Open Access Highly Accessed Research article

Proteome remodelling during development from blood to insect-form Trypanosoma brucei quantified by SILAC and mass spectrometry

Kapila Gunasekera13, Daniel Wüthrich1, Sophie Braga-Lagache2, Manfred Heller2 and Torsten Ochsenreiter1*

Author Affiliations

1 Institute for Cell Biology, University of Bern, Bern, Switzerland

2 Department of Clinical Research, University of Bern, Bern, Switzerland

3 Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland

For all author emails, please log on.

BMC Genomics 2012, 13:556  doi:10.1186/1471-2164-13-556

Published: 16 October 2012

Additional files

Additional file 1:

Figure S1. Comparison of procyclic T. brucei cell growth in different media. (A) Cells grown in SDM 79/80 with regular FCS and SDM 80 with dialyzed FCS (dFCS). (B) Comparison of procyclic T. brucei cell growth of cells in SDM 80 dFCS regular amino acids and cells in SDM 80, dFCS and heavy isotope labeled amino acids (Arg; Lys).

Figure S2. Labelling efficiency of procyclic T. brucei whole cell proteome after zero, two and 11 cell division cycles. (A) Box plot depicting mean ratios of heavy/light peptides from the whole proteome. (B) Shows the relative abundance shift of mass spectrometry peaks (m/z) during the course of labelling (0, 2 and 11 cell division cycles) with heavy amino acids towards higher m/z ratios. Data corresponds to one peptide of the triosephosphate isomerase gene (Tb11.02.3210).

Figure S3. Expression profile of 166 mitochondrial proteins during T. brucei development. Each circle indicates a cluster of co-regulated proteins. Circle size is proportional to the number of proteins in the cluster. The midpoint of the circle marks the mean fold change between the life cycle stages. Expression profile is depicted as fold change (log2) between the different life cycle stages.

Figure S4. Protein expression profile of oxidative phosphorylation complexes I-V during development. (A and B) Complex one. (C and D) Complex two. (E and F) Complex three. (G and H) Complex four. (I and J) Complex five. Each gene is assigned a sign. x-axis indicate the fold regulation in log2 between life stages.

Figure S5. Procyclic specific metabolism genes and their regulation during development. (A) Abundance profile of eight different proteins likely involved in pyruvate to acetate conversion in the mitochondrion of insect form trypanosomes. (B) Model depicting the conversion of pyruvate to acetate. Green arrow indicates activation of the pyruvate dehydrogenase complex through dephosphorylation.

Figure S6. Gene expression comparison between SLT, microarray and MS/MS. (A) A set of highly correlated genes between microarray (Jensen et al.) and SLT (Nilsson et al.). The Pearson’s product moment correlation is 0.82 (p-value < 2.2e-16). (B) Correlation of the same set between SLT and MS/MS. The Pearson’s product moment correlation is 0.35 (p-value < 2.2e-16). (C) Correlation of mRNA and protein changes between LS and PC. The Pearson’s product moment correlation is 0.28 (p-value < 2.2e-16). Colors of the circles in the scatter plot indicate correlation between the two studies (red high correlation, green low correlation).

Format: PDF Size: 2MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Table S13. Peptide information of PC/LS and PC/SS.

Format: XLS Size: 13.8MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

Table S1. Antibodies and conditions used in this study.

Format: PDF Size: 41KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

Table S2. Proteins detected in both the heavy fraction PC and light fraction LS. Raw – The raw excel sheet generated by MaxQuant system on heavy fraction PC and light fraction LS.

Table S3 – Proteins detected in both the heavy fraction PC and light fraction SS. Raw – The raw excel sheet generated by MaxQuant system on heavy fraction PC and light fraction SS.

Format: XLS Size: 4.7MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

Table S4. Proteins detected in both PC/LS and PC/SS experiments (overlaps).

Format: XLS Size: 754KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

Table S5. GO terms with gene IDs.

Format: XLS Size: 159KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 7:

Table S6. Proteins only detected in PC/LS experiment.

Format: XLS Size: 285KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 8:

Table S7. Proteins only detected in PC/SS experiment.

Format: XLS Size: 154KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 9:

Table S8. Proteins having difference in fold change >= 5 fold between Urbaniak and our study.

Format: XLS Size: 37KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 10:

Table S9. Alternative splicing to diversify protein production.

Format: XLS Size: 154KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 11:

Table S10. Change of mitochondrial protein abundance during differentiation. (PDF 53 kb)

Format: PDF Size: 54KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 12:

Table S11. Coverage of novel transcripts.

Format: PDF Size: 54KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 13:

Table S12. Overlaps of SLT and MS/MS data.

Format: XLS Size: 796KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data