Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' molybdopterin-guanine dinucleotide biosynthesis <br/><br/>
+
* '''Description:''' RNase J1<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'''
−
|''mobA''
+
|''rnjA ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykqC''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || molybdenum cofactor synthesis protein
+
|style="background:#ABCDEF;" align="center"| '''Product''' || RNase J1
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || nitrate respiration
+
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA processing
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 6.17  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 61 kDa, 5.902  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 597 bp, 199 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1665 bp, 555 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yknT]]'', ''[[moeB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[adeC]]'', ''[[ykzG]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13299&#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:CAB13326&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:mobA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ykqC_context.gif]]
 
  <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>
 
|-
 
|-
Line 38: Line 38:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 43: Line 45:
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12621]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11813]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' endonuclease and 5'-3' exonuclease
  
 
* '''Protein family:'''
 
* '''Protein family:'''
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[RnjB]]
 +
 
 +
=== RNAs  affected by ''rnjA'' ===
 +
 
 +
''[[hbs]]'', ''[[thrS]]''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 70: Line 76:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[RnjA]]-[[RnjB]], [[RnjA]]-[[PfkA]], [[RnjA]]-[[PnpA]], [[RnjA]]-[[Rny]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
  
 
* '''Localization:''' Cytoplasm
 
* '''Localization:''' Cytoplasm
Line 76: Line 82:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do;jsessionid=8B071C0C81B11ADEBA3DDC3FF3395811?structureId=3BK1 3BK1] (RNase J from ''Thermus thermophilus'') [http://www.pdb.org/pdb/explore/explore.do?structureId=3BK2 3BK2] (RNase J from ''Thermus thermophilus'', complex with UMP)
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14260]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14530]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
 +
 +
:* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 +
 +
required for ''[[thrS]]'' RNA processing, involved in maturation of the 5’-end of the16S rRNA, subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
  
 
=Expression and regulation=
 
=Expression and regulation=
Line 90: Line 100:
 
* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 96: Line 106:
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed],  subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
  
 
=Biological materials =
 
=Biological materials =
Line 108: Line 118:
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:'''  
+
* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
  
 
* '''Antibody:'''
 
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Harald Putzer]], IBPC Paris, France [http://www.ibpc.fr/UPR9073/putzer/recherches_harald.htm Homepage]
 +
 +
[[David Bechhofer]], Mount Sinai School, New York, USA [http://www.mountsinai.org/Research/Centers%20Laboratories%20and%20Programs/Bechhofer%20Laboratory?citype=Physician&ciid=Bechhofer%20David%20H%201255565 Homepage]
 +
 +
[[Ciaran Condon]], IBPC, Paris, France [http://www.ibpc.fr/UPR9073/condon/index_en.html Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 118: Line 134:
 
=References=
 
=References=
  
 +
# Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 +
# Even, S., Pellegrini, O., Zig, L., Labas, V., Vinh, J., Brechemmier-Baey, D., and Putzer, H. (2005) Ribonucleases J1 and J2: Two novel endoribonucleases in B. subtilis with functional  homology to E. coli RNase E. Nucl Acids Res 33, 2141-2152. [http://www.ncbi.nlm.nih.gov/sites/entrez/15831787 PubMed]
 +
# de la Sierra-Gallay IL, Zig L, Jamalli A, Putzer H. (2008 Structural insights into the dual activity of RNase J. Nat. Struct. Mol. Biol. 15:206-212. [http://www.ncbi.nlm.nih.gov/sites/entrez/18204464 PubMed]
 +
# Mäder, U., Zig, L., Kretschmer, J., Homuth, G., and Putzer, H. (2008) mRNA processing by RNases J1 and J2 affects Bacillus subtilis gene expression on a global scale. Mol Microbiol 70, 183-196. [http://www.ncbi.nlm.nih.gov/sites/entrez/18713320 PubMed]
 +
# Commichau, F. M., Rothe, F. M., Herzberg, C., Wagner, E., Hellwig, D., Lehnik-Habrink, M., Hammer, E., Völker, U. & Stülke, J. (2009) Novel activities of glycolytic enzymes in Bacillus subtilis: Interactions with essential proteins involved in mRNA processing. Mol. Cell. Proteomics in press [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
 +
# Hunt, A., Rawlins, J. P., Thomaides, H. B., and Errington, J. (2006) Functional analysis of 11 putative essential genes in Bacillus subtilis. Microbiology 152, 2895-2907. [http://www.ncbi.nlm.nih.gov/sites/entrez/17005971 PubMed]
 +
# Deikus, G., Condon, C. & Bechhofer, D. H. (2008). Role of ''Bacillus subtilis'' RNase J1 endonuclease and 5'-exonuclease activities in ''trp'' leader RNA turnover. J Biol Chem. 283:17158-17167. [http://www.ncbi.nlm.nih.gov/sites/entrez/18445592 PubMed]
 +
# Mathy, N., Bénard, L., Pellegrini, O., Daou, R., Wen, T. & Condon, C. (2007). 5'-to-3' exoribonuclease activity in bacteria: role of RNase J1 in rRNA maturation and 5' stability of mRNA. Cell 129:681-692. [http://www.ncbi.nlm.nih.gov/sites/entrez/17512403 PubMed]
 +
# Britton et al. (2007) Maturation of the 5' end of Bacillus subtilis 16S rRNA by the essential ribonuclease YkqC/RNase J1. Mol. Microbiol. 63: 127-138. [http://www.ncbi.nlm.nih.gov/sites/entrez/17229210 PubMed]
 +
# Yao, S., Blaustein, J. B. & Bechhofer, D. H. (2007). Processing of ''Bacillus subtilis'' small cytoplasmic RNA: evidence for an additional endonuclease cleavage site. Nucleic Acids Res. 35:4464-4473. [http://www.ncbi.nlm.nih.gov/sites/entrez/17576666 PubMed]
 +
# Daou-Chabo R, Mathy N, Bénard L, Condon C. (2009) Ribosomes initiating translation of the ''hbs'' mRNA protect it from 5'-to-3' exoribonucleolytic degradation by RNase J1.  ''Mol. Microbiol.'' '''71:''' 1538-1550. [http://www.ncbi.nlm.nih.gov/sites/entrez/19210617 PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 02:09, 30 April 2009

  • Description: RNase J1

Gene name rnjA
Synonyms ykqC
Essential yes PubMed
Product RNase J1
Function RNA processing
MW, pI 61 kDa, 5.902
Gene length, protein length 1665 bp, 555 aa
Immediate neighbours adeC, ykzG
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YkqC context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

essential PubMed

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: endonuclease and 5'-3' exonuclease
  • Protein family:
  • Paralogous protein(s): RnjB

RNAs affected by rnjA

hbs, thrS

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Localization: Cytoplasm

Database entries

  • Structure: 3BK1 (RNase J from Thermus thermophilus) 3BK2 (RNase J from Thermus thermophilus, complex with UMP)
  • Swiss prot entry:
  • KEGG entry: [2]
  • E.C. number:

Additional information

  • subject to Clp-dependent proteolysis upon glucose starvation PubMed

required for thrS RNA processing, involved in maturation of the 5’-end of the16S rRNA, subject to Clp-dependent proteolysis upon glucose starvation PubMed

Expression and regulation

  • Operon:
  • Sigma factor:
  • Regulation:
  • Regulatory mechanism:
  • Additional information: subject to Clp-dependent proteolysis upon glucose starvation PubMed, subject to Clp-dependent proteolysis upon glucose starvation PubMed

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab
  • Antibody:

Labs working on this gene/protein

Harald Putzer, IBPC Paris, France Homepage

David Bechhofer, Mount Sinai School, New York, USA Homepage

Ciaran Condon, IBPC, Paris, France Homepage

Your additional remarks

References

  1. Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 PubMed
  2. Even, S., Pellegrini, O., Zig, L., Labas, V., Vinh, J., Brechemmier-Baey, D., and Putzer, H. (2005) Ribonucleases J1 and J2: Two novel endoribonucleases in B. subtilis with functional homology to E. coli RNase E. Nucl Acids Res 33, 2141-2152. PubMed
  3. de la Sierra-Gallay IL, Zig L, Jamalli A, Putzer H. (2008 Structural insights into the dual activity of RNase J. Nat. Struct. Mol. Biol. 15:206-212. PubMed
  4. Mäder, U., Zig, L., Kretschmer, J., Homuth, G., and Putzer, H. (2008) mRNA processing by RNases J1 and J2 affects Bacillus subtilis gene expression on a global scale. Mol Microbiol 70, 183-196. PubMed
  5. Commichau, F. M., Rothe, F. M., Herzberg, C., Wagner, E., Hellwig, D., Lehnik-Habrink, M., Hammer, E., Völker, U. & Stülke, J. (2009) Novel activities of glycolytic enzymes in Bacillus subtilis: Interactions with essential proteins involved in mRNA processing. Mol. Cell. Proteomics in press PubMed
  6. Hunt, A., Rawlins, J. P., Thomaides, H. B., and Errington, J. (2006) Functional analysis of 11 putative essential genes in Bacillus subtilis. Microbiology 152, 2895-2907. PubMed
  7. Deikus, G., Condon, C. & Bechhofer, D. H. (2008). Role of Bacillus subtilis RNase J1 endonuclease and 5'-exonuclease activities in trp leader RNA turnover. J Biol Chem. 283:17158-17167. PubMed
  8. Mathy, N., Bénard, L., Pellegrini, O., Daou, R., Wen, T. & Condon, C. (2007). 5'-to-3' exoribonuclease activity in bacteria: role of RNase J1 in rRNA maturation and 5' stability of mRNA. Cell 129:681-692. PubMed
  9. Britton et al. (2007) Maturation of the 5' end of Bacillus subtilis 16S rRNA by the essential ribonuclease YkqC/RNase J1. Mol. Microbiol. 63: 127-138. PubMed
  10. Yao, S., Blaustein, J. B. & Bechhofer, D. H. (2007). Processing of Bacillus subtilis small cytoplasmic RNA: evidence for an additional endonuclease cleavage site. Nucleic Acids Res. 35:4464-4473. PubMed
  11. Daou-Chabo R, Mathy N, Bénard L, Condon C. (2009) Ribosomes initiating translation of the hbs mRNA protect it from 5'-to-3' exoribonucleolytic degradation by RNase J1. Mol. Microbiol. 71: 1538-1550. PubMed
  12. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=63942"