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. Finally, many interactions may be of a transient nature.
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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.
  
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==Methods to detect protein-protein interactions==
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<br/>
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*
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<big>'''Now online: A description of ''Subti''Wiki, ''Subti''Pathways, and ''Subt''Interact in the 2012 Database issue of Nucleic Acids Research'''</big>
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<pubmed> 22096228 </pubmed>
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=Methods to detect protein-protein interactions=
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* Bacterial Two Hybrid System: [[BACTH]] {{PubMed|9576956}}
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* Yeast Two Hybrid System {{PubMed|18218650,16806892,16262681,15064463,11769011,10967325,8816737,7894083}}
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* [[SPINE]]: A method to detect ''in vivo'' protein-protein interactions after cross-linking {{PubMed|17994626}}
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* TAP-Tag purification {{PubMed|10504710,11403571}}
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* ''in vivo'' detection of protein-protein interaction using [[DivIVA]] and GFP {{PubMed|19698693}}
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'''Attention:''' Each technique detects only about 33% of all interactions {{PubMed|20805792,19060903}}
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=Visualization of protein-protein interactions in ''B. subtilis''=
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* [http://cellpublisher.gobics.de/subtinteract/startpage/start/ interactive protein-protein interaction map]
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* the beta version of [http://subtiwiki.uni-goettingen.de/pathways/SubtInteract/demo_mitlinks/ SubtInteract]
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=Protein complexes in ''B. subtilis''=
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==Complexes in [[Cellular processes]]==
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=== [[cell wall synthesis]] and [[cell shape]]: the [[elongasome]]===
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=== [[cell division]]: the [[divisome]]===
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== Complexes in [[metabolism]], [[ATP synthesis]] and [[respiration]] ==
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=== the metabolons of glycolysis and the TCA cycle {{PubMed|19193632,20933603}}===
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=== the [[ATP synthase]] ===
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=== [[respiratory complexes and supercomplexes]] ===
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==Complexes in [[Information processing]]==
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=== Initiation of [[DNA replication]]: the [[primosome]]===
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=== [[DNA replication]]: the [[replisome]]===
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=== origin segregation: [[condensin]] ===
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=== [[transcription]]: [[RNA polymerase]]===
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=== [[translation]]: the [[ribosomal proteins|ribosome]]===
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=== synthesis of glutamyl-tRNA(Gln): the [[transamidosome]] ([[GatA]]-[[GatB]]-[[GatC]])-[[GltX]]-[[trnS-Gln]]===
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=== [[RNases|RNA processing and degradation]]: the [[RNA degradosome]]===
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=== [[protein secretion]]: the [[signal recognition particle]] ===
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==Complexes involved in [[Lifestyles]]==
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=== [[General stress proteins (controlled by SigB)|general stress response]]: the [[stressosome]]===
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=== DNA uptake: the [[pseudopilus]] {{PubMed|21278288,16751195}}===
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===spore [[germination]]: the [[germinosome]]===
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=Suspected hub proteins potentially involved in a large number of interactions (as deduced from a Yeast two-hybrid analysis)=
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* [[FruA]], [[SwrC]], [[XhlA]], [[YhaP]], [[YhgE]], [[YkcC]], [[PgpH]], [[CsbC]], [[CssS]], [[FliZ]], [[MreD]], [[PpsC]], [[RacA]], [[Smc]], [[YclI]], [[YdeL]], [[YdgH]], [[YdbI]], [[RhgR]], [[YkoT]], [[YopZ]], [[YqbD]], [[RmgR]], [[YueB]], [[YwqJ]], [[YyxA]]
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<pubmed> 21630458</pubmed>
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=Important publications=
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<pubmed>20658969 18228443 18219467 17953394 15264234 14706816 12127457 11827824 11377797 11306254 10851163 10842303 18366733 10694888 2200717 2441660  20969605 15451506 9787636 22790590 23808343 </pubmed>

Latest revision as of 13:48, 8 May 2015

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.


Now online: A description of SubtiWiki, SubtiPathways, and SubtInteract in the 2012 Database issue of Nucleic Acids Research

Ulrike Mäder, Arne G Schmeisky, Lope A Flórez, Jörg Stülke
SubtiWiki--a comprehensive community resource for the model organism Bacillus subtilis.
Nucleic Acids Res: 2012, 40(Database issue);D1278-87
[PubMed:22096228] [WorldCat.org] [DOI] (I p)


Methods to detect protein-protein interactions

  • Yeast Two Hybrid System PubMed
  • SPINE: A method to detect in vivo protein-protein interactions after cross-linking PubMed
  • in vivo detection of protein-protein interaction using DivIVA and GFP PubMed

Attention: Each technique detects only about 33% of all interactions PubMed

Visualization of protein-protein interactions in B. subtilis

Protein complexes in B. subtilis

Complexes in Cellular processes

cell wall synthesis and cell shape: the elongasome

cell division: the divisome

Complexes in metabolism, ATP synthesis and respiration

the metabolons of glycolysis and the TCA cycle PubMed

the ATP synthase

respiratory complexes and supercomplexes

Complexes in Information processing

Initiation of DNA replication: the primosome

DNA replication: the replisome

origin segregation: condensin

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

protein secretion: the signal recognition particle

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)

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

Ariel Fernández
Withdrawn: Supramolecular Evolution of Protein Organization.
Annu Rev Genet: 2013;
[PubMed:23808343] [WorldCat.org] [DOI] (I a)

Led Yered Jafet García Montes de Oca, Alicia Chagolla-López, Luis González de la Vara, Tecilli Cabellos-Avelar, Carlos Gómez-Lojero, Emma Berta Gutiérrez Cirlos
The composition of the Bacillus subtilis aerobic respiratory chain supercomplexes.
J Bioenerg Biomembr: 2012, 44(4);473-86
[PubMed:22790590] [WorldCat.org] [DOI] (I p)

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)

T Dandekar, B Snel, M Huynen, P Bork
Conservation of gene order: a fingerprint of proteins that physically interact.
Trends Biochem Sci: 1998, 23(9);324-8
[PubMed:9787636] [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)

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