Difference between revisions of "Metabolism of signalling nucleotides"

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* 2.5.4. [[Nucleotide metabolism/ other]]
 
* 2.5.4. [[Nucleotide metabolism/ other]]
 
|Related=
 
|Related=
−
none
+
* [[DAC domain]]
 +
* [[EAL domain]]
 +
* [[GGDEF domain]]
 
|}}
 
|}}
  
Line 15: Line 17:
 
===ppGpp synthesis and degradation===
 
===ppGpp synthesis and degradation===
 
* [[RelA]]
 
* [[RelA]]
−
* [[YjbM]]
+
* [[SasA]]
−
* [[YwaC]]
+
* [[SasB]]
  
 
===c-di-AMP synthesis===
 
===c-di-AMP synthesis===
 
* [[DisA]]
 
* [[DisA]]
−
* [[YbbP]]
+
* [[CdaA]]
−
* [[YojJ]]
+
* [[CdaS]]
 +
 
 +
=== Control of c-di-AMP synthesis ===
 +
* [[CdaR]] controls [[CdaA]] activity {{PubMed|23192352}}
 +
* [[RadA]] controls [[DisA]] activity {{PubMed|23760274}}
 +
Note that c-di-AMP is essential for the growth of B. subtilis, but accumulation of the nucleotide is detrimental as well {{PubMed|23192352}}
  
 
===c-di-AMP degradation===
 
===c-di-AMP degradation===
 
* [[GdpP]]
 
* [[GdpP]]
 +
* [[PgpH]]
 +
* [[YfkN]]
 +
 +
===Protein potentially involved in c-di-GMP metabolism and signalling===
  
−
===c-di-GMP degradation (presence of an EAL domain)===
+
==== Proteins containing a [[GGDEF domain]] (potential diguanylate cyclases) ====
−
* [[YkoW]]
+
* [[DgcK]], has cyclase activity
−
* [[YkuI]]
+
* [[DgcW]], has cyclase activity, contains both a GGDEF and an [[EAL domain]]
−
* [[YuxH]]
+
* [[DgcP]], has cyclase activity
 +
* [[YdaK]], no activity, degenerate [[GGDEF domain]]
 +
* [[GdpP]], no diguanylate cyclase activity, is c-di-AMP specific phosphodiesterase (see above), degenerate GGDEF domain
  
−
=== c-di-GMP synthesis/ based on similarity (presence of a GGDEF domain)===
+
==== Proteins containing an [[EAL domain]] (potential c-di-GMP phosphodiesterases) ====
−
* [[GdpP]]
+
* [[PdeH]], has phosphodiesterase activity
−
* [[YdaK]]
+
* [[YkuI]], no phosphodiesterase activity
−
* [[YhcK]]
+
* [[DgcW]], phosphodiesterase activity not demonstrated, contains both a GGDEF and an [[EAL domain]]
−
* [[YkoW]]
 
−
* [[YtrP]] (this enzyme may be inactive due to the lack of important residues)
 
  
 
=== Targets of signalling nucleotides ===
 
=== Targets of signalling nucleotides ===
 
* ppGpp targets
 
* ppGpp targets
 +
** [[DnaG]]
 
** [[GdpP]]
 
** [[GdpP]]
 +
** [[Gmk]]
 +
** [[GuaB]]
 +
** [[HprT]]
 +
** [[RbgA]]
 +
** [[Era]]
 +
** [[YnbA]]
  
 
* c-di-GMP targets
 
* c-di-GMP targets
−
** [[YpfA]] (contains a PilZ domain)
+
** [[DgrA]] (contains a PilZ domain)
 +
 
 +
* other c-di-GMP-binding proteins
 +
** [[YdaK]]
 +
** [[YkuI]]
 +
 
 +
* c-di-AMP targets
 +
** [[DarA]] {{PubMed|25433025}}
 +
** [[KtrC]] (binds c-di-AMP ''in vivo'') {{PubMed|23671116}}
 +
** the [[ydaO riboswitch]] {{PubMed|24141192}}
  
 
==Important original publications==
 
==Important original publications==
−
<pubmed>21566650</pubmed>
+
<pubmed>21566650 22981860 23192352 23671116 23893111 24141192 24163341 25433025 25605304 26951678 22821967 28965724 </pubmed>
 +
 
 
==Important reviews==
 
==Important reviews==
−
<pubmed>21255104 16045609 17208514 19756011 19287449 18714086</pubmed>
+
<pubmed>21255104 16045609 17208514 19756011 19287449 18714086 23023210 23812326 25636134 25869574,26773214 27354347
 +
    27149325</pubmed>
 +
 
 
=Back to [[categories]]=
 
=Back to [[categories]]=

Latest revision as of 10:10, 3 October 2017

Parent categories
Neighbouring categories
Related categories

Genes in this functional category

ppGpp synthesis and degradation

c-di-AMP synthesis

Control of c-di-AMP synthesis

Note that c-di-AMP is essential for the growth of B. subtilis, but accumulation of the nucleotide is detrimental as well PubMed

c-di-AMP degradation

Protein potentially involved in c-di-GMP metabolism and signalling

Proteins containing a GGDEF domain (potential diguanylate cyclases)

  • DgcK, has cyclase activity
  • DgcW, has cyclase activity, contains both a GGDEF and an EAL domain
  • DgcP, has cyclase activity
  • YdaK, no activity, degenerate GGDEF domain
  • GdpP, no diguanylate cyclase activity, is c-di-AMP specific phosphodiesterase (see above), degenerate GGDEF domain

Proteins containing an EAL domain (potential c-di-GMP phosphodiesterases)

  • PdeH, has phosphodiesterase activity
  • YkuI, no phosphodiesterase activity
  • DgcW, phosphodiesterase activity not demonstrated, contains both a GGDEF and an EAL domain

Targets of signalling nucleotides

  • c-di-GMP targets
    • DgrA (contains a PilZ domain)
  • other c-di-GMP-binding proteins

Important original publications


Important reviews

Erin B Purcell, Rita Tamayo
Cyclic diguanylate signaling in Gram-positive bacteria.
FEMS Microbiol Rev: 2016, 40(5);753-73
[PubMed:27354347] [WorldCat.org] [DOI] (I p)

Wieland Steinchen, Gert Bange
The magic dance of the alarmones (p)ppGpp.
Mol Microbiol: 2016, 101(4);531-44
[PubMed:27149325] [WorldCat.org] [DOI] (I p)

TuAnh Ngoc Huynh, Joshua J Woodward
Too much of a good thing: regulated depletion of c-di-AMP in the bacterial cytoplasm.
Curr Opin Microbiol: 2016, 30;22-29
[PubMed:26773214] [WorldCat.org] [DOI] (I p)

Fabian M Commichau, Achim Dickmanns, Jan Gundlach, Ralf Ficner, Jörg Stülke
A jack of all trades: the multiple roles of the unique essential second messenger cyclic di-AMP.
Mol Microbiol: 2015, 97(2);189-204
[PubMed:25869574] [WorldCat.org] [DOI] (I p)

Kuanqing Liu, Alycia N Bittner, Jue D Wang
Diversity in (p)ppGpp metabolism and effectors.
Curr Opin Microbiol: 2015, 24;72-9
[PubMed:25636134] [WorldCat.org] [DOI] (I p)

Rebecca M Corrigan, Angelika Gründling
Cyclic di-AMP: another second messenger enters the fray.
Nat Rev Microbiol: 2013, 11(8);513-24
[PubMed:23812326] [WorldCat.org] [DOI] (I p)

Dimpy Kalia, Gökçe Merey, Shizuka Nakayama, Yue Zheng, Jie Zhou, Yiling Luo, Min Guo, Benjamin T Roembke, Herman O Sintim
Nucleotide, c-di-GMP, c-di-AMP, cGMP, cAMP, (p)ppGpp signaling in bacteria and implications in pathogenesis.
Chem Soc Rev: 2013, 42(1);305-41
[PubMed:23023210] [WorldCat.org] [DOI] (I p)

Mark Gomelsky
cAMP, c-di-GMP, c-di-AMP and now cGMP: bacteria use them all!
Mol Microbiol: 2011, 79(3);562-5
[PubMed:21255104] [WorldCat.org] [DOI] (I p)

Tilman Schirmer, Urs Jenal
Structural and mechanistic determinants of c-di-GMP signalling.
Nat Rev Microbiol: 2009, 7(10);724-35
[PubMed:19756011] [WorldCat.org] [DOI] (I p)

Regine Hengge
Principles of c-di-GMP signalling in bacteria.
Nat Rev Microbiol: 2009, 7(4);263-73
[PubMed:19287449] [WorldCat.org] [DOI] (I p)

Ute Römling
Great times for small molecules: c-di-AMP, a second messenger candidate in Bacteria and Archaea.
Sci Signal: 2008, 1(33);pe39
[PubMed:18714086] [WorldCat.org] [DOI] (I e)

Peggy A Cotter, Scott Stibitz
c-di-GMP-mediated regulation of virulence and biofilm formation.
Curr Opin Microbiol: 2007, 10(1);17-23
[PubMed:17208514] [WorldCat.org] [DOI] (P p)

Ute Römling, Mark Gomelsky, Michael Y Galperin
C-di-GMP: the dawning of a novel bacterial signalling system.
Mol Microbiol: 2005, 57(3);629-39
[PubMed:16045609] [WorldCat.org] [DOI] (P p)


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