Editing Escherichia coli (section)

==Proteomics==

===Proteome===
The genome sequence of ''E. coli'' predicts 4288 protein-coding genes, of which 38 percent initially had no attributed function. Comparison with five other sequenced microbes reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within ''E. coli'' are also evident. The largest family of paralogous proteins contains 80 ABC transporters. The genome as a whole is strikingly organized with respect to the local direction of replication; guanines, oligonucleotides possibly related to replication and recombination, and most genes are so oriented. The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer.<ref name = "Blattner_1997" />

Several studies have experimentally investigated the [[proteome]] of ''E. coli''. By 2006, 1,627 (38%) of the predicted proteins ([[open reading frames]], ORFs) had been identified experimentally.<ref name="HanLee">{{cite journal | vauthors = Han MJ, Lee SY | title = The ''Escherichia coli'' proteome: past, present, and future prospects | journal = Microbiology and Molecular Biology Reviews | volume = 70 | issue = 2 | pages = 362–439 | date = June 2006 | pmid = 16760308 | pmc = 1489533 | doi = 10.1128/MMBR.00036-05 }}</ref> Mateus et al. 2020 detected 2,586 proteins with at least 2 peptides (60% of all proteins).<ref>{{cite journal | vauthors = Mateus A, Hevler J, Bobonis J, Kurzawa N, Shah M, Mitosch K, Goemans CV, Helm D, Stein F, Typas A, Savitski MM | display-authors = 6 | title = The functional proteome landscape of ''Escherichia coli'' | journal = Nature | volume = 588 | issue = 7838 | pages = 473–478 | date = December 2020 | pmid = 33299184 | pmc = 7612278 | doi = 10.1038/s41586-020-3002-5 | bibcode = 2020Natur.588..473M }}</ref>

=== Post-translational modifications (PTMs) ===
Although much fewer bacterial proteins seem to have [[post-translational modification]]s (PTMs) compared to [[Eukaryote|eukaryotic]] proteins, a substantial number of proteins are modified in ''E. coli''. For instance, Potel et al. (2018) found 227 [[phosphoprotein]]s of which 173 were phosphorylated on [[histidine]]. The majority of phosphorylated [[amino acid]]s were [[serine]] (1,220 sites) with only 246 sites on [[histidine]] and 501 phosphorylated [[threonine]]s and 162 [[tyrosine]]s.<ref>{{cite journal | vauthors = Potel CM, Lin MH, Heck AJ, Lemeer S | title = Widespread bacterial protein histidine phosphorylation revealed by mass spectrometry-based proteomics | journal = Nature Methods | volume = 15 | issue = 3 | pages = 187–190 | date = March 2018 | pmid = 29377012 | doi = 10.1038/nmeth.4580 | hdl = 1874/362159 | s2cid = 3367416 | hdl-access = free }}</ref>

===Interactome===
The [[interactome]] of ''E. coli'' has been studied by [[affinity purification]] and [[mass spectrometry]] (AP/MS) and by analyzing the binary interactions among its proteins.

'''Protein complexes'''. A 2006 study purified 4,339 proteins from cultures of strain K-12 and found interacting partners for 2,667 proteins, many of which had unknown functions at the time.<ref name="pmid16606699">{{cite journal | vauthors = Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H | display-authors = 6 | title = Large-scale identification of protein-protein interaction of ''Escherichia coli'' K-12 | journal = Genome Research | volume = 16 | issue = 5 | pages = 686–91 | date = May 2006 | pmid = 16606699 | pmc = 1457052 | doi = 10.1101/gr.4527806 }}</ref> A 2009 study found 5,993 interactions between proteins of the same ''E. coli'' strain, though these data showed little overlap with those of the 2006 publication.<ref name="pmid19402753">{{cite journal | vauthors = Hu P, Janga SC, Babu M, Díaz-Mejía JJ, Butland G, Yang W, Pogoutse O, Guo X, Phanse S, Wong P, Chandran S, Christopoulos C, Nazarians-Armavil A, Nasseri NK, Musso G, Ali M, Nazemof N, Eroukova V, Golshani A, Paccanaro A, Greenblatt JF, Moreno-Hagelsieb G, Emili A | display-authors = 6 | title = Global functional atlas of ''Escherichia coli'' encompassing previously uncharacterized proteins | journal = PLOS Biology | volume = 7 | issue = 4 | pages = e96 | date = April 2009 | pmid = 19402753 | pmc = 2672614 | doi = 10.1371/journal.pbio.1000096 | veditors = Levchenko A | doi-access = free }}</ref>

'''Binary interactions'''. Rajagopala ''et al.'' (2014) have carried out systematic yeast two-hybrid screens with most ''E. coli'' proteins, and found a total of 2,234 protein-protein interactions.<ref name="Rajagopala2014">{{cite journal | vauthors = Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Häuser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P | display-authors = 6 | title = The binary protein-protein interaction landscape of ''Escherichia coli'' | journal = Nature Biotechnology | volume = 32 | issue = 3 | pages = 285–90 | date = March 2014 | pmid = 24561554 | pmc = 4123855 | doi = 10.1038/nbt.2831 }}</ref> This study also integrated genetic interactions and protein structures and mapped 458 interactions within 227 [[multiprotein complex|protein complexes]].