The Yip1 domain family is a group of proteins involved in regulating secretory traffic in eukaryotes. The family consists of four members in yeast and nine members in humans. Family members have a shared architecture containing five transmembrane domains.
Yip1 domain family members are found in all eukaryotes. [1] The budding yeast Saccharomyces cerevisiae has four Yip1 domain family members: Yif1p, Yip1p, Yip4p, and Yip5p. [1] The amino acid sequence of the Yip domain family members divides them into two groups, called α-subunits and β-subunits. The α-subunits – in yeast Yip1p and Yip4p – are more closely related to each other than they are to the β-subunits, Yip5p and Yif1p. In mammals, both groups are expanded, with α-subunits YipF4, YipF5, YipF6, and YipF7; as well as β-subunits Yif1A, Yif1B, YipF1, YipF2, and YipF3. [1]
Yip1 domain family members localize to the Golgi apparatus, where they interact with each other to form complexes involved in trafficking cargo within the Golgi, and/or between the endoplasmic reticulum and Golgi. [2] The Yip1 domain family members are widely distributed throughout the body – with the exception of YipF7 found primarily in the skeletal muscle and tongue, while YipF1A is predominantly in the liver. [2] Within the cell, the different Yip family members have slightly different localizations, with YipF5, YipF7, Yif1A, and Yif1B (in yeast Yip1p and Yif1p) at the margin of the endoplasmic reticulum and Golgi; YipF3 and YipF4 at the cis-Golgi; and YipF1, YipF2, and Yipf6 (in yeast Yip4p and Yip5p) at the trans-Golgi. [1]
YipF1 was conditionally knocked-out in mice with no observable effect. [3]
A non-functional version of YipF6 exacerbated intestinal inflammation in mice, and sometimes resulted in spontaneous intestinal inflammatory disease. [4]
Each Yip1 domain family protein contains five transmembrane domains, with the N-terminus exposed to the cytosol and the C-terminus to the Golgi apparatus lumen. [1] Yip1 domain family members are thought to interact with a partner, with two molecules of each partner forming an active tetramer complex with 20 transmembrane segments. [1]
The endoplasmic reticulum (ER) is, in essence, the transportation system of the eukaryotic cell, and has many other important functions such as protein folding. It is a type of organelle made up of two subunits – rough endoplasmic reticulum (RER), and smooth endoplasmic reticulum (SER). The endoplasmic reticulum is found in most eukaryotic cells and forms an interconnected network of flattened, membrane-enclosed sacs known as cisternae, and tubular structures in the SER. The membranes of the ER are continuous with the outer nuclear membrane. The endoplasmic reticulum is not found in red blood cells, or spermatozoa.
The endomembrane system is composed of the different membranes that are suspended in the cytoplasm within a eukaryotic cell. These membranes divide the cell into functional and structural compartments, or organelles. In eukaryotes the organelles of the endomembrane system include: the nuclear membrane, the endoplasmic reticulum, the Golgi apparatus, lysosomes, vesicles, endosomes, and plasma (cell) membrane among others. The system is defined more accurately as the set of membranes that forms a single functional and developmental unit, either being connected directly, or exchanging material through vesicle transport. Importantly, the endomembrane system does not include the membranes of plastids or mitochondria, but might have evolved partially and from the actions of the latter.
The Golgi apparatus, also known as the Golgi complex, Golgi body, or simply the Golgi, is an organelle found in most eukaryotic cells. Part of the endomembrane system in the cytoplasm, it packages proteins into membrane-bound vesicles inside the cell before the vesicles are sent to their destination. It resides at the intersection of the secretory, lysosomal, and endocytic pathways. It is of particular importance in processing proteins for secretion, containing a set of glycosylation enzymes that attach various sugar monomers to proteins as the proteins move through the apparatus.
Protein targeting or protein sorting is the biological mechanism by which proteins are transported to their appropriate destinations within or outside the cell. Proteins can be targeted to the inner space of an organelle, different intracellular membranes, the plasma membrane, or to the exterior of the cell via secretion. Information contained in the protein itself directs this delivery process. Correct sorting is crucial for the cell; errors or dysfunction in sorting have been linked to multiple diseases.
A transmembrane domain (TMD) is a membrane-spanning protein domain. TMDs generally adopt an alpha helix topological conformation, although some TMDs such as those in porins can adopt a different conformation. Because the interior of the lipid bilayer is hydrophobic, the amino acid residues in TMDs are often hydrophobic, although proteins such as membrane pumps and ion channels can contain polar residues. TMDs vary greatly in length, sequence, and hydrophobicity, adopting organelle-specific properties.
A signal peptide is a short peptide present at the N-terminus of most newly synthesized proteins that are destined toward the secretory pathway. These proteins include those that reside either inside certain organelles, secreted from the cell, or inserted into most cellular membranes. Although most type I membrane-bound proteins have signal peptides, the majority of type II and multi-spanning membrane-bound proteins are targeted to the secretory pathway by their first transmembrane domain, which biochemically resembles a signal sequence except that it is not cleaved. They are a kind of target peptide.
COPI is a coatomer, a protein complex that coats vesicles transporting proteins from the cis end of the Golgi complex back to the rough endoplasmic reticulum (ER), where they were originally synthesized, and between Golgi compartments. This type of transport is retrograde transport, in contrast to the anterograde transport associated with the COPII protein. The name "COPI" refers to the specific coat protein complex that initiates the budding process on the cis-Golgi membrane. The coat consists of large protein subcomplexes that are made of seven different protein subunits, namely α, β, β', γ, δ, ε and ζ.
Calnexin (CNX) is a 67kDa integral protein of the endoplasmic reticulum (ER). It consists of a large N-terminal calcium-binding lumenal domain, a single transmembrane helix and a short, acidic cytoplasmic tail.
P24 protein family is a group of transmembrane proteins that are major components of COPI and COPII-coated vesicles. The family is also known as EMP24/GP25L/p24 family and TMP21-like proteins. The latter naming was after transmembrane emp24 domain-containing protein 10 that was found in the human brain. It was claimed to block the beta-amyloid peptide, which is implicated in the pathogenesis of Alzheimer's disease.
Endoplasmic-reticulum-associated protein degradation (ERAD) designates a cellular pathway which targets misfolded proteins of the endoplasmic reticulum for ubiquitination and subsequent degradation by a protein-degrading complex, called the proteasome.
The P-type ATPases, also known as E1-E2 ATPases, are a large group of evolutionarily related ion and lipid pumps that are found in bacteria, archaea, and eukaryotes. P-type ATPases are α-helical bundle primary transporters named based upon their ability to catalyze auto- (or self-) phosphorylation (hence P) of a key conserved aspartate residue within the pump and their energy source, adenosine triphosphate (ATP). In addition, they all appear to interconvert between at least two different conformations, denoted by E1 and E2. P-type ATPases fall under the P-type ATPase (P-ATPase) Superfamily (TC# 3.A.3) which, as of early 2016, includes 20 different protein families.
DNA damage-inducible transcript 3, also known as C/EBP homologous protein (CHOP), is a pro-apoptotic transcription factor that is encoded by the DDIT3 gene. It is a member of the CCAAT/enhancer-binding protein (C/EBP) family of DNA-binding transcription factors. The protein functions as a dominant-negative inhibitor by forming heterodimers with other C/EBP members, preventing their DNA binding activity. The protein is implicated in adipogenesis and erythropoiesis and has an important role in the cell's stress response.
Coatomer subunit alpha is a protein that in humans is encoded by the COPA gene.
KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 1, also known as KDELR1, is a protein which in humans is encoded by the KDELR1 gene.
Golgi reassembly-stacking protein of 55 kDa (GRASP55) also known as golgi reassembly-stacking protein 2 (GORASP2) is a protein that in humans is encoded by the GORASP2 gene. It was identified by its homology with GRASP65 and the protein's amino acid sequence was determined by analysis of a molecular clone of its complementary DNA. The first (N-terminus) 212 amino acid residues of GRASP55 are highly homologous to those of GRASP65, but the remainder of the 454 amino acid residues are highly diverged from GRASP65. The conserved region is known as the GRASP domain, and it is conserved among GRASPs of a wide variety of eukaryotes, but not plants. The C-terminus portion of the molecule is called the SPR domain. GRASP55 is more closely related to homologues in other species, suggesting that GRASP55 is ancestral to GRASP65. GRASP55 is found associated with the medial and trans cisternae of the Golgi apparatus.
Protein YIF1A is a Yip1 domain family proteins that in humans is encoded by the YIF1A gene.
Protein acetylation are acetylation reactions that occur within living cells as drug metabolism, by enzymes in the liver and other organs. Pharmaceuticals frequently employ acetylation to enable such esters to cross the blood-brain barrier, where they are deacetylated by enzymes (carboxylesterases) in a manner similar to acetylcholine. Examples of acetylated pharmaceuticals are diacetylmorphine (heroin), acetylsalicylic acid (aspirin), THC-O-acetate, and diacerein. Conversely, drugs such as isoniazid are acetylated within the liver during drug metabolism. A drug that depends on such metabolic transformations in order to act is termed a prodrug.
A target peptide is a short peptide chain that directs the transport of a protein to a specific region in the cell, including the nucleus, mitochondria, endoplasmic reticulum (ER), chloroplast, apoplast, peroxisome and plasma membrane. Some target peptides are cleaved from the protein by signal peptidases after the proteins are transported.
The endoplasmic reticulum membrane protein complex (EMC) is a putative endoplasmic reticulum-resident membrane protein (co-)chaperone. The EMC is evolutionarily conserved in eukaryotes, and its initial appearance might reach back to the last eukaryotic common ancestor (LECA). Many aspects of mEMC biology and molecular function remain to be studied.
The Golgi matrix is a collection of proteins involved in the structure and function of the Golgi apparatus. The matrix was first isolated in 1994 as an amorphous collection of 12 proteins that remained associated together in the presence of detergent and 150 mM NaCl. Treatment with a protease enzyme removed the matrix, which confirmed the importance of proteins for the matrix structure. Modern freeze etch electron microscopy (EM) clearly shows a mesh connecting Golgi cisternae and associated vesicles. Further support for the existence of a matrix comes from EM images showing that ribosomes are excluded from regions between and near Golgi cisternae.
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