Editing Interactome (section)

===Bacterial interactomes===
Relatively few bacteria have been comprehensively studied for their protein–protein interactions. However, none of these interactomes are complete in the sense that they captured all interactions. In fact, it has been estimated that none of them covers more than 20% or 30% of all interactions, primarily because most of these studies have only employed a single method, all of which discover only a subset of interactions.<ref name="Chen">{{Cite journal
| last1 = Chen | first1 = Y. C.
| last2 = Rajagopala | first2 = S. V.
| last3 = Stellberger | first3 = T.
| last4 = Uetz | first4 = P.
| title = Exhaustive benchmarking of the yeast two-hybrid system
| doi = 10.1038/nmeth0910-667
| journal = Nature Methods
| volume = 7
| issue = 9
| pages = 667–668; author 668 668
| year = 2010
| pmid = 20805792
| s2cid = 35834541
| pmc = 10332476
}}</ref> Among the published bacterial interactomes (including partial ones) are

{| class="wikitable sortable"
! Species
! proteins total
! interactions
! type
! reference
|-
| ''[[Helicobacter pylori]]'' ||1,553||~3,004||Y2H||<ref name="Rain">{{Cite journal | last1 = Rain | first1 = J. C. | last2 = Selig | first2 = L. | last3 = De Reuse | first3 = H. | last4 = Battaglia | first4 = V. R. | last5 = Reverdy | first5 = C. L. | last6 = Simon | first6 = S. P. | last7 = Lenzen | first7 = G. | last8 = Petel | first8 = F. | last9 = Wojcik | first9 = J. R. M. | last10 = Schächter | first10 = V. | last11 = Chemama | first11 = Y. | last12 = Labigne | first12 = A. S. | last13 = Legrain | first13 = P. | title = The protein–protein interaction map of Helicobacter pylori | journal = Nature | volume = 409 | issue = 6817 | pages = 211–215 | doi = 10.1038/35051615 | year = 2001 | pmid = 11196647 
| bibcode = 2001Natur.409..211R | s2cid = 4400094 }}</ref><ref name="Häuser2014">{{Cite journal | pmid = 24627523 | year = 2014 | last1 = Häuser | first1 = R | title = A Second-generation Protein–Protein Interaction Network of Helicobacter pylori | journal = Molecular & Cellular Proteomics | last2 = Ceol | first2 = A | last3 = Rajagopala | first3 = S. V. | last4 = Mosca | first4 = R | last5 = Siszler | first5 = G | last6 = Wermke | first6 = N | last7 = Sikorski | first7 = P | last8 = Schwarz | first8 = F | last9 = Schick | first9 = M | last10 = Wuchty | first10 = S | last11 = Aloy | first11 = P | last12 = Uetz | first12 = P | doi = 10.1074/mcp.O113.033571 | volume=13 | issue=5 | pages=1318–29 | doi-access = free | pmc = 4014287 }}</ref>
|-
| ''[[Campylobacter jejuni]]''||1,623||11,687||Y2H||<ref>{{cite journal|last=Parrish|first=JR|display-authors=etal|title=A proteome-wide protein interaction map for Campylobacter jejuni|journal=Genome Biol|year=2007|pmid=17615063|doi=10.1186/gb-2007-8-7-r130|pmc=2323224|volume=8|issue=7|pages=R130 |doi-access=free }}</ref>
|-
| ''[[Treponema pallidum]]'' ||1,040||3,649||Y2H||<ref name="Titz2008">{{Cite journal | last1 = Rajagopala | first1 = S. V. | last2 = Titz | first2 = B. R. | last3 = Goll | first3 = J. | last4 = Häuser | first4 = R. | last5 = McKevitt | first5 = M. T. | last6 = Palzkill | first6 = T. | last7 = Uetz | first7 = P. | editor1-last = Hall | editor1-first = Neil | title = The Binary Protein Interactome of Treponema pallidum – the Syphilis Spirochete | doi = 10.1371/journal.pone.0002292 | journal = PLOS ONE | volume = 3 | issue = 5 | pages = e2292 | year = 2008 | pmid = 18509523 | pmc =2386257 | bibcode = 2008PLoSO...3.2292T | doi-access = free }}</ref>
|-
| ''[[Escherichia coli]]'' ||4,288||(5,993)||AP/MS||<ref>{{cite journal|last=Hu|first=P|display-authors=etal|title=Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins|journal=PLOS Biol |year=2009|pmid=19402753|doi=10.1371/journal.pbio.1000096|pmc=2672614|volume=7|issue=4|pages=e96|editor1-last=Levchenko|editor1-first=Andre|doi-access=free}} {{open access}}</ref>
|-
| ''[[Escherichia coli]]'' || 4,288 ||2,234||Y2H||<ref name="Rajagopala2014">{{Cite journal | pmid = 24561554 | year = 2014 | last1 = Rajagopala | first1 = S. V. | title = The binary protein–protein interaction landscape of Escherichia coli | journal = Nature Biotechnology | last2 = Sikorski | first2 = P | last3 = Kumar | first3 = A | last4 = Mosca | first4 = R | last5 = Vlasblom | first5 = J | last6 = Arnold | first6 = R | last7 = Franca-Koh | first7 = J | last8 = Pakala | first8 = S. B. | last9 = Phanse | first9 = S | last10 = Ceol | first10 = A | last11 = Häuser | first11 = R | last12 = Siszler | first12 = G | last13 = Wuchty | first13 = S | last14 = Emili | first14 = A | last15 = Babu | first15 = M | last16 = Aloy | first16 = P | last17 = Pieper | first17 = R | last18 = Uetz | first18 = P | doi = 10.1038/nbt.2831 | volume=32 | issue=3 | pages=285–90 | pmc=4123855 }}</ref>
|-
| ''[[Mesorhizobium loti]]'' ||6,752||3,121||Y2H||<ref name="Mloti">{{Cite journal | last1 = Shimoda | first1 = Y. | last2 = Shinpo | first2 = S. | last3 = Kohara | first3 = M. | last4 = Nakamura | first4 = Y. | last5 = Tabata | first5 = S. | last6 = Sato | first6 = S. | doi = 10.1093/dnares/dsm028 | title = A Large Scale Analysis of Protein–Protein Interactions in the Nitrogen-fixing Bacterium Mesorhizobium loti | journal = DNA Research | volume = 15 | issue = 1 | pages = 13–23 | year = 2008 | pmid = 18192278 | pmc =2650630 }}</ref>
|-
| ''[[Mycobacterium tuberculosis]]'' ||3,959||>8000||B2H||<ref name="Mtub">{{Cite journal | last1 = Wang | first1 = Y. | last2 = Cui | first2 = T. | last3 = Zhang | first3 = C. | last4 = Yang | first4 = M. | last5 = Huang | first5 = Y. | last6 = Li | first6 = W. | last7 = Zhang | first7 = L. | last8 = Gao | first8 = C. | last9 = He | first9 = Y. | last10 = Li | doi = 10.1021/pr100808n | first10 = Y. | last11 = Huang | first11 = F. | last12 = Zeng | first12 = J. | last13 = Huang | first13 = C. | last14 = Yang | first14 = Q. | last15 = Tian | first15 = Y. | last16 = Zhao | first16 = C. | last17 = Chen | first17 = H. | last18 = Zhang | first18 = H. | last19 = He | first19 = Z. G. | title = Global Protein−Protein Interaction Network in the Human PathogenMycobacterium tuberculosisH37Rv | journal = Journal of Proteome Research | volume = 9 | issue = 12 | pages = 6665–6677 | year = 2010 | pmid = 20973567 }}</ref>
|-
| ''[[Mycoplasma genitalium]]'' ||482||||AP/MS||<ref name="Myco">{{Cite journal | last1 = Kuhner | first1 = S. | last2 = Van Noort | first2 = V. | last3 = Betts | first3 = M. J. | last4 = Leo-Macias | first4 = A. | last5 = Batisse | first5 = C. | last6 = Rode | first6 = M. | last7 = Yamada | first7 = T. | last8 = Maier | first8 = T. | last9 = Bader | first9 = S. | doi = 10.1126/science.1176343 | last10 = Beltran-Alvarez | first10 = P. | last11 = Castaño-Diez | first11 = D. | last12 = Chen | first12 = W. -H. | last13 = Devos | first13 = D. | last14 = Güell | first14 = M. | last15 = Norambuena | first15 = T. | last16 = Racke | first16 = I. | last17 = Rybin | first17 = V. | last18 = Schmidt | first18 = A. | last19 = Yus | first19 = E. | last20 = Aebersold | first20 = R. | last21 = Herrmann | first21 = R. | last22 = Böttcher | first22 = B. | last23 = Frangakis | first23 = A. S. | last24 = Russell | first24 = R. B. | last25 = Serrano | first25 = L. | last26 = Bork | first26 = P. | last27 = Gavin | first27 = A. -C. | title = Proteome Organization in a Genome-Reduced Bacterium | journal = Science | volume = 326 | issue = 5957 | pages = 1235–1240 | year = 2009 | pmid = 19965468 | bibcode = 2009Sci...326.1235K | s2cid = 19334426 }}</ref>
|-
| ''[[Synechocystis]]'' sp. PCC6803 ||3,264||3,236||Y2H||<ref name="Sato">{{Cite journal | last1 = Sato | first1 = S. | last2 = Shimoda | first2 = Y. | last3 = Muraki | first3 = A. | last4 = Kohara | first4 = M. | last5 = Nakamura | first5 = Y. | last6 = Tabata | first6 = S. | doi = 10.1093/dnares/dsm021 | title = A Large-scale Protein protein Interaction Analysis in Synechocystis sp. PCC6803 | journal = DNA Research | volume = 14 | issue = 5 | pages = 207–216 | year = 2007 | pmid = 18000013 | pmc =2779905 }}</ref>
|-
| ''[[Staphylococcus aureus]]'' (MRSA) ||2,656||13,219||AP/MS||<ref name="Cherkasov">{{Cite journal | pmid = 21166474 | year = 2011 | last1 = Cherkasov | first1 = A | title = Mapping the protein interaction network in methicillin-resistant ''Staphylococcus aureus'' | journal = Journal of Proteome Research | volume = 10 | issue = 3 | pages = 1139–50 | last2 = Hsing | first2 = M | last3 = Zoraghi | first3 = R | last4 = Foster | first4 = L. J. | last5 = See | first5 = R. H. | last6 = Stoynov | first6 = N | last7 = Jiang | first7 = J | last8 = Kaur | first8 = S | last9 = Lian | first9 = T | last10 = Jackson | first10 = L | last11 = Gong | first11 = H | last12 = Swayze | first12 = R | last13 = Amandoron | first13 = E | last14 = Hormozdiari | first14 = F | last15 = Dao | first15 = P | last16 = Sahinalp | first16 = C | last17 = Santos-Filho | first17 = O | last18 = Axerio-Cilies | first18 = P | last19 = Byler | first19 = K | last20 = McMaster | first20 = W. R. | last21 = Brunham | first21 = R. C. | last22 = Finlay | first22 = B. B. | last23 = Reiner | first23 = N. E. | doi = 10.1021/pr100918u }}</ref>
|}

The ''E. coli'' and ''Mycoplasma'' interactomes have been analyzed using large-scale protein complex affinity purification and mass spectrometry (AP/MS), hence it is not easily possible to infer direct interactions. The others have used extensive [[yeast two-hybrid]] (Y2H) screens. The ''Mycobacterium tuberculosis'' interactome has been analyzed using a [[bacterial two-hybrid screen]] (B2H).

Note that numerous additional interactomes have been predicted using computational methods (see section above).