Difference between revisions of "SubtInteract"
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Protein-protein interactions are essential for many activities of any living cell. These interactions involve multi-protein complexes that take part in central processes such as [[DNA replication]], [[transcription]] or [[translation]]. Protein-protein interactions may also be involved in a variety of regulatory events. Metabolic enzymes do often form transien complexes that represent a complete pathways. These complexes are called metabolon. Finally, many interactions may be of a transient nature. | Protein-protein interactions are essential for many activities of any living cell. These interactions involve multi-protein complexes that take part in central processes such as [[DNA replication]], [[transcription]] or [[translation]]. Protein-protein interactions may also be involved in a variety of regulatory events. Metabolic enzymes do often form transien complexes that represent a complete pathways. These complexes are called metabolon. Finally, many interactions may be of a transient nature. | ||
| − | + | =Methods to detect protein-protein interactions= | |
* Bacterial Two Hybrid System: [[BACTH]] {{PubMed|9576956}} | * Bacterial Two Hybrid System: [[BACTH]] {{PubMed|9576956}} | ||
| Line 14: | Line 14: | ||
'''Attention:''' Each technique detects only about 33% of all interactions {{PubMed|20805792,19060903}} | '''Attention:''' Each technique detects only about 33% of all interactions {{PubMed|20805792,19060903}} | ||
| − | + | =Visualization of protein-protein interactions in ''B. subtilis''= | |
* [http://cellpublisher.gobics.de/subtinteract/startpage/start/ interactive protein-protein interaction map] | * [http://cellpublisher.gobics.de/subtinteract/startpage/start/ interactive protein-protein interaction map] | ||
* the beta version of [http://subtiwiki.uni-goettingen.de/pathways/SubtInteract/demo_mitlinks/ SubtInteract] | * the beta version of [http://subtiwiki.uni-goettingen.de/pathways/SubtInteract/demo_mitlinks/ SubtInteract] | ||
| − | + | =Protein complexes in ''B. subtilis''= | |
| + | ==Complexes in [[Cellular processes]]== | ||
| + | === [[cell wall synthesis]] and [[cell shape]]: the [[cell wall biosynthhetic complex]]=== | ||
| + | === [[cell division]]: the [[divisome]]=== | ||
| + | |||
| + | ==Complexes in [[Metabolism]]== | ||
| + | === the metabolons of glycolysis and the TCA cycle {{PubMed|19193632,20933603}}=== | ||
| + | |||
| + | ==Complexes in [[Information processing]]== | ||
=== [[DNA replication]]: the [[replisome]]=== | === [[DNA replication]]: the [[replisome]]=== | ||
=== [[transcription]]: [[RNA polymerase]]=== | === [[transcription]]: [[RNA polymerase]]=== | ||
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=== synthesis of glutamyl-tRNA(Gln): the [[transamidosome]] ([[GatA]]-[[GatB]]-[[GatC]])-[[GltX]]-[[trnS-Gln]]=== | === synthesis of glutamyl-tRNA(Gln): the [[transamidosome]] ([[GatA]]-[[GatB]]-[[GatC]])-[[GltX]]-[[trnS-Gln]]=== | ||
=== [[RNases|RNA processing and degradation]]: the [[RNA degradosome]]=== | === [[RNases|RNA processing and degradation]]: the [[RNA degradosome]]=== | ||
| + | |||
| + | ==Complexes involved in [[Lifestyles]]== | ||
=== [[General stress proteins (controlled by SigB)|general stress response]]: the [[stressosome]]=== | === [[General stress proteins (controlled by SigB)|general stress response]]: the [[stressosome]]=== | ||
| − | |||
=== DNA uptake: the [[pseudopilus]] {{PubMed|21278288,16751195}}=== | === DNA uptake: the [[pseudopilus]] {{PubMed|21278288,16751195}}=== | ||
| − | |||
===spore [[germination]]: the [[germinosome]]=== | ===spore [[germination]]: the [[germinosome]]=== | ||
Revision as of 18:40, 10 July 2011
Protein-protein interactions are essential for many activities of any living cell. These interactions involve multi-protein complexes that take part in central processes such as DNA replication, transcription or translation. Protein-protein interactions may also be involved in a variety of regulatory events. Metabolic enzymes do often form transien complexes that represent a complete pathways. These complexes are called metabolon. Finally, many interactions may be of a transient nature.
Contents
- 1 Methods to detect protein-protein interactions
- 2 Visualization of protein-protein interactions in B. subtilis
- 3 Protein complexes in B. subtilis
Methods to detect protein-protein interactions
- Yeast Two Hybrid System PubMed
- TAP-Tag purification PubMed
Attention: Each technique detects only about 33% of all interactions PubMed
Visualization of protein-protein interactions in B. subtilis
- interactive protein-protein interaction map
- the beta version of SubtInteract
Protein complexes in B. subtilis
Complexes in Cellular processes
cell wall synthesis and cell shape: the cell wall biosynthhetic complex
cell division: the divisome
Complexes in Metabolism
the metabolons of glycolysis and the TCA cycle PubMed
Complexes in Information processing
DNA replication: the replisome
transcription: RNA polymerase
translation: the ribosome
synthesis of glutamyl-tRNA(Gln): the transamidosome (GatA-GatB-GatC)-GltX-trnS-Gln
RNA processing and degradation: the RNA degradosome
Complexes involved in Lifestyles
general stress response: the stressosome
DNA uptake: the pseudopilus PubMed
spore germination: the germinosome
Suspected hub proteins potentially involved in a large number of interactions (as deduced from a Yeast two-hybrid analysis)
- FruA, SwrC, XhlA, YhaP, YhgE, YkcC, YqfF, CsbC, CssS, FliZ, MreD, PpsC, RacA, Smc, YclI, YdeL, YdgH, YdbI, YesS, YkoT, YopZ, YqbD, YtdP, YueB, YwqJ, YyxA
Elodie Marchadier, Rut Carballido-López, Sophie Brinster, Céline Fabret, Peggy Mervelet, Philippe Bessières, Marie-Françoise Noirot-Gros, Vincent Fromion, Philippe Noirot
An expanded protein-protein interaction network in Bacillus subtilis reveals a group of hubs: Exploration by an integrative approach.
Proteomics: 2011, 11(15);2981-91
[PubMed:21630458]
[WorldCat.org]
[DOI]
(I p)
Important publications
Agnès Vendeville, Damien Larivière, Eric Fourmentin
An inventory of the bacterial macromolecular components and their spatial organization.
FEMS Microbiol Rev: 2011, 35(2);395-414
[PubMed:20969605]
[WorldCat.org]
[DOI]
(I p)
Mike P Williamson, Michael J Sutcliffe
Protein-protein interactions.
Biochem Soc Trans: 2010, 38(4);875-8
[PubMed:20658969]
[WorldCat.org]
[DOI]
(I p)
Patrick Amar, Guillaume Legent, Michel Thellier, Camille Ripoll, Gilles Bernot, Thomas Nystrom, Milton H Saier, Vic Norris
A stochastic automaton shows how enzyme assemblies may contribute to metabolic efficiency.
BMC Syst Biol: 2008, 2;27
[PubMed:18366733]
[WorldCat.org]
[DOI]
(I e)
Adam Brymora, Valentina A Valova, Phillip J Robinson
Protein-protein interactions identified by pull-down experiments and mass spectrometry.
Curr Protoc Cell Biol: 2004, Chapter 17;Unit 17.5
[PubMed:18228443]
[WorldCat.org]
[DOI]
(I p)
Hongtao Guan, Endre Kiss-Toth
Advanced technologies for studies on protein interactomes.
Adv Biochem Eng Biotechnol: 2008, 110;1-24
[PubMed:18219467]
[WorldCat.org]
[DOI]
(I p)
Vincent Collura, Guillaume Boissy
From protein-protein complexes to interactomics.
Subcell Biochem: 2007, 43;135-83
[PubMed:17953394]
[WorldCat.org]
[DOI]
(P p)
Philippe Noirot, Marie-Françoise Noirot-Gros
Protein interaction networks in bacteria.
Curr Opin Microbiol: 2004, 7(5);505-12
[PubMed:15451506]
[WorldCat.org]
[DOI]
(P p)
Barry Causier
Studying the interactome with the yeast two-hybrid system and mass spectrometry.
Mass Spectrom Rev: 2004, 23(5);350-67
[PubMed:15264234]
[WorldCat.org]
[DOI]
(P p)
Andrzej Dziembowski, Bertrand Séraphin
Recent developments in the analysis of protein complexes.
FEBS Lett: 2004, 556(1-3);1-6
[PubMed:14706816]
[WorldCat.org]
[DOI]
(P p)
Alfonso Valencia, Florencio Pazos
Computational methods for the prediction of protein interactions.
Curr Opin Struct Biol: 2002, 12(3);368-73
[PubMed:12127457]
[WorldCat.org]
[DOI]
(P p)
Peter Uetz
Two-hybrid arrays.
Curr Opin Chem Biol: 2002, 6(1);57-62
[PubMed:11827824]
[WorldCat.org]
[DOI]
(P p)
P Legrain, J Wojcik, J M Gauthier
Protein--protein interaction maps: a lead towards cellular functions.
Trends Genet: 2001, 17(6);346-52
[PubMed:11377797]
[WorldCat.org]
[DOI]
(P p)
C L Tucker, J F Gera, P Uetz
Towards an understanding of complex protein networks.
Trends Cell Biol: 2001, 11(3);102-6
[PubMed:11306254]
[WorldCat.org]
[DOI]
(P p)
P Uetz, R E Hughes
Systematic and large-scale two-hybrid screens.
Curr Opin Microbiol: 2000, 3(3);303-8
[PubMed:10851163]
[WorldCat.org]
[DOI]
(P p)
Z Chen, M Han
Building a protein interaction map: research in the post-genome era.
Bioessays: 2000, 22(6);503-6
[PubMed:10842303]
[WorldCat.org]
[DOI]
(P p)
P A Srere
Macromolecular interactions: tracing the roots.
Trends Biochem Sci: 2000, 25(3);150-3
[PubMed:10694888]
[WorldCat.org]
[DOI]
(P p)
P A Srere, J Ovadi
Enzyme-enzyme interactions and their metabolic role.
FEBS Lett: 1990, 268(2);360-4
[PubMed:2200717]
[WorldCat.org]
[DOI]
(P p)
P A Srere
Complexes of sequential metabolic enzymes.
Annu Rev Biochem: 1987, 56;89-124
[PubMed:2441660]
[WorldCat.org]
[DOI]
(P p)
