Difference between revisions of "Easter egg"

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Line 1: Line 1:
* '''Description:''' 6S RNA<br/><br/>
+
* '''Description:''' RNA component of [[RNase]] P <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'''
|''bsrA''
+
|''rnpB''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''rnaP ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || 6S RNA
+
|style="background:#ABCDEF;" align="center"| '''Product''' || RNA component of ribonuclease P <br/>([[RNase]] P) (catalytic subunit, ribozyme)
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || antagonist of [[SigA]]
+
|style="background:#ABCDEF;" align="center"|'''Function''' || cleavage of precursor sequences <br/>from the 5' ends of pre-tRNAs
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length''' ||  190 bp
+
|style="background:#ABCDEF;" align="center"| '''Gene length''' ||  401 bp
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yrvM]]'', ''[[aspS]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ypsC]]'', ''[[ypsB]]''
 
|-
 
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rnpB_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
 +
 
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:BsrA_context.jpeg]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:rnpB_context.gif]]
 +
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
 
|}
 
|}
Line 26: Line 28:
 
__TOC__
 
__TOC__
  
<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|[[sigma factors and their control]]}},
+
{{SubtiWiki category|[[Rnases]]}},
 +
{{SubtiWiki category|[[translation]]}},
 
{{SubtiWiki category|[[ncRNA]]}}
 
{{SubtiWiki category|[[ncRNA]]}}
  
Line 44: Line 46:
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
  
reduced growth rate  [http://www.ncbi.nlm.nih.gov/sites/entrez/12177353 PubMed]
+
=== Database entries ===
 +
 
 +
* '''DBTBS entry:''' no entry
 +
 
 +
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG00045]
 +
 
 +
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2A64 2A64] (from Geobacillus stearothermophilus),  [http://www.rcsb.org/pdb/explore.do?structureId=1NBS 1NBS] (specificity domain)
  
  
=== Database entries ===
 
  
* '''DBTBS entry:''' no entry
+
=The RNA=
  
* '''SubtiList entry:''' no entry
+
* '''Biological activity:''' 5' end maturation of precursor tRNAs
 
* '''Structure:'''  
 
  
=== Additional information===
+
* '''RNA family:'''
  
 +
* '''cofactor:''' divalent cations (Ca(II) or Mg (II)) for the stabilization of the complex with pre-tRNA {{PubMed|20434461}}
  
 +
* '''interaction:''' [[RnpA]]-RnpB
  
 +
=== Additional information===
  
 
=Expression and regulation=
 
=Expression and regulation=
  
* '''Operon:''' ''bsrA''  [http://www.ncbi.nlm.nih.gov/sites/entrez/12177353 PubMed]
+
* '''Operon:'''  
  
* '''Sigma factor:''' [[SigA]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/12177353 PubMed]
+
* '''Sigma factor:'''  
  
* '''Regulation:''' expressed in vegetative cells  [http://www.ncbi.nlm.nih.gov/sites/entrez/12177353 PubMed]
+
* '''Regulation:'''  
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
* '''Additional information:''' transcribed as 201 nt RNA, processed to mature 190 bp 6S RNA  [http://www.ncbi.nlm.nih.gov/sites/entrez/12177353 PubMed]
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 80: Line 88:
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
 +
* '''GFP fusion:'''
  
=Labs working on this gene/RNA=
+
* '''two-hybrid system:'''
  
Kouji Nakamura, Tsukuba, University, Japan
+
* '''Antibody:'''
  
[[Roland Hartmann]], Philipps-Universität Marburg, Marburg, Germany, [http://www.uni-marburg.de/fb16/ipc/ag_hartmann Homepage]
+
=Labs working on this gene/RNA=
 +
* [[Carol Fierke]], University of Michigan, Ann Arbor, USA [https://www.chem.lsa.umich.edu/chem/faculty/facultyDetail.php?Uniqname=fierke homepage]
 +
* [[Roland Hartmann]], Marburg University, Germany [http://www.pharmazie.uni-marburg.de/pharmchem/akhartmann/ag_hartmann.htm homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
  
 
=References=
 
=References=
 +
==Reviews==
 +
<pubmed> 19215776 17868095 14691942 16650980 16980936 16679018 14550630 </pubmed>
  
<pubmed>15811922,,12177353 15811922, </pubmed>
+
==Original Publications==
 +
<pubmed>16470227,17355991,11812129,10390342,11454206, 19549719,11454206, 19717440 ,20133747  19932118 20188108 20434461 17299131 14510496 12951523 12836338 11577704 20557101 </pubmed>
  
 
[[Category:small RNA]]
 
[[Category:small RNA]]

Revision as of 13:50, 8 December 2010

  • Description: RNA component of RNase P

Gene name rnpB
Synonyms rnaP
Essential no
Product RNA component of ribonuclease P
(RNase P) (catalytic subunit, ribozyme)
Function cleavage of precursor sequences
from the 5' ends of pre-tRNAs
Gene length 401 bp
Immediate neighbours ypsC, ypsB
Gene sequence (+200bp)
Genetic context
RnpB context.gif
This image was kindly provided by SubtiList








Categories containing this gene/protein

Rnases, translation, ncRNA

This gene is a member of the following regulons

The gene

Basic information

  • Locus tag:

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]
  • Structure: 2A64 (from Geobacillus stearothermophilus), 1NBS (specificity domain)


The RNA

  • Biological activity: 5' end maturation of precursor tRNAs
  • RNA family:
  • cofactor: divalent cations (Ca(II) or Mg (II)) for the stabilization of the complex with pre-tRNA PubMed
  • interaction: RnpA-RnpB

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/RNA

Your additional remarks

References

Reviews


Original Publications

Ruiting Liang, Elzbieta Kierzek, Ryszard Kierzek, Douglas H Turner
Comparisons between chemical mapping and binding to isoenergetic oligonucleotide microarrays reveal unexpected patterns of binding to the Bacillus subtilis RNase P RNA specificity domain.
Biochemistry: 2010, 49(37);8155-68
[PubMed:20557101] [WorldCat.org] [DOI] (I p)

John Hsieh, Kristin S Koutmou, David Rueda, Markos Koutmos, Nils G Walter, Carol A Fierke
A divalent cation stabilizes the active conformation of the B. subtilis RNase P x pre-tRNA complex: a role for an inner-sphere metal ion in RNase P.
J Mol Biol: 2010, 400(1);38-51
[PubMed:20434461] [WorldCat.org] [DOI] (I p)

Nathan J Baird, Haipeng Gong, Syed S Zaheer, Karl F Freed, Tao Pan, Tobin R Sosnick
Extended structures in RNA folding intermediates are due to nonnative interactions rather than electrostatic repulsion.
J Mol Biol: 2010, 397(5);1298-306
[PubMed:20188108] [WorldCat.org] [DOI] (I p)

Kristin S Koutmou, Anette Casiano-Negroni, Melissa M Getz, Samuel Pazicni, Andrew J Andrews, James E Penner-Hahn, Hashim M Al-Hashimi, Carol A Fierke
NMR and XAS reveal an inner-sphere metal binding site in the P4 helix of the metallo-ribozyme ribonuclease P.
Proc Natl Acad Sci U S A: 2010, 107(6);2479-84
[PubMed:20133747] [WorldCat.org] [DOI] (I p)

Kristin S Koutmou, Nathan H Zahler, Jeffrey C Kurz, Frank E Campbell, Michael E Harris, Carol A Fierke
Protein-precursor tRNA contact leads to sequence-specific recognition of 5' leaders by bacterial ribonuclease P.
J Mol Biol: 2010, 396(1);195-208
[PubMed:19932118] [WorldCat.org] [DOI] (I p)

Stefanie A Mortimer, Kevin M Weeks
C2'-endo nucleotides as molecular timers suggested by the folding of an RNA domain.
Proc Natl Acad Sci U S A: 2009, 106(37);15622-7
[PubMed:19717440] [WorldCat.org] [DOI] (I p)

John Hsieh, Carol A Fierke
Conformational change in the Bacillus subtilis RNase P holoenzyme--pre-tRNA complex enhances substrate affinity and limits cleavage rate.
RNA: 2009, 15(8);1565-77
[PubMed:19549719] [WorldCat.org] [DOI] (I p)

Barbara Wegscheid, Roland K Hartmann
In vivo and in vitro investigation of bacterial type B RNase P interaction with tRNA 3'-CCA.
Nucleic Acids Res: 2007, 35(6);2060-73
[PubMed:17355991] [WorldCat.org] [DOI] (I p)

Somashekarappa Niranjanakumari, Jeremy J Day-Storms, Mahiuddin Ahmed, John Hsieh, Nathan H Zahler, Ronald A Venters, Carol A Fierke
Probing the architecture of the B. subtilis RNase P holoenzyme active site by cross-linking and affinity cleavage.
RNA: 2007, 13(4);521-35
[PubMed:17299131] [WorldCat.org] [DOI] (P p)

Barbara Wegscheid, Ciarán Condon, Roland K Hartmann
Type A and B RNase P RNAs are interchangeable in vivo despite substantial biophysical differences.
EMBO Rep: 2006, 7(4);411-7
[PubMed:16470227] [WorldCat.org] [DOI] (P p)

Tomoaki Ando, Terumichi Tanaka, Yo Kikuchi
Bacterial ribonuclease P reaction is affected by substrate shape and magnesium ion concentration.
Nucleic Acids Res Suppl: 2003, (3);293-4
[PubMed:14510496] [DOI] (P p)

Tomoaki Ando, Terumichi Tanaka, Yo Kikuchi
Comparative analyses of hairpin substrate recognition by Escherichia coli and Bacillus subtilis ribonuclease P ribozymes.
Biosci Biotechnol Biochem: 2003, 67(8);1825-7
[PubMed:12951523] [WorldCat.org] [DOI] (P p)

Y Hori, T Tanaka, Y Kikuchi
In vitro hyperprocessing of tRNAs by Bacillus subtilis ribonuclease P RNA.
Nucleic Acids Res Suppl: 2001, (1);209-10
[PubMed:12836338] [DOI] (P p)

Christoph Rox, Ralph Feltens, Thomas Pfeiffer, Roland K Hartmann
Potential contact sites between the protein and RNA subunit in the Bacillus subtilis RNase P holoenzyme.
J Mol Biol: 2002, 315(4);551-60
[PubMed:11812129] [WorldCat.org] [DOI] (P p)

Y Hori, E Sakai, T Tanaka, Y Kikuchi
Hyperprocessing reaction of tRNA by Bacillus subtilis ribonuclease P ribozyme.
FEBS Lett: 2001, 505(2);337-9
[PubMed:11577704] [WorldCat.org] [DOI] (P p)

A Hansen, T Pfeiffer, T Zuleeg, S Limmer, J Ciesiolka, R Feltens, R K Hartmann
Exploring the minimal substrate requirements for trans-cleavage by RNase P holoenzymes from Escherichia coli and Bacillus subtilis.
Mol Microbiol: 2001, 41(1);131-43
[PubMed:11454206] [WorldCat.org] [DOI] (P p)

J M Warnecke, R Held, S Busch, R K Hartmann
Role of metal ions in the hydrolysis reaction catalyzed by RNase P RNA from Bacillus subtilis.
J Mol Biol: 1999, 290(2);433-45
[PubMed:10390342] [WorldCat.org] [DOI] (P p)