TopicPage for Inner Membrane Proteome of Escherichia coli K-12
| ||Membrane Proteome Inner Membrane         |
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)
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:
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.
Bibliography (25 total) : Review Only   Up
Bruni R, Kloss B (2013) High-throughput cloning and expression of integral membrane proteins in Escherichia coli. Curr Protoc Protein Sci 74:Unit 29.6.
Löw C, Moberg P, Quistgaard EM, Hedrén M, Guettou F, Frauenfeld J, Haneskog L, Nordlund P (2013) High-throughput analytical gel filtration screening of integral membrane proteins for structural studies. Biochim Biophys Acta 1830:3497-508
Papanastasiou M, Orfanoudaki G, Koukaki M, Kountourakis N, Sardis MF, Aivaliotis M, Karamanou S, Economou A (2013) The Escherichia coli peripheral inner membrane proteome. Mol Cell Proteomics 12:599-610
Vinothkumar KR, Edwards PC, Standfuss J (2013) Practical aspects in expression and purification of membrane proteins for structural analysis. Methods Mol Biol 955:17-30
Cymer F, Sanders CR, Schneider D (2013) Analyzing oligomerization of individual transmembrane helices and of entire membrane proteins in E. coli: A hitchhiker's guide to GALLEX. Methods Mol Biol 932:259-76
Schlegel S, Löfblom J, Lee C, Hjelm A, Klepsch M, Strous M, Drew D, Slotboom DJ, de Gier JW (2012) Optimizing membrane protein overexpression in the Escherichia coli strain Lemo21(DE3). J Mol Biol 423:648-59
Toddo S, Söderström B, Palombo I, von Heijne G, Nřrholm MH, Daley DO (2012) Application of split-green fluorescent protein for topology mapping membrane proteins in Escherichia coli. Protein Sci 21:1571-6
Wong WC, Maurer-Stroh S, Schneider G, Eisenhaber F (2012) Transmembrane helix: simple or complex. Nucleic Acids Res 40:W370-5
Luirink J, Yu Z, Wagner S, de Gier JW (2012) Biogenesis of inner membrane proteins in Escherichia coli. Biochim Biophys Acta 1817:965-76 Review
Granseth E, Daley DO, Rapp M, Melén K, von Heijne G (2005) Experimentally constrained topology models for 51,208 bacterial inner membrane proteins. J Mol Biol 352:489-94
Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005) Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth. Mol Cell Proteomics 4:1205-9
Daley DO, Rapp M, Granseth E, Melén K, Drew D, von Heijne G (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308:1321-3
Gao FP, Cross TA (2005) Recent developments in membrane-protein structural genomics. Genome Biol 6:244 Review
Luirink J, von Heijne G, Houben E, de Gier JW (2005) Biogenesis of inner membrane proteins in Escherichia coli. Annu Rev Microbiol 59:329-55 Review