The general structure of organelles annotated as vesicles is a round membrane-enclosed lumen that is less than 1 μm in diameter. Hence, there are only few differences in the structure of the vesicles which can be seen by light microscopy that allow a classification of the organelle, e.g. size, number or the position related to other organelles (Figure 3). Therefore, the true identity of the organelle is often only revealed by the detection of specific marker proteins in immunofluorescence images (see Table 1). Structural information about the organelles can be elucidated by electron microscopy and biochemical analyses.

Table 1. Selection of proteins suitable as markers for different vesicular organelles.

Endosomes
Endosomes can be further sub-classified into early, recycling, and late endosomes, and there is a continuous transition between these classes. Each of them can be defined by their function, by a distinct set of proteins (e.g. members of the Rab-family of proteins (Stenmark H. 2009)), or by morphological differences. The early endosome (EE) has a pleomorphic structure, which consists of cisternae. From these cisternae, two distinct subdomains emerge: vesicular structures with internal invaginations (300-400 nm diameter) and tubular extensions (60 nm diameter) (Gruenberg J. 2001). These two subdomains give rise to either recycling endosomes in the case of the tubular extension or form multivesicular bodies, which transport cargo to the late endosomes. Late endosomes (LE) have cisternal, tubular, and vesicular regions with numerous membrane invaginations, similar to those found in the EE (Griffiths G et al, 1988).

Lysosomes
The Belgian Nobel laureate de Duve discovered the lysosome in 1955 and named it after the richness in hydrolytic enzymes (De Duve C et al, 1955). Lysosomes have a tubular morphology of about 0.1-1.2 μm in size and a characteristic acidic pH-value of 4.5-5, which is ideal for the enzymes in the lysosomal lumen. The membrane of lysosomes is rich in glycoproteins and consists of an unusual lipid composition as a protection from the digestive enzymes (Schwake M et al, 2013).

Peroxisomes
The peroxisomes is another organelle discovered by de Duve in 1966 (De Duve C et al, 1966), and he named them because of their involvement in peroxidase reactions. Peroxisomes originate from the ER, but they are able to replicate themselves by division. They differ in size from 0.1-1 μm and have a dynamic structure, which is usually spherical. But the shape can change and become more elongated prior to division or in adaption to different conditions (Smith JJ et al, 2013). Elongated peroxisomes can help to distinguish peroxisomes from other vesicles in IF.

Lipid droplets
Lipid droplets (LDs) were known for a long time, but were believed to be a rather inert storage for lipids. The discovery of the first LD-associated protein in 1991 by Londos and coworkers (Greenberg AS et al, 1991) changed this view, and today LDs are considered as organelles. LDs are formed at the ER and have a simple, yet conserved structure: a hydrophobic core containing the lipids is surrounded by a membrane monolayer (instead of a bilayer found in all other organelles) to which proteins are attached (Walther TC et al, 2012). The size of LDs ranges from hundreds of nanometers to the single 100 micrometer large LD that fills adipocytes. Under normal conditions, cells have none or few small LDs, but if those few LDs are large enough, LD-associated proteins appear in perfectly round rings and the protein location can be annotated more precisely.

The function of the vesicles

Endosomes and lysosomes
Endocytic vesicles containing material such as receptors and their bound ligands are transported to the early endosome. An efficient sorting takes place in the endosomes. Some of the receptors are sent back to the plasma membranes for reuse, while other receptors are sorted into multivesicular bodies and transported to LEs, which later fuse with lysosomes for the degradation of the material. Many of the highest expressed proteins with a vesicular staining are involved in catabolic processes in the lysosome, e.g. PSAP (Table 2). Since endosomes and lysosomes take part in the regulation of receptors and transporters in the plasma membrane as well as in further distribution of endocytic material, a dysfunction of these organelles can cause human diseases. One example is the Niemann-Pick Type C Disease, where the intracellular cholesterol transport is disturbed leading to a neurologically progressive disease (Peake KB et al, 2010).

Peroxisomes
Peroxisomes are multifunctional organelles that harbor a variety of enzymes and are involved in several anabolic and catabolic cellular pathways. The main function of peroxisomes is β-oxidation of long- and very long-chain fatty acids. They also contribute to the utilization and production of reactive oxygen species in the cell. In addition, peroxisomes carry out important reactions such as phospholipid biosynthesis, chemical detoxification or oxidation of purines, polyamines, and some amino acids (Antonenkov VD et al, 2010).

Lipid droplets
Nearly all cells are able to form LDs and use them as the main storage site for cellular neutral lipids. These lipids, mainly triacylglycerol and cholesterol, are utilized for the generation of energy or serve as building blocks for the synthesis of other lipids. LDs are linked to a growing number of diseases, but most prominent is their role in obesity and diabetes (Walther TC et al, 2012).

Table 2. Highly expressed single localizing proteins with a vesicular staining across different cell lines.

Gene Ontology (GO)-based enrichment analysis of genes encoding proteins that localize mainly to vesicles reveals several functions associated with the group of organelles comprised of vesicles. In addition, it also indicates the organelles that are represented by the term vesicles. The highly enriched terms for the GO domain Biological Process are related mainly to lipid metabolism, which is connected to processes in peroxisomes, and processes related to the function of endosomes (Figure 4a). For the GO domain Molecular Function, vesicle proteins are enriched for sterol transport and receptor related actions (Figure 4b).

Vesicles proteins with multiple locations

Approximately 59% (n=1082) of the vesicle proteins detected in the Cell Atlas also localize to other compartments in the cell. The network plot (Figure 5) shows that the most overrepresented locations with vesicles are nucleoplasm, ER, and the Golgi apparatus. Given the function of vesicles, these multiple locations could highlight a higher activity in the secretory pathway. Examples of multilocalizing proteins within the proteome of vesicles can be seen in Figure 6.

Expression levels of vesicles proteins in tissue

The transcriptome analysis (figure 7) shows that vesicle proteins are less likely to be expressed in all tissues, but more likely to be enhanced or enriched in certain tissues compared to a background of all genes with protein data in the Cell Atlas. These results potentially reflect the variety of functions involving vesicle proteins, particularly in the transport of secretory proteins and other biomolecules to the outside of the cell.

Relevant links and publications

Antonenkov VD et al, 2010. Peroxisomes are oxidative organelles. Antioxid Redox Signal.
PubMed: 19958170 DOI: 10.1089/ars.2009.2996

De Duve C et al, 1966. Peroxisomes (microbodies and related particles). Physiol Rev.
PubMed: 5325972 

DE DUVE C et al, 1955. Tissue fractionation studies. 6. Intracellular distribution patterns of enzymes in rat-liver tissue. Biochem J.
PubMed: 13249955 

Greenberg AS et al, 1991. Perilipin, a major hormonally regulated adipocyte-specific phosphoprotein associated with the periphery of lipid storage droplets. J Biol Chem.
PubMed: 2040638 

Griffiths G et al, 1988. The mannose 6-phosphate receptor and the biogenesis of lysosomes. Cell.
PubMed: 2964276 

Gruenberg J. 2001. The endocytic pathway: a mosaic of domains. Nat Rev Mol Cell Biol.
PubMed: 11584299 DOI: 10.1038/35096054

Peake KB et al, 2010. Defective cholesterol trafficking in Niemann-Pick C-deficient cells. FEBS Lett.
PubMed: 20416299 DOI: 10.1016/j.febslet.2010.04.047

Schwake M et al, 2013. Lysosomal membrane proteins and their central role in physiology. Traffic.
PubMed: 23387372 DOI: 10.1111/tra.12056

Smith JJ et al, 2013. Peroxisomes take shape. Nat Rev Mol Cell Biol.
PubMed: 24263361 DOI: 10.1038/nrm3700

Stenmark H. 2009. Rab GTPases as coordinators of vesicle traffic. Nat Rev Mol Cell Biol.
PubMed: 19603039 DOI: 10.1038/nrm2728

Walther TC et al, 2012. Lipid droplets and cellular lipid metabolism. Annu Rev Biochem.
PubMed: 22524315 DOI: 10.1146/annurev-biochem-061009-102430