Eukaryote-wide sequence analysis of mitochondrial β-barrel outer membrane proteins

Abstract

Background: The outer membranes of mitochondria are thought to be homologous to the outer membranes of Gram negative bacteria, which contain 100's of distinct families of β-barrel membrane proteins (BOMPs) often forming channels for transport of nutrients or drugs. However, only four families of mitochondrial BOMPs (MBOMPs) have been confirmed to date. Although estimates as high as 100 have been made in the past, the number of yet undiscovered MBOMPs is an open question. Fortunately, the recent discovery of a membrane integration signal (the β-signal) for MBOMPs gave us an opportunity to look for undiscovered MBOMPs.

Results: We present the results of a comprehensive survey of eukaryotic protein sequences intended to identify new MBOMPs. Our search employs recent results on β-signals as well as structural information and a novel BOMP predictor trained on both bacterial and mitochondrial BOMPs. Our principal finding is circumstantial evidence suggesting that few MBOMPs remain to be discovered, if one assumes that, like known MBOMPs, novel MBOMPs will be monomeric and β-signal dependent. In addition to this, our analysis of MBOMP homologs reveals some exceptions to the current model of the β-signal, but confirms its consistent presence in the C-terminal region of MBOMP proteins. We also report a β-signal independent search for MBOMPs against the yeast and Arabidopsis proteomes. We find no good candidates MBOMPs in yeast but the Arabidopsis results are less conclusive.

Conclusions: Our results suggest there are no remaining MBOMPs left to discover in yeast; and if one assumes all MBOMPs are β-signal dependent, few MBOMP families remain undiscovered in any sequenced organism.

Figure 1

Sequence logos of proposed β-signal regions of combined ortholog sets. The upper figure is computed from all homologs in Uniprot and the bottom from the subset of those with confirmed expression.

Figure 2

Conserved β-signals and secondary structure prediction of yeast MBOMPs. In the top track, H, E, and C represented α-helix, β-strand and coil, as predicted by PSIPRED or from the experimentally determined structure in the case of VDAC (PDB:2K4T).

Figure 3

Informatics pipeline for searching for novel MBOMP candidates.

Figure 4

β-Signal matches not always in final predicted β-strand. Protein clusters which match our automatic criteria of a conserved β-signal, but with the matches outside of the final predicted β-signal are shown. The top track indicates predicted β -strand (E), coil (C), or α-helix (H), by PSIPRED. The colored residues occur in full or partial matches to the β-signal motif.

Figure 5

Examples which don't match the β-signal motif. (a) Putative MBOMP homologs, which do not match the β-signal motif, and (b) BBOMPs sorted to the mitochondrial outer membrane when expressed in yeast are shown. The C-terminus is indicated with an asterisk.

Figure 6

Overview of features used for MBOMP prediction by SVM.

Figure 7

Signal Peptide Model. The h-region is defined as the region of 20 residues around the position of the first peak of the hydrophobicity plot, and the n-region and c-region as the N-terminal and C-terminal flanking 5 residues, respectively, as shown at the top of this figure. The h-region is aligned to the first peak of the hydrophobicity plot (details in main text).