Escherichia coli K-12 substr. MG1655 Polypeptide: regulator of σ70D), stationary phase protein

Gene: rsd Accession Numbers: EG11738 (EcoCyc), b3995, ECK3987

Synonyms: yjaE

Regulation Summary Diagram: ?

Regulation summary diagram for rsd

The Rsd protein has been proposed to function as an anti-σ factor. It binds specifically to the major σ factor σ70 [Jishage98] with a stoichiometry of 1:1 [Westblade04, Piper09]. Rsd can interact simultaneously with regions 4 [Jishage98, Dove01, Jishage01, Westblade04, Sharma08a] and 2 of σ70 [Yuan08]. Region 4 is involved in recognition of the -35 promoter element, while region 2 is involved in the recognition of the -10 promoter element. Both regions also contain critical determinants for the interaction with core RNA polymerase (RNAP) [Campbell02a]. The crystal structure to 2.6 resolution of Rsd bound to region 4 of σ70 shows that Rsd binding directly interferes with both the core RNAP-binding and promoter-binding functions of region 4 [Patikoglou07].

It has been postulated that the function of Rsd is to sequester σ70 and displace RNAP core enzyme, which in turn becomes accessible for σS and possibly other σ factors in stationary phase [Jishage98, Mitchell07]. Three lines of evidence support this model. First, Rsd was initially isolated in a complex with σ70 from stationary-phase cell extracts [Jishage98]. Second, levels of Rsd increased upon entry into stationary phase [Jishage98, Piper09]. Third, it was shown that Rsd increased expression from a σS-dependent promoter and reduced expression from certain σ70-dependent promoters [Jishage99, Mitchell07].

Interestingly, pull-down experiments have demonstrated that Rsd levels are only twofold higher in stationary phase, with approximately 6,000 molecules per cell, compared to levels in exponentially growing cells [Piper09]. Therefore, the concentration of Rsd should be high enough in exponentially growing cells to allow binding to σ70. Yet, the complex between Rsd and σ70 can only be detected in stationary-phase extracts [Piper09].

Expression of rsd is under the control of two promoters, P1 and P2, where P1 is σS dependent and P2 is σ70 dependent [Jishage99, Piper09]. The P2 promoter is stronger than P1 and active in all phases of growth [Piper09].

Rsd: "regulator of sigma D" [Jishage98]

Reviews: [Campbell08a, Sharma10a]

Locations: cytosol

Map Position: [4,194,355 <- 4,194,831] (90.4 centisomes, 325°)
Length: 477 bp / 158 aa

Molecular Weight of Polypeptide: 18.243 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013059 , DIP:DIP-10800N , EchoBASE:EB1689 , EcoGene:EG11738 , EcoliWiki:b3995 , OU-Microarray:b3995 , PortEco:rsd , PR:PRO_000023876 , Pride:P0AFX4 , Protein Model Portal:P0AFX4 , RefSeq:NP_418423 , RegulonDB:EG11738 , SMR:P0AFX4 , String:511145.b3995 , UniProt:P0AFX4

Relationship Links: InterPro:IN-FAMILY:IPR007448 , InterPro:IN-FAMILY:IPR023785 , PDB:Structure:2p7v , Pfam:IN-FAMILY:PF04353

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0010468 - regulation of gene expression Inferred by computational analysis [GOA06]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Jishage98, Yuan08, Sharma08a, Arifuzzaman06, Dove01]
GO:0016989 - sigma factor antagonist activity Inferred from experiment [Jishage98, Patikoglou07]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

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

Essentiality data for rsd knockouts: ?

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

Sequence Features

Protein sequence of regulator of sigma70 (sigmaD), stationary phase protein with features indicated

Feature Class Location Citations Comment
Protein-Segment 59 -> 71
UniProt: Interaction with RpoD; Sequence Annotation Type: region of interest.
Protein-Segment 101 -> 108
UniProt: Interaction with RpoD; Sequence Annotation Type: region of interest.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


1/26/1998 (pkarp) Merged genes G7819/b3995 and EG11738/yjaE


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

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

Campbell02a: Campbell EA, Muzzin O, Chlenov M, Sun JL, Olson CA, Weinman O, Trester-Zedlitz ML, Darst SA (2002). "Structure of the bacterial RNA polymerase promoter specificity sigma subunit." Mol Cell 9(3);527-39. PMID: 11931761

Campbell08a: Campbell EA, Westblade LF, Darst SA (2008). "Regulation of bacterial RNA polymerase sigma factor activity: a structural perspective." Curr Opin Microbiol 11(2);121-7. PMID: 18375176

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

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

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Jishage01: Jishage M, Dasgupta D, Ishihama A (2001). "Mapping of the Rsd contact site on the sigma 70 subunit of Escherichia coli RNA polymerase." J Bacteriol 183(9);2952-6. PMID: 11292818

Jishage98: Jishage M, Ishihama A (1998). "A stationary phase protein in Escherichia coli with binding activity to the major sigma subunit of RNA polymerase." Proc Natl Acad Sci U S A 1998;95(9);4953-8. PMID: 9560209

Jishage99: Jishage M, Ishihama A (1999). "Transcriptional organization and in vivo role of the Escherichia coli rsd gene, encoding the regulator of RNA polymerase sigma D." J Bacteriol 181(12);3768-76. PMID: 10368152

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Mitchell07: Mitchell JE, Oshima T, Piper SE, Webster CL, Westblade LF, Karimova G, Ladant D, Kolb A, Hobman JL, Busby SJ, Lee DJ (2007). "The Escherichia coli regulator of sigma 70 protein, Rsd, can up-regulate some stress-dependent promoters by sequestering sigma 70." J Bacteriol 189(9);3489-95. PMID: 17351046

Patikoglou07: Patikoglou GA, Westblade LF, Campbell EA, Lamour V, Lane WJ, Darst SA (2007). "Crystal structure of the Escherichia coli regulator of sigma70, Rsd, in complex with sigma70 domain 4." J Mol Biol 372(3);649-59. PMID: 17681541

Piper09: Piper SE, Mitchell JE, Lee DJ, Busby SJ (2009). "A global view of Escherichia coli Rsd protein and its interactions." Mol Biosyst 5(12);1943-7. PMID: 19763331

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

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

Sharma10a: Sharma UK, Chatterji D (2010). "Transcriptional switching in Escherichia coli during stress and starvation by modulation of sigma activity." FEMS Microbiol Rev 34(5);646-57. PMID: 20491934

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

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

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

Westblade04: Westblade LF, Ilag LL, Powell AK, Kolb A, Robinson CV, Busby SJ (2004). "Studies of the Escherichia coli Rsd-sigma70 complex." J Mol Biol 335(3);685-92. PMID: 14687566

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

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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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