Plasma membrane

The plasma membrane, also known as the cell membrane or cytoplasmic membrane, is the barrier that encloses the cell and protects the intracellular components from the surroundings. The plasma membrane is a thin semi-permeable membrane consisting of a lipid bilayer and associated proteins, each constituting about 50% of the total mass of the cell membrane. Example images of proteins localized to the plasma membrane can be seen in Figure 1.

In the Cell Atlas, 2087 genes (11% of all protein-coding human genes) have been shown to encode proteins that localize to the plasma membrane (Figure 2). A Gene Ontology (GO)-based functional enrichment analysis of the plasma membrane proteome shows enrichment of terms for biological processes related to structural organization of the cell, cell signalling and cellular response to extracellular stimuli, transport across the plasma membrane, and cell adhesion. About 80% of the plasma membrane proteins localize to other cellular compartments in addition to the plasma membrane, with co-localization between the plasma membrane and actin filaments or the cytosol being overrepresented.

EGFR - A-431
CTNNB1 - A-431
EZR - A-431

Figure 1. Examples of proteins localized to the plasma membrane. EGFR is a transmembrane glycoprotein that binds to Epidermal Growth Factor (detected in A-431 cells). CTNNB1 is involved in signaling pathways (detected in A-431 cells). EZR plays a key role in cell surface structure adhesion, migration and organization (detected in A-431 cells).

Figure 2. 11% of all human protein-coding genes encode proteins localized to the plasma membrane. Each bar is clickable and gives a search result of proteins that belong to the selected category.

The structure of the plasma membrane

Substructures

• Plasma membrane: 1882
• Cell Junctions: 317

The plasma membrane is composed of a lipid bilayer, in which lipids constitute half and proteins the other half of the total mass in most human cell types. Phospholipids, which are composed of a hydrophilic phosphate group and two hydrophobic fatty-acid chains, make up the fundamental structural element in the plasma membrane (Jacobson K et al. (2019); Kobayashi T et al. (2018),Alberts B et al, 2002b. The inner and outer leaflet of the bilayer is held together by non-covalent interactions between the hydrophobic tails, which point towards each other and away from the hydrophilic faces of the membrane. In addition to phospholipids, the plasma membrane of animal cells contains two other major lipid classes; glycolipids and cholesterol. While cholesterol is usually almost as abundant as phospholipids, glycolipids only constitute about 2% of the lipids of the plasma membrane and are found only on the outer leaflet. The second major component of the plasma membrane is proteins. They can be divided into integral membrane proteins that cross the complete bilayer, peripheral membrane proteins that are anchored into one leaflet of the lipid bilayer, and surface proteins that bind to the polar heads of phospholipids or other membrane proteins. The composition of the plasma membrane is dynamic and adapts to changes in the environment as well as to the cell cycle. At physiological temperatures, the cell membrane is fluid and flexible, while at cooler temperatures, it becomes gel-like.

While the plasma membrane is behaving like a two-dimensional fluid, in which the lipids and proteins are not in fixed positions, it is still organized in different microdomains and specialized regions (Krapf D. (2018); Jacobson K et al. (2019); Kobayashi T et al. (2018)). These include lipid rafts, caveolae, protrusions and cell junctions. Cell junctions consist of regions with protein complexes that mediate contact or adhesion with neighbouring cells or with the extracellular matrix (Garcia MA et al. (2018)). The major types of cell junctions in vertebrates include gap junctions, tight junctions, and anchoring junctions. The latter includes desmosomes, hemidesmosomes and adherens junction. Desmosomes mediate cell-cell adhesion through transmembrane linker-proteins called cadherins, which connect to intermediate filaments within the cell and to cadherins on neighbouring cells. Hemi-desmosomes instead contain integrins, which also connect to intermediate filaments in the cytosol, but then also to components of the extracellular matrix, instead of neighbouring cells. Adherens junctions can contain cadherins or integrins, but in this case connecting to actin filaments in the cytosol.

Table 1. Selection of proteins suitable as markers for the plasma membrane.

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

A selection of proteins suitable to be used as markers for the plasma membrane is listed in Table 1. A list of highly expressed genes encoding proteins that localize to the plasma membrane can be found in Table 2.

CDH17 - CACO-2
CTNNA1 - CACO-2
DNAJC18 - HEK 293

GJB6 - RT4
TJP3 - CACO-2
C4orf19 - RT4

Figure 3. Examples of proteins localized to different types of cell junctions. CDH17 is a membrane-associated glycoprotein. Cadherins are calcium dependent cell adhesion proteins (detected in CACO-2 cells). CTNNA1 found at cell to cell and cell to matrix boundaries, associated with cadherins (detected in CACO-2 cells). DNAJC18 is not a very well characterized protein (detected in HEK 293 cells). GJB6 is a gap junction protein through which small materials diffuse into neighboring cells (detected in RT4 cells). TJP3 plays a role in the linkage between the actin cytoskeleton and tight junctions. Cadherins are calcium dependent cell adhesion proteins (detected in CACO-2 cells). C4orf19 is an uncharacterized protein (detected in RT4 cells).

Figure 4. 3D-view of the plasma membrane in U-2 OS, visualized by immunofluorescent staining of EZR. The morphology of cell junctions in human induced stem cells can be seen in the Allen Cell Explorer.

The function of the plasma membrane

The plasma membrane is involved in a variety of cellular processes (Alberts B et al, 2002b). The main function of the plasma membrane is to separate and protect the intracellular environment from the extracellular space. The plasma membrane is semi-permeable and selectively regulates the passage and transport of various molecules and compounds in and out of the cell. For small molecules, such as ions, cross-membrane cellular transport can occur by passive osmosis and diffusion, but transport against the concentration gradient requires the help of ion pumps. For larger molecules, like hormones and enzymes, transport occurs by endocytosis, exocytosis or with the help of transmembrane protein transporters or channels. The plasma membrane also provides structural integrity, shape and polarity to cells by anchoring the cytoskeleton and by attaching the cell to the extracellular matrix and to other cells (Orlando K et al. (2009)). These physical connections, as well as the presence of receptors or other factors with signal transduction role, are also essential for cell-cell and cell-ECM communication. Moreover, the plasma membrane has a central roles in cellular motility and polarity (Eaton RC et al. (1991)).

A rupture in the plasma membrane leads to the impairment of cell integrity and function, resulting in cell lysis and cell death unless rapidly repaired. Moreover, mutations in genes encoding proteins that localize to the plasma membrane have been associated with numerous human diseases. For example, mutations in genes encoding channel- and transporter proteins have been linked to including cystic fibrosis, cardiac arrhythmia, diabetes, skeletal muscle defects, and neurological disorders. Also, disturbances in the composition percentages of membrane lipids and proteins may lead to a variety of diseases related to lipid metabolism (Simons K et al. (2002)).

Gene Ontology (GO)-based functional enrichment analysis of genes encoding proteins localizing to the plasma membrane shows enrichment of terms describing functions that are well in-line with the known functions of the plasma membrane. The most highly enriched terms for the GO domain Biological Process are related to cellular responses to various stimuli, cell adhesion,cell signalling and structural organization of the plasma membrane (Figure 5a). Enrichment analysis of the GO domain Molecular Function gives top hits for terms related to binding to adhesion molecules and receptors, signal transduction, and channel activity (Figure 5b).

Figure 5a. Gene Ontology-based enrichment analysis for the plasma membrane 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 5b. Gene Ontology-based enrichment analysis for the plasma membrane 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.

Plasma membrane proteins with multiple locations

Approximately 81% (n=1685) of the plasma membrane proteins detected in the Cell Atlas also localize to other cellular compartments (Figure 6). The network plot shows that the most common additional locations for proteins that localize to the plasma membrane are the cytosol, nucleoplasm, vesicles and actin filaments. proteins that localize to both the plasma membrane and to the cytosol or vesicles are overrepresented. Indeed, most proteins that are targeted for the plasma membrane are carried through the secretory pathway to their destination by vesicles. Examples of multilocalizing proteins within the plasma membrane proteome can be seen in Figure 7.

Figure 6. Interactive network plot of the plasma membrane proteins with multiple localizations. The numbers in the connecting nodes show the proteins that are localized to the plasma membrane and to one or more additional locations. Only connecting nodes containing more than one protein and at least 0.5% of proteins in the plasma membrane 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.

BAIAP2 - U-2 OS
ADD1 - Hep G2
ARHGEF26 - U-251 MG

Figure 7. Examples of multilocalizing proteins in the plasma membrane proteome. BAIAP2 is an adapter protein that links membrane bound G-proteins, which plays a role in signal transduction, to cytoplasmic effector proteins. It has been shown to localize to both the cytoplasm and the plasma membrane (detected in U-2 OS cells). ADD1 is a heterodimeric protein. It binds with high affinity to Calmodulin and is a substrate for protein kinases. It has been shown to localize to both the nucleus and the plasma membrane (detected in Hep-G2 cells). ARHGEF26 is a member of the Rho-guanine nucleotide exchange factor (Rho-GEF). These proteins regulate Rho GTPases by catalyzing the exchange of GDP for GTP. GTPases act as molecular switches in intracellular signaling pathways. It has been shown that ARHGEF26 localizes to the nucleus, cytoplasm and plasma membrane (detected in U-251 cells).

Expression levels of plasma membrane proteins in tissue

Transcriptome analysis and classification of genes into tissue distribution categories (Figure 8) shows that a larger portion of the plasma membrane-associated protein-coding genes are detected in some or in many tissues, while a smaller portion are detected in all tissues, compared to all genes presented in the Cell Atlas. This indicates a more pronounced role for plasma membrane proteins in functions or structures specific to groups of tissues.

Figure 8. Bar plot showing the percentage of genes in different tissue distribution categories for plasma membrane-associated protein-coding genes, compared to all genes in the Cell Atlas. Asterisk marks a statistically significant deviation (p≤0.05) in the number of genes in a category based on a binomial statistical test. Each bar is clickable and gives a search result of proteins that belong to the selected category.

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