The Continual Movement and Exchange of Vesicles to and From the Plasmalemma is Called
Endomembrane System
The parts of the endomembrane system that are relevant to storage protein synthesis and deposition are shown schematically in Figure 1, while the processing events are summarized in Table 4.
From: Encyclopedia of Food Grains (Second Edition) , 2016
Basic Genetics: The Cell, Mitosis and Meiosis, and Mendelian Laws
Guan Wang , in Handbook of Pharmacogenomics and Stratified Medicine, 2014
2.1.2 Membrane-Bound Organelles in Eukaryotic Cells
The endomembrane system separates the cell into different compartments, or organelles, such as the nucleus, the endoplasmic reticulum (ER), the Golgi apparatus, and lysosomes (see Table 2.2). The endomembrane system is derived from the ER and flows to the Golgi apparatus, from which lysosomes bud. The ER is a continuous system of flattened membrane sacks and tubules that is specialized for protein processing and lipid biosynthesis. The endomembrane system is important for the cell's compartmental organization to function independently and properly. Ribosomes that synthesize proteins destined for insertion into cellular membranes or for export from the cell associate with specialized regions of the ER, called the rough ER owing to the attached ribosomes.
Table 2.2. Most Common Characteristics of Membrane-Bound Organelles in Animal Eukaryotic Cells
| Organelle | Feature | Function |
|---|---|---|
| Nucleus |
|
|
| Ribosomes |
|
|
| Endoplasmic reticulum (ER) |
|
|
| Golgi apparatus |
|
|
| Lysosomes |
|
|
| Peroxisomes |
|
|
| Mitochondria |
|
|
- a
- One of the two poles of the Golgi apparatus located near ER and receiving the content carried by transport vesicles from ER.
- b
- The other pole of the Golgi apparatus, giving rise to vesicles that travel to other sites.
For the most common organelles in eukaryotic cells, the structure and function of each are illustrated, using an animal cell as an example, in Figure 2.1 and Table 2.2.
Figure 2.1. The most common structures in an animal cell.
Genetic material, in the form of DNA, resides in the nucleus. Although vacuoles are included here, they generally exist in protists and plants.
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Extracellular Matrix
Randy Wayne , in Plant Cell Biology (Second Edition), 2019
20.5.3 Endomembrane System
The endomembrane system is fundamental in the synthesis and delivery of the components of the extracellular matrix ( Kim and Brandizzi, 2014, 2016 Kim and Brandizzi, 2014 Kim and Brandizzi, 2016 ; Lütz-Meindl, 2016; van de Meene et al., 2017). The synthesis of hemicellulose takes place predominantly or even exclusively in the Golgi apparatus (Zhang and Staehelin, 1992; Lynch and Staehelin, 1992; Staehelin et al., 1992). Many of the (100–1000) enzymes required for hemicellulose synthesis, including glucosyl, xylosyl, fucosyl, and arabinosyl transferases, have been localized in the Golgi apparatus (Ray et al., 1969; Gardiner and Chrispeels, 1975; Green and Northcote, 1978; James and Jones, 1979; Ray, 1980; Hayashi and Matsuda, 1981; Urbanowicz et al., 2004). The resulting hemicelluloses are transported to the plasma membrane through the secretory pathway.
The synthesis of pectins, including homogalacturonan, rhamnogalacturonan I, and rhamnogalacturonan II, also takes place in the Golgi apparatus (Zhang and Staehelin, 1992; Staehelin et al., 1992; Sherrier and VandenBosch, 1994; Staehelin and Moore, 1995; Sterling et al., 2001; Bosch and Hepler, 2005; Harholt et al., 2010; Anderson, 2016). The resulting pectins are transported to the plasma membrane through the secretory pathway (Toyooka et al., 2009).
The proteins that make up the cellulose-synthesizing centers pass through the Golgi apparatus (Haigler and Brown, 1986; Wightman and Turner, 2010a,b Wightman and Turner, 2010a Wightman and Turner, 2010b ; Bashline et al., 2011, 2014a,b Bashline et al., 2011 Bashline et al., 2014a Bashline et al., 2014b ; Cai et al., 2011; Oikawa et al., 2013; McFarlane et al., 2014). Perhaps, the same vesicles that contain the cellulose-synthesizing complexes also contain the hemicelluloses and pectins. Because the hemicelluloses and pectins in each cell type may be different, the enzymatic composition of the Golgi apparati in these cells must also be different. Moreover, the position of the Golgi body or the delivery of Golgi-derived vesicles to various sides of the cell must be regulated in cells that are surrounded by an extracellular matrix that is not uniform all the way around the cell. We do not know what controls the position of the Golgi apparatus and its enzymatic composition in these cases.
The synthesis of extracellular matrix proteins such as extensin begins when the gene becomes transcriptionally active. Then RNA polymerase II transcribes the DNA into hnRNA that subsequently binds to RNA-binding proteins and Small NUclear RibonucleoProteins (SNURPs) to form spliceosomes. The introns are then removed from the hnRNA to make mRNA and the 5′ end is capped with methylguanosine and the 3′ end is polyadenylated. The protein–mRNA complex then interacts with the nuclear pores and moves into the cytoplasm (see Chapter 16).
The mRNA for extensin must bind to the ribosomes, and as translation begins, the nascent polypeptide must bind the signal recognition particle and move to the endoplasmic reticulum (ER) where the signal recognition particle binds to its receptor (see Chapter 4). Subsequently, the amino-terminus containing the signal peptide is inserted through a protein-translocating channel of the ER and enters the secretory pathway, where it moves to the Golgi apparatus. The prolines participating in the O-linked glycosylations are hydroxylated in the ER (Hieta and Myllyharju, 2002; Tiainen et al., 2005). Extensin is glycosylated, and the O-linked arabinosylation of extensin begins in cis-Golgi cisternae (Moore et al., 1991). Double immunolabeling experiments with colloidal gold show that extensin moves through the entire Golgi apparatus and can be processed in the same Golgi stack as xyloglucan (Moore et al., 1991). Eventually, the extracellular matrix proteins end up in the lumen of a secretory vesicle (see Chapter 8).
Enzymes that affect the physicochemical properties of the extracellular matrix, including expansin (Vannerum et al., 2011; Cosgrove, 2016a,b Cosgrove, 2016a Cosgrove, 2016b ), yieldin (Okamoto-Nakazato, 2002), xyloglucan endotransglycosylase/hydrolase, polygalacturonase, pectate lyase, pectin methylesterase (Bosch et al., 2005; Tian et al., 2006), and pectin methylesterase inhibitor (Giovane et al., 2004), follow the same pathway as extensin, as they travel from the rough ER to the extracellular matrix.
The vesicles that bud off the Golgi cisternae or the trans-Golgi network move through the viscous cytosol (see Chapter 9) with the aid of a mechanochemical ATPase (see Chapters 10 and 11 Chapter 10 Chapter 11 ) to the plasma membrane. The vesicles fuse with the plasma membrane, and contents are secreted into the extracellular matrix. Of course, if too much plasma membrane is added relative to the wall material needed, the membrane is recycled by endocytosis (see Chapter 8; Moscatelli, 2008; Zonia and Munnik, 2008; Bashline et al., 2013). Moreover, the extracellular matrix is dynamic and is also undergoing turnover (Labavitch, 1981; Gorshkova et al., 1997). We do not know how the exocytotic and endocytotic vesicles that contain the cellulose-synthesizing complexes, hemicelluloses, pectins, and proteins are regulated, related, or coordinated.
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Membrane Trafficking in Autophagy
Kristiane Søreng , ... Anne Simonsen , in International Review of Cell and Molecular Biology, 2018
3 Membrane Trafficking
The endomembrane system permits various functions of the eukaryotic cell to be compartmentalized (e.g., protein degradation occurs in the lysosome), allowing a higher degree of cell specialization. The system relies on dynamic interactions between different compartments, facilitated by vesicle trafficking between them. In general, intracellular membrane trafficking involves the formation and budding of membrane vesicles from a donor membrane, their transport and subsequent fusion with target membranes, leading to transport of cargo from the donor to the target organelle ( Rothman, 2002). These events are orchestrated and regulated by several proteins and protein complexes, including adaptor and coat proteins, small GTP-binding proteins (also called GTPases), as well as SNARE and tethering proteins (Fig. 3A).
Fig. 3. General principles of membrane trafficking. (A) Intracellular membrane trafficking involves assembly of coat proteins at the donor membrane for generation of a transport vesicle (i) that pinches off and is transported to its target membrane for subsequent docking and fusion. Before docking, the coat proteins are released from the vesicle (ii) so a naked vesicle reaches its destination (iii). Direction of the vesicle to the correct target membrane is mediated by RAB, tethering, and SNARE proteins. Docking of the vesicle to the target membrane involves binding of tethering proteins to an active GTP-bound RAB protein in the vesicle membrane (iii). The following fusion involves formation of a SNARE complex between the SNARE proteins present in both membranes (iv). (B) RAB proteins are activated through conversion of their bound GDP to GTP by the action of a guanine nucleotide exchange factors (GEFs). The activated GTP-bound RAB can bind to various GTP-binding RAB-effector proteins. RAB GTP hydrolysis is activated by a RAB GTPase-activating protein (GAP), leading to RAB protein inactivation. Binding of a RAB GDP dissociation inhibitor (GDI) to prenylated RAB GDP inhibits RAB activation. A membrane bound RAB GDI displacement factor (GDF) releases the RAB protein from GDI allowing reactivation of the RAB protein by GDP exchange to GTP. (C) After tethering and docking of the vesicle on the target membrane a SNARE complex is formed by one R-SNARE located in the vesicle membrane and three Q-SNAREs in the target membrane. The SNARE proteins make up an α-helical bundle called a trans-SNARE complex that allows the two membranes to come in close proximity of each other for fusion to occur. Following fusion, the ATPase N-ethylmaleimide-sensitive factor (NSF) and its cofactor soluble NSF attachment protein (SNAP) mediates disassembly of the cis-SNARE complex, followed by sorting of the R-SNARE to the donor membrane.
Vesicle formation starts by recruitment and assembly of cytosolic coat proteins onto the membrane, leading to membrane budding and recruitment of cargo into the forming vesicle, which is eventually pinched off and transported to the donor membrane (Bonifacino and Lippincott-Schwartz, 2003; Kirchhausen, 2000). Several protein coat complexes have been identified, including clathrin-coats, COP-I, and COP-II. Clathrin is recruited to membranes through its binding to APs, including AP-2 which mediates vesicle formation from the plasma membrane (PM) through clathrin-mediated endocytosis and AP-1-mediating vesicle transport from the trans-Golgi network (TGN) (Schmid, 1997). Uptake of cargo from the PM can also occur independently of clathrin, involving other coats which facilitate micropinocytosis, phagocytosis, and other small-scale endocytic processes (Mayor et al., 2014). The nonclathrin coats COP-I and COP-II drive vesicle formation and transport from intra-Golgi/Golgi-to-ER and ER-to-ERGIC/Golgi, respectively (Barlowe et al., 1994; Letourneur et al., 1994).
The large superfamily of GTPases includes the RAS, Rho, ADP-ribosylation factor (ARF), and RAN and RRAB families that all function as molecular switches between an active state upon GTP-binding or inactive state when bound to GDP. Moreover, they have intrinsic GTPase activity leading to hydrolysis of their bound GTP to GDP and phosphate (Stenmark, 2009; Takai et al., 2001). The largest group of GTPases is the RAB proteins (Lamb et al., 2016a). RAB proteins localize to specific intracellular compartments where they regulate several steps of membrane trafficking, including vesicle formation, vesicle transport along actin and tubulin filaments as well as membrane tethering and fusion. The RAB proteins are prenylated and thus membrane anchored, giving them specific roles in trafficking of membrane vesicles. The activity of RAB proteins is tightly regulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). GEFs catalyze the dissociation of GDP allowing GTP to bind. The GTP-bound RAB protein is in its active state and can further bind effector proteins, e.g., a membrane-bound tethering protein (Fig. 3B). GAPs catalyze hydrolysis of the bound GTP to GDP resulting in the inactivation of the RAB protein and its displacement from the membrane. This occurs through the binding of guanosine nucleotide dissociation inhibitors (GDI) proteins, which bind the prenyl groups of RAB GDP and delivers that RAB to its original membrane (Cherfils and Zeghouf, 2013).
For a membrane vesicle to be able to fuse with other membrane vesicles or compartments, vesicle tethering proteins, and soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are involved. These are proteins located on both the vesicle membranes (v-SNAREs) and the target membranes (t-SNAREs). SNARE proteins share a similar SNARE motif, and depending on whether or not this motif contains a conserved glutamate (Q) or an arginine (R) residue, SNAREs can also be classified into Q-SNARES or R-SNARES. t-SNAREs belong to the group of Q-SNAREs, and include syntaxins (STX) and synaptosomal-associated protein 25 (SNAP-25) proteins, whereas V-SNAREs belong to R-SNAREs and include the VAMP family of proteins (vesicle-associated membrane protein, also called synaptobrevin) (Ungermann and Langosch, 2005). Upon fusion, one R-SNARE and three Q-SNAREs (Qa, Qb, and Qc) interact with each other forming a trans-SNARE complex (Fasshauer et al., 1998). The subsequent formation of a α-helical bundle allows the two membranes to come in close proximity, leading to the displacement of water molecules and membrane fusion (Fig. 3C). The energy required for the membrane fusion is produced by the formation of the SNARE bundle (Hong and Lev, 2014; Südhof and Rothman, 2009). After fusion, the AAA-ATPase NSF (N-ethylmaleimide-sensitive factor) and its cofactor SNAP (soluble NSF attachment protein) allow the remaining SNARE complex, also called a cis-SNARE complex, to disassemble and be ready for another round of vesicle fusion (Jahn et al., 2003). An overview of the membrane trafficking components implicated in the biogenesis, transport, and maturation of autophagosomes is shown in Tables 1 and 2 and these components are discussed in more detail below.
Table 1. Trafficking and Membrane Remodeling Proteins in Autophagosome Formation
| Proteins | Autophagic Function | References |
|---|---|---|
| RABs | ||
| RAB1/Ypt1 | Involved in autophagosome formation by regulating ULK1 and ATG9 traffic to the site of autophagosome formation | Zoppino et al. (2010), Kakuta et al. (2012), Lynch-Day et al. (2010), and Lamb et al. (2016b) |
| RAB4 | Colocalizes with both LC3 and mitochondria and promotes formation of LC3-positive autophagosomes. Regulates autophagy during laminar-shear stress | Talaber et al. (2014) and Yao et al. (2015) |
| RAB5 | Activates PIK3C3 and is involved in the clearance of mutant huntingtin-protein aggregates | Dou et al. (2013) and Ravikumar et al. (2008) |
| RAB11 | Recruits recruiting recycling endosomes to juxtanuclear region during autophagy | Knaevelsrud et al. (2013) and Longatti et al. (2012) |
| RAB12 | Regulates mTOR activity. Binds LC3 and is recruited to autophagosomes. May provide membrane input to autophagosomes from recycling endosomes | Matsui and Fukuda (2013) |
| RAB17 | Involved during formation of GAS-containing autophagosomes | Haobam et al. (2014) |
| RAB23 | Important for formation of GAS-containing autophagosomes | Nakagawa et al. (2004) |
| RAB26 | Mediates selective degradation of synapses through autophagy | Binotti et al. (2015) |
| RAB32 | Involved in formation of autophagosomes from the ER and autophagic clearance of protein aggregates. Also important for autophagy-mediated lipid storage in Drosophila fat body | Hirota and Tanaka (2009) |
| RAB33B | Regulates autophagy through interaction with ATG16L1 | Itoh et al. (2008) and Chandra et al. (2016) |
| SNAREs | ||
| STX17 | ER protein that recruits ATG14L to the ER-mitochondria contact sites during autophagy. Inserted into closed autophagosomes | Hamasaki et al. (2013a) |
| Sso1/2 | Yeast Q-SNARE involved during fusion of Atg9 vesicles at the PAS | Nair et al. (2011) |
| Sec9 | Yeast Q-SNARE that forms complex with the Q-SNAREs Sso1 and Tlg2 together with R-SNAREs Sec22 and Ykt6 during autophagosome formation | Nair et al. (2011) |
| Sec22 | Yeast R-SNARE involved in autophagosome formation | Nair et al. (2011) |
| Ykt6 | Yeast R-SNARE involved in autophagosome formation | Nair et al. (2011) |
| VAMP7 | R-SNARE in complex with the Q-SNAREs STX7, STX8, and VTI1B that regulates homotypic fusion of ATG16L1 precursor membranes | Moreau et al. (2011) |
| VAMP3 | R-SNARE acting during heterotypic fusion of ATG9- and ATG16L1-positive vesicles deriving from the plasma membrane. Necessary for autophagosome formation. Also important for fusion of recycling endosomes with GAS-containing autophagosomes | Puri et al. (2013) and Nozawa et al. (2017) |
| VAMP2 | R-SNARE involved in fusion of autophagic precursor membranes important for autophagosome formation | Moreau et al. (2014) |
| RAB GAPs and GEFs | ||
| TBC1D14 | Negative regulator of autophagosome formation | Longatti et al. (2012) |
| TRAPP III complex | RAB1/Ypt1 GEF regulating ATG9 trafficking | Lynch-Day et al. (2010), Kakuta et al. (2012), and Lamb et al. (2016b) |
| DENND3 | GEF for RAB12, activated by ULK1-phosphorylation | Xu et al. (2015) |
| Rabex-5 | GEF for RAB17 involved in formation of GAS-containing autophagosomes | Haobam et al. (2014) |
| TBC1D25/OATL1 | GAP for RAB33B, interacts with Atg8 homologs | Itoh et al. (2011) |
| Other proteins | ||
| Clathrin | Coat protein required for formation of ATG9 and ATG16-positive vesicles from the plasma membrane | Ravikumar et al. (2010) |
| PICALM | Clathrin assembly protein important for homotypic fusion of ATG16L1 vesicles | Moreau et al. (2014) |
| COP-I | Protein coat involved in vesicle formation between Golgi and ER, necessary for autophagy | Razi et al. (2009) and Karanasios et al. (2016) |
| COP-II | Protein coat involved in vesicle formation from ERES and ERGIC, important during autophagosome formation | Zoppino et al. (2010), Graef et al. (2013), and Ge et al. (2013) |
| Ema | Golgi protein important for autophagosome growth in Drosophila | Kim et al. (2012) |
| CLEC16A | Mammalian EMA ortholog, required for mitophagy and bulk autophagy | Soleimanpour et al. (2014) and Redmann et al. (2016) |
| SNX18 | Positive regulator of autophagosome formation and provides membrane input from recycling endosomes to the growing autophagosome | Knaevelsrud et al. (2013) |
| HS1BP3 | Negative regulator of autophagosome formation through binding to the lipid precursor phosphatidic acid | Holland et al. (2016) |
| C9orf72 | RAB1 effector protein that regulates trafficking of ULK1 complex to the phagophore | Webster et al. (2016), DeJesus-Hernandez et al. (2011), and Renton et al. (2011) |
| HAMM | Actin nucleation factor that generates actin filaments necessary for autophagosome formation | Kast et al. (2015) |
| JMY | Actin nucleation factor involved in autophagosome formation | Coutts and Thangue (2015) |
| CAPZ | PI3P-binding actin-capping protein that stabilizes actin filaments during autophagosome formation | Mi et al. (2015) |
Table 2. Trafficking and Membrane Remodeling Proteins in Autophagosome Maturation
| Proteins | Autophagic Function | References |
|---|---|---|
| RABs | ||
| RAB7/Ypt7 | Important for autophagosome–lysosome fusion both in yeast and mammalian cells | Kirisako et al. (1999), Gutierrez et al. (2004), Jäger et al. (2004), and Hu et al. (2015) |
| RAB8B | Involved in autophagosome–lysosome fusion during xenophagy | Pilli et al. (2012) |
| RAB9 | Mediates fusion of small GAS-containing autophagosomes into larger autophagosomes | Nozawa et al. (2012) |
| RAB11 | Involved in amphisome formation in mammalian cells and Drosophila | Fader et al. (2008) and Szatmári et al. (2014) |
| RAB21 | Important for endosomal sorting of VAMP8 to lysosomes and autophagosome–lysosome fusion | Jean et al. (2015) |
| RAB24 | Localizes to LC3-positive autophagosomes and is involved in protein aggregate clearance during basal conditions | Ylä-Anttila et al. (2015) |
| RAB25 | Prevents apoptosis and autophagy in ovarian and cancer cells, promoting cancer cell growth | Yang et al. (2006), Cheng et al. (2004), and Liu et al. (2012) |
| SNAREs | ||
| Vam3p | Yeast Q-SNARE regulating autophagosome–vacuole fusion | Wada et al. (1997), Darsow et al. (1997), and Ohashi and Munro (2010) |
| Vam7p | Yeast Q-SNARE forming complex with Vam3p | Sato et al. (1998) and Ohashi and Munro (2010) |
| Vti1p | Yeast Q-SNARE important for autophagosome–vacuole fusion during the Cvt-pathway and canonical autophagy | von Mollard and Stevens (1999) and Ishihara et al. (2001) |
| Ykt6p | Yeast R-SNARE forming SNARE complex with Vti1p, Vam3p, and Vam7p. Mediates fusion of autophagosomes and vacuoles | Dilcher et al. (2001) |
| VTI1B | Mammalian Vti1p-homolog and necessary for fusion between autophagosomes and lysosomes | Atlashkin et al. (2003) and Furuta et al. (2010) |
| VAMP7 | Lysosomal R-SNARE important for autophagosome maturation | Fader et al. (2009) |
| VAMP8 | Lysosomal R-SNARE mediating autophagosome–lysosome fusion. Forms SNARE complex with STX17 | Itakura et al. (2012b) |
| STX17 | Q-SNARE located in the autophagosomal membrane and mediates autophagosome fusion with lysosomes in mammalian cells and Drosophila | Itakura et al. (2012b) and Takáts et al. (2013) |
| SNAP-29 | Cytosolic Q-SNARE recruited to STX17 on the autophagosomes. Forms SNARE complex with STX17 and VAMP8 to mediate fusion of autophagosomes and lysosomes. | Itakura et al. (2012b) |
| Other proteins | ||
| JUMPY | Phosphatase that dephosphorylates PI3P and regulates autophagosome maturation | Vergne et al. (2009) |
| HOPS complex | RAB7 effector in both mammalian cells and Drosophila that binds STX17 and recruits UVRAG and PLEKHM1 to autophagosomes for autophagosome–lysosome fusion | Nickerson et al. (2009), Liang et al. (2008), Jiang et al. (2014), and Takáts et al. (2014) |
| TECPR1 | Binds to ATG5 and PI3P on autophagosomes to tether autophagosomes and lysosomes for fusion | Chen et al. (2012) and Kim et al. (2015a) |
| PLEKHM1 | Regulator of autophagosome maturation through interaction with RAB7 and HOPS in addition to LC3/GABARAP | Tabata et al. (2010), McEwan et al. (2015), and Nguyen et al. (2016) |
| PI4KII-α | Kinase generating PI4P important for autophagosome–lysosome fusion | Wang et al. (2015) |
| PIKfyve/FAB1 | Kinase in mammalian cells, Drosophila and C. elegans, generating PI(3,5)P2 from PI3P and is important for maturation of autophagosomes | Rusten et al. (2007), Martin et al. (2013), and Nicot et al. (2006) |
| INPP5E | Regulator of and autophagosome–lysosome fusion through conversion of PI(3,5)P2 to PI3P | Hasegawa et al. (2016) |
| RILP | RAB7-effector binding to LC3 and RAB7 on autophagosomes and the motor protein dynein, mediating minus-end traffic of autophagosomes | Bains et al. (2011) and Wijdeven et al. (2016) |
| FYCO1 | RAB7 effector which interacts with LC3 and PI3P-linking kinesin1 motor proteins to autophagosome for plus-end transport | Pankiv et al. (2010), Olsvik et al. (2015), and Raiborg et al. (2015) |
| ORP1 | Cholesterol-sensing RAB7-effector present on autophagosomes and mediates binding of RILP–RAB7–dynein complex for transport of autophagosomes | Wijdeven et al. (2016) |
| LRRK1 | Kinase regulating RAB7 activity during autophagosome maturation | Toyofuku et al. (2015) |
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Interplay between exosomes and autophagy: Are they partners in crime?
Malgorzata Czystowska , Theresa L. Whiteside , in Autophagy in Immune Response: Impact on Cancer Immunotherapy, 2020
Abstract
The eukaryotic endomembrane system plays a key role in responses of cells to stress and maintains cell homeostasis in health and disease. Its two components, exosome biogenesis and autophagy are linked through the shared molecular machinery in the endolysosomal pathway. The distinction between exosomes derived from the endosome and extracellular vesicles (EVs) produced by secretory autophagy is difficult, because of molecular crosstalk existing between the exosome and autophagy pathways. Dichotomous effects these EVs mediate in health and disease suggest they comprise vesicles derived from both pathways. The crosstalk between these pathways provides the host immune cells with context-dependent signals that might differentially drive innate and adaptive immune responses. The messages carried by autophagy-derived EVs may be distinct from messages exosomes deliver to immune cells and might induce immune responses that are qualitatively and quantitatively different. The presence of exosome biogenesis and autophagy might allow for the calibration of immune responses under various environmental stress conditions. This hypothesis is an attempt to explain why autophagy and exosome biogenesis exist as distinct albeit interactive and partially overlapping cellular pathways. By simultaneously engaging the host immune system, exosomes and autophagy maintain the balance required for cellular homeostasis under physiological and pathological conditions.
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Compartmentalization
M.A. De Matteis , C. Wilson , in Brenner's Encyclopedia of Genetics (Second Edition), 2013
Compartmentalization Ensures Fidelity and Directionality of Transport
The principal compartments of the endomembrane system are the nuclear envelope, the endoplasmic reticulum (ER), the Golgi apparatus, endosomes, and lysosomes ( Figure 1 ). Proteins destined to different compartments of the endomembrane system and those destined for secretion (approximately one-third of the proteins encoded by the human genome) are translocated into the ER during their synthesis on ER-attached ribosomes. The ER contains the machinery for the proper folding, assembly, and, in some cases, modification of the proteins to enhance their stability and render them suitable for further modification as they pass through the next compartment (i.e., the Golgi apparatus) along the secretory pathway. Incorrect assembly can lead to protein degradation, while correctly folded and modified proteins are selected and organized into domains that exit the ER in the membrane-bound carriers. The process involved in the formation of the carriers is mediated by a core set of evolutionarily conserved molecules called the COPII coat machinery that selects cargo molecules to be transported and bends the membrane to form small round or large pleomorphic membrane carriers. The carriers that leave the ER are then destined for the next compartment of the pathway, the Golgi apparatus. The membrane carriers fuse with the membrane of the Golgi and the proteins pass through a series of subcompartments (cisternae) where they may be sequentially modified to produce the mature functional form of the protein. Having traversed the Golgi, the proteins are then sorted for delivery to their final destination, such as lysosomes or the cell surface. This, so far incompletely understood, sorting process involves the interaction of sorting motifs on the cargo molecules with specific adaptor proteins and is also influenced by the lipid composition of the membranes. Here, for example, another vesicle coat, clathrin, mediates traffic from the trans-Golgi network (TGN) through the endocytic system. Efficient sorting may occur in endosomal compartments that also operate in the sorting of molecules that are endocytosed from the plasma membrane. Thus, the compartmental organization of the secretory pathway ensures fidelity and directionality and a stringent selection process so that the proteins are delivered to their target organelles/locations.
Figure 1. Compartmentalization of the endomembrane system. The endoplasmic reticulum (in orange), which is contiguous with the nuclear envelope, acts as a port of entry into the secretory system. Newly synthesized proteins are translocated into the ER where they are folded, assembled, and subjected to quality control. Proteins leave the ER in COPII-coated membrane carriers destined for the Golgi complex. In mammalian cells, these carriers may fuse with the ER–Golgi intermediate compartment (ERGIC), an intermediate sorting station. The transport carriers fuse with Golgi membranes and the cargo molecules pass through the cisternae of the Golgi where they are subjected to sequential modification reactions. Having traversed the Golgi, the cargo is sorted and packaged into new transport carriers in the TGN for transport to the cell surface and the endosomal system. Clathrin-coated vesicles mediate transport between the Golgi and the endosomal system. The endosomal system acts as a major sorting center that directs proteins coming from the cell surface and the Golgi to various destinations, such as the lysosome, but also recycles proteins back to the plasma membrane and the Golgi for reuse and to maintain compartmental identity and function. COPI-coated vesicles act to maintain compartmental identity and function by returning forward moving material to the correct compartment.
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Plastid Protein Targeting
P. Chotewutmontri , ... B.D. Bruce , in International Review of Cell and Molecular Biology, 2017
Abstract
Eukaryotic organisms are defined by their endomembrane system and various organelles. The membranes that define these organelles require complex protein sorting and molecular machines that selectively mediate the import of proteins from the cytosol to their functional location inside the organelle. The plastid possibly represents the most complex system of protein sorting, requiring many different translocons located in the three membranes found in this organelle. Despite having a small genome of its own, the vast majority of plastid-localized proteins is nuclear encoded and must be posttranslationally imported from the cytosol. These proteins are encoded as a larger molecular weight precursor that contains a special "zip code," a targeting sequence specific to the intended final destination of a given protein. The "zip code" is located at the precursor N-terminus, appropriately called a transit peptide (TP). We aim to provide an overview of plastid trafficking with a focus on the mechanism and regulation of the general import pathway, which serves as a central import hub for thousands of proteins that function in the plastid. We extend comparative analysis of plant proteomes to develop a better understanding of the evolution of TPs and differential TP recognition. We also review alternate import pathways, including vesicle-mediated trafficking, dual targeting, and import of signal-anchored and tail-anchored proteins.
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Movement within the Endomembrane System
Randy Wayne , in Plant Cell Biology, 2010
Publisher Summary
Proteins and polysaccharides move throughout the endomembrane system of the cell in 30–60 minutes. The ER and the Golgi apparatus cooperate in the synthesis and secretion of substances that are destined to go to either the vacuolar compartment or the plasma membrane. The plasma membrane and the vacuolar compartment are also in communication with each other through the endocytotic pathway, which includes the endosomes such as multivesicular bodies and partially coated reticulum and the trans-Golgi network. α-amylase follows the same secretory pathway in aleurone cells that it does in the pancreatic exocrine cells, whereas sterols are synthesized in the ER, transported through the Golgi apparatus, and then transferred to the plasma membrane with a half-time of about 30 minutes. This movement is inhibited by brefeldin A and monensin. The membrane proteins of the ER involved in lipid synthesis, ribosome docking, protein translocation, etc., as well as the chaperonins in the lumen of the ER, leave the transition ER by bulk flow in or on transition vesicles that are destined to arrive at the cis-Golgi network. The majority of proteins that are synthesized in the ER continue their movement to the Golgi apparatus. These proteins bleb off from the transition ER as transition vesicles and fuse with the Golgi apparatus and/or its cis-associated membranes.
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Protein targeting
Elizabeth Hood , ... Jianfeng Xu , in Plant Biotechnology and Agriculture, 2012
Accumulating proteins in the apoplast
Secretion is the default pathway of the plant endomembrane system and without addition of specific signals for sorting or retention, proteins that traffic through the endomembrane system will typically be secreted to the extracellular space. Most large recombinant proteins accumulate within the apoplast — the region between the plasma membrane and the cell wall — as diffusion through the cell wall matrix is size delimiting. However, recombinant protein strategies using plant cell cultures are often employed to recover the target protein in the culture medium, which decreases the complexity of the initial purification stream and minimizes exposure to vacuolar/intracellular proteinases. Strategies to direct and enhance recovery of secreted proteins in plant cell culture systems are discussed in the next section.
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Dynamic Remodeling of Membranes Catalyzed by Dynamin
Thomas J. Pucadyil , in Current Topics in Membranes, 2011
II Introduction
Eukaryotic cells are characterized by an elaborate endomembrane system encapsulated by the plasma membrane. Comprised of the endoplasmic reticulum, Golgi apparatus, endosomes and lysosomes, the endomembrane system, and the plasma membrane constitute a dynamic membrane network. Physical and functional compartmentalization of this network is achieved by the production and consumption of pools of compositionally distinct transport vesicles. Vesicles are produced from a donor compartment by membrane budding and fission and consumed at the acceptor compartment by membrane fusion. Owing to the development of assays that accurately report lipid and content mixing in membrane vesicles in the late 1970s and early 1980s ( Struck, Hoekstra, & Pagano, 1981; Wilschut & Papahadjopoulos, 1979), reconstitution of membrane fusion using viral and SNARE protein have significantly advanced our understanding of how transport vesicles are consumed at the acceptor compartment (Jahn & Sudhof, 1999). In contrast, mechanisms underlying membrane budding and fission remain largely unclear due to the lack of sensitive assays that can distinguish membrane fission from physical shearing of and protein desorption from membranes.
Of the numerous transport pathways involved in generation of vesicular intermediates in cells, the fission machinery involved in coated vesicular transport has been relatively well characterized. Coat complexes perform the dual role of concentrating proteins and budding membranes in the process of generating nascent transport vesicles (Brodsky, Chen, Knuehl, Towler, & Wakeham, 2001; Traub, 2009). Clathrin-coated vesicles mediate transport between the plasma membrane, endosome and trans Golgi compartments. Release of coated vesicles requires the membrane necks of coated buds to undergo scission, a process requiring GTP hydrolysis, and is catalyzed by members of the dynamin superfamily of large GTPases (Praefcke & McMahon, 2004). Early indication of the involvement of dynamin in scission of clathrin-coated endocytic buds came from analysis of a temperature sensitive Drosophila mutant shibire that displayed rapid paralysis at nonpermissive temperatures (Koenig & Ikeda, 1983). Thin-section electron micrographs of synaptic termini of paralyzed flies revealed a dramatic depletion of synaptic vesicles and accumulation of coated pits with electron dense material at the necks of coated pits resembling a collar. The shibire locus was subsequently identified as the Drosophila homologue of dynamin (van der Bliek & Meyerowitz, 1991).
In an attempt to understand the mechanistic basis of membrane fission, several reconstitution efforts have since been directed toward understanding dynamin behavior on artificial membrane templates. Much like the viral and SNARE proteins in membrane fusion research, these studies constitute a framework to understand membrane fission mechanisms.
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Metabolism, Structure and Function of Plant Tetrapyrroles: Introduction, Microbial and Eukaryotic Chlorophyll Synthesis and Catabolism
Jaromír Cihlář Zoltán Füssy Miroslav Oborník , in Advances in Botanical Research, 2019
Conventional routes for proteins translocated to the endomembrane system, mitochondria, and plastids include passing through protein complexes at their membranes, referred to as translocons. Targeting sequences recognized by the translocons are encoded at proteins' N-termini (i.e., they are presequences) and have a character of amphipathic or slightly hydrophobic helices ( Kunze & Berger, 2015). These characteristics have been used by prediction algorithms to assess the probability of a given protein to be recognized for translocation into a membrane-bound compartment, when experimental data are lacking. There is a wide variety of localization predictors, and the most widely used include SignalP (Emanuelsson et al., 2007) for ER-targeted proteins, TargetP (Emanuelsson et al., 2007) for mitochondrial, plastid, and cytosolic proteins (invokes SignalP to predict signal peptides), TMHMM (Krogh, Larsson, von Heijne, & Sonnhammer, 2001) to predict membrane-anchored proteins and domains, MultiLoc2 to determine the highest probability of multiple localizations, including peroxisomes and Golgi, and HECTAR (Gschloessl, Guermeur, & Cock, 2008) and ASAFind (Gruber, Rocap, Kroth, Armbrust, & Mock, 2015) specifically trained to sort stramenopile proteins. Combined presequence analyses (signal and transit peptides) are needed to detect complex plastid-targeted proteins.
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https://www.sciencedirect.com/science/article/pii/S0065229618300983
Source: https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/endomembrane-system
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