Document Type

Article

Original Publication Date

2015

Journal/Book/Conference Title

PLoS Computational Biology

Volume

11

Issue

2

DOI of Original Publication

10.1371/journal.pcbi.1004107

Comments

Originally published at http://dx.doi.org/10.1371/journal.pcbi.1004107

Date of Submission

November 2015

Abstract

Large-scale analyses of protein complexes have recently become available for Escherichia coliand Mycoplasma pneumoniae, yielding 443 and 116 heteromultimeric soluble protein complexes, respectively. We have coupled the results of these mass spectrometry-characterized protein complexes with the 285 “gold standard” protein complexes identified by EcoCyc. A comparison with databases of gene orthology, conservation, and essentiality identified proteins conserved or lost in complexes of other species. For instance, of 285 “gold standard” protein complexes in E. coli, less than 10% are fully conserved among a set of 7 distantly-related bacterial “model” species. Complex conservation follows one of three models: well-conserved complexes, complexes with a conserved core, and complexes with partial conservation but no conserved core. Expanding the comparison to 894 distinct bacterial genomes illustrates fractional conservation and the limits of co-conservation among components of protein complexes: just 14 out of 285 model protein complexes are perfectly conserved across 95% of the genomes used, yet we predict more than 180 may be partially conserved across at least half of the genomes. No clear relationship between gene essentiality and protein complex conservation is observed, as even poorly conserved complexes contain a significant number of essential proteins. Finally, we identify 183 complexes containing well-conserved components and uncharacterized proteins which will be interesting targets for future experimental studies.

Rights

Caufield, J. H., Abreu, M., & Wimble, C., et al. Protein Complexes in Bacteria. PLoS Computational Biology, 11, e1004107. Copyright © 2015 Caufield et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Is Part Of

VCU Study of Biological Complexity Publications

S1_Fig.pdf (505 kB)
All EcoCyc complexes and their fractional conservation in selected bacterial species.

S1_Table.xlsx (13 kB)
Key to protein complex IDs as shown in Fig. 5.

S1_Text.docx (21 kB)
Guide to content provided in the supporting tables.

S2_Fig.pdf (504 kB)
All EcoCyc complexes and their fractional essentiality in selected bacterial species.

S2_Table.xlsx (3977 kB)
Protein complex conservation across bacteria.

S3_Fig.pdf (230 kB)
Cross-species conservation of experimentally-observed protein complexes and the sums of the counts of potential paralogs of their components.

S3_Table.xlsx (13 kB)
Conservation of orthologous groups between species pairs.

S4_Fig.pdf (363 kB)
Essentiality of protein complexes and their average paralogy.

S4_Table.xlsx (152 kB)
Conservation across numerous bacterial species.

S5_Fig.pdf (1855 kB)
E. coli literature-curated complex conservation across bacteria corresponds to taxonomic boundaries.

S5_Table.xlsx (158 kB)
Conservation of E. coli complexes from Hu et al. (2009).

S6_Fig.pdf (3375 kB)
E. coli experimentally-observed complex conservation across bacteria corresponds to taxonomic boundaries.

S6_Table.xlsx (118 kB)
Essentiality of E. coli complexes from Hu et al. (2009).

S7_Table.xlsx (100 kB)
Conservation of E. coli complexes from EcoCyc.

S8_Table.xlsx (452 kB)
Essentiality of E. coli complexes from EcoCyc.

S9_Table.xlsx (208 kB)
Conservation of Mycoplasma pneumoniae complexes from Kühner et al. (2009).

S10_Table.xlsx (218 kB)
Essentiality of Mycoplasma pneumoniae complexes from Kühner et al. (2009).

S11_Table.xlsx (15 kB)
Experimental protein complexes containing uncharacterized components.

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