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Escherichia coli K-12 substr. MG1655 Polypeptide: SdiA DNA-binding transcriptional dual regulator



Gene: sdiA Accession Numbers: EG10935 (EcoCyc), b1916, ECK1915

Regulation Summary Diagram: ?

Summary:
The transcription factor SdiA, for "Suppressor of the cell division inhibitor," is possibly positively autoregulated and controls the transcription of the genes involved in cell division [GarciaLara96, Sitnikov96, Yamamoto01, Wang91, Wei01a]. SdiA has been shown to increase transcription from the P2 promoter of the ftsQAZ operon [Sitnikov96] by facilitating RNA polymerase binding to the promoter region [Yamamoto01]. SdiA activates the expression of ydiV, which is involved in the interaction between two quorum-sensing systems. An sdiA ydiV double mutant reduces cAMP levels, which inhibits quorum-sensing system 2 [Zhou08]. Expression of sdiAitself is regulated by a mechanism similar to quorum sensing: exposure to conditioned medium results in a 50-80% decrease in sdiA expression [GarciaLara96]. The transcriptional activity of SdiA is affected not only by quorum signaling but also by other environmental factors, such as oxidation [Kim14].

Overexpression of SdiA speeds up cell division [Wang91] and causes apparently concomitant morphological changes; in both exponential and stationary phases, cells appear rounder and shorter [Wei01b]. Overexpression of SdiA also leads to resistance to the DNA-damaging agent mitomycin C as well as to other drugs [Wei01b, Wei01a], while an sdiA null mutant strain was not hypersensitive to mitomycin C [Wei01b] but was more sensitive to flouroquinolones [Rahmati02]. In addition, SdiA also affects the expression of a number of genes, including a decrease in expression of several motility [Dyszel10] and chemotaxis [Wei01a] genes, a pleiotropic effect over the expression of genes involved in cell division, drug sensitivity, DNA replication and repair, macromolecular metabolism [Wei01a], genes involved in the glutamate-dependent acid resistance systems (AR-2) [Dyszel10], and an increase in the expression of the AcrAB multidrug efflux pump proteins [Rahmati02].

On the other hand, SdiA is highly homologous to quorum-sensing transcription factors that belong to the LuxR family [Michael01, Ahmer04, Kanamaru00, Yao06]. The molecule inducer is represented by different N-acyl-L-homoserine lactones (AHLs), which are signaling molecules involved in communication between bacteria (quorum-sensing systems) [Ahmer04, Van06, Lee09d, DeLisa01a, Lindsay05, Walters06, GarciaLara96, Dyszel10, Kim14]. AHLs might control the transcriptional activity of SdiA by enhancing its stability rather than by directly affecting its DNA-binding affinity [Kim14]. Lee et al. showed that the transcription which SdiA mediates is controlled by indole, but whether this effect is indirect or direct is not known [Lee07i, Lee08a]. However, it was experimentally shown that SdiA does not respond to indole, although it can inhibit SdiA activity [SabagDaigle12]. On the other hand Dyszel et al. showed that the SdiA protein is partially dependent upon a diffusible molecule [N-(3-oxo-hexanoyl)-L-homoserine lactone] [Lee07i, Lee08a, Dyszel10].

Accordingly, this family protein is composed of two domains: a conserved C-terminal domain which contains the DNA-binding region [Kanamaru00] and the N-terminal domain, which is involved in effector binding [Yao06].

The crystal structure of intact SdiA has been determined [Kim14].

Review:[Ahmer04].

Microarray analysis:[Wei01a]

Gene Citations: [Yakhnin11]

Locations: cytosol

Map Position: [1,994,134 <- 1,994,856] (42.98 centisomes)
Length: 723 bp / 240 aa

Molecular Weight of Polypeptide: 28.117 kD (from nucleotide sequence)

pI: 6.86

Unification Links: ASAP:ABE-0006381 , CGSC:30919 , EchoBASE:EB0928 , EcoGene:EG10935 , EcoliWiki:b1916 , ModBase:P07026 , OU-Microarray:b1916 , PortEco:sdiA , PR:PRO_000023922 , Pride:P07026 , Protein Model Portal:P07026 , RefSeq:NP_416426 , RegulonDB:EG10935 , SMR:P07026 , String:511145.b1916 , UniProt:P07026

Relationship Links: InterPro:IN-FAMILY:IPR000792 , InterPro:IN-FAMILY:IPR005143 , InterPro:IN-FAMILY:IPR011991 , InterPro:IN-FAMILY:IPR016032 , PDB:Structure:2AVX , Pfam:IN-FAMILY:PF00196 , Pfam:IN-FAMILY:PF03472 , Prints:IN-FAMILY:PR00038 , Prosite:IN-FAMILY:PS00622 , Prosite:IN-FAMILY:PS50043 , Smart:IN-FAMILY:SM00421

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0032467 - positive regulation of cytokinesis Inferred from experiment [Wang91]
GO:2000144 - positive regulation of DNA-templated transcription, initiation Inferred from experiment [Wang91]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0007049 - cell cycle Inferred by computational analysis [UniProtGOA11]
GO:0051301 - cell division Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell processes cell division
information transfer RNA related Transcription related
regulation genetic unit regulated operon
regulation type of regulation transcriptional level activator

DNA binding site length: 18 base-pairs

Symmetry: Inverted Repeat

Regulated Transcription Units (4 total): ?

Notes:

Essentiality data for sdiA knockouts: ?

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

Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 120 -> 128
[Sharma86, UniProt10]
Alternate sequence: TQYLMLPNR → HSVFNAAQTG; UniProt: (in Ref. 1; CAA27327);
Sequence-Conflict 140
[Sharma86, UniProt10]
Alternate sequence: A → R; UniProt: (in Ref. 1; CAA27327);
Conserved-Region 173 -> 238
[UniProt09]
UniProt: HTH luxR-type;
DNA-Binding-Region 197 -> 216
[UniProt10a]
UniProt: H-T-H motif; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b1916 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10935; confirmed by SwissProt match.


References

Ahmer04: Ahmer BM (2004). "Cell-to-cell signalling in Escherichia coli and Salmonella enterica." Mol Microbiol 52(4);933-45. PMID: 15130116

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

DeLisa01a: DeLisa MP, Valdes JJ, Bentley WE (2001). "Mapping stress-induced changes in autoinducer AI-2 production in chemostat-cultivated Escherichia coli K-12." J Bacteriol 183(9);2918-28. PMID: 11292813

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

Dyszel10: Dyszel JL, Soares JA, Swearingen MC, Lindsay A, Smith JN, Ahmer BM (2010). "E. coli K-12 and EHEC genes regulated by SdiA." PLoS One 5(1);e8946. PMID: 20126629

GarciaLara96: Garcia-Lara J, Shang LH, Rothfield LI (1996). "An extracellular factor regulates expression of sdiA, a transcriptional activator of cell division genes in Escherichia coli." J Bacteriol 178(10);2742-8. PMID: 8631660

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

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

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

Kanamaru00: Kanamaru K, Kanamaru K, Tatsuno I, Tobe T, Sasakawa C (2000). "SdiA, an Escherichia coli homologue of quorum-sensing regulators, controls the expression of virulence factors in enterohaemorrhagic Escherichia coli O157:H7." Mol Microbiol 38(4);805-16. PMID: 11115115

Kim14: Kim T, Duong T, Wu CA, Choi J, Lan N, Kang SW, Lokanath NK, Shin D, Hwang HY, Kim KK (2014). "Structural insights into the molecular mechanism of Escherichia coli SdiA, a quorum-sensing receptor." Acta Crystallogr D Biol Crystallogr 70(Pt 3);694-707. PMID: 24598739

Lee07i: Lee J, Jayaraman A, Wood TK (2007). "Indole is an inter-species biofilm signal mediated by SdiA." BMC Microbiol 7;42. PMID: 17511876

Lee08a: Lee J, Zhang XS, Hegde M, Bentley WE, Jayaraman A, Wood TK (2008). "Indole cell signaling occurs primarily at low temperatures in Escherichia coli." ISME J 2(10);1007-23. PMID: 18528414

Lee09d: Lee J, Maeda T, Hong SH, Wood TK (2009). "Reconfiguring the quorum-sensing regulator SdiA of Escherichia coli to control biofilm formation via indole and N-acylhomoserine lactones." Appl Environ Microbiol 75(6);1703-16. PMID: 19168658

Lindsay05: Lindsay A, Ahmer BM (2005). "Effect of sdiA on biosensors of N-acylhomoserine lactones." J Bacteriol 187(14);5054-8. PMID: 15995228

Michael01: Michael B, Smith JN, Swift S, Heffron F, Ahmer BM (2001). "SdiA of Salmonella enterica is a LuxR homolog that detects mixed microbial communities." J Bacteriol 183(19);5733-42. PMID: 11544237

Rahmati02: Rahmati S, Yang S, Davidson AL, Zechiedrich EL (2002). "Control of the AcrAB multidrug efflux pump by quorum-sensing regulator SdiA." Mol Microbiol 43(3);677-85. PMID: 11929524

SabagDaigle12: Sabag-Daigle A, Soares JA, Smith JN, Elmasry ME, Ahmer BM (2012). "The Acyl Homoserine Lactone Receptor, SdiA, of Escherichia coli and Salmonella enterica Serovar Typhimurium Does Not Respond to Indole." Appl Environ Microbiol 78(15);5424-31. PMID: 22610437

Sharma86: Sharma S, Stark TF, Beattie WG, Moses RE (1986). "Multiple control elements for the uvrC gene unit of Escherichia coli." Nucleic Acids Res 14(5);2301-18. PMID: 3515318

Sitnikov96: Sitnikov DM, Schineller JB, Baldwin TO (1996). "Control of cell division in Escherichia coli: regulation of transcription of ftsQA involves both rpoS and SdiA-mediated autoinduction." Proc Natl Acad Sci U S A 1996;93(1);336-41. PMID: 8552633

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

Van06: Van Houdt R, Aertsen A, Moons P, Vanoirbeek K, Michiels CW (2006). "N-acyl-L-homoserine lactone signal interception by Escherichia coli." FEMS Microbiol Lett 256(1);83-9. PMID: 16487323

Walters06: Walters M, Sperandio V (2006). "Quorum sensing in Escherichia coli and Salmonella." Int J Med Microbiol 296(2-3);125-31. PMID: 16487745

Wang91: Wang XD, de Boer PA, Rothfield LI (1991). "A factor that positively regulates cell division by activating transcription of the major cluster of essential cell division genes of Escherichia coli." EMBO J 1991;10(11);3363-72. PMID: 1915297

Wei01a: Wei Y, Lee JM, Smulski DR, LaRossa RA (2001). "Global impact of sdiA amplification revealed by comprehensive gene expression profiling of Escherichia coli." J Bacteriol 2001;183(7);2265-72. PMID: 11244066

Wei01b: Wei Y, Vollmer AC, LaRossa RA (2001). "In vivo titration of mitomycin C action by four Escherichia coli genomic regions on multicopy plasmids." J Bacteriol 2001;183(7);2259-64. PMID: 11244065

Yakhnin11: Yakhnin H, Baker CS, Berezin I, Evangelista MA, Rassin A, Romeo T, Babitzke P (2011). "CsrA represses translation of sdiA, which encodes the N-acylhomoserine-L-lactone receptor of Escherichia coli, by binding exclusively within the coding region of sdiA mRNA." J Bacteriol 193(22);6162-70. PMID: 21908661

Yamamoto01: Yamamoto K, Yata K, Fujita N, Ishihama A (2001). "Novel mode of transcription regulation by SdiA, an Escherichia coli homologue of the quorum-sensing regulator." Mol Microbiol 41(5);1187-98. PMID: 11555297

Yao06: Yao Y, Martinez-Yamout MA, Dickerson TJ, Brogan AP, Wright PE, Dyson HJ (2006). "Structure of the Escherichia coli quorum sensing protein SdiA: activation of the folding switch by acyl homoserine lactones." J Mol Biol 355(2);262-73. PMID: 16307757

Zhou08: Zhou X, Meng X, Sun B (2008). "An EAL domain protein and cyclic AMP contribute to the interaction between the two quorum sensing systems in Escherichia coli." Cell Res 18(9);937-48. PMID: 18560382

Other References Related to Gene Regulation

Ghosh09: Ghosh D, Roy K, Williamson KE, Srinivasiah S, Wommack KE, Radosevich M (2009). "Acyl-homoserine lactones can induce virus production in lysogenic bacteria: an alternative paradigm for prophage induction." Appl Environ Microbiol 75(22);7142-52. PMID: 19783745

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

Vakulskas14: Vakulskas CA, Pannuri A, Cortes-Selva D, Zere TR, Ahmer BM, Babitzke P, Romeo T (2014). "Global effects of the DEAD-box RNA helicase DeaD (CsdA) on gene expression over a broad range of temperatures." Mol Microbiol 92(5);945-58. PMID: 24708042


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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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