Table 1.
Summary of subcellular compartments represented in the spatial proteomes for each cell-type. An extended version of Table 1 is available in Supplementary Data 7
| Compartment | Description | Examplesa | Compartment groupingb |
|---|---|---|---|
| Acidocalcisomes | Small membranous acidified vacuoles present in the cytoplasm. | VIT1, VTC1, VTC4 | Acidocalcisomes |
| Cytosol | The intracellular contents of the cell within the bounds of the plasma membrane not otherwise contained in organelles or the cytoskeleton. | ECT, GMPS, NBP2, pdxK | Cytosol |
| Endoplasmic reticulum (ER) | The membrane and lumen of the membranous network of the ER including sub-domains in addition to nuclear envelope. Compartment set includes ER and nuclear envelope proteins. | DPMS, ELO1, GPI16, SPT | Endoplasmic reticulum (ER) |
| Flagellum 1 | Core cytoskeletal components of the flagellum including the axoneme and paraflagellar rod. | CARP1, CMF10, DRC4, PFC12, SAXO1, TRYPARP | Flagellum |
| Flagellum 2 | A subset of the flagellum 1 compartment set separately resolved in TcBSF only. | PFC1, PFC7 | Flagellum |
| Glycosomes | Small membranous peroxisome-like organelles containing glycosomal matrix and membrane proteins. | GAT1, PEX10, TFEalpha1 | Glycosomes |
| Intraflagellar transport | Intraflagellar transport proteins which comprise a set of proteins involved in the construction of the flagellum. | IFT46, IFT52, PIFTB2 | Intraflagellar transport |
| Microtubule structures 1 | Cytoskeletal proteins associated with flagellar and microtubule proximal structures. | BOH1, POC11 | Microtubule structures 1 |
| Microtubule structures 2 | Cytoskeleton interacting proteins including those involved in cytoskeleton organisation, microtubule-based movement and cell division. | KAT60A, KIN13-5, KH1 | Microtubule structures 2 |
| Mitochondrion - matrix 1 | Mitochondrial matrix including ribosomal proteins. | MRPS6, MRPS11, KRIPP8 | Mitochondrion - matrix |
| Mitochondrion - matrix 2 | Mitochondrial matrix including proteins involved in matrix-localised processes, i.e. RNA editing and iron-sulfur cluster assembly and ribosomal proteins in TcPCF. | FHm, KREPA1, PAMC1, NFU1, TOP2 | Mitochondrion - matrix |
| Mitochondrion - matrix 3 | Mitochondrial matrix including large ribosomal proteins separately resolved in TcBSF only. | MRPL2, MRPL15 | Mitochondrion - matrix |
| Mitochondrion – inner membrane (IM) | Mitochondrial IM including components of the electron transport chain and mitochondrial inner membrane import machinery. |
AOX, TIM62, SDH5, MIC10-1 |
Mitochondrion - membranes |
| Mitochondrion – outer membrane (OM) | Mitochondrial OM including components of the mitochondrial outer membrane import machinery. | ATOM40, POMP1 | Mitochondrion - membranes |
| Nucleus | Nucleolar proteins as well as non-chromatin components of the nucleus. | NOP105, U2AF35, KKIP2 | Nucleus |
| Nucleus – chromatin | Chromatin component of nucleus including DNA interacting proteins. | CITFA-4, H3V, ISWI, NLP | Nucleus – chromatin |
| Proteasome | Alpha and beta sub-units of the proteasome. | PSA4, PSB4 | Proteasome |
| Proteasome regulatory particle | Regulatory particle sub-units of the proteasome. | RPN1, RPT2 | Proteasome regulatory particle |
| Ribonucleoproteins 1 | Ribosomal proteins and translation initiation factors. In TbBSF, this also included stress granule proteins. | 40S and 60S ribosomal proteins | Ribonucleoproteins |
| Ribonucleoproteins 2 | A subset of 60 S ribosomal proteins was separately resolved in TcBSF only. | 60S ribosomal protein | Ribonucleoproteins |
|
Secretory/ endocytic 1 |
Secretory pathway, surface and endocytic compartments, including trafficking, golgi, putative surface, endosomal, and lysosomal proteins. | ABCG5, GLP1, syntaxin 5, VCL2, VCL3 |
Secretory/ endocytic |
|
Secretory/ endocytic 2 |
Secretory pathway, surface and endosomal compartments, including putative surface transporters. | AQPs, AA transporters, glucose transporters |
Secretory/ endocytic |
|
Secretory/ endocytic 3 |
Secretory pathway, surface and endosomal compartments, including putative surface and endosomal proteins. | ISG64 (TbBSF), ACP3 (TbPCF), VSG domain proteins (TcBSF) |
Secretory/ endocytic |
a Protein names based on TriTrypDB annotation of T. brucei genes.
b Grouped compartment name for downstream comparative analysis.