:4KN4, PDB:Structure:4KN7, PDB:Structure:4MEX, PDB:Structure:4MEY, PDB:Structure:4YG2, PDB:Structure:4YLN, PDB:Structure:4YLO, PDB:Structure:4YLP, Pfam:IN-FAMILY:PF00623, Pfam:IN-FAMILY:PF04983, Pfam:IN-FAMILY:PF04997, Pfam:IN-FAMILY:PF04998, Pfam:IN-FAMILY:PF05000, Smart:IN-FAMILY:SM00663

Along with its β partner, the β' subunit of is integrally involved in the enzymatic function of RNA polymerase, especially at the promoter melting stage.

Both the β and β' subunits interact with DNA and may contribute to the polymerase active site [Chenchik82, Simpson79, Ross93, Nedea99].

Though β' is not required for interaction with the initiating nucleotide, it binds RNA polymerase, sigma 70 (sigma D) factor and makes contact at the same points on the nontemplate strand as RNA polymerase, sigma 70 (sigma D) factor [Naryshkina01, Luo96, Arthur98, Brodolin00]. The minimal set of RNA polymerase components needed for promoter melting consists of the RpoC amino-terminus and a portion of a sigma factor [Young04]. The "jaw" domain of RpoC stabilizes the open promoter complex [Wigneshweraraj05].

RpoC is involved in chelating a magnesium ion that is required for RNA polymerase catalysis [Zaychikov96]. RpoC also coordinates a zinc ion that is required for it to maintain its functional conformation [Markov99].

The carboxy-terminus of RpoC interacts with DNA topoisomerase I, which must act on DNA to prevent excessive negative supercoiling in the wake of RNA polymerase [Cheng03].

Essentiality data for rpoC knockouts:

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

Subunit of RNA polymerase, core enzyme: RNA polymerase, β subunit

Synonyms: Stl, Stv, TabD, SdgB, Ron, Rif, NitB, GroN, FtsR, RpoB

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

Locations: cytosol, membrane

Sequence Length: 1342 AAs

Molecular Weight: 150.63 kD (from nucleotide sequence)

GO Terms:
Biological Process:
Inferred by computational analysisGO:0006351 - transcription, DNA-templated [GOA06, GOA01a]
Molecular Function:
Inferred from experimentGO:0005515 - protein binding [Rajagopala14, Arifuzzaman06, Butland05, Weerasekera07]
Inferred by computational analysisGO:0003677 - DNA binding [GOA06, GOA01a]
Inferred by computational analysisGO:0003899 - DNA-directed RNA polymerase activity [UniProtGOA11a, GOA06, GOA01, GOA01a]
Inferred by computational analysisGO:0016740 - transferase activity [UniProtGOA11a]
Inferred by computational analysisGO:0016779 - nucleotidyltransferase activity [UniProtGOA11a]
Inferred by computational analysisGO:0032549 - ribonucleoside binding [GOA01a]
Cellular Component:
Inferred from experimentGO:0005737 - cytoplasm [Lasserre06]
Inferred from experimentInferred by computational analysisGO:0005829 - cytosol [DiazMejia09, Ishihama08, LopezCampistrou05]
Inferred from experimentGO:0016020 - membrane [Lasserre06]
Inferred by computational analysisGO:0000428 - DNA-directed RNA polymerase complex [Gaudet10]

MultiFun Terms: information transferRNA relatedTranscription related

Unification Links: DIP:DIP-35777N, EcoliWiki:b3987, Mint:MINT-1222430, ModBase:P0A8V2, PR:PRO_000023845, Pride:P0A8V2, Protein Model Portal:P0A8V2, RefSeq:NP_418414, SMR:P0A8V2, 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, PDB:Structure:3IYD, PDB:Structure:3LTI, PDB:Structure:3LU0, PDB:Structure:3T72, PDB:Structure:3TBI, PDB:Structure:4JK1, PDB:Structure:4JK2, PDB:Structure:4KMU, PDB:Structure:4KN4, PDB:Structure:4KN7, PDB:Structure:4MEX, PDB:Structure:4MEY, PDB:Structure:4YG2, PDB:Structure:4YLN, PDB:Structure:4YLO, PDB:Structure:4YLP, 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

Along with its β' partner, the β subunit 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 [Wang97d].

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].

Essentiality data for rpoB knockouts:

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

Subunit of RNA polymerase sigma 70: RNA polymerase, sigma 70 (sigma D) factor

Synonyms: Alt, RpoD, sigma D factor, sigma 70 factor, σ70

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

Locations: cytosol

Sequence Length: 613 AAs

Molecular Weight: 70.263 kD (from nucleotide sequence)

GO Terms:
Biological Process:
Inferred from experimentGO:0009408 - response to heat [Chuang93]
Inferred by computational analysisGO:0001123 - transcription initiation from bacterial-type RNA polymerase promoter [GOA06]
Inferred by computational analysisGO:0006351 - transcription, DNA-templated [UniProtGOA11a]
Inferred by computational analysisGO:0006352 - DNA-templated transcription, initiation [GOA01a]
Inferred by computational analysisGO:0006355 - regulation of transcription, DNA-templated [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0010468 - regulation of gene expression [GOA06]
Molecular Function:
Inferred from experimentGO:0005515 - protein binding [Rajagopala14, Yuan08, Sharma08a, Dove01, Arifuzzaman06, Butland05, Arthur00]
Inferred from experimentInferred by computational analysisGO:0016987 - sigma factor activity [UniProtGOA11a, GOA06, GOA01a, Burgess69]
Inferred by computational analysisGO:0003677 - DNA binding [UniProtGOA11a, GOA06, GOA01a]
Inferred by computational analysisGO:0003700 - transcription factor activity, sequence-specific DNA binding [GOA01a]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005829 - cytosol [DiazMejia09, Ishihama08]
Inferred by computational analysisGO:0005737 - cytoplasm [UniProtGOA11, UniProtGOA11a, GOA06]

MultiFun Terms: information transferRNA relatedTranscription related
regulationgenetic unit regulatedstimulon
regulationtype of regulationtranscriptional levelsigma factors, anti-sigmafactors

Unification Links: DIP:DIP-10773N, EcoliWiki:b3067, Mint:MINT-1220595, ModBase:P00579, PR:PRO_000023847, Pride:P00579, Protein Model Portal:P00579, RefSeq:NP_417539, SMR:P00579, 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, InterPro:IN-FAMILY:IPR028630, 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, PDB:Structure:4LJZ, PDB:Structure:4LK0, PDB:Structure:4LK1, PDB:Structure:4LLG, PDB:Structure:4MEX, PDB:Structure:4MEY, PDB:Structure:4YFK, PDB:Structure:4YFN, PDB:Structure:4YFX, PDB:Structure:4YG2, PDB:Structure:4YLN, PDB:Structure:4YLO, PDB:Structure:4YLP, 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

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 [Maciag11a].

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 [Gill91, 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 [Chen03c]. 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 ]

Essentiality data for rpoD knockouts:

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


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

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

Arthur98: Arthur TM, Burgess RR (1998). "Localization of a sigma70 binding site on the N terminus of the Escherichia coli RNA polymerase beta' subunit." J Biol Chem 273(47);31381-7. PMID: 9813048

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

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

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

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

Brodolin00: Brodolin K, Mustaev A, Severinov K, Nikiforov V (2000). "Identification of RNA polymerase beta' subunit segment contacting the melted region of the lacUV5 promoter." J Biol Chem 275(5);3661-6. PMID: 10652363

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

Burns99: Burns HD, Ishihama A, Minchin SD (1999). "Open complex formation during transcription initiation at the Escherichia coli galP1 promoter: the role of the RNA polymerase alpha subunit at promoters lacking an UP-element." Nucleic Acids Res 27(9);2051-6. PMID: 10198440

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

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

Chen03c: 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

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

Cheng03: Cheng B, Zhu CX, Ji C, Ahumada A, Tse-Dinh YC (2003). "Direct interaction between Escherichia coli RNA polymerase and the zinc ribbon domains of DNA topoisomerase I." J Biol Chem 278(33);30705-10. PMID: 12788950

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

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

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

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

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

Davis05: 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

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

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

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

Fredrick97: Fredrick K, Helmann JD (1997). "RNA polymerase sigma factor determines start-site selection but is not required for upstream promoter element activation on heteroduplex (bubble) templates." Proc Natl Acad Sci U S A 94(10);4982-7. PMID: 9144176

Fujita00: Fujita N, Endo S, Ishihama A (2000). "Structural requirements for the interdomain linker of alpha subunit of Escherichia coli RNA polymerase." Biochemistry 39(20);6243-9. PMID: 10821700

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

Gamper82: Gamper HB, Hearst JE (1982). "A topological model for transcription based on unwinding angle analysis of E. coli RNA polymerase binary, initiation and ternary complexes." Cell 29(1);81-90. PMID: 6286146

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

Garland99: Garland CS, Tarien E, Nirmala R, Clark P, Rifkind J, Eichhorn GL (1999). "Curvature of dinucleotide poised for formation of trinucleotide in transcription with Escherichia coli RNA polymerase." Biochemistry 38(11);3421-5. PMID: 10079088

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

Geiduschek61: Geiduschek EP, Nakamoto T, Weiss SB (1961). "The enzymatic synthesis of RNA: complementary interaction with DNA." Proc Natl Acad Sci U S A 47;1405-15. PMID: 13704191

Geszvain04: Geszvain K, Gruber TM, Mooney RA, Gross CA, Landick R (2004). "A hydrophobic patch on the flap-tip helix of E.coli RNA polymerase mediates sigma(70) region 4 function." J Mol Biol 343(3);569-87. PMID: 15465046

Gill91: 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

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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."

Grachev80: Grachev MA, Zaychikov EF (1980). "Initiation by Escherichia coli RNA-polymerase: transformation of abortive to productive complex." FEBS Lett 115(1);23-6. PMID: 6156091

Groomes91: Groomes TE, Huang CT (1991). "Orthostatic hypotension after spinal cord injury: treatment with fludrocortisone and ergotamine." Arch Phys Med Rehabil 72(1);56-8. PMID: 1985624

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

Gulland92: Gulland U, Hillen W (1992). "The Tn10-encoded tetR mRNA has heterogeneous 5' ends in vivo and in vitro." Gene 114(1);97-101. PMID: 1316869

Hansen80: Hansen UM, McClure WR (1980). "Role of the sigma subunit of Escherichia coli RNA polymerase in initiation. II. Release of sigma from ternary complexes." J Biol Chem 255(20);9564-70. PMID: 7000759

Harley87: Harley CB, Reynolds RP (1987). "Analysis of E. coli promoter sequences." Nucleic Acids Res 15(5);2343-61. PMID: 3550697

Harrison82: Harrison CA, Turner DH, Hinkle DC (1982). "Laser crosslinking of E. coli RNA polymerase and T7 DNA." Nucleic Acids Res 10(7);2399-414. PMID: 7045809

Hawley83: Hawley DK, McClure WR (1983). "Compilation and analysis of Escherichia coli promoter DNA sequences." Nucleic Acids Res 11(8);2237-55. PMID: 6344016

Hein14: Hein PP, Kolb KE, Windgassen T, Bellecourt MJ, Darst SA, Mooney RA, Landick R (2014). "RNA polymerase pausing and nascent-RNA structure formation are linked through clamp-domain movement." Nat Struct Mol Biol 21(9);794-802. PMID: 25108353

Heyduk01: Heyduk E, Baichoo N, Heyduk T (2001). "Interaction of the alpha-subunit of Escherichia coli RNA polymerase with DNA: rigid body nature of the protein-DNA contact." J Biol Chem 276(48);44598-603. PMID: 11571305

Hinkle72: Hinkle DC, Chamberlin MJ (1972). "Studies of the binding of Escherichia coli RNA polymerase to DNA. I. The role of sigma subunit in site selection." J Mol Biol 70(2);157-85. PMID: 4562312

Hofer82: Hofer B, Ruhe G, Koch A, Koster H (1982). "Primary and secondary structure specificity of the cleavage of 'single-stranded' DNA by endonuclease Hinf I." Nucleic Acids Res 10(9);2763-73. PMID: 6285307

Hofer85: Hofer B, Muller D, Koster H (1985). "The pathway of E. coli RNA polymerase-promoter complex formation as visualized by footprinting." Nucleic Acids Res 13(16);5995-6013. PMID: 3898021

Holmes06: Holmes SF, Santangelo TJ, Cunningham CK, Roberts JW, Erie DA (2006). "Kinetic investigation of Escherichia coli RNA polymerase mutants that influence nucleotide discrimination and transcription fidelity." J Biol Chem 281(27);18677-83. PMID: 16621791

HookBarnard06: Hook-Barnard I, Johnson XB, Hinton DM (2006). "Escherichia coli RNA polymerase recognition of a sigma70-dependent promoter requiring a -35 DNA element and an extended -10 TGn motif." J Bacteriol 188(24);8352-9. PMID: 17012380

Houman90: Houman F, Diaz-Torres MR, Wright A (1990). "Transcriptional antitermination in the bgl operon of E. coli is modulated by a specific RNA binding protein." Cell 62(6);1153-63. PMID: 1698125

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

Ishihama81: Ishihama A (1981). "Subunit of assembly of Escherichia coli RNA polymerase." Adv Biophys 14;1-35. PMID: 7015808

Jeon97: Jeon YH, Yamazaki T, Otomo T, Ishihama A, Kyogoku Y (1997). "Flexible linker in the RNA polymerase alpha subunit facilitates the independent motion of the C-terminal activator contact domain." J Mol Biol 267(4);953-62. PMID: 9135123

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

Kainz98: Kainz M, Gourse RL (1998). "The C-terminal domain of the alpha subunit of Escherichia coli RNA polymerase is required for efficient rho-dependent transcription termination." J Mol Biol 284(5);1379-90. PMID: 9878357

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

Kasas97: Kasas S, Thomson NH, Smith BL, Hansma HG, Zhu X, Guthold M, Bustamante C, Kool ET, Kashlev M, Hansma PK (1997). "Escherichia coli RNA polymerase activity observed using atomic force microscopy." Biochemistry 36(3);461-8. PMID: 9012661

Kashlev90: Kashlev M, Lee J, Zalenskaya K, Nikiforov V, Goldfarb A (1990). "Blocking of the initiation-to-elongation transition by a transdominant RNA polymerase mutation." Science 248(4958);1006-9. PMID: 1693014

Kirkegaard83: Kirkegaard K, Buc H, Spassky A, Wang JC (1983). "Mapping of single-stranded regions in duplex DNA at the sequence level: single-strand-specific cytosine methylation in RNA polymerase-promoter complexes." Proc Natl Acad Sci U S A 80(9);2544-8. PMID: 6573669

Kobayashi90: Kobayashi M, Nagata K, Ishihama A (1990). "Promoter selectivity of Escherichia coli RNA polymerase: effect of base substitutions in the promoter -35 region on promoter strength." Nucleic Acids Res 18(24);7367-72. PMID: 2259628

Komissarova97: Komissarova N, Kashlev M (1997). "RNA polymerase switches between inactivated and activated states By translocating back and forth along the DNA and the RNA." J Biol Chem 272(24);15329-38. PMID: 9182561

Komissarova98: Komissarova N, Kashlev M (1998). "Functional topography of nascent RNA in elongation intermediates of RNA polymerase." Proc Natl Acad Sci U S A 95(25);14699-704. PMID: 9843952

Kovacic87: Kovacic RT (1987). "The 0 degree C closed complexes between Escherichia coli RNA polymerase and two promoters, T7-A3 and lacUV5." J Biol Chem 262(28);13654-61. PMID: 3308880

Krummel89: Krummel B, Chamberlin MJ (1989). "RNA chain initiation by Escherichia coli RNA polymerase. Structural transitions of the enzyme in early ternary complexes." Biochemistry 28(19);7829-42. PMID: 2482070

Krummel92: Krummel B, Chamberlin MJ (1992). "Structural analysis of ternary complexes of Escherichia coli RNA polymerase. Deoxyribonuclease I footprinting of defined complexes." J Mol Biol 225(2);239-50. PMID: 1593619

Krummel92a: Krummel B, Chamberlin MJ (1992). "Structural analysis of ternary complexes of Escherichia coli RNA polymerase. Individual complexes halted along different transcription units have distinct and unexpected biochemical properties." J Mol Biol 225(2);221-37. PMID: 1593618

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

Kuznedelov02: Kuznedelov K, Minakhin L, Niedziela-Majka A, Dove SL, Rogulja D, Nickels BE, Hochschild A, Heyduk T, Severinov K (2002). "A role for interaction of the RNA polymerase flap domain with the sigma subunit in promoter recognition." Science 295(5556);855-7. PMID: 11823642

Landick90: Landick R, Stewart J, Lee DN (1990). "Amino acid changes in conserved regions of the beta-subunit of Escherichia coli RNA polymerase alter transcription pausing and termination." Genes Dev 4(9);1623-36. PMID: 2253882

Larson14: Larson MH, Mooney RA, Peters JM, Windgassen T, Nayak D, Gross CA, Block SM, Greenleaf WJ, Landick R, Weissman JS (2014). "A pause sequence enriched at translation start sites drives transcription dynamics in vivo." Science 344(6187);1042-7. PMID: 24789973

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

Lee92a: Lee DN, Landick R (1992). "Structure of RNA and DNA chains in paused transcription complexes containing Escherichia coli RNA polymerase." J Mol Biol 228(3);759-77. PMID: 1281887

Leirmo91: Leirmo S, Gourse RL (1991). "Factor-independent activation of Escherichia coli rRNA transcription. I. Kinetic analysis of the roles of the upstream activator region and supercoiling on transcription of the rrnB P1 promoter in vitro." J Mol Biol 220(3);555-68. PMID: 1870123

Levin87: Levin JR, Chamberlin MJ (1987). "Mapping and characterization of transcriptional pause sites in the early genetic region of bacteriophage T7." J Mol Biol 196(1);61-84. PMID: 2821285

Li84: Li SC, Squires CL, Squires C (1984). "Antitermination of E. coli rRNA transcription is caused by a control region segment containing lambda nut-like sequences." Cell 38(3);851-60. PMID: 6091902

Lisser93: Lisser S, Margalit H (1993). "Compilation of E. coli mRNA promoter sequences." Nucleic Acids Res 21(7);1507-16. PMID: 8479900

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

Luo96: Luo J, Sharif KA, Jin R, Fujita N, Ishihama A, Krakow JS (1996). "Molecular anatomy of the beta' subunit of the E. coli RNA polymerase: identification of regions involved in polymerase assembly." Genes Cells 1(9);819-27. PMID: 9077436

Maciag11a: 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

Mah00: Mah TF, Kuznedelov K, Mushegian A, Severinov K, Greenblatt J (2000). "The alpha subunit of E. coli RNA polymerase activates RNA binding by NusA." Genes Dev 14(20);2664-75. PMID: 11040219

Mahadevan87: Mahadevan S, Wright A (1987). "A bacterial gene involved in transcription antitermination: regulation at a rho-independent terminator in the bgl operon of E. coli." Cell 50(3);485-94. PMID: 3301003

Malan84: Malan TP, Kolb A, Buc H, McClure WR (1984). "Mechanism of CRP-cAMP activation of lac operon transcription initiation activation of the P1 promoter." J Mol Biol 180(4);881-909. PMID: 6098691

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

Markov99: Markov D, Naryshkina T, Mustaev A, Severinov K (1999). "A zinc-binding site in the largest subunit of DNA-dependent RNA polymerase is involved in enzyme assembly." Genes Dev 13(18);2439-48. PMID: 10500100

Martin80: Martin FH, Tinoco I (1980). "DNA-RNA hybrid duplexes containing oligo(dA:rU) sequences are exceptionally unstable and may facilitate termination of transcription." Nucleic Acids Res 8(10);2295-9. PMID: 6159577

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

Mecsas91: Mecsas J, Cowing DW, Gross CA (1991). "Development of RNA polymerase-promoter contacts during open complex formation." J Mol Biol 220(3);585-97. PMID: 1651395

Meng00: Meng W, Savery NJ, Busby SJ, Thomas MS (2000). "The Escherichia coli RNA polymerase alpha subunit linker: length requirements for transcription activation at CRP-dependent promoters." EMBO J 19(7);1555-66. PMID: 10747024

Meng01: Meng W, Belyaeva T, Savery NJ, Busby SJ, Ross WE, Gaal T, Gourse RL, Thomas MS (2001). "UP element-dependent transcription at the Escherichia coli rrnB P1 promoter: positional requirements and role of the RNA polymerase alpha subunit linker." Nucleic Acids Res 29(20);4166-78. PMID: 11600705

Michalke69: Michalke H, Bremer H (1969). "RNA synthesis in Escherichia coli after irradiation with ultraviolet light." J Mol Biol 41(1);1-23. PMID: 4896016

Miksch05: Miksch G, Bettenworth F, Friehs K, Flaschel E (2005). "The sequence upstream of the -10 consensus sequence modulates the strength and induction time of stationary-phase promoters in Escherichia coli." Appl Microbiol Biotechnol 69(3);312-20. PMID: 16088348

Milan99: Milan S, D'Ari L, Chamberlin MJ (1999). "Structural analysis of ternary complexes of Escherichia coli RNA polymerase: ribonuclease footprinting of the nascent RNA in complexes." Biochemistry 38(1);218-25. PMID: 9890901

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

Morgan83: Morgan WD, Bear DG, von Hippel PH (1983). "Rho-dependent termination of transcription. II. Kinetics of mRNA elongation during transcription from the bacteriophage lambda PR promoter." J Biol Chem 258(15);9565-74. PMID: 6223930

Mosteller70: Mosteller RD, Yanofsky C (1970). "Transcription of the tryptophan operon in Escherichia coli: rifampicin as an inhibitor of initiation." J Mol Biol 48(3);525-31. PMID: 4986890

Mulligan85: Mulligan ME, Brosius J, McClure WR (1985). "Characterization in vitro of the effect of spacer length on the activity of Escherichia coli RNA polymerase at the TAC promoter." J Biol Chem 260(6);3529-38. PMID: 3882710

Munson81: Munson LM, Reznikoff WS (1981). "Abortive initiation and long ribonucleic acid synthesis." Biochemistry 20(8);2081-5. PMID: 6165380

Murakami97: Murakami K, Kimura M, Owens JT, Meares CF, Ishihama A (1997). "The two alpha subunits of Escherichia coli RNA polymerase are asymmetrically arranged and contact different halves of the DNA upstream element." Proc Natl Acad Sci U S A 94(5);1709-14. PMID: 9050843

Naryshkina01: Naryshkina T, Mustaev A, Darst SA, Severinov K (2001). "The beta ' subunit of Escherichia coli RNA polymerase is not required for interaction with initiating nucleotide but is necessary for interaction with rifampicin." J Biol Chem 276(16);13308-13. PMID: 11278820

Nedea99: Nedea EC, Markov D, Naryshkina T, Severinov K (1999). "Localization of Escherichia coli rpoC mutations that affect RNA polymerase assembly and activity at high temperature." J Bacteriol 181(8);2663-5. PMID: 10198039

Neuman03: Neuman KC, Abbondanzieri EA, Landick R, Gelles J, Block SM (2003). "Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking." Cell 115(4);437-47. PMID: 14622598

Newlands91: Newlands JT, Ross W, Gosink KK, Gourse RL (1991). "Factor-independent activation of Escherichia coli rRNA transcription. II. characterization of complexes of rrnB P1 promoters containing or lacking the upstream activator region with Escherichia coli RNA polymerase." J Mol Biol 220(3);569-83. PMID: 1651394

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

NiedzielaMajka05: Niedziela-Majka A, Heyduk T (2005). "Escherichia coli RNA polymerase contacts outside the -10 promoter element are not essential for promoter melting." J Biol Chem 280(46);38219-27. PMID: 16169843

Nudler94: Nudler E, Goldfarb A, Kashlev M (1994). "Discontinuous mechanism of transcription elongation." Science 265(5173);793-6. PMID: 8047884

Nudler95: Nudler E, Kashlev M, Nikiforov V, Goldfarb A (1995). "Coupling between transcription termination and RNA polymerase inchworming." Cell 81(3);351-7. PMID: 7736587

Nudler97: Nudler E, Mustaev A, Lukhtanov E, Goldfarb A (1997). "The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase." Cell 89(1);33-41. PMID: 9094712

NussbaumShochat99: Nussbaum-Shochat A, Amster-Choder O (1999). "BglG, the transcriptional antiterminator of the bgl system, interacts with the beta' subunit of the Escherichia coli RNA polymerase." Proc Natl Acad Sci U S A 96(8);4336-41. PMID: 10200263

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

Otomo00: Otomo T, Yamazaki T, Murakami K, Ishihama A, Kyogoku Y (2000). "Structural study of the N-terminal domain of the alpha subunit of Escherichia coli RNA polymerase solubilized with non-denaturing detergents." J Biochem (Tokyo) 128(2);337-44. PMID: 10920271

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

Park80: Park CS, Hillel Z, Wu CW (1980). "DNA strand specificity in promoter recognition by RNA polymerase." Nucleic Acids Res 8(23);5895-912. PMID: 7008032

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

Rao94: Rao L, Ross W, Appleman JA, Gaal T, Leirmo S, Schlax PJ, Record MT, Gourse RL (1994). "Factor independent activation of rrnB P1. An "extended" promoter with an upstream element that dramatically increases promoter strength." J Mol Biol 235(5);1421-35. PMID: 8107083

Ray05: Ray P, Hall RJ, Finn RD, Chen S, Patwardhan A, Buck M, van Heel M (2005). "Conformational changes of Escherichia coli sigma54-RNA-polymerase upon closed-promoter complex formation." J Mol Biol 354(2);201-5. PMID: 16246367

Rees93: Rees WA, Keller RW, Vesenka JP, Yang G, Bustamante C (1993). "Evidence of DNA bending in transcription complexes imaged by scanning force microscopy." Science 260(5114);1646-9. PMID: 8503010

Rippa10: Rippa V, Cirulli C, Di Palo B, Doti N, Amoresano A, Duilio A (2010). "The ribosomal protein L2 interacts with the RNA polymerase alpha subunit and acts as a transcription modulator in Escherichia coli." J Bacteriol 192(7);1882-9. PMID: 20097853

Rivetti99: Rivetti C, Guthold M, Bustamante C (1999). "Wrapping of DNA around the E.coli RNA polymerase open promoter complex." EMBO J 18(16);4464-75. PMID: 10449412

Roberts14: Roberts JW (2014). "Molecular biology. Molecular basis of transcription pausing." Science 344(6189);1226-7. PMID: 24926002

Ross01: Ross W, Ernst A, Gourse RL (2001). "Fine structure of E. coli RNA polymerase-promoter interactions: alpha subunit binding to the UP element minor groove." Genes Dev 15(5);491-506. PMID: 11238372

Ross93: Ross W, Gosink KK, Salomon J, Igarashi K, Zou C, Ishihama A, Severinov K, Gourse RL (1993). "A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase." Science 262(5138);1407-13. PMID: 8248780

Ross98: Ross W, Aiyar SE, Salomon J, Gourse RL (1998). "Escherichia coli promoters with UP elements of different strengths: modular structure of bacterial promoters." J Bacteriol 180(20);5375-83. PMID: 9765569

Ryan83: Ryan T, Chamberlin MJ (1983). "Transcription analyses with heteroduplex trp attenuator templates indicate that the transcript stem and loop structure serves as the termination signal." J Biol Chem 258(8);4690-3. PMID: 6339503

SakataSogawa04: Sakata-Sogawa K, Shimamoto N (2004). "RNA polymerase can track a DNA groove during promoter search." Proc Natl Acad Sci U S A 101(41);14731-5. PMID: 15469913

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

SasseDwight89: Sasse-Dwight S, Gralla JD (1989). "KMnO4 as a probe for lac promoter DNA melting and mechanism in vivo." J Biol Chem 264(14);8074-81. PMID: 2722774

Schauer96: Schauer AT, Cheng SW, Zheng C, St Pierre L, Alessi D, Hidayetoglu DL, Costantino N, Court DL, Friedman DI (1996). "The alpha subunit of RNA polymerase and transcription antitermination." Mol Microbiol 21(4);839-51. PMID: 8878045

Schickor90: Schickor P, Metzger W, Werel W, Lederer H, Heumann H (1990). "Topography of intermediates in transcription initiation of E.coli." EMBO J 9(7);2215-20. PMID: 2192861

Schulz98: Schulz A, Mucke N, Langowski J, Rippe K (1998). "Scanning force microscopy of Escherichia coli RNA polymerase.sigma54 holoenzyme complexes with DNA in buffer and in air." J Mol Biol 283(4);821-36. PMID: 9790843

Shaevitz03: Shaevitz JW, Abbondanzieri EA, Landick R, Block SM (2003). "Backtracking by single RNA polymerase molecules observed at near-base-pair resolution." Nature 426(6967);684-7. PMID: 14634670

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

Sidorenkov98: Sidorenkov I, Komissarova N, Kashlev M (1998). "Crucial role of the RNA:DNA hybrid in the processivity of transcription." Mol Cell 2(1);55-64. PMID: 9702191

Siebenlist79: Siebenlist U (1979). "RNA polymerase unwinds an 11-base pair segment of a phage T7 promoter." Nature 279(5714);651-2. PMID: 450114

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

Simpson79: Simpson RB (1979). "The molecular topography of RNA polymerase-promoter interaction." Cell 18(2);277-85. PMID: 387258

Squires93: Squires CL, Greenblatt J, Li J, Condon C, Squires CL (1993). "Ribosomal RNA antitermination in vitro: requirement for Nus factors and one or more unidentified cellular components." Proc Natl Acad Sci U S A 90(3);970-4. PMID: 8430111

Stefano82: Stefano JE, Gralla JD (1982). "Spacer mutations in the lac ps promoter." Proc Natl Acad Sci U S A 79(4);1069-72. PMID: 6951162

Strainic98: Strainic MG, Sullivan JJ, Velevis A, deHaseth PL (1998). "Promoter recognition by Escherichia coli RNA polymerase: effects of the UP element on open complex formation and promoter clearance." Biochemistry 37(51);18074-80. PMID: 9922176

Straney87: Straney DC, Crothers DM (1987). "A stressed intermediate in the formation of stably initiated RNA chains at the Escherichia coli lac UV5 promoter." J Mol Biol 193(2);267-78. PMID: 2439694

Suh93: Suh WC, Ross W, Record MT (1993). "Two open complexes and a requirement for Mg2+ to open the lambda PR transcription start site." Science 259(5093);358-61. PMID: 8420002

Szoke87: Szoke PA, Allen TL, deHaseth PL (1987). "Promoter recognition by Escherichia coli RNA polymerase: effects of base substitutions in the -10 and -35 regions." Biochemistry 26(19);6188-94. PMID: 2961367

Tagami99: Tagami H, Aiba H (1999). "An inactive open complex mediated by an UP element at Escherichia coli promoters." Proc Natl Acad Sci U S A 96(13);7202-7. PMID: 10377392

TolicNorrelykke04: Tolic-Norrelykke SF, Engh AM, Landick R, Gelles J (2004). "Diversity in the rates of transcript elongation by single RNA polymerase molecules." J Biol Chem 279(5);3292-9. PMID: 14604986

Toulokhonov01: Toulokhonov I, Artsimovitch I, Landick R (2001). "Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins." Science 292(5517);730-3. PMID: 11326100

Toulokhonov06: Toulokhonov I, Landick R (2006). "The role of the lid element in transcription by E. coli RNA polymerase." J Mol Biol 361(4);644-58. PMID: 16876197

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

Tsujikawa02: Tsujikawa L, Strainic MG, Watrob H, Barkley MD, DeHaseth PL (2002). "RNA polymerase alters the mobility of an A-residue crucial to polymerase-induced melting of promoter DNA." Biochemistry 41(51);15334-41. PMID: 12484772

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

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."

Vogel94: Vogel U, Jensen KF (1994). "The RNA chain elongation rate in Escherichia coli depends on the growth rate." J Bacteriol 176(10);2807-13. PMID: 7514589

Vvedenskaya14: Vvedenskaya IO, Vahedian-Movahed H, Bird JG, Knoblauch JG, Goldman SR, Zhang Y, Ebright RH, Nickels BE (2014). "Transcription. Interactions between RNA polymerase and the "core recognition element" counteract pausing." Science 344(6189);1285-9. PMID: 24926020

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

Wang95a: Wang D, Meier TI, Chan CL, Feng G, Lee DN, Landick R (1995). "Discontinuous movements of DNA and RNA in RNA polymerase accompany formation of a paused transcription complex." Cell 81(3);341-50. PMID: 7537637

Wang97d: Wang Y, Severinov K, Loizos N, Fenyo D, Heyduk E, Heyduk T, Chait BT, Darst SA (1997). "Determinants for Escherichia coli RNA polymerase assembly within the beta subunit." J Mol Biol 270(5);648-62. PMID: 9245594

Wang98e: Wang MD, Schnitzer MJ, Yin H, Landick R, Gelles J, Block SM (1998). "Force and velocity measured for single molecules of RNA polymerase." Science 282(5390);902-7. PMID: 9794753

Weerasekera07: Weerasekera R, She YM, Markham KA, Bai Y, Opalka N, Orlicky S, Sicheri F, Kislinger T, Schmitt-Ulms G (2007). "Interactome and interface protocol (2IP): a novel strategy for high sensitivity topology mapping of protein complexes." Proteomics 7(21);3835-52. PMID: 17960736

Wigneshweraraj03: Wigneshweraraj SR, Kuznedelov K, Severinov K, Buck M (2003). "Multiple roles of the RNA polymerase beta subunit flap domain in sigma 54-dependent transcription." J Biol Chem 278(5);3455-65. PMID: 12424241

Wigneshweraraj05: Wigneshweraraj SR, Burrows PC, Severinov K, Buck M (2005). "Stable DNA opening within open promoter complexes is mediated by the RNA polymerase beta'-jaw domain." J Biol Chem 280(43);36176-84. PMID: 16123036

Xiong93: Xiong XF, Reznikoff WS (1993). "Transcriptional slippage during the transcription initiation process at a mutant lac promoter in vivo." J Mol Biol 231(3);569-80. PMID: 7685823

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

Yang89a: Yang MT, Gardner JF (1989). "Transcription termination directed by heteroduplex thr attenuator templates. Evidence that the transcript stem and loop structure is the termination signal." J Biol Chem 264(5);2634-9. PMID: 2464590

Yarnell99: Yarnell WS, Roberts JW (1999). "Mechanism of intrinsic transcription termination and antitermination." Science 284(5414);611-5. PMID: 10213678

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

Yuan08: 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

Zaychikov96: Zaychikov E, Martin E, Denissova L, Kozlov M, Markovtsov V, Kashlev M, Heumann H, Nikiforov V, Goldfarb A, Mustaev A (1996). "Mapping of catalytic residues in the RNA polymerase active center." Science 273(5271);107-9. PMID: 8658176

Zaychikov99: Zaychikov E, Denissova L, Guckenberger R, Heumann H (1999). "Escherichia coli RNA polymerase translocation is accompanied by periodic bending of the DNA." Nucleic Acids Res 27(18);3645-52. PMID: 10471732

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

Zhang98c: Zhang G, Darst SA (1998). "Structure of the Escherichia coli RNA polymerase alpha subunit amino-terminal domain." Science 281(5374);262-6. PMID: 9657722

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

Zou97: Zou C, Thomas MS, Keen J, Glass RE (1997). "A nested set of C-terminal deletions of the alpha subunit of Escherichia coli RNA polymerase define regions concerned with assembly, proteolysis, stabilization and transcriptional activation in vivo." Genes Cells 2(1);81-94. PMID: 9112442

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