Revision as of 18:55, 10 June 2009

Description: extracellular alkaline serine protease (subtilisin E)

Gene name	aprE
Synonyms	sprE
Essential	no
Product	extracellular alkaline serine protease (subtilisin E))
Function	protein degradation
MW, pI	39 kDa, 9.342
Gene length, protein length	1143 bp, 381 aa
Immediate neighbours	yhfN, yhfO
Get the DNA and protein sequences (Barbe et al., 2009)
Genetic context This image was kindly provided by SubtiList

The gene

Basic information

Locus tag: BSU10300

Phenotypes of a mutant

Database entries

DBTBS entry: [1]

SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

Catalyzed reaction/ biological activity: Hydrolysis of proteins with broad specificity for peptide bonds, and a preference for a large uncharged residue in P1 (according to Swiss-Prot)

Protein family: peptidase S8 family (according to Swiss-Prot)

Paralogous protein(s):

Extended information on the protein

Kinetic information:

Domains:

Modification:

Cofactor(s):

Effectors of protein activity:

Interactions: AprE-PaiA

Localization: secreted (according to Swiss-Prot), extracellular (signal peptide) PubMed

Database entries

Structure: 1SBC

Swiss prot entry: P04189

KEGG entry: [3]

E.C. number:

Additional information

Expression and regulation

Operon:

Sigma factor:

Regulation: repressed during logrithmic growth (AbrB)

Regulatory mechanism:

Additional information: the mRNA is extremely stable (more than 25 min) PubMed

Biological materials

Mutant:

Expression vector:

lacZ fusion:

GFP fusion:

two-hybrid system:

Antibody:

Labs working on this gene/protein

Your additional remarks

References

Voigt et al. (2009) Cell physiology and protein secretion of Bacillus licheniformis compared to Bacillus subtilis. J Mol Microbiol Biotechnol. 16: 53-68 PubMed
Hambraeus, G., Persson, M. & Rutberg, B. (2000). The aprE leader is a determinant of extreme mRNA stability in Bacillus subtilis. Microbiology 146, 3051-3059. PubMed
Hambraeus, G., Karhumaa, K. & Rutberg, B. (2002). A 5' stem-loop and ribosome binding but not translation are important for the stability of Bacillus subtilis aprE leader mRNA. Microbiology 148, 1795-1803. PubMed
Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed

@@ Line 1: / Line 1: @@
-* '''Description:''' transcriptional regulator of transition state genes <br/><br/>
+* '''Description:''' extracellular alkaline serine protease (subtilisin E) <br/><br/>
 {| align="right" border="1" cellpadding="2"
 |-
 |style="background:#ABCDEF;" align="center"|'''Gene name'''
-|''abrB''
+|''aprE''
 |-
-|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''cpsX ''
+|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''sprE ''
 |-
 |style="background:#ABCDEF;" align="center"| '''Essential''' || no
 |-
-|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
+|style="background:#ABCDEF;" align="center"| '''Product''' || extracellular alkaline serine protease (subtilisin E))
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of gene expression during the transition <br/>from growth to stationary phase
+|style="background:#ABCDEF;" align="center"|'''Function''' || protein degradation
 |-
-|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 10 kDa, 6.57
+|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 39 kDa, 9.342
 |-
-|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 288 bp, 96 aa
+|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1143 bp, 381 aa
 |-
-|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yabC]]'', ''[[metS]]''
+|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhfN]]'', ''[[yhfO]]''
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11813&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12870&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 |-
-|colspan="2" | '''Genetic context''' <br/> [[Image:abrB_context.gif]]
+|-
+|-
+|colspan="2" | '''Genetic context''' <br/> [[Image:aprE_context.gif]]
   <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 |-
@@ Line 35: / Line 37: @@
 === Basic information ===
-* '''Locus tag:''' BSU00370
+* '''Locus tag:''' BSU10300
 ===Phenotypes of a mutant ===
-No swarming motility on B medium. [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 PubMed]
 === Database entries ===
-* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/abrB.html]
+* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/aprE.html]
-* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10100]
+* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10190]
 === Additional information===
@@ Line 54: / Line 54: @@
 === Basic information/ Evolution ===
-* '''Catalyzed reaction/ biological activity:'''
+* '''Catalyzed reaction/ biological activity:''' Hydrolysis of proteins with broad specificity for peptide bonds, and a preference for a large uncharged residue in P1 (according to Swiss-Prot)
-* '''Protein family:'''
-* '''Paralogous protein(s):''' [[Abh]], [[SpoVT]] (only N-terminal domain)
-=== Genes/ operons controlled by AbrB ===
-* '''Activated by AbrB:''' ''[[citB]]'', ''[[comK]], [[hpr]]'', ''[[rbsR]]-[[rbsK]]-[[rbsD]]-[[rbsA]]-[[rbsC]]-[[rbsB]]''
+* '''Protein family:''' peptidase S8 family (according to Swiss-Prot)
-* ''' Repressed by AbrB:''' ''[[abrB]], [[aprE]], [[ftsA]]-[[ftsZ]], [[kinC]], [[motA]], [[nprE]], [[pbpE]], [[spo0H]], [[spoVG]], [[spo0E]], [[tycA]], [[sbo]]-[[alb]], [[yqxM]]-[[sipW]]-[[tasA]]''
+* '''Paralogous protein(s):'''
 === Extended information on the protein ===
@@ Line 76: / Line 70: @@
 * '''Cofactor(s):'''
-* '''Effectors of protein activity:''' interaction with [[AbbA]] results in inactivation of AbrB [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
+* '''Effectors of protein activity:'''
-* '''Interactions:''' [[AbrB]]-[[AbbA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
+* '''Interactions:''' [[AprE]]-[[PaiA]]
-* '''Localization:'''
+* '''Localization:''' secreted (according to Swiss-Prot),  extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
 === Database entries ===
-* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1Z0R 1Z0R] (N-terminal DNA recognition domain), 	1Z0R (N-terminal DNA recognition domain)  [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=32611 NCBI] [http://www.ncbi.nlm.nih.gov/sites/entrez/16223496 PubMed]
+* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1SBC 1SBC]
-* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P08874 P08874]
+* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P04189 P04189]
-* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00370]
+* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU10300]
+* '''E.C. number:'''
 === Additional information===
 =Expression and regulation=
-* '''Operon:''' ''abrB'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
+* '''Operon:'''
-* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
+* '''[[Sigma factor]]:'''
-* '''Regulation:''' repressed during logrithmic growth ([[AbrB]]) expressed at the onset of stationary phase [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
+* '''Regulation:''' repressed during logrithmic growth ([[AbrB]])
-* '''Regulatory mechanism:''' repressed by [[Spo0A]]-P [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
+* '''Regulatory mechanism:'''
-* '''Additional information:'''
+* '''Additional information:''' the mRNA is extremely stable (more than 25 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/11101663 PubMed]
 =Biological materials =
-* '''Mutant:''' TT731 (aphA3)
+* '''Mutant:'''
 * '''Expression vector:'''
@@ Line 120: / Line 115: @@
 =Labs working on this gene/protein=
-[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]
-[[Mark Strauch]], Baltimore, USA [http://lifesciences.umaryland.edu/Pages/faculty_profile.aspx?ID=212 homepage]
 =Your additional remarks=
@@ Line 129: / Line 120: @@
 =References=
-<pubmed>18840696 3145384 8821944 8576231 11101897 11395475 11583849 11964117 11751836 12123659 12076816 12591885 15610005 16223496 16159768 16702211 17660417 17720793 19202088 7592460, 19465659   </pubmed>
+<pubmed>18957862 11101663 12055299, </pubmed>
-# Banse et al. (2008) Parallel pathways of repression and antirepression governing the transition to stationary phase in ''Bacillus subtilis''.''Proc. Natl. Acad. Sci. USA'' '''105:''' 15547-15552. [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
+# Voigt et al. (2009) Cell physiology and protein secretion of ''Bacillus licheniformis'' compared to ''Bacillus subtilis''. ''J Mol Microbiol Biotechnol.'' '''16:''' 53-68 [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
-# Perego et al. (1988) Structure of the gene for the transition state regulator, ''abrB'': regulator synthesis is controlled by the ''spo0A'' sporulation gene in ''Bacillus subtilis''. ''Mol. Microbiol.'' '''2:''' 689-699. [http://www.ncbi.nlm.nih.gov/sites/entrez/3145384 PubMed]
+# Hambraeus, G., Persson, M. & Rutberg, B. (2000). The ''aprE'' leader is a determinant of extreme mRNA stability in ''Bacillus subtilis''. Microbiology 146, 3051-3059. [http://www.ncbi.nlm.nih.gov/sites/entrez/11101663 PubMed]
-# Xu, K. and M.A. Strauch. (1996) In vitro selection of optimal AbrB-binding sites: comparison to known in vivo sites indicates flexibility in AbrB-binding and recognition of three-dimensional DNA structures. Molec. Microbiol. 19: 145-158 [http://www.ncbi.nlm.nih.gov/sites/entrez/8821944 PubMed]
+# Hambraeus, G., Karhumaa, K. & Rutberg, B. (2002). A 5' stem-loop and ribosome binding but not translation are important for the stability of ''Bacillus subtilis aprE'' leader mRNA. Microbiology 148, 1795-1803. [http://www.ncbi.nlm.nih.gov/sites/entrez/12055299 PubMed]
-# Xu, K., D. Clark and M.A. Strauch. (1996) Analysis of abrB mutations, mutant proteins, and why abrB does not utilize a perfect consensus in the –35 region of its sigmaA promoter.J. Biol. Chem. 271:2621-2626 [http://www.ncbi.nlm.nih.gov/sites/entrez/8576231 PubMed]
-# Vaughn, J.L., Feher V., Naylor, S., Strauch, M.A. and J. Cavanagh. (2000) Novel DNA binding domain and genetic regulation model of Bacillus subtilis transition state regulator AbrB. Nature Structural Biology 7:1139-1146; [http://www.ncbi.nlm.nih.gov/sites/entrez/11101897 PubMed], Corrigendum appears in Nature Stuctural & Molecular Biology (2005) 12:380
-# Xu, K. and M.A. Strauch. (2001) DNA-binding activity of amino-terminal domains of the Bacillus subtilis AbrB protein. J. Bacteriol. 183:4094-4098 [http://www.ncbi.nlm.nih.gov/sites/entrez/11395475 PubMed]
-# Phillips, Z. E.V. and M.A. Strauch. (2001) Role of Cys54 in AbrB multimerization and DNA-binding activity. FEMS Microbiol. Letters. 203:207-210 [http://www.ncbi.nlm.nih.gov/sites/entrez/11583849 PubMed]
-# Phillips, Z.E.V. and M.A. Strauch. (2002) Bacillus subtilis sporulation and stationary phase gene expression. Cellular and Molecular Life Sciences 59:392-402 [http://www.ncbi.nlm.nih.gov/sites/entrez/11964117 PubMed]
-# Shafikhani, S.H., Mandic-Mulec, I., Strauch, M.A., Smith, I. and T. Leighton. (2002) Postexponential regulation of sin operon expression in Bacillus subtilis. J. Bacteriol. 184:564-571 [http://www.ncbi.nlm.nih.gov/sites/entrez/11751836 PubMed]
-# Benson, L. M., Vaughn, J. L., Strauch, M. A., Bobay, B. G., Thompson, R., Naylor, S. and J. Cavanagh (2002). Macromolecular assembly of the transition state regulator AbrB in its unbound and complexed states probed by microelectrospray ionization mass spectrometry. Analytical Biochemistry 306:222-227 [http://www.ncbi.nlm.nih.gov/sites/entrez/12123659 PubMed]
-# Qian, Q., Lee, C.Y., Helmann, J. and M.A. Strauch. (2002) AbrB regulation of the sigmaW regulon of Bacillus subtilis. FEMS Microbiol. Letters 211:219-223. [http://www.ncbi.nlm.nih.gov/sites/entrez/12076816 PubMed]
-# Kim, H. J., S. I. Kim, M. Ratnayake-Lecamwasam, K. Tachikawa, A. L. Sonenshein, and M. Strauch. (2003) Complex regulation of the Bacillus subtilis aconitase gene. J. Bacteriol. 185:1672-1680. [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed]
-# Bobay, B.G., Benson, L., Naylor, S., Feeney, B., Clark, A.C., Goshe, M.B., Strauch, M.A., Thompson, R., and J.Cavanagh. (2004) Evaluation of the DNA binding tendencies of the transition state regulator AbrB. Biochemistry. 43:16106-16118. [http://www.ncbi.nlm.nih.gov/sites/entrez/15610005 PubMed]
-# Bobay et al.(2005) Revised structure of the AbrB N-terminal domain unifies a diverse superfamily of putative DNA-binding proteins. FEBS Lett. 579:5669-5674. [http://www.ncbi.nlm.nih.gov/sites/entrez/16223496 PubMed]
-# Yao, F and M.A. Strauch (2005) Independent and Interchangeable Multimerization Domains of the AbrB, Abh and SpoVT Global Regulatory Proteins. J. Bacteriol. 187:6354-6362 [http://www.ncbi.nlm.nih.gov/sites/entrez/16159768 PubMed]
-# Bobay, B.G., Mueller, G.A., Thompson, R.J., Venters, R.A., Murzin, A.G., Strauch, M.A. & J. Cavanagh (2006) NMR structure of AbhN and comparison with AbrBN: First Insights into the DNA-binding Promiscuity and Specificity of AbrB-like Transition-state Regulator Proteins. J. Biol. Chem. 281:21399-21409  [http://www.ncbi.nlm.nih.gov/sites/entrez/16702211 PubMed]
-# Jordan S. Rietkötter E. Strauch MA. Kalamorz F. Butcher BG. Helmann JD. Mascher T. (2007) LiaRS-dependent gene expression is embedded in transition state regulation in Bacillus subtilis. Microbiology. 153: 2530-2540. [http://www.ncbi.nlm.nih.gov/sites/entrez/17660417 PubMed]
-# Strauch MA. Bobay BG. Cavanagh J. Yao F. Wilson A. Le Breton Y. (2007) Abh and AbrB control of Bacillus subtilis antimicrobial gene expression. J. of Bacteriol. 189:7720-7732. [http://www.ncbi.nlm.nih.gov/sites/entrez/17720793 PubMed]
-# Hamze et al. (2009) Identification of genes required for different stages of dendritic swarming in ''Bacillus subtilis'', with a novel role for ''phrC''.  ''Microbiology'' '''155:''' 398-412. [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 PubMed]
-# Strauch MA. (1995) AbrB modulates expression and catabolite repression of a Bacillus subtilis ribose transport operon. ''J Bacteriol.'' '''Dec;177(23):'''6727-31. [http://www.ncbi.nlm.nih.gov/sites/entrez/7592460 PubMed]
 # Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Difference between revisions of "Sandbox"

Revision as of 18:55, 10 June 2009

Contents

The gene

Basic information

Phenotypes of a mutant

Database entries

Additional information

The protein

Basic information/ Evolution

Extended information on the protein

Database entries

Additional information

Expression and regulation

Biological materials

Labs working on this gene/protein

Your additional remarks

References

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