THE HUMAN CELL


The cytosol is the semi-fluid substance filling the cytoplasm of the cell; where it embeds the cellular organelles. All the organelles, except the nucleus, suspended in the cytosol make up the cytoplasm (Clegg JS, 1984). The cytosol itself is enclosed by the cell membrane. Examples of images proteins localized to the cytosol can be seen in Figure 1.

Of all human proteins, 4341 (22%) have been experimentally shown to localize to the cytosol (Figure 2). Analysis of the cytosolic proteome shows highly enriched terms for biological processes related to translation, post-translational modifications, signaling pathways, and cell death. About 75% (n=3270) of the cytosolic proteins localize to other cellular compartments in addition to the cytosol, mainly the nucleus and the plasma membrane.

G3BP1 - U-251 MG
QARS - U-2 OS
MTHFS - U-2 OS

Figure 1. Examples of proteins localized to the cytosol. G3BP1 is an enzyme localized in the cytosol and plays a role in signal transduction pathway (detected in U-251 MG cells). QARS catalyze the aminoacylation of tRNA by their associated amino acid (detected in U-2 OS cells). MTHFS is an enzyme involved in metabolic processes (detected in U-2 OS cells).

  • 22% (4341 proteins) of all human proteins have been experimentally detected in the cytosol by the Human Protein Atlas.
  • 1587 proteins in the cytosol are supported by experimental evidence and out of these 400 proteins are validated by the Human Protein Atlas.
  • 3270 proteins in the cytosol have multiple locations.
  • 397 proteins in the cytosol show a cell to cell variation. Of these 300 show a variation in intensity and 109 a spatial variation.
  • Proteins are mainly involved in translation, post-translational modifications, signaling pathways and cell death.

Figure 2. 22% of all human protein-coding genes encode proteins localized to the cytosol. Each bar is clickable and gives a search result of proteins that belong to the selected category.

The composition of the cytosol


Substructures

  • Aggresome: 17
  • Cytosol: 4289
  • Cytoplasmic bodies: 48
  • Rods & Rings: 18

    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.

    MTHFD1 - A-431
    MTHFD1 - U-251 MG
    MTHFD1 - U-2 OS

    Figure 3. Examples of the morphology of the cytosol in different cell lines, represented by immunofluorescent staining of protein MTHFD1 in A-431, U-251 MG and U-2 OS cells.

    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.

    Gene

    Description

    Substructure

    ADSL Adenylosuccinate lyase Cytosol
    ATXN2 Ataxin 2 Cytosol
    G3BP2 GTPase activating protein (SH3 domain) binding protein 2 Cytosol
    AIMP1 Aminoacyl tRNA synthetase complex-interacting multifunctional protein 1 Cytosol
    YARS Tyrosyl-tRNA synthetase Cytosol
    DARS Aspartyl-tRNA synthetase Cytosol
    SERBP1 SERPINE1 mRNA binding protein 1 Cytosol
    CCDC43 Coiled-coil domain containing 43 Cytosol
    EPRS Glutamyl-prolyl-tRNA synthetase Cytosol
    HARS Histidyl-tRNA synthetase Cytosol
    ATXN2L Ataxin 2-like Cytosol
    AMPD2 Adenosine monophosphate deaminase 2 Cytosol
    RABGAP1 RAB GTPase activating protein 1 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).

    Figure 4a. Gene Ontology-based enrichment analysis for the cytosol 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 cytosol 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 single localizing cytosolic proteins across different cell lines.

    Gene

    Description

    Average TPM

    TPT1 Tumor protein, translationally-controlled 1 3052
    RPL23 Ribosomal protein L23 2108
    RPS12 Ribosomal protein S12 1988
    PKM Pyruvate kinase, muscle 1512
    HSP90AB1 Heat shock protein 90kDa alpha (cytosolic), class B member 1 1379
    S100A6 S100 calcium binding protein A6 1341
    HSP90AA1 Heat shock protein 90kDa alpha (cytosolic), class A member 1 1152
    PABPC1 Poly(A) binding protein, cytoplasmic 1 1143
    ALDOA Aldolase A, fructose-bisphosphate 1142
    LDHB Lactate dehydrogenase B 1116

    Cytosol proteins with multiple locations


    Approximately 75% (n=3270) 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.

    Figure 5. Interactive network plot of the cytosol proteins with multiple localizations. The numbers in the connecting nodes show the proteins that are localized to the cytosol and to one or more additional locations. Only connecting nodes containing more than one protein and at least 0.5% of proteins in the cytosolic 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.

    RPL10A - U-2 OS
    UBE2L3 - A-431
    DDX55 - A-431

    Figure 6. Examples of multilocalizing proteins in the cytosolic proteome. RPL10A is a known ribosomal protein, which is required for formation of the 60S ribosomal subunits. It has been shown to localize both to the nucleoli and the cytosol (detected in U-2 OS cells). UBE2L3 is a member of the E2 ubiquitin-conjugating enzyme family, involved in the ubiquitination of several proteins including p53. It has been shown to localize both to the nucleus and the cytosol (detected in A-431 cells). DDX55 is a member of DEAD box protein family implicated in several cellular processes involving alteration of RNA secondary structure. It has been shown to localize to the nucleus, nucleoli and cytosol (detected in A-431 cells).

    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.

    Figure 7. Bar plot showing the distribution of expression categories, based on the gene expression in tissues, for cytosol-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


    Aizer A et al, 2008. 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