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Escherichia coli K-12 substr. MG1655 Polypeptide: SeqA, negative modulator of initiation of replication



Gene: seqA Accession Numbers: EG12197 (EcoCyc), b0687, ECK0675

Synonyms: hsm-1

Regulation Summary Diagram: ?

Summary:
The SeqA protein is a negative modulator of the initiation of chromosome replication and is involved in sequestration of oriC, ensuring a single round of chromosome replication per cell cycle [Lu94a, vonFreiesleben94, Boye96]. SeqA binds hemimethylated GATC sequences in the wake of the advancing replication fork [Brendler95, Yamazoe05, Waldminghaus12] and inhibits open complex formation [Torheim99], delaying reinitiation at the hemimethylated oriC until it is fully methylated by Dam [vonFreiesleben00]. Regulation of replication by SeqA is important for survival of replication fork damage [Sutera06]. Colocalization of sister origins in rapidly growing cells [Fossum07] and cell cycle arrest during the stringent response [Ferullo08] are dependent on SeqA.

In vitro, SeqA inhibits both the formation of the pre-priming complex as well as replication from an established pre-priming complex and alters dependence on the concentration of DnaA [Wold98]. In vivo, SeqA blocks binding of DnaA to its lower-affinity sites near oriC, but not to the high-affinity sites [Nievera06]. The ability of SeqA dimers to form higher-order complexes is required for origin sequestration [Guarne05, Odsbu05]. There is disagreement over whether [Molina04] or not [denBlaauwen06] SeqA foci represent the location of replication forks. SeqA foci localize to the midcell in newborn cells; after the FtsZ ring is formed, the SeqA foci migrate towards the cell quarter sites [Hiraga98, Onogi99, Hiraga00, Ohsumi01]. MukB protein is required for correct SeqA localization [Hiraga98, Onogi99].

Multiple molecules of SeqA interact with fully methylated oriC sequences and with hemimethylated oriC and non-oriC sequences [Slater95]. The DNA binding properties of SeqA have been extensively investigated [Brendler99, Kang99, Taghbalout00, Fossum03, Han03a, Fujikawa04, Han04a, Kang05]. SeqA binds specifically and cooperatively to two sites surrounding the DnaA binding site R1 in fully or hemimethylated oriC [Skarstad00, Skarstad01]. Binding is dependent on the alignment of the sites on the same face of the helix [Brendler00] and requires at least three base pairs flanking both sides of the GmATC sequence [Fujikawa03]. Chromosome-wide binding of SeqA was investigated by ChIP-Chip [SanchezRomero10a, Waldminghaus10].

SeqA protein forms a homotetramer; the E9K mutant is defective in both tetramer formation and hemimethylated DNA binding [Lee01]. The N-terminal domain (residues 1-59) of SeqA is involved in self-association, while the C-terminal domain (residues 71-181) contains the specific DNA binding activity [Fujikawa03]. The hinge region between the two domains is required for aggregation and formation of SeqA foci [Kang07]. Crystal structures of the C-terminal DNA binding domain in complex with normal and mismatched hemimethylated GATC sites have been determined [Guarn02, Fujikawa04]. A crystal structure of the oligomerization domain shows it to form dimers that assemble into a helical filament [Guarne05]. A crystal structure of a dimeric mutant form of SeqA in complex with DNA is available [Chung08, Chung09], and a structural model has been proposed [Daghfous09]. In an aphA null mutant, the membrane contains 6-fold more SeqA protein than the parental strain [Kohiyama98].

SeqA modulates superhelicity of the E. coli chromosome [Weitao00, Skarstad01, Klungs04]. SeqA was found to interact with the C-terminal domain of ParC, a subunit of topoisomerase IV (topo IV); purified SeqA specifically stimulates topo IV activity, while excess SeqA inhibits all topoisomerases [Kang03]. Genetic analysis suggests that SeqA stabilizes sister chromatid cohesion by antagonizing their topo IV-mediated resolution [Joshi13].

SeqA stimulates transcription from the methylated or hemimethylated bacteriophage λ pR promoter [SlomiDska01, Lyzen06] and may cooperate with CII in stimulating transcription from pI and paQ promoters [Slominska03].

A seqA null mutant is viable, but newly replicated origins are not sequestered and the frequency of replication initiation is increased [Lu94a, vonFreiesleben94], leading to a significantly shortened eclipse period [Olsson02]. In a recBC(Ts) background, seqA mutants display chromosomal fragmentation [Kouzminova04, Rotman14]. seqA mutants are sensitive to UV irradiation and HU [Sutera06]. A non-polar ΔseqA mutant shows synthetic lethality with ΔrecA at 22°C and a high ratio of ori to ter sequences, indicating a number of incomplete replication cycles. Loss of function in LPS biosynthesis enzymes (rfaQGP) suppresses the ori/ter effects of seqA mutation, but not the chromosomal fragmentation phenotype [Rotman09]. The seqA2 and seqA4 point mutations cause defects in self-association of the SeqA protein [Fossum03, Odsbu05]. A microarray analysis of transcription patterns in wild type vs. a seqA mutant has been performed [LobnerOlesen03]. Overexpression of SeqA leads to an extended period of oriC hemimethylation and sequestration as well as other cell division phenotypes [Bach03] and a mutator phenotype [Yang04b]. One of the mutations that suppresses the effect of an hda deletion, hsm-1, results in upregulated expression of seqA [Charbon11].

SeqA: "sequestration protein A"

Reviews: [Baker94, Norris00, Hiraga00a, Dasgupta00, Boye00, Nordstrom01, Sawitzke01, Kaguni06, ZakrzewskaCzerw07, Waldminghaus09, Katayama10, Dame11]

Citations: [Garwood96, Bahloul96, Zhou97, Katayama97, Bogan97, Shakibai98, Wegrzyn99, dAlencon99, Torheim00, Azam00, Onogi00, Correnti02, Norris02, Slominska03a, Slominska03b, Bae03, Strzelczyk03, Olsson03, Bach04, Camara05, Daghfous06, Narajczyk07, Foti07, Babic08, Lyzen08, Bach08, Morigen09, Fujimitsu09, Felczak09, Kaminska10, Drew11, Douraid11, SanchezRomero11, Chung12, Cagliero13]

Gene Citations: [Lu94]

Locations: cytosol

Map Position: [712,210 -> 712,755] (15.35 centisomes)
Length: 546 bp / 181 aa

Molecular Weight of Polypeptide: 20.315 kD (from nucleotide sequence), 22.0 kD (experimental) [Brendler95 ]

Unification Links: ASAP:ABE-0002343 , CGSC:31506 , DIP:DIP-48017N , EchoBASE:EB2114 , EcoGene:EG12197 , EcoliWiki:b0687 , Mint:MINT-1238758 , ModBase:P0AFY8 , OU-Microarray:b0687 , PortEco:seqA , PR:PRO_000023934 , Pride:P0AFY8 , Protein Model Portal:P0AFY8 , RefSeq:NP_415213 , RegulonDB:EG12197 , SMR:P0AFY8 , String:511145.b0687 , Swiss-Model:P0AFY8 , UniProt:P0AFY8

Relationship Links: InterPro:IN-FAMILY:IPR005621 , InterPro:IN-FAMILY:IPR010985 , InterPro:IN-FAMILY:IPR013321 , InterPro:IN-FAMILY:IPR026577 , PDB:Structure:1IU3 , PDB:Structure:1J3E , PDB:Structure:1LRR , PDB:Structure:1XRX , PDB:Structure:2CH3 , PDB:Structure:3FMT , Pfam:IN-FAMILY:PF03925

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0007062 - sister chromatid cohesion Inferred from experiment [Joshi13]
GO:0032297 - negative regulation of DNA-dependent DNA replication initiation Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, vonFreiesleben94, Lu94a]
GO:0051289 - protein homotetramerization Inferred from experiment [Lee01]
GO:0090143 - nucleoid organization Inferred from experiment [Weitao99]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [GOA01a]
GO:0008156 - negative regulation of DNA replication Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0003688 - DNA replication origin binding Inferred from experiment [Brendler95]
GO:0005515 - protein binding Inferred from experiment [Kang03, Rajagopala14]
GO:0010385 - double-stranded methylated DNA binding Inferred from experiment [Slater95]
GO:0042802 - identical protein binding Inferred from experiment [Rajagopala14, Guarne05, Guarn02]
GO:0042803 - protein homodimerization activity Inferred from experiment [Kang05]
GO:0044729 - hemi-methylated DNA-binding Inferred from experiment [Brendler95]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11, GOA06, GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:1990097 - SeqA-DNA complex Inferred from experiment [Slater95]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06]

MultiFun Terms: information transfer DNA related DNA replication

Essentiality data for seqA 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]

Credits:
Last-Curated ? 13-Jun-2014 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Protein-Segment 87 -> 88
[UniProt11a]
UniProt: Interaction with DNA; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 116
[Fujikawa04, UniProt12a]
Alternate sequence: R → A; UniProt: Strongly reduced DNA binding.
Protein-Segment 116 -> 120
[UniProt11a]
UniProt: Interaction with DNA; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 118
[Fujikawa04, UniProt12a]
Alternate sequence: R → A; UniProt: Strongly reduced DNA binding.
Mutagenesis-Variant 149
[Fujikawa04, UniProt12a]
Alternate sequence: T → A; UniProt: Strongly reduced DNA binding.
Mutagenesis-Variant 150
[Fujikawa04, UniProt12a]
Alternate sequence: N → D; UniProt: Strongly reduced DNA binding.
Alternate sequence: N → A; UniProt: Strongly reduced DNA binding.
Protein-Segment 150 -> 156
[UniProt11a]
UniProt: Interaction with DNA; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 151
[Fujikawa04, UniProt12a]
Alternate sequence: T → A; UniProt: Reduced DNA binding.
Mutagenesis-Variant 152
[Fujikawa04, UniProt12a]
Alternate sequence: N → D; UniProt: Strongly reduced DNA binding.
Mutagenesis-Variant 155
[Fujikawa04, UniProt12a]
Alternate sequence: R → A; UniProt: Strongly reduced DNA binding.
Mutagenesis-Variant 156
[Fujikawa04, UniProt12a]
Alternate sequence: K → A; UniProt: Strongly reduced DNA binding.


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b0687 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12197; confirmed by SwissProt match.


References

Azam00: Azam TA, Hiraga S, Ishihama A (2000). "Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid." Genes Cells 5(8);613-26. PMID: 10947847

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

Babic08: Babic A, Lindner AB, Vulic M, Stewart EJ, Radman M (2008). "Direct visualization of horizontal gene transfer." Science 319(5869);1533-6. PMID: 18339941

Bach03: Bach T, Krekling MA, Skarstad K (2003). "Excess SeqA prolongs sequestration of oriC and delays nucleoid segregation and cell division." EMBO J 22(2);315-23. PMID: 12514137

Bach04: Bach T, Skarstad K (2004). "Re-replication from non-sequesterable origins generates three-nucleoid cells which divide asymmetrically." Mol Microbiol 51(6);1589-600. PMID: 15009887

Bach08: Bach T, Morigen , Skarstad K (2008). "The initiator protein DnaA contributes to keeping new origins inactivated by promoting the presence of hemimethylated DNA." J Mol Biol 384(5);1076-85. PMID: 18835566

Bae03: Bae SH, Cheong HK, Cheong C, Kang S, Hwang DS, Choi BS (2003). "Structure and dynamics of hemimethylated GATC sites: implications for DNA-SeqA recognition." J Biol Chem 278(46);45987-93. PMID: 12944412

Bahloul96: Bahloul A, Meury J, Kern R, Garwood J, Guha S, Kohiyama M (1996). "Co-ordination between membrane oriC sequestration factors and a chromosome partitioning protein, TolC (MukA)." Mol Microbiol 22(2);275-82. PMID: 8930912

Baker94: Baker TA (1994). "Replication initiation. A new controller in Escherichia coli." Curr Biol 4(10);945-6. PMID: 7850437

Bogan97: Bogan JA, Helmstetter CE (1997). "DNA sequestration and transcription in the oriC region of Escherichia coli." Mol Microbiol 1997;26(5);889-96. PMID: 9426127

Boye00: Boye E, Lobner-Olesen A, Skarstad K (2000). "Limiting DNA replication to once and only once." EMBO Rep 1(6);479-83. PMID: 11263490

Boye96: Boye E, Stokke T, Kleckner N, Skarstad K (1996). "Coordinating DNA replication initiation with cell growth: differential roles for DnaA and SeqA proteins." Proc Natl Acad Sci U S A 93(22);12206-11. PMID: 8901558

Brendler00: Brendler T, Sawitzke J, Sergueev K, Austin S (2000). "A case for sliding SeqA tracts at anchored replication forks during Escherichia coli chromosome replication and segregation." EMBO J 19(22);6249-58. PMID: 11080170

Brendler95: Brendler T, Abeles A, Austin S (1995). "A protein that binds to the P1 origin core and the oriC 13mer region in a methylation-specific fashion is the product of the host seqA gene." EMBO J 14(16);4083-9. PMID: 7664748

Brendler99: Brendler T, Austin S (1999). "Binding of SeqA protein to DNA requires interaction between two or more complexes bound to separate hemimethylated GATC sequences." EMBO J 18(8);2304-10. PMID: 10205183

Cagliero13: Cagliero C, Grand RS, Jones MB, Jin DJ, O'Sullivan JM (2013). "Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription." Nucleic Acids Res 41(12);6058-71. PMID: 23632166

Camara05: Camara JE, Breier AM, Brendler T, Austin S, Cozzarelli NR, Crooke E (2005). "Hda inactivation of DnaA is the predominant mechanism preventing hyperinitiation of Escherichia coli DNA replication." EMBO Rep 6(8);736-41. PMID: 16041320

Charbon11: Charbon G, Riber L, Cohen M, Skovgaard O, Fujimitsu K, Katayama T, Lobner-Olesen A (2011). "Suppressors of DnaA(ATP) imposed overinitiation in Escherichia coli." Mol Microbiol 79(4);914-28. PMID: 21299647

Chung08: Chung YS, Guarne A (2008). "Crystallization and preliminary X-ray diffraction analysis of SeqA bound to a pair of hemimethylated GATC sites." Acta Crystallogr Sect F Struct Biol Cryst Commun 64(Pt 6);567-71. PMID: 18540078

Chung09: Chung YS, Brendler T, Austin S, Guarne A (2009). "Structural insights into the cooperative binding of SeqA to a tandem GATC repeat." Nucleic Acids Res 37(10);3143-52. PMID: 19304745

Chung12: Chung YS, Guarne A (2012). "Iterative optimization of DNA duplexes for crystallization of SeqA-DNA complexes." J Vis Exp (69);e4266. PMID: 23149570

Correnti02: Correnti J, Munster V, Chan T, Woude M (2002). "Dam-dependent phase variation of Ag43 in Escherichia coli is altered in a seqA mutant." Mol Microbiol 44(2);521-32. PMID: 11972788

Daghfous06: Daghfous D, Chatti A, Marzouk B, Landoulsi A (2006). "Phospholipid changes in seqA and dam mutants of Escherichia coli." C R Biol 329(4);271-6. PMID: 16644499

Daghfous09: Daghfous D, Chatti A, Hammami R, Landoulsi A (2009). "Modeling of the full-length Escherichia coli SeqA protein, in complex with DNA." Pathol Biol (Paris) 57(3);e61-6. PMID: 18849124

dAlencon99: d'Alencon E, Taghbalout A, Kern R, Kohiyama M (1999). "Replication cycle dependent association of SeqA to the outer membrane fraction of E. coli." Biochimie 81(8-9);841-6. PMID: 10572297

Dame11: Dame RT, Kalmykowa OJ, Grainger DC (2011). "Chromosomal macrodomains and associated proteins: implications for DNA organization and replication in gram negative bacteria." PLoS Genet 7(6);e1002123. PMID: 21698131

Dasgupta00: Dasgupta S, Maisnier-Patin S, Nordstr?m K (2000). "New genes with old modus operandi. The connection between supercoiling and partitioning of DNA in Escherichia coli." EMBO Rep 1(4);323-7. PMID: 11269497

denBlaauwen06: den Blaauwen T, Aarsman ME, Wheeler LJ, Nanninga N (2006). "Pre-replication assembly of E. coli replisome components." Mol Microbiol 62(3);695-708. PMID: 16999830

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

Douraid11: Douraid D, Ahmed L (2011). "SeqA, the Escherichia coli origin sequestration protein, can regulate the replication of the pBR322 plasmid." Plasmid 65(1);15-9. PMID: 20875449

Drew11: Drew DA, Koch GA, Hitchcock S, Kowalski J, Talati R, Valakh V (2011). "A mathematical model for timing the release from sequestration and the resultant Brownian migration of SeqA clusters in E. coli." Bull Math Biol 73(6);1271-91. PMID: 20640526

Felczak09: Felczak MM, Kaguni JM (2009). "DnaAcos hyperinitiates by circumventing regulatory pathways that control the frequency of initiation in Escherichia coli." Mol Microbiol 72(6);1348-63. PMID: 19432804

Ferullo08: Ferullo DJ, Lovett ST (2008). "The stringent response and cell cycle arrest in Escherichia coli." PLoS Genet 4(12);e1000300. PMID: 19079575

Fossum03: Fossum S, Soreide S, Skarstad K (2003). "Lack of SeqA focus formation, specific DNA binding and proper protein multimerization in the Escherichia coli sequestration mutant seqA2." Mol Microbiol 47(3);619-32. PMID: 12535065

Fossum07: Fossum S, Crooke E, Skarstad K (2007). "Organization of sister origins and replisomes during multifork DNA replication in Escherichia coli." EMBO J 26(21);4514-22. PMID: 17914458

Foti07: Foti JJ, Persky NS, Ferullo DJ, Lovett ST (2007). "Chromosome segregation control by Escherichia coli ObgE GTPase." Mol Microbiol 65(2);569-81. PMID: 17578452

Fujikawa03: Fujikawa N, Kurumizaka H, Yamazoe M, Hiraga S, Yokoyama S (2003). "Identification of functional domains of the Escherichia coli SeqA protein." Biochem Biophys Res Commun 300(3);699-705. PMID: 12507506

Fujikawa04: Fujikawa N, Kurumizaka H, Nureki O, Tanaka Y, Yamazoe M, Hiraga S, Yokoyama S (2004). "Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein." Nucleic Acids Res 32(1);82-92. PMID: 14704346

Fujimitsu09: Fujimitsu K, Senriuchi T, Katayama T (2009). "Specific genomic sequences of E. coli promote replicational initiation by directly reactivating ADP-DnaA." Genes Dev 23(10);1221-33. PMID: 19401329

Garwood96: Garwood J, Kohiyama M (1996). "A novel cytoplasmic hemimethylated oriC binding activity." J Biol Chem 271(13);7404-11. PMID: 8631765

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."

Guarn02: Guarn? A, Zhao Q, Ghirlando R, Yang W (2002). "Insights into negative modulation of E. coli replication initiation from the structure of SeqA-hemimethylated DNA complex." Nat Struct Biol 9(11);839-43. PMID: 12379844

Guarne05: Guarne A, Brendler T, Zhao Q, Ghirlando R, Austin S, Yang W (2005). "Crystal structure of a SeqA-N filament: implications for DNA replication and chromosome organization." EMBO J 24(8);1502-11. PMID: 15933720

Han03a: Han JS, Kang S, Lee H, Kim HK, Hwang DS (2003). "Sequential binding of SeqA to paired hemi-methylated GATC sequences mediates formation of higher order complexes." J Biol Chem 278(37);34983-9. PMID: 12824161

Han04a: Han JS, Kang S, Kim SH, Ko MJ, Hwang DS (2004). "Binding of SeqA protein to hemi-methylated GATC sequences enhances their interaction and aggregation properties." J Biol Chem 279(29);30236-43. PMID: 15151991

Hiraga00: Hiraga S, Ichinose C, Onogi T, Niki H, Yamazoe M (2000). "Bidirectional migration of SeqA-bound hemimethylated DNA clusters and pairing of oriC copies in Escherichia coli." Genes Cells 5(5);327-41. PMID: 10886362

Hiraga00a: Hiraga S (2000). "Dynamic localization of bacterial and plasmid chromosomes." Annu Rev Genet 34;21-59. PMID: 11092821

Hiraga98: Hiraga S, Ichinose C, Niki H, Yamazoe M (1998). "Cell cycle-dependent duplication and bidirectional migration of SeqA-associated DNA-protein complexes in E. coli." Mol Cell 1(3);381-7. PMID: 9660922

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

Joshi13: Joshi MC, Magnan D, Montminy TP, Lies M, Stepankiw N, Bates D (2013). "Regulation of sister chromosome cohesion by the replication fork tracking protein SeqA." PLoS Genet 9(8);e1003673. PMID: 23990792

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

Kaguni06: Kaguni JM (2006). "DnaA: controlling the initiation of bacterial DNA replication and more." Annu Rev Microbiol 60;351-75. PMID: 16753031

Kaminska10: Kaminska R, van der Woude MW (2010). "Establishing and maintaining sequestration of Dam target sites for phase variation of agn43 in Escherichia coli." J Bacteriol 192(7);1937-45. PMID: 20118257

Kang03: Kang S, Han JS, Park JH, Skarstad K, Hwang DS (2003). "SeqA protein stimulates the relaxing and decatenating activities of topoisomerase IV." J Biol Chem 278(49);48779-85. PMID: 14512422

Kang05: Kang S, Han JS, Kim KP, Yang HY, Lee KY, Hong CB, Hwang DS (2005). "Dimeric configuration of SeqA protein bound to a pair of hemi-methylated GATC sequences." Nucleic Acids Res 33(5);1524-31. PMID: 15767277

Kang07: Kang S, Han JS, Kim SH, Park JH, Hwang DS (2007). "Aggregation of SeqA protein requires positively charged amino acids in the hinge region." Biochem Biophys Res Commun 360(1);63-9. PMID: 17586464

Kang99: Kang S, Lee H, Han JS, Hwang DS (1999). "Interaction of SeqA and Dam methylase on the hemimethylated origin of Escherichia coli chromosomal DNA replication." J Biol Chem 274(17);11463-8. PMID: 10206949

Katayama10: Katayama T, Ozaki S, Keyamura K, Fujimitsu K (2010). "Regulation of the replication cycle: conserved and diverse regulatory systems for DnaA and oriC." Nat Rev Microbiol 8(3);163-70. PMID: 20157337

Katayama97: Katayama T, Akimitsu N, Mizushima T, Miki T, Sekimizu K (1997). "Overinitiation of chromosome replication in the Escherichia coli dnaAcos mutant depends on activation of oriC function by the dam gene product." Mol Microbiol 25(4);661-70. PMID: 9379896

Klungs04: Klungs?yr HK, Skarstad K (2004). "Positive supercoiling is generated in the presence of Escherichia coli SeqA protein." Mol Microbiol 54(1);123-31. PMID: 15458410

Kohiyama98: Kohiyama M, Bahloul A, Kern R, Meury J, Reshetnyak E, Malki A, Guha S (1998). "Increased expression of a hemimethylated oriC binding protein, SeqA, in an aphA mutant." Biochimie 80(12);1043-6. PMID: 9924983

Kouzminova04: Kouzminova EA, Rotman E, Macomber L, Zhang J, Kuzminov A (2004). "RecA-dependent mutants in Escherichia coli reveal strategies to avoid chromosomal fragmentation." Proc Natl Acad Sci U S A 101(46);16262-7. PMID: 15531636

Lee01: Lee H, Kang S, Bae SH, Choi BS, Hwang DS (2001). "SeqA protein aggregation is necessary for SeqA function." J Biol Chem 276(37);34600-6. PMID: 11457824

LobnerOlesen03: Lobner-Olesen A, Marinus MG, Hansen FG (2003). "Role of SeqA and Dam in Escherichia coli gene expression: a global/microarray analysis." Proc Natl Acad Sci U S A 100(8);4672-7. PMID: 12682301

Lu94: Lu M, Kleckner N (1994). "Molecular cloning and characterization of the pgm gene encoding phosphoglucomutase of Escherichia coli." J Bacteriol 176(18);5847-51. PMID: 8083177

Lu94a: Lu M, Campbell JL, Boye E, Kleckner N (1994). "SeqA: a negative modulator of replication initiation in E. coli." Cell 77(3);413-26. PMID: 8011018

Lyzen06: Lyzen R, Wegrzyn G, Wegrzyn A, Szalewska-Palasz A (2006). "Stimulation of the lambda pR promoter by Escherichia coli SeqA protein requires downstream GATC sequences and involves late stages of transcription initiation." Microbiology 152(Pt 10);2985-92. PMID: 17005979

Lyzen08: Lyzen R, Kochanowska M, Wegrzyn G, Szalewska-Palasz A (2008). "IHF- and SeqA-binding sites, present in plasmid cloning vectors, may significantly influence activities of promoters." Plasmid 60(2);125-30. PMID: 18590762

Molina04: Molina F, Skarstad K (2004). "Replication fork and SeqA focus distributions in Escherichia coli suggest a replication hyperstructure dependent on nucleotide metabolism." Mol Microbiol 52(6);1597-612. PMID: 15186411

Morigen09: Morigen , Odsbu I, Skarstad K (2009). "Growth rate dependent numbers of SeqA structures organize the multiple replication forks in rapidly growing Escherichia coli." Genes Cells 14(5);643-57. PMID: 19371375

Narajczyk07: Narajczyk M, Baranska S, Szambowska A, Glinkowska M, Wegrzyn A, Wegrzyn G (2007). "Modulation of lambda plasmid and phage DNA replication by Escherichia coli SeqA protein." Microbiology 153(Pt 5);1653-63. PMID: 17464080

Nievera06: Nievera C, Torgue JJ, Grimwade JE, Leonard AC (2006). "SeqA blocking of DnaA-oriC interactions ensures staged assembly of the E. coli pre-RC." Mol Cell 24(4);581-92. PMID: 17114060

Nordstrom01: Nordstrom K, Dasgupta S (2001). "Partitioning of the Escherichia coli chromosome: superhelicity and condensation." Biochimie 83(1);41-8. PMID: 11254973

Norris00: Norris V, Fralick J, Danchin A (2000). "A SeqA hyperstructure and its interactions direct the replication and sequestration of DNA." Mol Microbiol 37(4);696-702. PMID: 10972793

Norris02: Norris V, Demarty M, Raine D, Cabin-Flaman A, Le Sceller L (2002). "Hypothesis: hyperstructures regulate initiation in Escherichia coli and other bacteria." Biochimie 84(4);341-7. PMID: 12106913

Odsbu05: Odsbu I, Klungsoyr HK, Fossum S, Skarstad K (2005). "Specific N-terminal interactions of the Escherichia coli SeqA protein are required to form multimers that restrain negative supercoils and form foci." Genes Cells 10(11);1039-49. PMID: 16236133

Ohsumi01: Ohsumi K, Yamazoe M, Hiraga S (2001). "Different localization of SeqA-bound nascent DNA clusters and MukF-MukE-MukB complex in Escherichia coli cells." Mol Microbiol 40(4);835-45. PMID: 11401691

Olsson02: Olsson J, Dasgupta S, Berg OG, Nordstrom K (2002). "Eclipse period without sequestration in Escherichia coli." Mol Microbiol 44(6);1429-40. PMID: 12067334

Olsson03: Olsson JA, Nordstrom K, Hjort K, Dasgupta S (2003). "Eclipse-synchrony relationship in Escherichia coli strains with mutations affecting sequestration, initiation of replication and superhelicity of the bacterial chromosome." J Mol Biol 334(5);919-31. PMID: 14643657

Onogi00: Onogi T, Yamazoe M, Ichinose C, Niki H, Hiraga S (2000). "Null mutation of the dam or seqA gene suppresses temperature-sensitive lethality but not hypersensitivity to novobiocin of muk null mutants." J Bacteriol 182(20);5898-901. PMID: 11004192

Onogi99: Onogi T, Niki H, Yamazoe M, Hiraga S (1999). "The assembly and migration of SeqA-Gfp fusion in living cells of Escherichia coli." Mol Microbiol 31(6);1775-82. PMID: 10209749

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

Rotman09: Rotman E, Bratcher P, Kuzminov A (2009). "Reduced lipopolysaccharide phosphorylation in Escherichia coli lowers the elevated ori/ter ratio in seqA mutants." Mol Microbiol 72(5);1273-92. PMID: 19432803

Rotman14: Rotman E, Khan SR, Kouzminova E, Kuzminov A (2014). "Replication fork inhibition in seqA mutants of Escherichia coli triggers replication fork breakage." Mol Microbiol. PMID: 24806348

SanchezRomero10a: Sanchez-Romero MA, Busby SJ, Dyer NP, Ott S, Millard AD, Grainger DC (2010). "Dynamic distribution of SeqA protein across the chromosome of Escherichia coli K-12." MBio 1(1). PMID: 20689753

SanchezRomero11: Sanchez-Romero MA, Molina F, Jimenez-Sanchez A (2011). "Organization of ribonucleoside diphosphate reductase during multifork chromosome replication in Escherichia coli." Microbiology 157(Pt 8);2220-5. PMID: 21659325

Sawitzke01: Sawitzke J, Austin S (2001). "An analysis of the factory model for chromosome replication and segregation in bacteria." Mol Microbiol 40(4);786-94. PMID: 11401686

Shakibai98: Shakibai N, Ishidate K, Reshetnyak E, Gunji S, Kohiyama M, Rothfield L (1998). "High-affinity binding of hemimethylated oriC by Escherichia coli membranes is mediated by a multiprotein system that includes SeqA and a newly identified factor, SeqB." Proc Natl Acad Sci U S A 95(19);11117-21. PMID: 9736699

Skarstad00: Skarstad K, Lueder G, Lurz R, Speck C, Messer W (2000). "The Escherichia coli SeqA protein binds specifically and co-operatively to two sites in hemimethylated and fully methylated oriC." Mol Microbiol 36(6);1319-26. PMID: 10931282

Skarstad01: Skarstad K, Torheim N, Wold S, Lurz R, Messer W, Fossum S, Bach T (2001). "The Escherichia coli SeqA protein binds specifically to two sites in fully and hemimethylated oriC and has the capacity to inhibit DNA replication and affect chromosome topology." Biochimie 83(1);49-51. PMID: 11254974

Slater95: Slater S, Wold S, Lu M, Boye E, Skarstad K, Kleckner N (1995). "E. coli SeqA protein binds oriC in two different methyl-modulated reactions appropriate to its roles in DNA replication initiation and origin sequestration." Cell 82(6);927-36. PMID: 7553853

SlomiDska01: SlomiDska M, Wegrzyn A, Konopa G, Skarstad K, Wegrzyn G (2001). "SeqA, the Escherichia coli origin sequestration protein, is also a specific transcription factor." Mol Microbiol 40(6);1371-9. PMID: 11442835

Slominska03: Slominska M, Konopa G, Ostrowska J, Kedzierska B, Wegrzyn G, Wegrzyn A (2003). "SeqA-mediated stimulation of a promoter activity by facilitating functions of a transcription activator." Mol Microbiol 47(6);1669-79. PMID: 12622820

Slominska03a: Slominska M, Wahl A, Wegrzyn G, Skarstad K (2003). "Degradation of mutant initiator protein DnaA204 by proteases ClpP, ClpQ and Lon is prevented when DNA is SeqA-free." Biochem J 370(Pt 3);867-71. PMID: 12479794

Slominska03b: Slominska M, Konopa G, Baranska S, Wegrzyn G, Wegrzyn A (2003). "Interplay between DnaA and SeqA proteins during regulation of bacteriophage lambda pR promoter activity." J Mol Biol 329(1);59-68. PMID: 12742018

Strzelczyk03: Strzelczyk B, Slominska-Wojewodzka M, Wegrzyn G, Wegrzyn A (2003). "Non-random distribution of GATC sequences in regions of promoters stimulated by the SeqA protein of Escherichia coli." Acta Biochim Pol 50(4);941-5. PMID: 14739988

Sutera06: Sutera VA, Lovett ST (2006). "The role of replication initiation control in promoting survival of replication fork damage." Mol Microbiol 60(1);229-39. PMID: 16556234

Taghbalout00: Taghbalout A, Landoulsi A, Kern R, Yamazoe M, Hiraga S, Holland B, Kohiyama M, Malki A (2000). "Competition between the replication initiator DnaA and the sequestration factor SeqA for binding to the hemimethylated chromosomal origin of E. coli in vitro." Genes Cells 5(11);873-884. PMID: 11122375

Torheim00: Torheim NK, Boye E, Lobner-Olesen A, Stokke T, Skarstad K (2000). "The Escherichia coli SeqA protein destabilizes mutant DnaA204 protein." Mol Microbiol 37(3);629-38. PMID: 10931356

Torheim99: Torheim NK, Skarstad K (1999). "Escherichia coli SeqA protein affects DNA topology and inhibits open complex formation at oriC." EMBO J 18(17);4882-8. PMID: 10469666

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UniProt12a: UniProt Consortium (2012). "UniProt version 2012-02 released on 2012-02-29 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."

vonFreiesleben00: von Freiesleben U, Krekling MA, Hansen FG, Lobner-Olesen A (2000). "The eclipse period of Escherichia coli." EMBO J 19(22);6240-8. PMID: 11080169

vonFreiesleben94: von Freiesleben U, Rasmussen KV, Schaechter M (1994). "SeqA limits DnaA activity in replication from oriC in Escherichia coli." Mol Microbiol 14(4);763-72. PMID: 7891562

Waldminghaus09: Waldminghaus T, Skarstad K (2009). "The Escherichia coli SeqA protein." Plasmid 61(3);141-50. PMID: 19254745

Waldminghaus10: Waldminghaus T, Skarstad K (2010). "ChIP on Chip: surprising results are often artifacts." BMC Genomics 11;414. PMID: 20602746

Waldminghaus12: Waldminghaus T, Weigel C, Skarstad K (2012). "Replication fork movement and methylation govern SeqA binding to the Escherichia coli chromosome." Nucleic Acids Res 40(12);5465-76. PMID: 22373925

Wegrzyn99: Wegrzyn A, Wrobel B, Wegrzyn G (1999). "Altered biological properties of cell membranes in Escherichia coli dnaA and seqA mutants." Mol Gen Genet 261(4-5);762-9. PMID: 10394913

Weitao00: Weitao T, Nordstr?m K, Dasgupta S (2000). "Escherichia coli cell cycle control genes affect chromosome superhelicity." EMBO Rep 1(6);494-9. PMID: 11263493

Weitao99: Weitao T, Nordstr?m K, Dasgupta S (1999). "Mutual suppression of mukB and seqA phenotypes might arise from their opposing influences on the Escherichia coli nucleoid structure." Mol Microbiol 34(1);157-68. PMID: 10540294

Wold98: Wold S, Boye E, Slater S, Kleckner N, Skarstad K (1998). "Effects of purified SeqA protein on oriC-dependent DNA replication in vitro." EMBO J 17(14);4158-65. PMID: 9670030

Yamazoe05: Yamazoe M, Adachi S, Kanaya S, Ohsumi K, Hiraga S (2005). "Sequential binding of SeqA protein to nascent DNA segments at replication forks in synchronized cultures of Escherichia coli." Mol Microbiol 55(1);289-98. PMID: 15612935

Yang04b: Yang H, Wolff E, Kim M, Diep A, Miller JH (2004). "Identification of mutator genes and mutational pathways in Escherichia coli using a multicopy cloning approach." Mol Microbiol 53(1);283-95. PMID: 15225322

ZakrzewskaCzerw07: Zakrzewska-Czerwinska J, Jakimowicz D, Zawilak-Pawlik A, Messer W (2007). "Regulation of the initiation of chromosomal replication in bacteria." FEMS Microbiol Rev 31(4);378-87. PMID: 17459114

Zhou97: Zhou P, Bogan JA, Welch K, Pickett SR, Wang HJ, Zaritsky A, Helmstetter CE (1997). "Gene transcription and chromosome replication in Escherichia coli." J Bacteriol 179(1);163-9. PMID: 8981994

Other References Related to Gene Regulation

Lee01a: Lee H, Kim HK, Kang S, Hong CB, Yim J, Hwang DS (2001). "Expression of the seqA gene is negatively modulated by the HU protein in Escherichia coli." Mol Gen Genet 264(6);931-5. PMID: 11254141


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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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