Difference between revisions of "Sandbox"
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− | * ''' | + | * '''Description:''' AAA+ ATPase, replication initiation protein <br/><br/> |
+ | |||
{| align="right" border="1" cellpadding="2" | {| align="right" border="1" cellpadding="2" | ||
− | |- | + | |- |
|style="background:#ABCDEF;" align="center"|'''Gene name''' | |style="background:#ABCDEF;" align="center"|'''Gene name''' | ||
− | |'' | + | |''dnaA'' |
− | |||
− | |||
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"| ''' | + | |style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dnaH, dnaJ, dnaK '' |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"| ''' | + | |style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed] |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"|''' | + | |style="background:#ABCDEF;" align="center"| '''Product''' || replication initiation protein |
|- | |- | ||
− | | | + | |style="background:#ABCDEF;" align="center"|'''Function''' || [[DNA replication]] |
|- | |- | ||
− | |colspan="2" style="background:#FAF8CC;" align="center"| ''' | + | |colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00010 dnaA] |
|- | |- | ||
− | |colspan="2" style="background:#FAF8CC;" align="center"| ''' | + | |colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=DnaA DnaA] |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"| '''MW, pI''' || | + | |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 6.035 |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || | + | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1338 bp, 446 aa |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ | + | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rpmH]]'', ''[[dnaN]]'' |
|- | |- | ||
− | |style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object= | + | |style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00010 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00010 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00010 DNA_with_flanks] |
|- | |- | ||
− | |colspan="2" | '''Genetic context''' <br/> [[Image: | + | |colspan="2" | '''Genetic context''' <br/> [[Image:DnaA_dnaN_yaaA_recF_yaaB_gyrB_context.png]] |
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div> | <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div> | ||
|- | |- | ||
− | |colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id= | + | |colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dnaA_410_1750_1 Expression at a glance]'''   {{PubMed|22383849}}<br/>[[Image:dnaA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00010]] |
|- | |- | ||
|} | |} | ||
Line 38: | Line 37: | ||
<br/><br/><br/><br/> | <br/><br/><br/><br/> | ||
<br/><br/><br/><br/> | <br/><br/><br/><br/> | ||
− | + | <br/><br/> | |
− | |||
− | |||
− | |||
− | |||
= [[Categories]] containing this gene/protein = | = [[Categories]] containing this gene/protein = | ||
− | {{SubtiWiki category|[[ | + | {{SubtiWiki category|[[DNA replication]]}}, |
− | {{SubtiWiki category|[[ | + | {{SubtiWiki category|[[essential genes]]}} |
= This gene is a member of the following [[regulons]] = | = This gene is a member of the following [[regulons]] = | ||
− | {{SubtiWiki regulon|[[ | + | {{SubtiWiki regulon|[[Spo0A regulon]]}} |
− | =The [[ | + | =The [[DnaA regulon]]= |
− | |||
− | |||
=The gene= | =The gene= | ||
=== Basic information === | === Basic information === | ||
− | * '''Locus tag:''' | + | * '''Locus tag:''' BSU00010 |
===Phenotypes of a mutant === | ===Phenotypes of a mutant === | ||
+ | |||
+ | essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed] | ||
=== Database entries === | === Database entries === | ||
− | * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ | + | * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dnaAN.html] |
− | * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+ | + | * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10065] |
=== Additional information=== | === Additional information=== | ||
− | |||
− | |||
Line 77: | Line 70: | ||
* '''Catalyzed reaction/ biological activity:''' | * '''Catalyzed reaction/ biological activity:''' | ||
+ | ** binds multiple regions in the oriC region, required for recruitment of proteins needed to load the replicative helicase [[DnaC]] | ||
− | * '''Protein family:''' | + | * '''Protein family:''' dnaA family (according to Swiss-Prot) |
* '''Paralogous protein(s):''' | * '''Paralogous protein(s):''' | ||
Line 86: | Line 80: | ||
* '''Kinetic information:''' | * '''Kinetic information:''' | ||
− | * '''Domains:''' | + | * '''Domains:''' AAA+ domain |
* '''Modification:''' | * '''Modification:''' | ||
Line 93: | Line 87: | ||
* '''Effectors of protein activity:''' | * '''Effectors of protein activity:''' | ||
+ | ** [[SirA]] displaces [[DnaA]] from the replication origin {{PubMed|19682252}} | ||
+ | ** [[YabA]] inhibits co-operative binding of DnaA to the ''oriC'' DNA {{PubMed|21895792}} | ||
+ | ** DnaA helix formation (and thus replication initiation) is inhibited by the interaction of either [[Soj]], [[YabA]] or [[DnaN]] with the AAA+ domain of DnaA {{PubMed|23909787,22286949}} | ||
+ | ** interaction with [[DnaD]] inhibits the ability of [[DnaA]] to cooperatively bind to DNA {{PubMed|22821970}} | ||
* '''[[SubtInteract|Interactions]]:''' | * '''[[SubtInteract|Interactions]]:''' | ||
+ | ** [[DnaA]] assembles into a right-handed helical oligomer built upon interactions between neighbouring AAA+ domains {{PubMed|23909787}} | ||
+ | ** [[Soj]]-[[DnaA]] {{PubMed|22286949}} | ||
+ | ** [[DnaA]]-[[YabA]] {{PubMed|23909787,12060778}} | ||
+ | ** [[DnaA]]-[[YabA]]-[[DnaN]] {{PubMed|12060778}} | ||
+ | ** [[DnaA]]-[[DnaD]] {{PubMed|22821970,11222620}} | ||
+ | ** [[SirA]]-[[DnaA]] {{PubMed|19682252,21239581}} | ||
+ | ** [[YqaH]]-[[DnaA]] {{PubMed|12060778}} | ||
+ | ** part of the [[primosome]]: [[DnaA]]-[[DnaG]]-[[DnaC]]-[[DnaI]]-[[DnaD]]-[[DnaB]] {{PubMed|22797751}} | ||
− | * '''[[Localization]]:''' | + | * '''[[Localization]]:''' |
+ | ** throughout the cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/10844689 PubMed] | ||
=== Database entries === | === Database entries === | ||
Line 102: | Line 109: | ||
* '''Structure:''' | * '''Structure:''' | ||
− | * '''UniProt:''' [http://www.uniprot.org/uniprot/ | + | * '''UniProt:''' [http://www.uniprot.org/uniprot/P05648 P05648] |
− | * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu: | + | * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00010] |
* '''E.C. number:''' | * '''E.C. number:''' | ||
Line 112: | Line 119: | ||
=Expression and regulation= | =Expression and regulation= | ||
− | * '''Operon:''' ''[[ | + | * '''Operon:''' ''[[dnaA]]-[[dnaN]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed] |
− | * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id= | + | * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dnaA_410_1750_1 dnaA] {{PubMed|22383849}} |
− | * '''Sigma factor:''' [[SigA]] | + | * '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed] |
* '''Regulation:''' | * '''Regulation:''' | ||
− | ** | + | ** negatively controlled by [[DnaA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2168872 PubMed] and [[Spo0A]] [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed] |
+ | ** repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed] | ||
* '''Regulatory mechanism:''' | * '''Regulatory mechanism:''' | ||
− | ** [[ | + | ** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed] |
* '''Additional information:''' | * '''Additional information:''' | ||
Line 129: | Line 137: | ||
* '''Mutant:''' | * '''Mutant:''' | ||
− | |||
* '''Expression vector:''' | * '''Expression vector:''' | ||
Line 142: | Line 149: | ||
=Labs working on this gene/protein= | =Labs working on this gene/protein= | ||
− | + | * [[Philippe Noirot]], Jouy-en-Josas, France [http://locus.jouy.inra.fr/cms/index.php?id=18 homepage] | |
− | [[ | + | * [[Peter Graumann]], Freiburg University, Germany [http://www.biologie.uni-freiburg.de/data/bio2/graumann/index.htm homepage] |
+ | * [[Alan Grossman]], MIT, Cambridge, MA, USA | ||
+ | * [[Heath Murray]], Centre for Bacterial Cell Biology, Newcastle, UK [http://www.ncl.ac.uk/camb/staff/profile/heath.murray homepage] | ||
=Your additional remarks= | =Your additional remarks= | ||
=References= | =References= | ||
+ | ==Reviews== | ||
+ | <pubmed> 20157337 21035377 21639790 22575476 22797751</pubmed> | ||
− | <pubmed> | + | ==The [[DnaA regulon]]== |
+ | <pubmed> 16120674, </pubmed> | ||
+ | ==Original publications== | ||
+ | <pubmed>18854156,19011033, 11222620,14651647,17140409 10844689 ,11222620 12060778 16461910 2987848 2168872 11207367, 19737352 19081080 17932079 19968790 19682252 20511500 21097613 21239581 21895792 22286949 22821970 23909787 22396664,21911367</pubmed> | ||
− | [[Category:Protein-coding genes]] | + | [[Category:Protein-coding genes]] |
Revision as of 14:26, 11 November 2013
- Description: AAA+ ATPase, replication initiation protein
Gene name | dnaA |
Synonyms | dnaH, dnaJ, dnaK |
Essential | yes PubMed |
Product | replication initiation protein |
Function | DNA replication |
Gene expression levels in SubtiExpress: dnaA | |
Interactions involving this protein in SubtInteract: DnaA | |
MW, pI | 50 kDa, 6.035 |
Gene length, protein length | 1338 bp, 446 aa |
Immediate neighbours | rpmH, dnaN |
Sequences | Protein DNA DNA_with_flanks |
Genetic context This image was kindly provided by SubtiList
| |
Expression at a glance PubMed |
Contents
Categories containing this gene/protein
DNA replication, essential genes
This gene is a member of the following regulons
The DnaA regulon
The gene
Basic information
- Locus tag: BSU00010
Phenotypes of a mutant
essential PubMed
Database entries
- DBTBS entry: [1]
- SubtiList entry: [2]
Additional information
The protein
Basic information/ Evolution
- Catalyzed reaction/ biological activity:
- binds multiple regions in the oriC region, required for recruitment of proteins needed to load the replicative helicase DnaC
- Protein family: dnaA family (according to Swiss-Prot)
- Paralogous protein(s):
Extended information on the protein
- Kinetic information:
- Domains: AAA+ domain
- Modification:
- Cofactor(s):
- Effectors of protein activity:
- SirA displaces DnaA from the replication origin PubMed
- YabA inhibits co-operative binding of DnaA to the oriC DNA PubMed
- DnaA helix formation (and thus replication initiation) is inhibited by the interaction of either Soj, YabA or DnaN with the AAA+ domain of DnaA PubMed
- interaction with DnaD inhibits the ability of DnaA to cooperatively bind to DNA PubMed
- Localization:
- throughout the cytoplasm PubMed
Database entries
- Structure:
- UniProt: P05648
- KEGG entry: [3]
- E.C. number:
Additional information
Expression and regulation
- Regulation:
- Additional information:
Biological materials
- Mutant:
- Expression vector:
- lacZ fusion:
- GFP fusion:
- two-hybrid system:
- Antibody:
Labs working on this gene/protein
- Philippe Noirot, Jouy-en-Josas, France homepage
- Peter Graumann, Freiburg University, Germany homepage
- Alan Grossman, MIT, Cambridge, MA, USA
- Heath Murray, Centre for Bacterial Cell Biology, Newcastle, UK homepage
Your additional remarks
References
Reviews
The DnaA regulon
Original publications
Graham Scholefield, Heath Murray
YabA and DnaD inhibit helix assembly of the DNA replication initiation protein DnaA.
Mol Microbiol: 2013, 90(1);147-59
[PubMed:23909787]
[WorldCat.org]
[DOI]
(I p)
Carla Y Bonilla, Alan D Grossman
The primosomal protein DnaD inhibits cooperative DNA binding by the replication initiator DnaA in Bacillus subtilis.
J Bacteriol: 2012, 194(18);5110-7
[PubMed:22821970]
[WorldCat.org]
[DOI]
(I p)
Norbert S Hill, Ryosuke Kadoya, Dhruba K Chattoraj, Petra Anne Levin
Cell size and the initiation of DNA replication in bacteria.
PLoS Genet: 2012, 8(3);e1002549
[PubMed:22396664]
[WorldCat.org]
[DOI]
(I p)
Graham Scholefield, Jeff Errington, Heath Murray
Soj/ParA stalls DNA replication by inhibiting helix formation of the initiator protein DnaA.
EMBO J: 2012, 31(6);1542-55
[PubMed:22286949]
[WorldCat.org]
[DOI]
(I p)
Hajime Okumura, Mika Yoshimura, Mikako Ueki, Taku Oshima, Naotake Ogasawara, Shu Ishikawa
Regulation of chromosomal replication initiation by oriC-proximal DnaA-box clusters in Bacillus subtilis.
Nucleic Acids Res: 2012, 40(1);220-34
[PubMed:21911367]
[WorldCat.org]
[DOI]
(I p)
Houra Merrikh, Alan D Grossman
Control of the replication initiator DnaA by an anti-cooperativity factor.
Mol Microbiol: 2011, 82(2);434-46
[PubMed:21895792]
[WorldCat.org]
[DOI]
(I p)
Lilah Rahn-Lee, Houra Merrikh, Alan D Grossman, Richard Losick
The sporulation protein SirA inhibits the binding of DnaA to the origin of replication by contacting a patch of clustered amino acids.
J Bacteriol: 2011, 193(6);1302-7
[PubMed:21239581]
[WorldCat.org]
[DOI]
(I p)
Wiep Klaas Smits, Houra Merrikh, Carla Yaneth Bonilla, Alan D Grossman
Primosomal proteins DnaD and DnaB are recruited to chromosomal regions bound by DnaA in Bacillus subtilis.
J Bacteriol: 2011, 193(3);640-8
[PubMed:21097613]
[WorldCat.org]
[DOI]
(I p)
Sharon E Hoover, Weihong Xu, Wenzhong Xiao, William F Burkholder
Changes in DnaA-dependent gene expression contribute to the transcriptional and developmental response of Bacillus subtilis to manganese limitation in Luria-Bertani medium.
J Bacteriol: 2010, 192(15);3915-24
[PubMed:20511500]
[WorldCat.org]
[DOI]
(I p)
Wiep Klaas Smits, Alexi I Goranov, Alan D Grossman
Ordered association of helicase loader proteins with the Bacillus subtilis origin of replication in vivo.
Mol Microbiol: 2010, 75(2);452-61
[PubMed:19968790]
[WorldCat.org]
[DOI]
(I p)
Alexi I Goranov, Adam M Breier, Houra Merrikh, Alan D Grossman
YabA of Bacillus subtilis controls DnaA-mediated replication initiation but not the transcriptional response to replication stress.
Mol Microbiol: 2009, 74(2);454-66
[PubMed:19737352]
[WorldCat.org]
[DOI]
(I p)
Jennifer K Wagner, Kathleen A Marquis, David Z Rudner
SirA enforces diploidy by inhibiting the replication initiator DnaA during spore formation in Bacillus subtilis.
Mol Microbiol: 2009, 73(5);963-74
[PubMed:19682252]
[WorldCat.org]
[DOI]
(I p)
Clarisse Defeu Soufo, Hervé Joël Defeu Soufo, Marie-Françoise Noirot-Gros, Astrid Steindorf, Philippe Noirot, Peter L Graumann
Cell-cycle-dependent spatial sequestration of the DnaA replication initiator protein in Bacillus subtilis.
Dev Cell: 2008, 15(6);935-41
[PubMed:19081080]
[WorldCat.org]
[DOI]
(I p)
Adam M Breier, Alan D Grossman
Dynamic association of the replication initiator and transcription factor DnaA with the Bacillus subtilis chromosome during replication stress.
J Bacteriol: 2009, 191(2);486-93
[PubMed:19011033]
[WorldCat.org]
[DOI]
(I p)
Heath Murray, Jeff Errington
Dynamic control of the DNA replication initiation protein DnaA by Soj/ParA.
Cell: 2008, 135(1);74-84
[PubMed:18854156]
[WorldCat.org]
[DOI]
(I p)
Shu Ishikawa, Yoshitoshi Ogura, Mika Yoshimura, Hajime Okumura, Eunha Cho, Yoshikazu Kawai, Ken Kurokawa, Taku Oshima, Naotake Ogasawara
Distribution of stable DnaA-binding sites on the Bacillus subtilis genome detected using a modified ChIP-chip method.
DNA Res: 2007, 14(4);155-68
[PubMed:17932079]
[WorldCat.org]
[DOI]
(P p)
Melanie B Berkmen, Alan D Grossman
Subcellular positioning of the origin region of the Bacillus subtilis chromosome is independent of sequences within oriC, the site of replication initiation, and the replication initiator DnaA.
Mol Microbiol: 2007, 63(1);150-65
[PubMed:17140409]
[WorldCat.org]
[DOI]
(P p)
Marie-Françoise Noirot-Gros, M Velten, M Yoshimura, S McGovern, T Morimoto, S D Ehrlich, N Ogasawara, P Polard, Philippe Noirot
Functional dissection of YabA, a negative regulator of DNA replication initiation in Bacillus subtilis.
Proc Natl Acad Sci U S A: 2006, 103(7);2368-73
[PubMed:16461910]
[WorldCat.org]
[DOI]
(P p)
Virginie Molle, Masaya Fujita, Shane T Jensen, Patrick Eichenberger, José E González-Pastor, Jun S Liu, Richard Losick
The Spo0A regulon of Bacillus subtilis.
Mol Microbiol: 2003, 50(5);1683-701
[PubMed:14651647]
[WorldCat.org]
[DOI]
(P p)
Marie-Françoise Noirot-Gros, Etienne Dervyn, Ling Juan Wu, Peggy Mervelet, Jeffery Errington, S Dusko Ehrlich, Philippe Noirot
An expanded view of bacterial DNA replication.
Proc Natl Acad Sci U S A: 2002, 99(12);8342-7
[PubMed:12060778]
[WorldCat.org]
[DOI]
(P p)
D Ishigo-Oka, N Ogasawara, S Moriya
DnaD protein of Bacillus subtilis interacts with DnaA, the initiator protein of replication.
J Bacteriol: 2001, 183(6);2148-50
[PubMed:11222620]
[WorldCat.org]
[DOI]
(P p)
W F Burkholder, I Kurtser, A D Grossman
Replication initiation proteins regulate a developmental checkpoint in Bacillus subtilis.
Cell: 2001, 104(2);269-79
[PubMed:11207367]
[WorldCat.org]
[DOI]
(P p)
Y Imai, N Ogasawara, D Ishigo-Oka, R Kadoya, T Daito, S Moriya
Subcellular localization of Dna-initiation proteins of Bacillus subtilis: evidence that chromosome replication begins at either edge of the nucleoids.
Mol Microbiol: 2000, 36(5);1037-48
[PubMed:10844689]
[WorldCat.org]
[DOI]
(P p)
T Fukuoka, S Moriya, H Yoshikawa, N Ogasawara
Purification and characterization of an initiation protein for chromosomal replication, DnaA, in Bacillus subtilis.
J Biochem: 1990, 107(5);732-9
[PubMed:2168872]
[WorldCat.org]
[DOI]
(P p)
N Ogasawara, S Moriya, H Yoshikawa
Structure and function of the region of the replication origin of the Bacillus subtilis chromosome. IV. Transcription of the oriC region and expression of DNA gyrase genes and other open reading frames.
Nucleic Acids Res: 1985, 13(7);2267-79
[PubMed:2987848]
[WorldCat.org]
[DOI]
(P p)