Centrosome


The Microtubule Organizing Center (MTOC) is a structure from which microtubules emerge. The concept of MTOCs was established due to advances in microscopy techniques, enabling researchers to visualize structures that assemble and organize microtubules. The most well-studied MTOCs are the centrosome in animal cells and the spindle pole body in yeast, however there are also other sites within cells where organization of microtubules occur (Lüders J et al, 2007.). In mammalian cells, the most prominent and well-known MTOC is the centrosome, which has been widely studied ever since Theodor Bovery first described it in 1888 (Bovery, T, 1900). Although the centrosome is a small organelle, its impact on cellular function is of great importance. Located adjacent to the nucleus, the major role of the centrosome is to regulate the intracellular organization of the microtubules, which is important during cell division when the mitotic spindle is formed. The centrosome is the key responsible organelle for the correct orientation of the poles of the mitotic spindle, facilitating the segregation of the chromosomes, and the subsequent distribution to the daughter cells (Nigg EA et al, 2011).

Of all proteins detected in the Cell Atlas, 481 proteins (2%) have been experimentally shown to localize to the MTOC. In images where it has been possible to distinguish the centrioles, proteins have been annotated with the location Centrosome. In images where the centrioles have not been detected, but the protein localizes to the center of the microtubules, proteins have been annotated with the location MTOC (Figure 1-2). Functional enrichment analysis of the MTOC proteome shows highly enriched terms for biological processes related to organization of the microtubules and cell cycle progression (Figure 3).

RAB11FIP5 - A-431
PCNT - U-251 MG
MKKS - U-2 OS

Figure 1. Examples for proteins localized to the MTOC and the centrosome. RAB11FIP5 is involved in intracellular transport and has previously not been shown to localize to the MTOC. By using independent antibodies, RAB11FIP5 is localized to the MTOC (detected in A-431 cells). PCNT is a well-characterized protein component of the filamentous matrix of the centrosome with important roles in both mitosis and meiosis (detected in U-251 cells). MKKS is a centrosome-shuttling protein that localizes to a tube-like structure around the centrioles in the pericentriolar material (PCM) and is important for cell division (detected in U-2 OS cells). Normally, MKKS shuttles between the centrosome and the cytosol throughout the cell cycle but when mutated, it fails to localize to the centrosome, leading to the McKusick Kaufman syndrome, a disease that manifests with impaired development, especially of hands and feet, as well as heart and genital defects.

  • 2% (481 proteins) of all human proteins have been experimentally detected in the centrosome by the Human Protein Atlas.
  • 142 proteins in the centrosome are supported by experimental evidence and out of these 27 proteins are enhanced by the Human Protein Atlas.
  • 370 proteins in the centrosome have multiple locations.
  • 11 proteins in the centrosome show a cell to cell variation. Of these 10 show a variation in intensity and 1 a spatial variation.
  • Proteins are mainly involved in microtubule organization and cell cycle progression.

Figure 2. 2% of all human protein-coding genes encode proteins localized to the MTOC. Each bar is clickable and gives a search result of proteins that belong to the selected category.

The structure of the centrosome


Structures

  • Microtubule organizing center: 145
  • Centrosome: 338

    The centrosome is a small non-membranous MTOC organelle occupying about 1-2 μm3 of the cytoplasmic volume (Doxsey S, 2001). It is composed of two barrel shaped centrioles, each having nine proximal triplets organized into a symmetric structure, which maintain both the stability and functional activity of the centrosome. The centrioles are organized in a matrix together with proteins, commonly referred to as the pericentriolar material (PCM). Among the proteins of this complex, there are many important cell cycle regulators and other signaling molecules essential for the function of the centrosome. Pericentrin (Figure 1), aurora kinases, ninein and centriolin are some examples (Doxsey S, 2001). Also, several of the proteins that are localized to MTOC belong to these PCM proteins. One of the most well studied constituents of the PCM is the highly conserved γ-tubulin protein complex, which is organized into an open ring structure with around 25 nm in diameter, responsible for the nucleation of the microtubules. As a key regulator of mitosis, the MTOC displays a highly dynamic structure that undergoes dramatic organizational changes throughout the cell cycle (Bornens M, 2002; Conduit PT et al, 2015).

    Table 1. Selection of proteins suitable as markers for the MTOC.

    Gene Description Substructure
    MKKS McKusick-Kaufman syndrome Centrosome
    ODF2 Outer dense fiber of sperm tails 2 Centrosome
    CEP97 Centrosomal protein 97 Cytosol
    Microtubule organizing center
    KIF5B Kinesin family member 5B Cytosol
    Microtubule organizing center
    PIBF1 Progesterone immunomodulatory binding factor 1 Microtubule organizing center

    See the morphology of centrosomes in human induced stem cells in the Allen Cell Explorer.

    The function of the centrosome


    The major functional role of MTOCs is to manage the organization of the microtubules in the cell; they thereby possess an important influence over the cellular shape, polarity, proliferation and mobility. In eukaryotic cells, one of the major MTOCs is the well-studied centrosome that is associated with spindle formation during cell division. During S-phase the centrioles are first duplicated into daughter centrioles that start to move apart as the cell enters mitosis (G2-M phases) and the amount of surrounding PCM increases. Proteins in the PCM contribute to the assembly and orientation of the mitotic spindle by organizing into a scaffold structure around the mother centrioles, where they facilitate spindle formation through different functions. Increasing evidence suggest a more versatile function of the centrosome, especially pointing to its ability to coordinate a myriad of cellular functions by serving as a compact hub where cytoplasmic proteins can interact at higher concentrations (Doxsey S, 2001; Rieder CL et al, 2001). As a key regulator of the cell cycle, abnormalities in number, size and morphology of the centrosome is commonly observed in cells undergoing tumorigenesis. Centrosomal abnormalities are also observed in several other diseases. Dysfunction in the ubiquitin-proteasome degradation that has implications in several neurodegenerative disorders is one example (Badano JL et al, 2005).

    Gene Ontology (GO)-based analysis of the corresponding genes in the MTOC proteome shows functions that are well in-line with existing literature on MTOC and centrosome function. The most highly enriched terms for the GO domain Biological Process are related to the organization of the microtubules, cell division and cilium morphogenesis (Figure 3a). Enrichment analysis of the GO domain Molecular Function, also generates expected results showing dynein- and tubulin binding together with motor activity as the most enriched significant terms (Figure 3b). A list of highly expressed MTOC and centrosome proteins are summarized in Table 2.

    Figure 3a. Gene Ontology-based enrichment analysis for the centrosome proteome showing the significantly enriched terms for the GO domain Biological Process. Each bar is clickable and gives a search result of proteins that belong to the selected category.

    Figure 3b. Gene Ontology-based enrichment analysis for the centrosome proteome showing the significantly enriched terms for the GO domain Molecular Function. Each bar is clickable and gives a search result of proteins that belong to the selected category.

    Table 2. Highly expressed MTOC and centrosome marker proteins, in different cell lines.

    Gene Description Average TPM
    DCTN2 Dynactin subunit 2 110
    MKKS McKusick-Kaufman syndrome 82
    PAFAH1B1 Platelet activating factor acetylhydrolase 1b regulatory subunit 1 52
    ODF2 Outer dense fiber of sperm tails 2 50
    CETN3 Centrin 3 31
    CEP250 Centrosomal protein 250 28
    SLC1A4 Solute carrier family 1 member 4 27
    CCDC14 Coiled-coil domain containing 14 26
    FGFR1OP FGFR1 oncogene partner 25
    KLHL21 Kelch like family member 21 25

    Centrosome and the MTOC proteins with multiple locations


    Approximately 77% (n=370) of the centrosome and MTOC proteins detected in the cell atlas also localize to other cellular compartments (Figure 4). The network plot shows that the most common locations shared with Centrosome and MTOC are the cytoplasm, nucleus and vesicles.

    Figure 4. Interactive network plot of microtubule proteins with multiple localizations. The numbers in the connecting nodes show the proteins that are localized to MTOCs and to one or more additional locations. Only connecting nodes containing more than one protein and at least 0.5% of proteins in the MTOC proteome are shown. The circle sizes are related to the number of proteins. The cyan colored nodes show combinations that are significantly overrepresented, while magenta colored nodes show combinations that are significantly underrepresented as compared to the probability of observing that combination based on the frequency of each annotation and a hypergeometric test (p≤0.05). Note that this calculation is only done for proteins with dual localizations. Each node is clickable and results in a list of all proteins that are found in the connected organelles.

    Expression levels of centrosome proteins in tissue


    Transcriptome analysis (Figure 5) shows that centrosome and MTOC proteins are less likely to be expressed at equal levels in all tissue types, compared to all genes with protein data in the Cell Atlas.

    Figure 5. Bar plot showing the distribution of expression categories, based on the gene expression in tissues, for centrosome-associated protein-coding genes compared to all genes in the Cell Atlas. Asterisk marks statistically significant deviation(s) (p≤0.05) from all other organelles based on a binomial statistical test. Note that this calculation is only done for proteins with dual localizations. Each bar is clickable and gives a search result of proteins that belong to the selected category.

    Relevant links and publications


    Badano JL et al, 2005. The centrosome in human genetic disease. Nat Rev Genet.
    PubMed: 15738963 DOI: 10.1038/nrg1557

    Bornens M. 2002. Centrosome composition and microtubule anchoring mechanisms. Curr Opin Cell Biol.
    PubMed: 11792541 

    Bovery T. 1900. Zellen-Studien. Verlag von Gustav Fischer.

    Conduit PT et al, 2015. Centrosome function and assembly in animal cells. Nat Rev Mol Cell Biol.
    PubMed: 26373263 DOI: 10.1038/nrm4062

    Doxsey S. 2001. Re-evaluating centrosome function. Nat Rev Mol Cell Biol.
    PubMed: 11533726 DOI: 10.1038/35089575

    L├╝ders J et al, 2007. Microtubule-organizing centres: a re-evaluation. Nat Rev Mol Cell Biol.
    PubMed: 17245416 DOI: 10.1038/nrm2100

    Nigg EA et al, 2011. The centrosome cycle: Centriole biogenesis, duplication and inherent asymmetries. Nat Cell Biol.
    PubMed: 21968988 DOI: 10.1038/ncb2345

    Rieder CL et al, 2001. The centrosome in vertebrates: more than a microtubule-organizing center. Trends Cell Biol.
    PubMed: 11567874