To study biogenesis of this organelle, several mutants that show a reduction or loss of gut granules were isolated and referred to as the (gut granule loss) mutants (). In the and mutant, gut granules are lost at the bean-stage of embryogenesis, apparently by fusion with the apical intestinal membrane, dumping the autofluorescent and birefringent material into the lumen. The phenotype is similar, but some gut granules are retained. Notably, the activity and distribution of the conventional endocytic pathway appears largely unaffected in these mutants (; ). encodes a Rab GTPase homologous to mammalian Rab38, a protein involved in the biogenesis of the mammalian LROs such as melanosomes and platelet dense granules (; ). Likewise the homolog Rab-RP1/Lightnoid is required for another type of LRO, the pigment granules found in retinal pigment cells (; ). GLO-1 is highly expressed in the intestine and localizes to the gut granules (). GLO-4 is a homolog of Claret, which is a putative nucleotide exchange factor of Rab-RP1 (). and are epistatic to mutations in AP3 components. and are also expressed in neurons and required for RPM-1-mediated axon termination and synaptogenesis possibly by regulating the formation or accumulation of late endosomes in neurons ().
In addition to conventional lysosomes, intestinal cells contain abundant autofluorescent and birefringent lysosome-related organelles (LROs) called gut granules (; ). gut granules were recently discovered to perform an essential role in zinc storage (). Since gut granules are stained with lysosome-specific fluorescent dyes such as acridine orange and lysotracker, these are thought to be acidified LROs like melanosomes and platelet dense granules in mammals (: ). Biogenesis of gut granules requires clathrin-adaptor AP3-components (, , , ) but not AP1 or AP2 components, suggesting that AP3-mediaed lysosomal trafficking is involved in gut granule formation ().
While mutations in retromer subunits and produce strong defects in Wnt signaling, and in the retrograde recycling of MIG-14, loss of the other core component of the retromer cargo-selective complex, VPS-29, produces only minor defects in MIG-14 sorting, and Wnt signaling is hardly affected (). However, mutant phenotypes are strongly enhanced when combined with loss of other retrograde recycling regulators that also produce weak phenotypes on their own, such as and (; ). In fact, a synthetic or enhanced Wnt-related phenotype when a mutation is combined with is often used as supporting evidence when testing for the involvement of a new protein in retrograde transport (; ). Given that VPS-29 co-purifies with VPS-26 and VPS-35 in many other organisms, VPS-29 is most likely a constitutive component of the cargo recognition complex, but in VPS-29 appears to play a supporting role in retrograde recycling, or may be more important for retromer cargo other than MIG-14.
The ultimate destination for cargo that enters the degradative pathway is the lysosome, an organelle packed with digestive enzymes and transporters, capable of breaking down most macromolecules into constituent parts small enough to be transported through the lysosomal membrane into the cytoplasm, providing small molecules that support new macromolecular synthesis and provide energy (). How cargo reaches the lysosome, and the dynamics of lysosomal membranes, remain important topics of study. Lysosomes are often called terminal compartments, but many studies indicate that lysosomes are dynamic interconnected organelles, and can fuse with the plasma membrane under certain conditions ().
As a matter of fact, protein biosynthesis is entirely controlled by RNA molecules including mRNA (genetic information), transfer RNA (tRNA) for translating the DNA code into amino acid code, and ribosomal RNA (rRNA) that provide the enzymatic linkage (chemical bond formation) of amino acids into proteins.
One aspect that defines and distinguishes membrane-bound organelles from one-another is their phophatidylinositide (PI) lipid composition (). The inositol head group of PIs are often phosphorylated at defined positions around the inositol ring, giving rise to functionally distinct lipids. Many peripheral membrane proteins involved in membrane transport contain lipid binding domains with distinct preferences for particular phosphoinositide species. Such domains include the FYVE, PH, PX, and GRAM (). The distribution and importance for particular PI lipids appears largely conserved between mammals and . Some examples include the enrichment of PI(4)P on the Golgi, PI(4,5)P2 on the plasma membrane and to a lesser extent on recycling endosomes, PI(3)P on early endosomes, and PI(3,5)P2 on late endosomes/lysosomes (). The control of the phosphorylation status of the inositol head group on particular membranes provides membrane identity, and has strong effects on which trafficking regulators are recruited and activated on particular organelles.
One prevalent model for late endosome to lysosome transport is that late endosomes fuse with pre-exisiting lysosomes to form hybrid organelles, followed by reformation of lysosomes (). ARL-8 is a small GTPase of Arf family, which mainly localizes to lysosomes in (). In mutants, RAB-7-positive late endosomes, including endocytosed macromolecules, fail to fuse with lysosomes containing the aspartic protease ASP-1 (). In addition, mutants suppress the formation of the enlarged late endosome-lysosome hybrid organelles of mutants, indicating that ARL-8 functions upstream of CUP-5 (see CUP-5 description below). ARL-8 is also involved in apoptotic cell removal, mediating fusion of phagosomes with lysosomes after phagocytosis (). The number of cell corpses significantly increases in the hermaphrodite gonad of the mutant and cell corpses engulfed by the sheath cells accumulate in RAB-7-positive phagosomes. ARL-8 is mainly localized to lysosomes but is also recruited to phagosomes at the late stages of phagosome maturation. This transient recruitment to phagosomes is regulated by RAB-7 and the HOPS complex, both of which mediate phagosome-lysosome fusion (; ). VPS-41, a component of the HOPS complex preferentially binds to the GTP-form of ARL-8, suggesting that it functions as one of the effectors of ARL-8 in the phagocytic pathway.
While all these organelles are found in animal cells, plant cells in addition contain a central vacuole that controls pressure to stabilize the cell and chloroplasts, the site of photosynthesis or light depended biosynthesis of sugars (carbohydrates).
Early/Medial Golgi cisternae can be visualized by GFP-tagged AMAN-2 (also called MANS/mannosidase) and RER-1 (a homolog of the yeast retrieval receptor for ER membrane proteins) (). GFP-tagged SYN-16 (a syntaxin 16 homolog) and RAB-6.2 mark late-Golgi compartments (; ; ; ; ). Most of early Golgi compartments appear directly juxtaposed to late Golgi compartments, indicating that Golgi mini-stacks contain early and late compartments in , which is similar to mammals but distinct from budding yeast where early and late Golgi compartments are spatially separated (). Depending upon their sorting in the TGN, newly synthesized proteins are transported to the plasma membrane or endosomes. Lysosomal hydrolases are typically sorted in the TGN for delivery to endosomes by mannose-6-phosphate receptors or Vps10/sortillin type receptors in other organisms. However, does not have any obvious homologs of mannose-6-phosphate receptors or Vps10/sortillin type receptors, leaving it a mystery for the moment as to how the sorting of lysosomal hydrolases is achieved. Interestingly, Golgi compartments are often observed closely juxtaposed to RAB-5-positive endosomes and partly to RME-1 positive tubulo-vesicular recycling endosomes, consistent with the existence of transport pathways linking these organelles (; ; ).
Macroautophagy (hereafter called autophagy) is a transport pathway leading to lysosomes (). In autophagy, cytosolic proteins and organelles are sequestered by double-membrane autophagosomes. Autophagosomes then fuse with lysosomes, resulting in degradation of their contents. The bulk degradation of cytoplasm by autophagy is essential for cell survival under starvation conditions, promoting the recycling of cellular materials such as amino acids and lipids. In addition to bulk degradation, autophagy could be a selective process, which mediates the degradation of specific targets such as pathogens, protein aggregates, and organelles. Many proteins, including ATG proteins, have been identified as regulators of autophagy in yeast and mammals, and most of them are conserved in (see WormBook chapter ). In , autophagy is involved in various physiological processes including dauer formation (), survival of L1 larvae under starvation condition (), longevity (; ; ; ; ; ) and necrotic-like degeneration of neurons (; ). Autophagy genes also play a role in apoptotic cell corpse degradation during development (; ; ). More information about this work is summarized in detail in .
In addition to these functions, recent studies have revealed that autophagy also plays unique physiological roles during early embryogenesis. ATG8/LC3 generally serves as a marker of the autophagosomal membrane in other systems, and the worm has two ATG8/LC3 homologs, LGG-1 and LGG-2 (). When autophagic activity is monitored in embryos, autophagosomes labeled with GFP::LGG-1/2 surround the penetrating paternal pronucleus in the fertilized 1-cell-stage embryos (; ). In addition to the 1-cell stage embryos, puncta of GFP::LGG-1 are induced in whole embryos around the 32- to 64-cell stages, suggesting multiple rounds of induction of autophagy during embryogenesis (). The first induction of autophagy in 1-cell stage embryos depends on fertilization, because autophagy is not induced in unfertilized eggs of the mutant that has infertile sperm but shows normal oocyte maturation and ovulation. Interestingly, in polyspermic embryos autophagosomes surround each penetrating sperm. This observation suggests that autophagy is induced by sperm entry to remove some of the paternally provided components. In fact, it was determined that these autophagosomes selectively sequester paternally inherited organelles such as mitochondria and membranous organelles (MOs), and target them to lysosomal degradation (; ). MOs are sperm-specific post-Golgi organelles essential for sperm fertility and enter the ooplasm upon fertilization together with sperm mitochondria (). This type of autophagy is referred to as “allophagy” for allogeneic (non-self) organelle autophagy (). Allophagy could also explain the mechanism of maternal inheritance of mitochondrial DNA (mtDNA). Maternal (uniparental) inheritance of mtDNA is observed in many species, although the precise mechanism has not been clear (). mtDNA is maternally inherited in wild-type . However, in autophagy-defective mutants, paternal mtDNA is abnormally transmitted to the next generation, suggesting that paternal mtDNA is eliminated from embryos by allophagy (; ). More work will be required to understand how the paternal organelles are recognized and targeted to autophagosomes. Ubiquitylation may be involved in MO recognition because a strong ubiquitylation signal is detectable on MOs in fertilized embryos. In addition to autophagy, it has been reported that RNAi of some proteasomal subunits results in the defective elimination of paternal mtDNA from embryos (), implying that the proteasomal system is also involved in degradation of paternal mitochondria.