Research Article

Proteome Organization in a Genome-Reduced Bacterium

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Science  27 Nov 2009:
Vol. 326, Issue 5957, pp. 1235-1240
DOI: 10.1126/science.1176343

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  1. Fig. 1

    Synopsis of the genome-wide screen of complexes in M. pneumoniae.

  2. Fig. 2

    Proteome organization is only partially reflected by other biological data sets. (A) General overlap between TAP and interactions inferred from other data sets: coexpression (24, 28), operons (24), STRING (21), and pathways (48). Numbers refer to the interacting pairs within the different data sets. The fraction of TAP interactions that cluster into complexes and are covered by other data sets is given between brackets. For TAP-interacting protein pairs the cutoff was set at 80% accuracy. Cutoffs for other data sets were optimized for coverage (accuracies from 40 to 100%). (B) Frequent functional cross-talk in the protein complex data set. All proteins within high confidence pairs were functionally annotated according to the COG (Clusters of Orthologous Groups of Proteins) database (49). Boxed areas are colored proportionally to the number of interactions linking two functional classes. The scales represent the total (top) and normalized (bottom) number of interactions (23). Category Q (secondary metabolites) contains only two proteins. The category most frequently linked is J (translation) with itself; however, it contains the highest number of proteins. The highest proportion of interactions is between proteins within category K (transcription).

  3. Fig. 3

    Higher level of proteome organization. (A) The RNA polymerase–ribosome assembly. Core components are represented by circles, attachments by diamonds. The line attribute corresponds to socio-affinity indices: dashed lines, 0.5 to 0.86; plain lines, >0.86. Color code and shaded yellow circles around groups of proteins refer to individual complexes: RNA polymerase (pink), ribosome (purple), and translation elongation factor (green). The bottom graph shows that the ribosomal protein RpsD (23 kD) and the α subunit of the RNA polymerase, RpoA-TAP (57 kD), co-elute in high molecular weight fractions (MD range) during gel filtration chromatography. (B) DNA topoisomerase (diameter ~ 12 nm) is a heterodimer in bacteria: ParE (ATPase and DNA binding domains) and ParC (cleavage and C-terminal domains). The interaction between ParE-DNA–binding and ParC–cleavage domains was modeled by using yeast topoisomerase II as a template [Protein Data Bank (PDB) code 2rgr], and ParE-ATPase and ParC–C-terminal domains were modeled separately on structures of gyrase homologs (PDB 1kij and 1suu). All four domains were fitted into the electron microscopy density. Gyrase (~12 nm) is similarly split in bacteria into GyrA/GyrB, which are paralogs of ParE/ParC, and was modeled and fitted by using PDB 1bjt as a template for the GyrB-DNA–binding and GyrA-cleavage domains interaction. (C) Protein multifunctionality in M. pneumoniae illustrated with the AARS complexes.

  4. Fig. 4

    From proteomics to the cell. By a combination of pattern recognition and classification algorithms, the following TAP-identified complexes from M. pneumoniae, matching to existing electron microscopy and x-ray and tomogram structures (A), were placed in a whole-cell tomogram (B): the structural core of pyruvate dehydrogenase in blue (~23 nm), the ribosome in yellow (~26 nm), RNA polymerase in purple (~17 nm), and GroEL homomultimer in red (~20 nm). Cell dimensions are ~300 nm by 700 nm. The cell membrane is shown in light blue. The rod, a prominent structure filling the space of the tip region, is depicted in green. Its major structural elements are HMW2 (Mpn310) in the core and HMW3 (Mpn452) in the periphery, stabilizing the rod (42).The individual complexes (A) are not to scale, but they are shown to scale within the bacterial cell (B).

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