Microtubules are one of the principal components of the cytoskeleton that build up the structure and shape of the cell
(Figure 1). They are also important in a number of other cellular processes, such as cell division and transportation. Extending from a central
microtubule-organizing center, they display a polar structure that is highly conserved in evolution, reflected in a striking similarity of
microtubules across almost all species (Janke C, 2014).Mitotic spindle: 16
Microtubules are physically robust polymers made up of α/β-Tubulin dimers called protofilaments assembled into
groups of 13 around a hollow core about 25 nm in diameter. When these dimer complexes polymerize, they form linear microtubule filaments
that display a polar structure with two growing ends. One fast-growing plus-end with exposed β-subunits and one slow-growing minus-end with
exposed α-subunits. Microtubules display a highly dynamic structure due to their ability to polymerize or depolymerize rapidly from
end-to-end, two counteracting processes that are both regulated by the binding of GTP. The ability of microtubules to maintain highly dynamic
polymerization patterns is vital for the cell's ability to adapt its spatial arrangements in response to different environmental conditions,
and to execute mechanical work. A characteristic feature of microtubules is that they never reach a steady-state length and thus remain constantly
in the process of elongation (polymerization) or shrinkage (depolymerization), a phenomenon known as dynamic instability
(Desai A et al, 1997; Conde C et al, 2009). In the Cell Atlas, several substructures of the microtubule cytoskeleton are classified; the cytokinetic bridge, microtubule ends, midbody, midbody ring and the mitotic spindle (Figure 3).
Figure 3. Examples of the substructures of the microtubules.
Midbody ring: APC2 is localized to the midbody ring (detected in U-2 OS cells).
Cytokinetic bridge: CCSAP is a spindle-associated protein that is localized to the cytokinetic bridge (detected in U-2 OS cells).
Mitotic spindle: C12orf66 is localized to the mitotic spindle (detected in MCF-7 cells).
Microtubules are subjected to a number of different post-translational modifications that influence the structure in order to meet the
requirements for their different functions, for example acetylation of lysine residues, detyrosination, glycylation and glutamylation
(Janke C, 2014; Wloga D et al, 2010). A selection of proteins suitable to be used as markers for microtubules and the substructures are listed in Table 1.
Table 1. Selection of proteins suitable as markers for the microtubules structure or its substructures.
||Tubulin, alpha 1a
||Dystrobrevin binding protein 1
||Calmodulin regulated spectrin-associated protein family, member 2
The function of the microtubules
One major function of the microtubule cytoskeleton is to supply mechanical strength to the cytoplasm and maintain the
intracellular organization of the organelles. Microtubules are vital for cell migration and for the mobility of organelles within the cell.
They make up eukaryotic cilia and flagella, and act as substrates for motor proteins that can move along the filaments to convert chemical energy
into mechanical energy, which facilitates movement. Dynein and kinesin are the two largest families of motor proteins. The dyneins move in direction
towards the microtubule organizing center (MTOC) whereas the kinesins are directed away from the MTOC. As an important platform for organelle movement, the microtubule skeleton is a
key member of the secretory pathway, where it channels the post-Golgi vesicles out to the plasma membrane. This is done by the help of
motor proteins that attach to the vesicles
(Schmoranzer J et al, 2003). Another highly important and well studied function of the microtubules is to participate in cell
division. Here, they form the mitotic spindle (see Figure 3) in order to properly segregate the chromosomes during mitosis, a function with significant implications
in cancer where the mitotic rate is out of control. During the last steps of mitosis, a protein structure called the midbody (see Figure 3) is compacted between the
two daughter cells, held together by the cytokinetic bridge (see Figure 3)
(Skop AR et al, 2004).
Several diseases are linked to defective cellular transport due to abnormalities in the microtubules.
Many efficient anti-cancer drugs therefore target the microtubules
(Jordan MA et al, 2004). Hereditary diseases associated with defects in
cilia, known as ciliopathies, and several neurodegenerative disorders such as Parkinson's syndrome are two of such diseases
(Waters AM et al, 2011; Cappelletti G et al, 2015).
Gene Ontology (GO)-based analysis of the corresponding genes in the microtubule proteome shows functions highly in line with existing
literature. The most highly enriched terms for the GO domain Biological Process are related to microtubule-based processes such as cytoskeleton
organization, cilium morphogenesis and cell division (Figure 4a). Enrichment analysis of the GO domain Molecular Function also shows top hits for
enriched terms related to motor activity and tubulin binding (Figure 4b).
Figure 4a. Gene Ontology-based enrichment analysis for the microtubules 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 4b. Gene Ontology-based enrichment analysis for the microtubules 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 microtubules proteins across different cell lines.
||Tubulin, alpha 1b
||Tubulin, beta 4B class IVb
||Tubulin, alpha 1a
||Tubulin, beta class I
||Baculoviral IAP repeat containing 5
||Tubulin, alpha 4a
||Tubulin, beta 2A class IIa
||Sprouty RTK signaling antagonist 2
||Vacuolar protein sorting 4 homolog A (S. cerevisiae)
||Spindle and kinetochore associated complex subunit 1
Microtubules proteins with multiple locations
Approximately 70% (n=262) of the microtubule-localizing proteins detected in the Cell Atlas also localize to other compartments in the cell (Figure 5). The network plot shows that the most common locations shared with microtubules are the nucleoplasm, the cytosol and vesicles. As the microtubules are essential for intracellular transport, often utilized by molecules encapsulated in vesicles, the dual locations of these proteins reflect the important role of the microtubules as a transport system in the cell.
Figure 5. Interactive network plot of microtubule proteins with multiple localizations.
The numbers in the connecting nodes show the proteins that are localized to the microtubules and to one or more additional locations. Only connecting nodes containing more than one protein and at least 0.5% of proteins in the microtubule 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).
Each node is clickable and results in a list of all proteins that are found in the connected organelles.
Expression levels of microtubules proteins in tissue
Transcriptome analysis (Figure 6) shows that microtubule-localizing proteins are less likely to be expressed in all tissues, compared to all genes with protein data in the Cell Atlas.
Figure 6. Bar plot showing the distribution of expression categories, based on the gene expression in tissues, for microtubules-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. Each bar is clickable and gives a search result of proteins that belong to the selected category.
Relevant links and publications
Cappelletti G et al, 2015. Linking microtubules to Parkinson's disease: the case of parkin. Biochem Soc Trans.
PubMed: 25849932 DOI: 10.1042/BST20150007
Conde C et al, 2009. Microtubule assembly, organization and dynamics in axons and dendrites. Nat Rev Neurosci.
PubMed: 19377501 DOI: 10.1038/nrn2631
Desai A et al, 1997. Microtubule polymerization dynamics. Annu Rev Cell Dev Biol.
PubMed: 9442869 DOI: 10.1146/annurev.cellbio.13.1.83
Janke C. 2014. The tubulin code: molecular components, readout mechanisms, and functions. J Cell Biol.
PubMed: 25135932 DOI: 10.1083/jcb.201406055
Jordan MA et al, 2004. Microtubules as a target for anticancer drugs. Nat Rev Cancer.
PubMed: 15057285 DOI: 10.1038/nrc1317
Schmoranzer J et al, 2003. Role of microtubules in fusion of post-Golgi vesicles to the plasma membrane. Mol Biol Cell.
PubMed: 12686609 DOI: 10.1091/mbc.E02-08-0500
Skop AR et al, 2004. Dissection of the mammalian midbody proteome reveals conserved cytokinesis mechanisms. Science.
PubMed: 15166316 DOI: 10.1126/science.1097931
Waters AM et al, 2011. Ciliopathies: an expanding disease spectrum. Pediatr Nephrol.
PubMed: 21210154 DOI: 10.1007/s00467-010-1731-7
Wloga D et al, 2010. Post-translational modifications of microtubules. J Cell Sci.
PubMed: 20930140 DOI: 10.1242/jcs.063727