THE HUMAN CELL


The plasma membrane also known as cell membrane or cytoplasmic membrane is the barrier that encloses the cell and protects the intracellular components from the cell's surroundings. The Plasma membrane is a thin semi-permeable membrane consisting of a lipid bilayer and associated proteins, each constituting 50% of the mass of the cell membrane (Cooper GM, 2000a). Example images of proteins localized to the plasma membrane can be seen in Figure 1.

Of all human proteins, 1661 (8%) have been experimentally shown to localize to the plasma membrane (Figure 2). Analysis of the plasma membrane proteome shows highly enriched terms for biological processes related to endocytosis and cellular response to extracellular stimuli, as well as cell adhesion. About 80% of the plasma membrane proteins localize to other cellular compartments in addition to the plasma membrane, the most represented ones being actin filaments and cytoplasm.

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).

  • 8% (1661 proteins) of all human proteins have been experimentally detected in the plasma membrane by the Human Protein Atlas.
  • 566 proteins in the plasma membrane are supported by experimental evidence and out of these 117 proteins are validated by the Human Protein Atlas.
  • 1334 proteins in the plasma membrane have multiple locations.
  • 124 proteins in the plasma membrane show a cell to cell variation. Of these 113 show a variation in intensity and 12 a spatial variation.
  • Proteins are mainly involved in endocytosis and cellular response to extracellular stimuli, as well as cell adhesion.

Figure 2. 8% 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: 1467
  • Cell Junctions: 285

    Phospholipids, composed of a hydrophilic phosphate group and two hydrophobic fatty-acid chains, constitute the fundamental structural element in plasma membranes. Lipids constitute 50% of the mass of the cell membrane and proteins the other half (1). These phospholipids form an inner and outer leaflet with the hydrophobic fatty-acid chains turned inwards within the bilayer. This bilayer functions as a barrier between two aqueous compartments impermeable to the passage of water-soluble molecules. In addition to the phospholipids, the plasma membrane of animal cells contains two major lipid classes, glycolipids and cholesterol. Glycolipids only constitute about 2% of the lipids of the plasma membrane and are found only on the outer leaflet (Cooper GM, 2000b). Cholesterol is as abundant as phospholipids within the lipid bilayer; each constitutes 20% of the lipids (Cell Membranes. Nature.com). This composition provides additional structural integrity to the cell membrane.

    The second major component of the plasma membrane is proteins. The membrane proteins are responsible for carrying out specific functions. They can be divided into integral proteins, which cross the complete bilayer; peripheral proteins, which are only inserted in one monolayer; and surface proteins, which bind to the polar heads of phospholipids or other membrane proteins (Alberts B et al, 2002a). At physiological temperatures, cell membranes are fluid and flexible, at cooler temperatures, they become gel-like (Cell Membranes. Nature.com). Phospholipids and proteins are not in a fixed position within the plasma membrane. In fact, the fluid mosaic membrane model describes the asymmetric distribution and mobility capacity of the proteins in the cell membrane matrix (Nicolson GL. 2014). A turning point to this model came with the hypothesis of the existence of lipid rafts in the exoplasmic leaflet of the bilayer. Lipid rafts consist of dynamic assemblies of cholesterol and sphingolipids and are specialized areas that differ from cell type to cell type. They play an essential role for example in signal transduction (Simons K et al, 2000). A selection of proteins suitable to be used as marker for the plasma membrane is listed in Table 1.

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

    Gene

    Description

    Substructure

    RDX Radixin Plasma membrane
    STX4 Syntaxin 4 Plasma membrane
    SLC16A1 Solute carrier family 16 (monocarboxylate transporter), member 1 Cell Junctions
    Plasma membrane
    BAIAP2L1 BAI1-associated protein 2-like 1 Cytosol
    Plasma membrane
    EZR Ezrin Plasma membrane
    EPB41L3 Erythrocyte membrane protein band 4.1-like 3 Plasma membrane
    CTNNB1 Catenin (cadherin-associated protein), beta 1, 88kDa Plasma membrane
    ANK3 Ankyrin 3, node of Ranvier (ankyrin G) Plasma membrane
    SLC41A3 Solute carrier family 41, member 3 Plasma membrane

    Cell junctions
    Cell junctions can be considered as plasma membrane micro-domains (Giepmans BN et al, 2009). Cell junctions are essential to maintain the integrity of tissue connectivity. Cell junctions contain transmembrane proteins that promote cell to cell or cell to extracellular matrix adhesion. These transmembrane proteins are associated with cytoplasmic and cytoskeletal proteins, allowing cell signaling and communication. Based on their molecular composition and structural morphology cell junctions can be distinguished to three major types. Tight junctions are typically residing at the apical end of the lateral membrane and their role is to function as para-cellular gates that select diffusion based on size and charge (Zihni C et al, 2016). Members of the claudin protein family are one of the most representative components of tight junctions. Gap junctions or communicating junctions allow direct communication between adjacent cells through diffusion, which is done through a channel formed by six connexin proteins that form a cylinder. Anchoring junctions allow cells to anchor to each other and to the extracellular matrix. Transmembrane proteins such as cadherins and integrins link cytoskeletal proteins from neighbouring cells to each other and proteins in the extracellular matrix. Example images of proteins localized to cell junctions can be seen in Figure 3.

    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).

    The function of the plasma membrane


    The plasma membrane is involved in a variety of cellular processes. The main function of the plasma membrane is to protect the intracellular environment from the extracellular space. The plasma membrane selectively regulates the exchange of matter in and out the cell. For small molecules, ions and gases, the cross-membrane cellular transport is allowed by osmosis and diffusion. For larger molecules the transport occurs by endocytosis. Hormones and enzymes are transported by exocytosis or by the help of transmembrane proteins forming membrane channels (Lodish H et al, 2000). There are also ion pumps that actively transport ions against the concentration gradient, which creates the membrane potential that is found in nerve and muscle cells (Alberts B et al, 2002b). In addition, other transmembrane proteins are receptors and enzymes having signal transduction roles.

    The plasma membrane also provides structural integrity by anchoring the cytoskeleton to give shape to the cell as well as attaching the cell to the extracellular matrix and to other cells allowing cell-cell interaction and cross-communication. A rupture in the plasma membrane leads to the impairment of cell integrity and function resulting in cell lysis and eventually to cell death.

    Another central function of the plasma membrane lies in maintaining cellular motility and polarity (Orlando K et al, 2009; Singer SJ et al, 1972; Keren K. 2011). Disturbances in these characteristics may lead to tissue disorganization, which is a hallmark of cancer (Lee M et al, 2008). 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). A list of highly expressed plasma membrane proteins is summarized in Table 2. Gene Ontology (GO)-based analysis of the proteins mainly localizing to the plasma membrane shows functions that are well in-line with the known functions of the plasma membrane. The most highly enriched terms for biological processes are related to cellular response, endocytosis, cellular maintenance and integrity (Figure 4a). Enrichment analysis of molecular function gives top hits for terms related to cell-cell adhesion, cadherin binding, which have an important role in cell adhesion or cell junctions that allows cell-to-cell adhesion (Figure 4b).

    Figure 4.a 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 4.b 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.

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

    Gene

    Description

    Average TPM

    AP2M1 Adaptor-related protein complex 2, mu 1 subunit 400
    S100A4 S100 calcium binding protein A4 394
    MSN Moesin 327
    CD81 CD81 molecule 301
    CD9 CD9 molecule 225
    ATP1B3 ATPase, Na+/K+ transporting, beta 3 polypeptide 186
    EZR Ezrin 183
    SLC1A5 Solute carrier family 1 (neutral amino acid transporter), member 5 182
    CTNNB1 Catenin (cadherin-associated protein), beta 1, 88kDa 177
    EGFR Epidermal growth factor receptor 121

    Plasma membrane proteins with multiple locations


    Approximately 80% (n=1334) of the plasma membrane proteins detected in Human Protein Atlas also localize to other cellular compartments (Figure 5). The network plot shows that the most common shared compartments with the plasma membrane are the cytosol and actin filaments. Given that many plasma membrane proteins play a role in signal transduction, these multiple locations could highlight the enzymes and receptors involved in cell signaling pathways. Examples of multilocalizing proteins within the plasma membrane proteome can be seen in Figure 6.

    Figure 5. 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 6. 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


    The transcriptome analysis (Figure 7) shows that plasma membrane proteins have slightly different distribution of tissue expression levels, compared to all localized genes in the cell atlas. The plasma membrane has more proteins specific for some tissues and fewer proteins expressed in all tissues.

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


    Alberts B et al, 2002a. Molecular Biology of the Cell. 4th edition. Membrane Proteins. New York: Garland Science.

    Alberts B et al, 2002b. Molecular Biology of the Cell. 4th edition. Ion Channels and the Electrical Properties of Membranes. New York: Garland Science.

    Cell Membranes. Nature.com. Accessed November 24, 2016. http://www.nature.com/scitable/topicpage/cell-membranes-14052567.

    Cooper GM, 2000a. The Cell: A Molecular Approach. 2nd edition. Cell Membranes. Sunderland (MA): Sinauer Associates.

    Cooper GM, 2000b. The Cell: A Molecular Approach. 2nd edition. Structure of the Plasma Membrane. Sunderland (MA): Sinauer Associates.

    Giepmans BN et al, 2009. Epithelial cell-cell junctions and plasma membrane domains. Biochim Biophys Acta.
    PubMed: 18706883 DOI: 10.1016/j.bbamem.2008.07.015

    Keren K. 2011. Cell motility: the integrating role of the plasma membrane. Eur Biophys J.
    PubMed: 21833780 DOI: 10.1007/s00249-011-0741-0

    Lee M et al, 2008. Cell polarity and cancer--cell and tissue polarity as a non-canonical tumor suppressor. J Cell Sci.
    PubMed: 18388309 DOI: 10.1242/jcs.016634

    Lodish H et al, 2000. Transport across Cell Membranes. 4th edition. Membrane Proteins. New York: W. H. Freeman.

    Nicolson GL. 2014. The Fluid-Mosaic Model of Membrane Structure: still relevant to understanding the structure, function and dynamics of biological membranes after more than 40 years. Biochim Biophys Acta.
    PubMed: 24189436 DOI: 10.1016/j.bbamem.2013.10.019

    Orlando K et al, 2009. Membrane organization and dynamics in cell polarity. Cold Spring Harb Perspect Biol.
    PubMed: 20066116 DOI: 10.1101/cshperspect.a001321

    Simons K et al, 2002. Cholesterol, lipid rafts, and disease. J Clin Invest.
    PubMed: 12208858 DOI: 10.1172/JCI16390

    Simons K et al, 2000. Lipid rafts and signal transduction. Nat Rev Mol Cell Biol.
    PubMed: 11413487 DOI: 10.1038/35036052

    Singer SJ et al, 1972. The fluid mosaic model of the structure of cell membranes. Science.
    PubMed: 4333397 

    Zihni C et al, 2016. Tight junctions: from simple barriers to multifunctional molecular gates. Nat Rev Mol Cell Biol.
    PubMed: 27353478 DOI: 10.1038/nrm.2016.80