The cytosol is a highly crowded and complex medium (Luby-Phelps K, 2013). It is often described as a hydrophilic jelly-like matrix, and makes up about 70% of the cell volume. This allows for free movement of ions, hydrophilic molecules and proteins, but also larger structures such as protein complexes or vesicles across the cytosol. The cytosol is mainly composed of water (approximately 80%) (Luby-Phelps K, 2000), and proteins. The amount of proteins is high, close to 200 mg/ml, occupying about 20-30% of the volume of the cytosol (Ellis RJ, 2001). Example images of the protein coded by MTHFD1 stained in 3 different cell lines can be seen in Figure 3.

Ions such as potassium, sodium, bicarbonate, chloride, calcium, magnesium and amino acids are also contained in the cytosol. In addition, there is a gradient in concentration of these ions between the cytosol and the extracellular fluid or cytosolic organelles. These gradients are essential for cellular functions, for example cell-to-cell communication at the synapses of nerve cells. Human cytosolic pH ranges between 7.0 - 7.4 and is usually higher if the cell is growing (Bright GR et al, 1987).

The cytosol also contains cytoplasmic inclusions such as glycogen, pigments and crystalline inclusions, and cytoplasmic bodies such as P bodies. Cytoplasmic bodies are not bound by a membrane and function in RNA turnover, translational repression, RNA-mediated silencing, and RNA storage (AAizer A et al, 2008). In the cytosol, other non-membrane bound structures can also be found such as aggresomes and rods & rings.

A selection of proteins suitable to be used as markers for the cytosol is listed in Table 1.

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

The function of the cytosol

Many cellular processes, mainly of metabolic character, occur in the cytosol. These processes include protein synthesis known as translation, the first stage of cellular respiration known as glycolysis and cell division known as mitosis and meiosis. The cytosol allows intracellular transport of molecules across the cell and between cellular organelles. Metabolites can be transported across the cytosol from the area of their production to the site where they are needed. Hydrophobic molecules are transported by protein binding or in capsuled vesicles (Pelham HR, 1999).

The cytosol plays a pivotal role in maintaining the action potential of the cell. As the protein concentration is high within the cytosol compared to the extracellular fluid, the differences in ion concentrations inside and outside of the cell becomes important to regulate osmosis, to maintaining the water balance within the cell and protecting the cell from bursting (Lang F, 2007).

A list of highly expressed cytosolic proteins is summarized in Table 2. Gene Ontology (GO)-based analysis of the cytosolic core proteome shows functions that are well in-line with the known functions of the cytoplasm. The most highly enriched terms for the GO domain Biological Process are related to translation, post-translational modifications, signaling pathways, and cell death (Figure 4a). Enrichment analysis of the GO domain Molecular Function also shows significant enrichment for terms related to translation and protein metabolism (Figure 4b).

Table 2. Highly expressed single localizing cytosolic proteins across different cell lines.

Cytosol proteins with multiple locations

Approximately 76% (n=3308) of the cytosolic proteome detected in Human Protein Atlas also localizes to other cellular compartment (Figure 5). The network plot shows that the most represented compartments shared with the cytosol are the nucleus, plasma membrane and nucleoli. Given that many proteins continuously shuttle between the nucleus and the cytoplasm and between the nucleoli and the cytoplasm, these dual locations could highlight proteins that function as transcription factors, which are transported into the nucleus from their site of synthesis in the cytoplasm. Similarly, ribosomal proteins are transferred, after translation, from the cytoplasm to the nucleolus where they are assembled and exported back to the cytoplasm for final maturation. Examples of multilocalizing proteins within the cytosolic proteome can be seen in Figure 6.

Expression levels of cytosol proteins in tissue

The transcriptome analysis (Figure 7) shows that cytosolic proteins are more likely to be expressed in all tissues and less likely to be tissue enhanced or enriched, compared to all other genes with protein data in the Cell Atlas. The distribution reflects that a large portion of the cytosolic proteome is needed for housekeeping purposes.

Relevant links and publications

Aizer A et al, 0. Intracellular trafficking and dynamics of P bodies. Prion.
PubMed: 19242093 

Bright GR et al, 1987. Fluorescence ratio imaging microscopy: temporal and spatial measurements of cytoplasmic pH. J Cell Biol.
PubMed: 3558476 

Clegg JS. 1984. Properties and metabolism of the aqueous cytoplasm and its boundaries. Am J Physiol.
PubMed: 6364846 

Ellis RJ. 2001. Macromolecular crowding: obvious but underappreciated. Trends Biochem Sci.
PubMed: 11590012 

Lang F. 2007. Mechanisms and significance of cell volume regulation. J Am Coll Nutr.
PubMed: 17921474 

Luby-Phelps K. 2000. Cytoarchitecture and physical properties of cytoplasm: volume, viscosity, diffusion, intracellular surface area. Int Rev Cytol.
PubMed: 10553280 

Luby-Phelps K. 2013. The physical chemistry of cytoplasm and its influence on cell function: an update. Mol Biol Cell.
PubMed: 23989722 DOI: 10.1091/mbc.E12-08-0617

Pelham HR. 1999. The Croonian Lecture 1999. Intracellular membrane traffic: getting proteins sorted. Philos Trans R Soc Lond B Biol Sci.
PubMed: 10515003 DOI: 10.1098/rstb.1999.0491