RegulonDB RegulonDB 11.0: Gene Form
   

seqA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

pgm ybfF seqA anti-terminator anti-anti-terminator TSS_826 TSS_826 TSS_825 TSS_825 seqAp seqAp TSS_824 (cluster) TSS_824 (cluster) TSS_823 TSS_823 ybfFp1 ybfFp1 TSS_822 TSS_822

Gene      
Name: seqA    Texpresso search in the literature
Synonym(s): ECK0675, EG12197, b0687, hsm-1
Genome position(nucleotides): 712987 --> 713532
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 49.63
External database links:  
ASAP:
 ABE-0002343
CGSC:
 31506
ECHOBASE:
 EB2114
ECOLIHUB:
 seqA
OU-MICROARRAY:
 b0687
STRING:
 511145.b0687
COLOMBOS: seqA


Product      
Name: negative modulator of initiation of replication
Synonym(s): SeqA
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 20.315
Isoelectric point: 9.048
Motif(s):
 
Type Positions Sequence Comment
1 -> 36 MKTIEVDDELYSYIASHTKHIGESASDILRRMLKFS
71 -> 179 AMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITNTNTGRKCSMIEHIMQSMQFPAELIEKVCG
87 -> 88 AV UniProt: Interaction with DNA; Sequence Annotation Type: region of interest.
116 -> 116 R UniProt: Strongly reduced DNA binding..
118 -> 118 R UniProt: Strongly reduced DNA binding..

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.1 - DNA related --> 2.1.1 - DNA replication
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0032991 - protein-containing complex
GO:1990097 - SeqA-DNA complex
molecular_function GO:0003677 - DNA binding
GO:0005515 - protein binding
GO:0003688 - DNA replication origin binding
GO:0042802 - identical protein binding
GO:0042803 - protein homodimerization activity
GO:0010385 - double-stranded methylated DNA binding
GO:0044729 - hemi-methylated DNA-binding
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0009314 - response to radiation
GO:0008156 - negative regulation of DNA replication
GO:0032297 - negative regulation of DNA-templated DNA replication initiation
GO:0007062 - sister chromatid cohesion
GO:0090143 - nucleoid organization
Note(s): Note(s): ...[more].
Evidence: [APPH] Assay of protein purified to homogeneity
Reference(s): [1] Azam TA., et al., 2000
[2] Babic A., et al., 2008
[3] Bach T., et al., 2008
[4] Bach T., et al., 2004
[5] Bae SH., et al., 2003
[6] Bahloul A., et al., 1996
[7] Bogan JA., et al., 1997
[8] Cagliero C., et al., 2013
[9] Camara JE., et al., 2005
[10] Chung YS., et al., 2012
[11] Correnti J., et al., 2002
[12] Daghfous D., et al., 2006
[13] Douraid D., et al., 2011
[14] Drew DA., et al., 2011
[15] Felczak MM., et al., 2009
[16] Fossum-Raunehaug S., et al., 2014
[17] Foti JJ., et al., 2007
[18] Fujimitsu K., et al., 2009
[19] Garwood J., et al., 1996
[20] Joshi MC., et al., 2013
[21] Kaminska R., et al., 2010
[22] Katayama T., et al., 1997
[23] Lyzen R., et al., 2008
[24] Morigen., et al., 2009
[25] Narajczyk M., et al., 2007
[26] Norris V., et al., 2002
[27] Olsson JA., et al., 2003
[28] Onogi T., et al., 2000
[29] Sanchez-Romero MA., et al., 2011
[30] Shakibai N., et al., 1998
[31] Slater S., et al., 1995
[32] Slominska M., et al., 2003
[33] Slominska M., et al., 2003
[34] Strzelczyk B., et al., 2003
[35] Torheim NK., et al., 2000
[36] Wegrzyn A., et al., 1999
[37] Zhou P., et al., 1997
[38] d'Alencon E., et al., 1999
External database links:  
ALPHAFOLD:
 P0AFY8
DIP:
 DIP-48017N
ECOCYC:
 EG12197-MONOMER
ECOLIWIKI:
 b0687
INTERPRO:
 IPR036835
INTERPRO:
 IPR013321
INTERPRO:
 IPR010985
INTERPRO:
 IPR005621
INTERPRO:
 IPR033761
INTERPRO:
 IPR026577
MODBASE:
 P0AFY8
PDB:
 3FMT
PDB:
 1XRX
PDB:
 1LRR
PDB:
 1J3E
PDB:
 1IU3
PDB:
 2CH3
PFAM:
 PF17206
PFAM:
 PF03925
PRIDE:
 P0AFY8
PRODB:
 PRO_000023934
REFSEQ:
 NP_415213
SMR:
 P0AFY8
SWISSMODEL:
 P0AFY8
UNIPROT:
 P0AFY8


Operon      
Name: seqA-pgm         
Operon arrangement:
Transcription unit        Promoter
seqA-pgm


Transcriptional Regulation      
Display Regulation             
Repressed by: HU


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_822 712843 reverse nd [RS-EPT-CBR] [39]
  promoter ybfFp1 712846 reverse nd [ICWHO] [40]
  promoter TSS_823 712851 forward nd [RS-EPT-CBR] [39]
  promoter TSS_824 (cluster) 712916 forward nd [RS-EPT-CBR] [39]
  promoter TSS_825 713180 forward nd [RS-EPT-CBR] [39]
  promoter TSS_826 713441 forward nd [RS-EPT-CBR] [39]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [ICWHO] Inferred computationally without human oversight


Reference(s)    

 [1] 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

 [2] Babic A., Lindner AB., Vulic M., Stewart EJ., Radman M., 2008, Direct visualization of horizontal gene transfer., Science 319(5869):1533-6

 [3] 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

 [4] Bach T., Skarstad K., 2004, Re-replication from non-sequesterable origins generates three-nucleoid cells which divide asymmetrically., Mol Microbiol 51(6):1589-600

 [5] 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

 [6] 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

 [7] Bogan JA., Helmstetter CE., 1997, DNA sequestration and transcription in the oriC region of Escherichia coli., Mol Microbiol 26(5):889-96

 [8] 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

 [9] 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

 [10] Chung YS., Guarne A., 2012, Iterative optimization of DNA duplexes for crystallization of SeqA-DNA complexes., J Vis Exp (69):e4266

 [11] Correnti J., Munster V., Chan T., Woude Mv., 2002, Dam-dependent phase variation of Ag43 in Escherichia coli is altered in a seqA mutant., Mol Microbiol 44(2):521-32

 [12] 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

 [13] 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

 [14] 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

 [15] 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

 [16] Fossum-Raunehaug S., Helgesen E., Stokke C., Skarstad K., 2014, Escherichia coli SeqA Structures Relocalize Abruptly upon Termination of Origin Sequestration during Multifork DNA Replication., PLoS One 9(10):e110575

 [17] Foti JJ., Persky NS., Ferullo DJ., Lovett ST., 2007, Chromosome segregation control by Escherichia coli ObgE GTPase., Mol Microbiol 65(2):569-81

 [18] 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

 [19] Garwood J., Kohiyama M., 1996, A novel cytoplasmic hemimethylated oriC binding activity., J Biol Chem 271(13):7404-11

 [20] 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

 [21] 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

 [22] 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

 [23] 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

 [24] 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

 [25] 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

 [26] 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

 [27] 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

 [28] 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

 [29] 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

 [30] 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

 [31] 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

 [32] 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

 [33] 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

 [34] 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

 [35] 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

 [36] 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

 [37] 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

 [38] 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

 [39] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [40] 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

RegulonDB