Inner Membrane Proteome

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The proven and predicted Inner Membrane (IM) proteins of E. coli K-12, also known as the Cytoplasmic Membrane (CM) proteins, are grouped into this Topic's GeneSet. Two studies are being used to seed the IM Proteome Topic.

The Global Topology Analysis of Daley (2005) as summarized in their Supplementary Table S1

was used to initially identify the Verified and Predicted Inner Membrane Proteins in EcoGene.

The Inner Membrane Proteins of E. coli K-12 have been broken into subTopics in EcoGene based on these results:

1) IMemProt_Ei = Experimentally determined C-terminus in cytoplasm(inside)

2) IMemProt_Eo = Experimentally determined C-terminus in periplasm(outside)

3) IMemProt_Pi = Predicted inside topology based on paralogs

4) IMemProt_Po = Predicted outside topology based on paralogs

5) IMemProt_Pred = Predicted membrane proteins >100 aa, no experimental result, no verified paralog

6) IMem_Loc_2DMS = an additional subTopic added based on Lopez-Campistrous (2005) and Lai (2004).


Daley (2005) have Experimentally (E) determined the periplasmic (o) or cytoplasmic (i) location of these membrane protein C-terminal tails verified using C-terminal GFP (Cytoplasmic) and AP (Periplasmic) tagged membrane proteins.
The predictions (P) subtopics include proteins whose topology is predicted using the experimentally determined C-terminal orientation of a verified paralog.

Some proteins predicted by TMHMM , but without paralogs or experimental data, were also listed by Daley (2005), if they were >100 amino acids long. Daley (2005) did not predict the number of TM helices for this third group

The Daley (2005) IMemProt assignments include
514 IMemProt_E class, 99 IMemProt_P class and 124 IMemProt_Pred class for a total of 737 IMemProt integral membrane protein assignments. Using this dataset as a starting point, more information about additional verification studies, the unverified (prediction-only) IMemProts, the small <100 aa) inner membrane proteins, and inner-membrane associated proteins will be included.

76 proteins have been identified in inner membrane preparations by 2D-gel fractionation and MS identification of many protein isoform spots:
Lopez-Campistrous (2005)

The 76 proteins localized to the inner membrane, as identified in Supplementary Table 3 of Lopez-Campistrous( 2005), are labeled in EcoGene as IMem_Loc_2DMS. Unlike the IMemProt, the IMem_Loc_2DMS proteins are not all predicted to have membrane spanning regions or to be integral membrane proteins.

Many of these IM-localized proteins bind to integral membrane proteins or have single membrane spanning domains predicted. In fact, only 7/738 IMemProts were identified among the 76 IMem_Loc_2DMS proteins: cld, msbA, mtlA, pntB, sohB, tsr and yqiK.

The 2D gel step may have enriched for membrane-associated proteins with soluble domains, including some lipoproteins (LipoProt) excluded from the IMemProt classification. Some proteins with known or suspected cytoplasmic, periplasmic and outer membrane locations were assigned an inner membrane location in this study. This may result from some proteins sticking to inner membranes during sample preparation or from cross-contamination of cell fractions. However, it is likely that most, if not all, of these proteins do associate with the inner membrane, or inner membrane complexes, in vivo, in physiologiocally relevant interactions.
In another study using 2D_MS to identify membrane proteins, Lai (2004) examined total membrane preparations from minicells and rods to look for proteins with polar and septal localization. OmpW was identified as an outer membrane protein localized to the cell poles and the inner membrane protein YiaF was identified as having a polar and septal location bias.

The five inner membrane proteins identified by Lai (2004) include AtpA, YiaF and AcrA, all also localized to the IM by Lopez-Campistrous (2005), IMemProt_E protein AtpB, and FtsZ, an inner membrane associated protein bound to the cytoplasmic side that was identified by Lopez-Campistrous (2005) as a periplasmic protein, perhaps artifactually. ftsZ and atpB are included in the IMem_Loc_2DMS subTopic based on the Lai (2004) results.