Pathway Analysis Report Gene Name This report contains the pathway analysis results for the submitted sample 'Gene Name'. Analysis was performed against Reactome version 66 on 04/12/2018. The web link to these results is: https://reactome.org/PathwayBrowser/#/ANALYSIS=MjAxODEyMDQwMjI0MjhfNDA4MA%3D%3D Please keep in mind that analysis results are temporarily stored on our server. The storage period depends on usage of the service but is at least 7 days. As a result, please note that this URL is only valid for a limited time period and it might have expired.
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Pathway Analysis Report
Gene Name
This report contains the pathway analysis results for the submitted sample 'Gene Name'. Analysis was performed against Reactome version 66 on 04/12/2018. The web link to these results is:
Please keep in mind that analysis results are temporarily stored on our server. The storage period depends on usage of the service but is at least 7 days. As a result, please note that this URL is only
valid for a limited time period and it might have expired.
Reactome is a curated database of pathways and reactions in human biology. Reactions can be con-sidered as pathway 'steps'. Reactome defines a 'reaction' as any event in biology that changes the state of a biological molecule. Binding, activation, translocation, degradation and classical bio-chemical events involving a catalyst are all reactions. Information in the database is authored by expert biologists, entered and maintained by Reactome’s team of curators and editorial staff. Re-actome content frequently cross-references other resources e.g. NCBI, Ensembl, UniProt, KEGG (Gene and Compound), ChEBI, PubMed and GO. Orthologous reactions inferred from annotation for Homo sapiens are available for 17 non-human species including mouse, rat, chicken, puffer fish, worm, fly, yeast, rice, and Arabidopsis. Pathways are represented by simple diagrams follow-ing an SBGN-like format.
Reactome's annotated data describe reactions possible if all annotated proteins and small mo-lecules were present and active simultaneously in a cell. By overlaying an experimental dataset on these annotations, a user can perform a pathway over-representation analysis. By overlaying quantitative expression data or time series, a user can visualize the extent of change in affected pathways and its progression. A binomial test is used to calculate the probability shown for each result, and the p-values are corrected for the multiple testing (Benjamini–Hochberg procedure) that arises from evaluating the submitted list of identifiers against every pathway.
To learn more about our Pathway Analysis, please have a look at our relevant publications:
Fabregat A, Sidiropoulos K, Garapati P, Gillespie M, Hausmann K, Haw R, … D’Eustachio P (2016). The reactome pathway knowledgebase. Nucleic Acids Research, 44(D1), D481–D487.
https://doi.org/10.1093/nar/gkv1351.
Fabregat A, Sidiropoulos K, Viteri G, Forner O, Marin-Garcia P, Arnau V, … Hermjakob H (2017). Reactome pathway analysis: a high-performance in-memory approach. BMC Bioinformatics, 18.
This is an expression analysis: The numbers are used to produce a scaled coloured overlay over Reactome pathway diagrams, as a means to visualize relative expression levels. Note that the numeric values do not have to be expression data, for instance by using gene association
scores the same analysis can be used to visualize genotyping results.
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703 out of 1159 identifiers in the sample were found in Reactome, where 1337 pathways were hit by at least one of them.
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All non-human identifiers have been converted to their human equivalent. •
This report is filtered to show only results for species 'Homo sapiens' and resource 'all re-sources'.
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The unique ID for this analysis (token) is MjAxODEyMDQwMjI0MjhfNDA4MA%3D%3D. This ID is valid for at least 7 days in Reactome’s server. Use it to access Reactome services with your data.
This figure shows a genome-wide overview of the results of your pathway analysis. Reactome path-ways are arranged in a hierarchy. The center of each of the circular "bursts" is the root of one top-
level pathway, for example "DNA Repair". Each step away from the center represents the next level lower in the pathway hierarchy. The color code denotes over-representation of that pathway in your input dataset. Light grey signifies pathways which are not significantly over-represented.
For every pathway of the most significant pathways, we present its diagram, as well as a short sum-mary, its bibliography and the list of inputs found in it.
Interleukin-4 and Interleukin-13 signaling (R-HSA-6785807)1.
Interleukin-4 (IL4) is a principal regulatory cytokine during the immune response, crucially im-portant in allergy and asthma (Nelms et al. 1999). When resting T cells are antigen-activated and ex-pand in response to Interleukin-2 (IL2), they can differentiate as Type 1 (Th1) or Type 2 (Th2) T helper cells. The outcome is influenced by IL4. Th2 cells secrete IL4, which both stimulates Th2 in an autocrine fashion and acts as a potent B cell growth factor to promote humoral immunity (Nelms et al. 1999).
Interleukin-13 (IL13) is an immunoregulatory cytokine secreted predominantly by activated Th2 cells. It is a key mediator in the pathogenesis of allergic inflammation. IL13 shares many functional properties with IL4, stemming from the fact that they share a common receptor subunit. IL13 re-ceptors are expressed on human B cells, basophils, eosinophils, mast cells, endothelial cells, fibro-blasts, monocytes, macrophages, respiratory epithelial cells, and smooth muscle cells, but unlike IL4, not T cells. Thus IL13 does not appear to be important in the initial differentiation of CD4 T cells into Th2 cells, rather it is important in the effector phase of allergic inflammation (Hershey et al. 2003). IL4 and IL13 induce “alternative activation” of macrophages, inducing an anti-inflammatory phen-otype by signaling through IL4R alpha in a STAT6 dependent manner. This signaling plays an im-portant role in the Th2 response, mediating anti-parasitic effects and aiding wound healing (Go-rdon & Martinez 2010, Loke et al. 2002) There are two types of IL4 receptor complex (Andrews et al. 2006). Type I IL4R (IL4R1) is predomin-antly expressed on the surface of hematopoietic cells and consists of IL4R and IL2RG, the common gamma chain. Type II IL4R (IL4R2) is predominantly expressed on the surface of nonhematopoietic cells, it consists of IL4R and IL13RA1 and is also the type II receptor for IL13. (Obiri et al. 1995, Aman et al. 1996, Hilton et al. 1996, Miloux et al. 1997, Zhang et al. 1997). The second receptor for IL13 consists of IL4R and Interleukin-13 receptor alpha 2 (IL13RA2), sometimes called Interleukin-13 binding protein (IL13BP). It has a high affinity receptor for IL13 (Kd = 250 pmol/L) but is not suf-ficient to render cells responsive to IL13, even in the presence of IL4R (Donaldson et al. 1998). It is reported to exist in soluble form (Zhang et al. 1997) and when overexpressed reduces JAK-STAT sig-naling (Kawakami et al. 2001). It's function may be to prevent IL13 signalling via the functional IL4R:IL13RA1 receptor. IL13RA2 is overexpressed and enhances cell invasion in some human can-cers (Joshi & Puri 2012).
The first step in the formation of IL4R1 (IL4:IL4R:IL2RB) is the binding of IL4 with IL4R (Hoffman et al. 1995, Shen et al. 1996, Hage et al. 1999). This is also the first step in formation of IL4R2 (IL4:IL4R:IL13RA1). After the initial binding of IL4 and IL4R, IL2RB binds (LaPorte et al. 2008), to form IL4R1. Alternatively, IL13RA1 binds, forming IL4R2. In contrast, the type II IL13 complex (IL13R2) forms with IL13 first binding to IL13RA1 followed by recruitment of IL4R (Wang et al. 2009).
Crystal structures of the IL4:IL4R:IL2RG, IL4:IL4R:IL13RA1 and IL13:IL4R:IL13RA1 complexes have been determined (LaPorte et al. 2008). Consistent with these structures, in monocytes IL4R is tyr-osine phosphorylated in response to both IL4 and IL13 (Roy et al. 2002, Gordon & Martinez 2010) while IL13RA1 phosphorylation is induced only by IL13 (Roy et al. 2002, LaPorte et al. 2008) and IL2RG phosphorylation is induced only by IL4 (Roy et al. 2002).
Both IL4 receptor complexes signal through Jak/STAT cascades. IL4R is constitutively-associated with JAK2 (Roy et al. 2002) and associates with JAK1 following binding of IL4 (Yin et al. 1994) or IL13 (Roy et al. 2002). IL2RG constitutively associates with JAK3 (Boussiotis et al. 1994, Russell et al. 1994). IL13RA1 constitutively associates with TYK2 (Umeshita-Suyama et al. 2000, Roy et al. 2002, LaPorte et al. 2008, Bhattacharjee et al. 2013).
IL4 binding to IL4R1 leads to phosphorylation of JAK1 (but not JAK2) and STAT6 activation (Takeda et al. 1994, Ratthe et al. 2007, Bhattacharjee et al. 2013).
IL13 binding increases activating tyrosine-99 phosphorylation of IL13RA1 but not that of IL2RG. IL4 binding to IL2RG leads to its tyrosine phosphorylation (Roy et al. 2002). IL13 binding to IL4R2 leads to TYK2 and JAK2 (but not JAK1) phosphorylation (Roy & Cathcart 1998, Roy et al. 2002).
Phosphorylated TYK2 binds and phosphorylates STAT6 and possibly STAT1 (Bhattacharjee et al. 2013).
A second mechanism of signal transduction activated by IL4 and IL13 leads to the insulin receptor substrate (IRS) family (Kelly-Welch et al. 2003). IL4R1 associates with insulin receptor substrate 2 and activates the PI3K/Akt and Ras/MEK/Erk pathways involved in cell proliferation, survival and translational control. IL4R2 does not associate with insulin receptor substrate 2 and consequently the PI3K/Akt and Ras/MEK/Erk pathways are not activated (Busch-Dienstfertig & González-Rodríguez 2013).
References
Nelms K, Keegan AD, Zamorano J, Ryan JJ & Paul WE (1999). The IL-4 receptor: signaling mechan-
isms and biologic functions. Annu. Rev. Immunol., 17, 701-38.
Hershey GK (2003). IL-13 receptors and signaling pathways: an evolving web. J. Allergy Clin. Im-
DDR1 dimerCollagen type I, II, III, IV, V, XICollagen type I, II, III, IV, V, XICollagen type I, II, III, IV, V, XIfibrilsfibrilsfibrils
Collagen types I-V, VIICollagen types I-V, VIICollagen types I-V, VII
DDR1 dimer:Collagen type I, II, III, IV, V, XIDDR1 dimer:Collagen type I, II, III, IV, V, XIDDR1 dimer:Collagen type I, II, III, IV, V, XIfibrilsfibrilsfibrils
Laminins are a large family of conserved, multidomain trimeric basement membrane proteins. There are many theoretical trimer combinations but only 18 have been described (Domogatskaya et al. 2012, Miner 2008, Macdonald et al. 2010) and the existence of isoforms laminin-212 and/or laminin-222 (Durbeej et al. 2010) awaits further confirmation. The chains assemble through coiled-coil domains at their C-terminal end. Alpha chains additionally have a large C-terminal globular do-main containing five LG subdomains (LG1-5). The N termini are often referred to as the short arms. These have varying numbers of laminin-type epidermal growth factor-like (LE) repeats. Trimer as-sembly is controlled by highly specific coiled-coil interactions (Domogatskaya et al. 2012). Some laminin isoforms are modified extracellularly by proteolytic processing at the N- or C-terminal ends prior to their binding to cellular receptors or other matrix molecules (Tzu & Marinkovitch 2008).
The cell adhesion properties of laminins are mediated primarily through the alpha chain G domain to integrins, dystroglycan, Lutheran glycoprotein, or sulfated glycolipids. The N-terminal globular domains of the alpha-1 (Colognato-Pyke et al. 1995) and alpha-2 chains (Colognato et al. 1997) and globular domains VI (Nielsen & Yamada 2001) and IVa (Sasaki & Timpl 2001) of the alpha-5 chain can bind to several integrin isoforms (alpha1beta1, alpha2beta1, alpha3beta1, and alphaVbeta3), which enables cell binding at both ends of laminins with these alpha chains.
References
Domogatskaya A, Rodin S & Tryggvason K (2012). Functional diversity of laminins. Annu. Rev. Cell
Dev. Biol., 28, 523-53.
Edit history
Date Action Author
2008-05-07 Reviewed Hynes R, Humphries MJ, Yamada KM
DDR1 dimerCollagen type I, II, III, IV, V, XICollagen type I, II, III, IV, V, XICollagen type I, II, III, IV, V, XIfibrilsfibrilsfibrils
Collagen types I-V, VIICollagen types I-V, VIICollagen types I-V, VII
DDR1 dimer:Collagen type I, II, III, IV, V, XIDDR1 dimer:Collagen type I, II, III, IV, V, XIDDR1 dimer:Collagen type I, II, III, IV, V, XIfibrilsfibrilsfibrils
Several non-integrin membrane proteins interact with extracellular matrix proteins. Transmem-brane proteoglycans may associate with integrins and growth factor receptors to influence their function, or they can signal independently, often influencing the actin cytoskeleton.
References
Rosso F, Giordano A, Barbarisi M & Barbarisi A (2004). From cell-ECM interactions to tissue engin-
Collagen type VII hexamerCollagen type VII hexamerCollagen type VII hexamer
Collagen type I fibrils with histidino-hydroxylysinoleucine cross-links
2 Collagen type IV networks withCollagen type IV networks withCollagen type IV networks withsulfilimine cross-linkssulfilimine cross-linkssulfilimine cross-links
Collagen type XVII fibril:Integrin alpha6beta4
BPAG1e:PlectinBPAG1e:PlectinBPAG1e:Plectin
Collagen type VII fibril:Collagen type VII fibril:Collagen type VII fibril:Laminin-332Laminin-332Laminin-332
CD151 Type I hemidesmosomeType I hemidesmosomeType I hemidesmosomecomplexcomplexcomplex
Collagen type I fibrils with hydroxylysino-5-Collagen type I fibrils with hydroxylysino-5-Collagen type I fibrils with hydroxylysino-5-ketonorleucine crosslinksketonorleucine crosslinksketonorleucine crosslinks
Collagen type 1 fibrils cross-linked bydehydro-lysinonorleucine crosslinks
Collagen alpha-1(VII) NC2 regionCollagen alpha-1(VII) NC2 regionCollagen alpha-1(VII) NC2 region
Tropocollagens
Collagen type I fibrils withCollagen type I fibrils withCollagen type I fibrils withhydroxylysyl-pyrrole cross-linkshydroxylysyl-pyrrole cross-linkshydroxylysyl-pyrrole cross-links
Collagen type VII -NC2Collagen type VII -NC2Collagen type VII -NC2hexamerhexamerhexamer
Collagen fibres
Laminin-332Laminin-332Laminin-332
Collagen type VII fibril
Collagen type IV networksCollagen type IV networksCollagen type IV networks
Collagen type I fibrils with lysyl-pyridinolineCollagen type I fibrils with lysyl-pyridinolineCollagen type I fibrils with lysyl-pyridinolinecross-linkscross-linkscross-links
Collagen type I fibrils with hydroxylysyl-Collagen type I fibrils with hydroxylysyl-Collagen type I fibrils with hydroxylysyl-pyridinoline cross-linkspyridinoline cross-linkspyridinoline cross-links
H2O2
Collagen type II fibril
NH3
Lysyl oxidases:Cu2+
Collagen type I fibril withhydroxyallysines
Collagen type II fibril:Collagentype IX
H2O
Collagen type XII, XIV fibrils
Collagen type I fibril withallysines
Collagen type I fibrils with lysyl-pyrroleCollagen type I fibrils with lysyl-pyrroleCollagen type I fibrils with lysyl-pyrrolecross-linkscross-linkscross-links
Collagen type I, II fibrils
Collagen type I,II:XII,XIV fibrils
Collagen type I fibrils with lysino-5-Collagen type I fibrils with lysino-5-Collagen type I fibrils with lysino-5-ketonorleucine cross-linksketonorleucine cross-linksketonorleucine cross-links
Collagen type X network
Collagen type X:type II fibrils
1.4E2
-1.96E1
Cellular compartments: extracellular region.
Collagen VII forms anchoring fibrils, composed of antiparallel dimers that connect the dermis to the epidermis (Bruckner-Tuderman 2009, Has & Kern 2010). During fibrillogenesis, the nascent type VII procollagen molecules dimerize in an antiparallel manner. The C-propeptide is then re-moved by Bone morphogenetic protein 1 (Rattenholl et al. 2002) and the processed antiparallel di-mers laterally aggregate (Villone et al. 2008, Gordon & Hahn 2010).
References
Chung HJ & Uitto J (2010). Type VII collagen: the anchoring fibril protein at fault in dystrophic epi-
MET receptor activates the focal adhesion kinase PTK2 (FAK1) in a process that depends on the simultaneous interaction of PTK2 with integrins and with MET. SRC is needed for PTK2 to become fully active. Activation of PTK2 is needed for HGF-induced cell motility (Beviglia et al. 1999, Parr et al. 2001, Chen and Chen 2006, Lietha et al. 2007, Chen et al. 2011, Brami-Cherrier et al. 2014).
References
Beviglia L & Kramer RH (1999). HGF induces FAK activation and integrin-mediated adhesion in
MTLn3 breast carcinoma cells. Int. J. Cancer, 83, 640-9.
Chen SY & Chen HC (2006). Direct interaction of focal adhesion kinase (FAK) with Met is required for FAK to promote hepatocyte growth factor-induced cell invasion. Mol. Cell. Biol., 26, 5155-67.
Parr C, Davies G, Nakamura T, Matsumoto K, Mason MD & Jiang WG (2001). The HGF/SF-induced phosphorylation of paxillin, matrix adhesion, and invasion of prostate cancer cells were sup-
pressed by NK4, an HGF/SF variant. Biochem. Biophys. Res. Commun., 285, 1330-7.
Brami-Cherrier K, Gervasi N, Arsenieva D, Walkiewicz K, Boutterin MC, Ortega A, ... Arold ST (2014). FAK dimerization controls its kinase-dependent functions at focal adhesions. EMBO J.,
33, 356-70.
Lietha D, Cai X, Ceccarelli DF, Li Y, Schaller MD & Eck MJ (2007). Structural basis for the autoinhib-
ition of focal adhesion kinase. Cell, 129, 1177-87.
Both Follistatin (FST) and Follistatin-like-3 (FSTL3) irreversibly bind Activin dimers and prevent Activin from interacting with its receptor (reviewed in Schneyer et al. 2004, Xia and Schneyer 2009). Though functionally similar in vitro, FST and FSTL3 do not function identically in vivo. Mice lack-ing FST die shortly after birth due to defects in muscle and bone (Matzuk et al. 1995); mice lacking FSTL3 are viable but have altered glucose metabolism (Mukherjee et al. 2007).
References
Schneyer A, Sidis Y, Xia Y, Saito S, del Re E, Lin HY & Keutmann H (2004). Differential actions of
follistatin and follistatin-like 3. Mol. Cell. Endocrinol., 225, 25-8.
Xia Y & Schneyer AL (2009). The biology of activin: recent advances in structure, regulation and
function. J. Endocrinol., 202, 1-12.
Matzuk MM, Lu N, Vogel H, Sellheyer K, Roop DR & Bradley A (1995). Multiple defects and perinat-
al death in mice deficient in follistatin. Nature, 374, 360-3.
Mukherjee A, Sidis Y, Mahan A, Raher MJ, Xia Y, Rosen ED, ... Schneyer AL (2007). FSTL3 deletion reveals roles for TGF-beta family ligands in glucose and fat homeostasis in adults. Proc. Natl.
Collagen type VII hexamerCollagen type VII hexamerCollagen type VII hexamer
Collagen type I fibrils with histidino-hydroxylysinoleucine cross-links
2 Collagen type IV networks withCollagen type IV networks withCollagen type IV networks withsulfilimine cross-linkssulfilimine cross-linkssulfilimine cross-links
Collagen type XVII fibril:Integrin alpha6beta4
BPAG1e:PlectinBPAG1e:PlectinBPAG1e:Plectin
Collagen type VII fibril:Collagen type VII fibril:Collagen type VII fibril:Laminin-332Laminin-332Laminin-332
CD151 Type I hemidesmosomeType I hemidesmosomeType I hemidesmosomecomplexcomplexcomplex
Collagen type I fibrils with hydroxylysino-5-Collagen type I fibrils with hydroxylysino-5-Collagen type I fibrils with hydroxylysino-5-ketonorleucine crosslinksketonorleucine crosslinksketonorleucine crosslinks
Collagen type 1 fibrils cross-linked bydehydro-lysinonorleucine crosslinks
Collagen alpha-1(VII) NC2 regionCollagen alpha-1(VII) NC2 regionCollagen alpha-1(VII) NC2 region
Tropocollagens
Collagen type I fibrils withCollagen type I fibrils withCollagen type I fibrils withhydroxylysyl-pyrrole cross-linkshydroxylysyl-pyrrole cross-linkshydroxylysyl-pyrrole cross-links
Collagen type VII -NC2Collagen type VII -NC2Collagen type VII -NC2hexamerhexamerhexamer
Collagen fibres
Laminin-332Laminin-332Laminin-332
Collagen type VII fibril
Collagen type IV networksCollagen type IV networksCollagen type IV networks
Collagen type I fibrils with lysyl-pyridinolineCollagen type I fibrils with lysyl-pyridinolineCollagen type I fibrils with lysyl-pyridinolinecross-linkscross-linkscross-links
Collagen type I fibrils with hydroxylysyl-Collagen type I fibrils with hydroxylysyl-Collagen type I fibrils with hydroxylysyl-pyridinoline cross-linkspyridinoline cross-linkspyridinoline cross-links
H2O2
Collagen type II fibril
NH3
Lysyl oxidases:Cu2+
Collagen type I fibril withhydroxyallysines
Collagen type II fibril:Collagentype IX
H2O
Collagen type XII, XIV fibrils
Collagen type I fibril withallysines
Collagen type I fibrils with lysyl-pyrroleCollagen type I fibrils with lysyl-pyrroleCollagen type I fibrils with lysyl-pyrrolecross-linkscross-linkscross-links
Collagen type I, II fibrils
Collagen type I,II:XII,XIV fibrils
Collagen type I fibrils with lysino-5-Collagen type I fibrils with lysino-5-Collagen type I fibrils with lysino-5-ketonorleucine cross-linksketonorleucine cross-linksketonorleucine cross-links
Collagen type X network
Collagen type X:type II fibrils
1.4E2
-1.96E1
Collagen trimers in triple-helical form, referred to as procollagen or collagen molecules, are expor-ted from the ER and trafficked through the Golgi network before secretion into the extracellular space. For fibrillar collagens namely types I, II, III, V, XI, XXIV and XXVII (Gordon & Hahn 2010, Ricard-Blum 2011) secretion is concomitant with processing of the N and C terminal collagen propeptides. These processed molecules are known as tropocollagens, considered to be the units of higher order collagen structures. They form within the extracellular space via a process that can proceed spontaneously, but in the cellular environment is regulated by many collagen binding pro-teins such as the FACIT (Fibril Associated Collagens with Interrupted Triple helices) family colla-gens and Small Leucine-Rich Proteoglycans (SLRPs). The architecture formed ultimately depends on the collagen subtype and the cellular conditions. Structures include the well-known fibrils and fibres formed by the major structural collagens type I and II plus several different types of supra-molecular assembly (Bruckner 2010). The mechanical and physical properties of tissues depend on the spatial arrangement and composition of these collagen-containing structures (Kadler et al. 1996, Shoulders & Raines 2009, Birk & Bruckner 2011).
Fibrillar collagen structures are frequently heterotypic, composed of a major collagen type in asso-ciation with smaller amounts of other types, e.g. type I collagen fibrils are associated with types III and V, while type II fibrils frequently contain types IX and XI (Wess 2005). Fibres composed exclus-ively of a single collagen type probably do not exist, as type I and II fibrils require collagens V and XI respectively as nucleators (Kadler et al. 2008, Wenstrup et al. 2011). Much of the structural un-derstanding of collagen fibrils has been obtained with fibril-forming collagens, particularly type I, but some central features are believed to apply to at least the other fibrillar collagen subtypes (Wess 2005). Fibril diameter and length varies considerably, depending on the tissue and collagen types (Fang et al. 2012). The reasons for this are poorly understood (Wess 2005).
Some tissues such as skin have fibres that are approximately the same diameter while others such as tendon or cartilage have a bimodal distribution of thick and thin fibrils. Mature type I collagen fibrils in tendon are up to 1 cm in length, with a diameter of approx. 500 nm. An individual fibrillar collagen triple helix is less than 1.5 nm in diameter and around 300 nm long; collagen molecules must assemble to give rise to the higher-order fibril structure, a process known as fibrillogenesis, prevented by the presence of C-terminal propeptides (Kadler et al. 1987). In electron micrographs, fibrils have a banded appearance, due to regular gaps where fewer collagen molecules overlap, which occur because the fibrils are aligned in a quarter-stagger arrangement (Hodge & Petruska 1963). Collagen microfibrils are believed to have a quasi-hexagonal unit cell, with tropocollagen ar-ranged to form supertwisted, right-handed microfibrils that interdigitate with neighbouring mi-crofibrils, leading to a spiral-like structure for the mature collagen fibril (Orgel et al. 2006, Holmes & Kadler 2006).
Neighbouring tropocollagen monomers interact with each other and are cross-linked covalently by lysyl oxidase (Orgel et al. 2000, Maki 2006). Mature collagen fibrils are stabilized by lysyl oxidase-mediated cross-links. Hydroxylysyl pyridinoline and lysyl pyridinoline cross-links form between (hydroxy) lysine and hydroxylysine residues in bone and cartilage (Eyre et al. 1984). Arginoline cross-links can form in cartilage (Eyre et al. 2010); mature bovine articular cartilage contains roughly equimolar amounts of arginoline and hydroxylysyl pyridinoline based on peptide yields. Mature collagen fibrils in skin are stabilized by the lysyl oxidase-mediated cross-link histidino-hydroxylysinonorleucine (Yamauch et al. 1987). Due to the quarter-staggered arrangement of colla-gen molecules in a fibril, telopeptides most often interact with the triple helix of a neighbouring collagen molecule in the fibril, except for collagen molecules in register staggered by 4D from an-other collagen molecule. Fibril aggregation in vitro can be unipolar or bipolar, influenced by tem-perature and levels of C-proteinase, suggesting a role for the N- and C- propeptides in regulation of the aggregation process (Kadler et al. 1996). In vivo, collagen molecules at the fibril surface may re-tain their N-propeptides, suggesting that this may limit further accretion, or alternatively repres-ents a transient stage in a model whereby fibrils grow in diameter through a cycle of deposition, cleavage and further deposition (Chapman 1989).
In vivo, fibrils are often composed from more than one type of collagen. Type III collagen is found associated with type I collagen in dermal fibrils, with the collagen III on the periphery, suggesting a regulatory role (Fleischmajer et al. 1990). Type V collagen associates with type I collagen fibrils, where it may limit fibril diameter (Birk et al. 1990, White et al. 1997). Type IX associates with the surface of narrow diameter collagen II fibrils in cartilage and the cornea (Wu et al. 1992, Eyre et al. 2004). Highly specific patterns of crosslinking sites suggest that collagen IX functions in interfibril-lar networking (Wess 2005). Type XII and XIV collagens are localized near the surface of banded collagen I fibrils (Nishiyama et al. 1994). Certain fibril-associated collagens with interrupted triple helices (FACITs) associate with the surface of collagen fibrils, where they may serve to limit fibril fusion and thereby regulate fibril diameter (Gordon & Hahn 2010). Collagen XV, a member of the multiplexin family, is almost exclusively associated with the fibrillar collagen network, in very close proximity to the basement membrane. In human tissues collagen XV is seen linking banded collagen fibers subjacent to the basement membrane (Amenta et al. 2005). Type XIV collagen, SLRPs and discoidin domain receptors also regulate fibrillogenesis (Ansorge et al. 2009, Kalamajski et al. 2010, Flynn et al. 2010).
Collagen IX is cross-linked to the surface of collagen type II fibrils (Eyre et al. 1987). Type XII and XIV collagens are found in association with type I (Walchli et al. 1994) and type II (Watt et al. 1992, Eyre 2002) fibrils in cartilage. They are thought to associate non-covalently via their COL1/NC1 do-mains (Watt et al. 1992, Eyre 2002).
Some non-fibrillar collagens form supramolecular assemblies that are distinct from typical fibrils. Collagen VII forms anchoring fibrils, composed of antiparallel dimers that connect the dermis to the epidermis (Bruckner-Tuderman 2009). During fibrillogenesis, the nascent type VII procollagen molecules dimerize in an antiparallel manner. The C-propeptides are then removed by Bone morphogenetic protein 1 (Rattenholl et al. 2002) and the processed antiparallel dimers aggregate laterally. Collagens VIII and X form hexagonal networks and collagen VI forms beaded filament (Gordon & Hahn 2010, Ricard-Blum et al. 2011).
References
Kadler KE, Holmes DF, Trotter JA & Chapman JA (1996). Collagen fibril formation. Biochem J, 316,
1-11.
Orgel JP, San Antonio JD & Antipova O (2011). Molecular and structural mapping of collagen fibril
Interleukin-7 (IL7) is produced primarily by T zone fibroblastic reticular cells found in lymphoid organs, and also expressed by non-hematopoietic stromal cells present in other tissues including the skin, intestine and liver. It is an essential survival factor for lymphocytes, playing a key anti-ap-optotic role in T-cell development, as well as mediating peripheral T-cell maintenance and prolifer-ation. This dual function is reflected in a dose-response relationship that distinguishes the survival function from the proliferative activity; low doses of IL7 (<1 ng/ml) sustain only survival, higher doses (>1 ng/ml) promote survival and cell cycling (Kittipatarin et al. 2006, Swainson et al. 2007).
The IL7 receptor is a heterodimeric complex of the the common cytokine-receptor gamma chain (IL2RG, CD132, or Gc) and the IL7-receptor alpha chain (IL7R, IL7RA, CD127). Both chains are members of the type 1 cytokine family. Neither chain is unique to the IL7 receptor as IL7R is util-ized by the receptor for thymic stromal lymphopoietin (TSLP) while IL2RG is shared with the re-ceptors for IL2, IL4, IL9, IL15 and IL21. IL2RG consists of a single transmembrane region and a 240aa extracellular region that includes a fibronectin type III (FNIII) domain thought to be involved in receptor complex formation. It is expressed on most lymphocyte populations. Null mutations of IL2RG in humans cause X-linked severe combined immunodeficiency (X-SCID), which has a pheno-type of severely reduced T-cell and natural killer (NK) cell populations, but normal numbers of B cells. In addition to reduced T- and NK-cell numbers, Il2rg knockout mice also have dramatically reduced B-cell populations suggesting that Il2rg is more critical for B-cell development in mice than in humans. Patients with severe combined immunodeficiency (SCID) phenotype due to IL7R mutations (see Puel & Leonard 2000), or a partial deficiency of IL7R (Roifman et al. 2000) have markedly reduced circulating T cells, but normal levels of peripheral blood B cells and NK cells, similar to the phenotype of IL2RG mutations, highlighting a requirement for IL7 in T cell lymph-opoiesis. It has been suggested that IL7 is essential for murine, but not human B cell development, but recent studies indicate that IL7 is essential for human B cell production from adult bone mar-row and that IL7-induced expansion of the progenitor B cell compartment is increasingly critical for human B cell production during later stages of development (Parrish et al. 2009).
IL7 has been shown to induce rapid and dose-dependent tyrosine phosphorylation of JAKs 1 and 3, and concomitantly tyrosine phosphorylation and DNA-binding activity of STAT5a/b (Foxwell et al. 1995). IL7R was shown to directly induce the activation of JAKs and STATs by van der Plas et al. (1996). Jak1 and Jak3 knockout mice displayed severely impaired thymic development, further sup-porting their importance in IL7 signaling (Rodig et al. 1998, Nosaka et al. 1995).
The role of STAT5 in IL7 signaling has been studied largely in mouse models. Tyr449 in the cyto-plasmic domain of IL7RA is required for T-cell development in vivo and activation of JAK/STAT5 and PI3k/Akt pathways (Jiang et al. 2004, Pallard et al. 1999). T-cells from an IL7R Y449F knock-in mouse did not activate STAT5 (Osbourne et al. 2007), indicating that IL7 regulates STAT5 activity via this key tyrosine residue. STAT5 seems to enhance proliferation of multiple cell lineages in mouse models but it remains unclear whether STAT5 is required solely for survival signaling or also for the induction of proliferative activity (Kittipatarin & Khaled, 2007).
The model for IL7 receptor signaling is believed to resemble that of other Gc family cytokines, based on detailed studies of the IL2 receptor, where IL2RB binds constitutively to JAK1 while JAK3 is pre-associated uniquely with the IL2RG chain. Extending this model to IL7 suggests a similar series of events: IL7R constitutively associated with JAK1 binds IL7, the resulting trimer recruits IL2RG:JAK3, bringing JAK1 and JAK3 into proximity. The association of both chains of the IL7 re-ceptor orients the cytoplasmic domains of the receptor chains so that their associated kinases (Janus and phosphatidylinositol 3-kinases) can phosphorylate sequence elements on the cytoplas-mic domains (Jiang et al. 2005). JAKs have low intrinsic enzymatic activity, but after mutual phos-phorylation acquire much higher activity, leading to phosphorylation of the critical Y449 site on IL7R. This site binds STAT5 and possibly other signaling adapters, they in turn become phos-phorylated by JAK1 and/or JAK3. Phosphorylated STATs translocate to the nucleus and trigger the transcriptional events of their target genes.
The role of the PI3K/AKT pathway in IL7 signaling is controversial. It is a potential T-cell survival pathway because in many cell types PI3K signaling regulates diverse cellular functions such as cell cycle progression, transcription, and metabolism. The ERK/MAPK pathway does not appear to be involved in IL7 signaling (Crawley et al. 1996).
It is not clear how IL7 influences cell proliferation. In the absence of a proliferative signal such as IL7 or IL3, dependent lymphocytes arrest in the G0/G1 phase of the cell cycle. To exit this phase, cells typically activate specific G1 Cyclin-dependent kinases/cyclins and down regulate cell cycle in-hibitors such as Cyclin-dependent kinase inhibitor 1B (Cdkn1b or p27kip1). There is indirect evid-ence suggesting a possible role for IL7 stimulated activation of PI3K/AKT signaling, obtained from transformed cell lines and thymocytes, but not confirmed by observations using primary T-cells (Kittipatarin & Khaled, 2007). IL7 withdrawal results in G1/S cell cycle arrest and is correlated with loss of cdk2 activity (Geiselhart et al. 2001), both events which are known to be regulated by the de-phosphorylating activity of Cdc25A. Expression of a p38 MAPK-resistant Cdc25A mutant in an IL-7-dependent T-cell line as well as in peripheral, primary T-cells was sufficient to sustain cell survival and promote cell cycling for several days in the absence of IL7 (Khaled et al. 2005). Cdkn1b is a member of the CIP/KIP family of cyclin-dependent cell cycle inhibitors (CKIs) that negatively regu-lates the G1/S transition. In IL7 dependent T-cells, the expression of Cdkn1b was sufficient to cause G1 arrest in the presence of IL7. Withdrawal of IL7 induced the upregulation of Cdkn1b and arres-ted cells in G1 while siRNA knockout of Cdkn1b enhanced cell cycle progression. However, adopt-ive transfer of Cdkn1b-deficient lymphocytes into IL7 deficient mice indicated that loss of Cdkn1b could only partially compensate for the IL7 signal needed by T-cells to expand in a lymphopenic en-vironment (Li et al. 2006), so though Cdkn1b may be involved in negative regulation of the cell cycle through an effect on cdk2 activity, its absence is not sufficient to fully induce cell cycling under lymphopenic conditions.
C-linked procollagen type IC-linked procollagen type IC-linked procollagen type Itrimertrimertrimer
3Alpha-1(II) propeptides C-linked procollagen type IItrimer
3Alpha-1(III) propeptidesAlpha-1(III) propeptidesAlpha-1(III) propeptidesC-linked procollagen type IIIC-linked procollagen type IIIC-linked procollagen type III
3Alpha-1(VII) chainsAlpha-1(VII) chainsAlpha-1(VII) chains C-linked procollagen type VIIC-linked procollagen type VIIC-linked procollagen type VIItrimertrimertrimer
2
Alpha-2(VIII) chains
Alpha-1(VIII) chains
C-linked procollagen type VIIItrimer
Alpha-2(IX) chains
Alpha-1(IX) chains
Alpha-3(IX) chains
C-linked procollagen type IXtrimer
3Alpha-1(X) chains C-linked procollagen type Xtrimer
3Alpha-1(XIII) chains C-linked procollagen type XIIItrimer
3Alpha-1(XIV) chains C-linked procollagen type XIVtrimer
3Alpha-1(XIX) chainsC-linked procollagen type XIX
trimer
3Alpha-1(XV) chainsAlpha-1(XV) chainsAlpha-1(XV) chains C-linked procollagen type XVC-linked procollagen type XVC-linked procollagen type XVtrimertrimertrimer
3Alpha-1(XVI) chainsC-linked procollagen type XVI
trimer 3Alpha-1(XVII) chains C-linked procollagen type XVIItrimer
3Alpha-1(XXVIII) chainsC-linked procollagen type XXVIII
trimer
3Collagen alpha-1(XVIII)chains
C-linked procollagen type XVIIItrimer
3Alpha-1(XX) chainsC-linked procollagen type XX
trimer 3Alpha-1(XXI) chains C-linked procollagen type XXItrimer
3Alpha-1(XXII) chainsC-linked procollagen type XXII
trimer
3Alpha-1(XXIII) chains C-linked procollagen type XXIIItrimer
3Alpha-1(XXIV)propeptides
C-linked procollagen type XXIVtrimer
3Alpha-1(XXV) chainsC-linked procollagen type XXV
trimer
3Alpha-1(XXVI) chains C-linked procollagen type XXVItrimer
C-linked procollagen type XXVIIC-linked procollagen type XXVIIC-linked procollagen type XXVIItrimertrimertrimer
1.4E2
-1.96E1
The C-propeptides of collagen propeptide chains are essential for the association of three peptide chains into a trimeric but non-helical procollagen. This initial binding event determines the com-position of the trimer, brings the individual chains into the correct register and initiates formation of the triple helix at the C-terminus, which then proceeds towards the N-terminus in a zipper-like fashion (Engel & Prockop 1991). Most early refolding studies were performed with collagen type III, which contains a disulfide linkage at the C-terminus of its triple helix (Bächinger et al. 1978, Bruck-ner et al. 1978) that acts as a permanent linker even after removal of the non-collagenous domains.
Mutations within the C-propeptides further suggest that they are crucial for the correct interaction of the three polypeptide chains and for subsequent correct folding (refs. in Boudko et al. 2011).
References
Byers PH, Click EM, Harper E & Bornstein P (1975). Interchain disulfide bonds in procollagen are located in a large nontriple-helical COOH-terminal domain. Proc Natl Acad Sci U S A, 72, 3009-13
.
Bächinger HP, Brückner P, Timpl R & Engel J (1978). The role of cis-trans isomerization of peptide bonds in the coil leads to and comes from triple helix conversion of collagen. Eur J Biochem, 90,
Leptin (LEP, OB, OBS), a circulating adipokine, and its receptor LEPR (DB, OBR) control food intake and energy balance and are implicated in obesity-related diseases (recently reviewed in Amitani et al. 2013, Dunmore and Brown 2013, Cottrell and Mercer 2012, La Cava 2012, Marroqui et al. 2012, Paz-Filho et al. 2012, Denver et al. 2011, Lee 2011, Marino et al. 2011, Morton and Schwartz 2011, Scherer and Buettner 2011, Shan and Yeo 2011, Wauman and Tavernier 2011, Dardeno et al. 2010, Bjorbaek 2009, Morris and Rui 2009, Myers et al. 2008), including cancer (Guo et al. 2012), inflam-mation (Newman and Gonzalez-Perez 2013, Iikuni et al. 2008), and angiogenesis (Gonzalez-Perez et al. 2013).
The identification of spontaneous mutations in the leptin gene (ob or LEP) and the leptin receptor gene (Ob-R, db or LEPR) genes in mice opened up a new field in obesity research. Leptin was dis-covered as the product of the gene affected by the ob (obesity) mutation, which causes obesity in mice. Likewise LEPR is the product of the gene affected by the db (diabetic) mutation. Leptin bind-ing to LEPR induces canonical (JAK2/STATs; MAPK/ERK 1/2, PI-3K/AKT) and non-canonical signal-ing pathways (PKC, JNK, p38 MAPK and AMPK) in diverse cell types. The binding of leptin to the long isoform of LEPR (OB-Rl) initiates a phosphorylation cascade that results in transcriptional ac-tivation of target genes by STAT5 and STAT3 and activation of the PI3K pathway(not shown here), the MAPK/ERK pathway, and the mTOR/S6K pathway. Shorter LEPR isoforms with truncated intra-cellular domains are unable to activate the STAT pathway, but can transduce signals by way of ac-tivation of JAK2, IRS-1 or ERKs, including MAPKs.
LEPR is constitutively bound to the JAK2 kinase. Binding of LEP to LEPR causes a conformational change in LEPR that activates JAK2 autophosphorylation followed by phosphorylation of LEPR by JAK2. Phosphorylated LEPR binds STAT3, STAT5, and SHP2 which are then phosphorylated by JAK2. Phosphorylated JAK2 binds SH2B1 which then binds IRS1/2, resulting in phosphorylation of IRS1/2 by JAK2. Phosphorylated STAT3 and STAT5 dimerize and translocate to the nucleus where they activate transcription of target genes (Jovanovic et al. 2010). SHP2 activates the MAPK path-way. IRS1/2 activate the PI3K/AKT pathway which may be the activator of mTOR/S6K.
Several isoforms of LEPR have been identified (reviewed in Gorska et al. 2010). The long isoform (LEPRb, OBRb) is expressed in the hypothalamus and all types of immune cells. It is the only iso-form known to fully activate signaling pathways in response to leptin. Shorter isoforms (LEPRa, LEPRc, LEPRd, and a soluble isoform LEPRe) are able to interact with JAK kinases and activate oth-er pathways, however their roles in energy homeostasis are not fully characterized.
Association of RUNX3 with the TEADs:YAP1 complex inhibits loading of the TEADs:YAP1 to the CT-GF promoter, thus negatively regulating transcription of the CTGF gene which encodes the Con-nective tissue growth factor (Yagi et al. 1999, Zhao et al. 2008, Qiao et al. 2016).
References
Yagi R, Chen LF, Shigesada K, Murakami Y & Ito Y (1999). A WW domain-containing yes-associated
protein (YAP) is a novel transcriptional co-activator. EMBO J., 18, 2551-62.
Qiao Y, Lin SJ, Chen Y, Voon DC, Zhu F, Chuang LS, ... Ito Y (2016). RUNX3 is a novel negative regu-
lator of oncogenic TEAD-YAP complex in gastric cancer. Oncogene, 35, 2664-74.
Zhao B, Ye X, Yu J, Li L, Li W, Li S, ... Guan KL (2008). TEAD mediates YAP-dependent gene induc-
MET is a receptor tyrosine kinase (RTK) (Cooper et al. 1984, Park et al. 1984) activated by binding to its ligand, Hepatocyte growth factor/Scatter factor (HGF/SF) (Bottaro et al. 1991, Naldini et al. 1991). Similar to other related RTKs, such as EGFR, ligand binding induces MET dimerization and trans-autophosphorylation, resulting in the active MET receptor complex (Ferracini et al. 1991, Longati et al. 1994, Rodrigues and Park 1994, Kirchhofer et al. 2004, Stamos et al. 2004, Hays and Watowich 2004). Phosphorylated tyrosines in the cytoplasmic tail of MET serve as docking sites for binding of adapter proteins, such as GRB2, SHC1 and GAB1, which trigger signal transduction cascades that activate PI3K/AKT, RAS, STAT3, PTK2, RAC1 and RAP1 signaling (Ponzetto et al. 1994, Pelicci et al. 1995, Weidner et al. 1995, Besser et al. 1997, Shen and Novak 1997, Beviglia and Kramer 1999, Rodrigues et al. 2000, Sakkab et al. 2000, Schaeper et al. 2000, Lamorte et al. 2002, Wang et al. 2002, Chen and Chen 2006, Palamidessi et al. 2008, Chen et al. 2011, Murray et al. 2014).
Activation of PLC gamma 1 (PLCG1) signaling by MET remains unclear. It has been reported that PLCG1 can bind to MET directly (Ponzetto et al. 1994) or be recruited by phosphorylated GAB1 (Gual et al. 2000). Tyrosine residue Y307 of GAB1 that serves as docking sites for PLCG1 may be phosphorylated either by activated MET (Watanabe et al. 2006) or SRC (Chan et al. 2010). Another PCLG1 docking site on GAB1, tyrosine residue Y373, was reported as the SRC target, while the kinase for the main PLCG1 docking site, Y407 of GAB1, is not known (Chan et al. 2010).
Signaling by MET promotes cell growth, cell survival and motility, which are essential for embryon-ic development (Weidner et al. 1993, Schmidt et al. 1995, Uehara et al. 1995, Bladt et al. 1995, Maina et al. 1997, Maina et al. 2001, Helmbacher et al. 2003) and tissue regeneration (Huh et al. 2004, Borowiak et al. 2004, Liu 2004, Chmielowiec et al. 2007). MET signaling is frequently aberrantly ac-tivated in cancer, through MET overexpression or activating MET mutations (Schmidt et al. 1997, Pennacchietti et al. 2003, Smolen et al. 2006, Bertotti et al. 2009).
Considerable progress has recently been made in the development of HGF-MET inhibitors in can-cer therapy. These include inhibitors of HGF activators, HGF inhibitors and MET antagonists, which are protein therapeutics that act outside the cell. Kinase inhibitors function inside the cell and have constituted the largest effort towards MET-based therapeutics (Gherardi et al. 2012).
Pathogenic bacteria of the species Listeria monocytogenes, exploit MET receptor as an entryway to host cells (Shen et al. 2000, Veiga and Cossart 2005, Neimann et al. 2007).
For review of MET signaling, please refer to Birchmeier et al. 2003, Trusolino et al. 2010, Gherardi et al. 2012, Petrini 2015.
References
Ponzetto C, Bardelli A, Zhen Z, Maina F, dalla Zonca P, Giordano S, ... Comoglio PM (1994). A multi-functional docking site mediates signaling and transformation by the hepatocyte growth
Gual P, Giordano S, Williams TA, Rocchi S, Van Obberghen E & Comoglio PM (2000). Sustained re-cruitment of phospholipase C-gamma to Gab1 is required for HGF-induced branching tubulo-
genesis. Oncogene, 19, 1509-18.
Chan PC, Sudhakar JN, Lai CC & Chen HC (2010). Differential phosphorylation of the docking pro-tein Gab1 by c-Src and the hepatocyte growth factor receptor regulates different aspects of cell
functions. Oncogene, 29, 698-710.
Ferracini R, Longati P, Naldini L, Vigna E & Comoglio PM (1991). Identification of the major auto-phosphorylation site of the Met/hepatocyte growth factor receptor tyrosine kinase. J. Biol.
Chem., 266, 19558-64.
Longati P, Bardelli A, Ponzetto C, Naldini L & Comoglio PM (1994). Tyrosines1234-1235 are critical for activation of the tyrosine kinase encoded by the MET proto-oncogene (HGF receptor). Onco-
DNA DNA DSBs:p-MRN:p-S1981,Ac-K3016-ATM:KAT5:K63PolyUb-K14,K16,p-S139-H2AFX,DNA DNA DSBs:p-MRN:p-S1981,Ac-K3016-ATM:KAT5:K63PolyUb-K14,K16,p-S139-H2AFX,DNA DNA DSBs:p-MRN:p-S1981,Ac-K3016-ATM:KAT5:K63PolyUb-K14,K16,p-S139-H2AFX,Me2K21-HIST1H4A-Nucleosome:p-5T-MDC1:p-S102-WHSC1:RNF8:Zn2+:SUMO1:p-T4827-Me2K21-HIST1H4A-Nucleosome:p-5T-MDC1:p-S102-WHSC1:RNF8:Zn2+:SUMO1:p-T4827-Me2K21-HIST1H4A-Nucleosome:p-5T-MDC1:p-S102-WHSC1:RNF8:Zn2+:SUMO1:p-T4827-HERC2:UBE2N:UBE2V2:RNF168:PIAS4:p-S25,S1778-TP53BP1:p-4S,2T-BRCA1-A complex:HERC2:UBE2N:UBE2V2:RNF168:PIAS4:p-S25,S1778-TP53BP1:p-4S,2T-BRCA1-A complex:HERC2:UBE2N:UBE2V2:RNF168:PIAS4:p-S25,S1778-TP53BP1:p-4S,2T-BRCA1-A complex:
CHEK2CHEK2CHEK2
ATP ADP
DNA DNA DSBs:p-MRN:p-S1981,Ac-K3016-ATM:KAT5:K63PolyUb-K14,K16,p-DNA DNA DSBs:p-MRN:p-S1981,Ac-K3016-ATM:KAT5:K63PolyUb-K14,K16,p-DNA DNA DSBs:p-MRN:p-S1981,Ac-K3016-ATM:KAT5:K63PolyUb-K14,K16,p-S139-H2AFX,Me2K21-HIST1H4A-Nucleosome:p-5T-MDC1:p-S102-WHSC1:S139-H2AFX,Me2K21-HIST1H4A-Nucleosome:p-5T-MDC1:p-S102-WHSC1:S139-H2AFX,Me2K21-HIST1H4A-Nucleosome:p-5T-MDC1:p-S102-WHSC1:
p53 causes G1 arrest by inducing the expression of a cell cycle inhibitor, p21 (El-Deiry et al, 1993; Harper et al, 1993; Xiong et al, 1993). P21 binds and inactivates Cyclin-Cdk complexes that mediate G1/S progression, resulting in lack of phosphorylation of Rb, E2F sequestration and cell cycle arrest at the G1/S transition. Mice with a homozygous deletion of p21 gene are deficient in their ability to undergo a G1/S arrest in response to DNA damage (Deng et al, 1995).
References
el-Deiry WS, Tokino T, Velculescu VE, Levy DB, Parsons R, Trent JM, ... Vogelstein B (1993). WAF1,
a potential mediator of p53 tumor suppression. Cell, 75, 817-25.
Harper JW, Adami GR, Wei N, Keyomarsi K & Elledge SJ (1993). The p21 Cdk-interacting protein
Cip1 is a potent inhibitor of G1 cyclin-dependent kinases. Cell, 75, 805-16.
Xiong Y, Hannon GJ, Zhang H, Casso D, Kobayashi R & Beach D (1994). p21 is a universal inhibitor
of cyclin kinases. Nature, 366, 701-4.
Deng C, Zhang P, Harper JW, Elledge SJ & Leder P (1995). Mice lacking p21CIP1/WAF1 undergo nor-
mal development, but are defective in G1 checkpoint control. Cell, 82, 675-84.
DNA DNA DSBs:p-MRN:p-S1981,Ac-K3016-ATM:KAT5:K63PolyUb-K14,K16,p-S139-H2AFX,DNA DNA DSBs:p-MRN:p-S1981,Ac-K3016-ATM:KAT5:K63PolyUb-K14,K16,p-S139-H2AFX,DNA DNA DSBs:p-MRN:p-S1981,Ac-K3016-ATM:KAT5:K63PolyUb-K14,K16,p-S139-H2AFX,Me2K21-HIST1H4A-Nucleosome:p-5T-MDC1:p-S102-WHSC1:RNF8:Zn2+:SUMO1:p-T4827-Me2K21-HIST1H4A-Nucleosome:p-5T-MDC1:p-S102-WHSC1:RNF8:Zn2+:SUMO1:p-T4827-Me2K21-HIST1H4A-Nucleosome:p-5T-MDC1:p-S102-WHSC1:RNF8:Zn2+:SUMO1:p-T4827-HERC2:UBE2N:UBE2V2:RNF168:PIAS4:p-S25,S1778-TP53BP1:p-4S,2T-BRCA1-A complex:HERC2:UBE2N:UBE2V2:RNF168:PIAS4:p-S25,S1778-TP53BP1:p-4S,2T-BRCA1-A complex:HERC2:UBE2N:UBE2V2:RNF168:PIAS4:p-S25,S1778-TP53BP1:p-4S,2T-BRCA1-A complex:
CHEK2CHEK2CHEK2
ATP ADP
DNA DNA DSBs:p-MRN:p-S1981,Ac-K3016-ATM:KAT5:K63PolyUb-K14,K16,p-DNA DNA DSBs:p-MRN:p-S1981,Ac-K3016-ATM:KAT5:K63PolyUb-K14,K16,p-DNA DNA DSBs:p-MRN:p-S1981,Ac-K3016-ATM:KAT5:K63PolyUb-K14,K16,p-S139-H2AFX,Me2K21-HIST1H4A-Nucleosome:p-5T-MDC1:p-S102-WHSC1:S139-H2AFX,Me2K21-HIST1H4A-Nucleosome:p-5T-MDC1:p-S102-WHSC1:S139-H2AFX,Me2K21-HIST1H4A-Nucleosome:p-5T-MDC1:p-S102-WHSC1:
Both p53-independent and p53-dependent mechanisms of induction of p21 mRNA have been demonstrated. p21 is transcriptionally activated by p53 after DNA damage (el-Deiry et al., 1993).
References
el-Deiry WS, Tokino T, Velculescu VE, Levy DB, Parsons R, Trent JM, ... Vogelstein B (1993). WAF1,
a potential mediator of p53 tumor suppression. Cell, 75, 817-25.
The biosynthesis of collagen is a multistep process. Collagen propeptides are cotranslationally translocated into the ER lumen. Propeptides undergo a number of post-translational modifications. Proline and lysine residues may be hydroxylated by prolyl 3-, prolyl 4- and lysyl hydroxylases. 4-hy-droxyproline is essential for intramolecular hydrogen bonding and stability of the triple helical col-lagenous domain. In fibril forming collagens approximately 50% of prolines are 4-hydroxylated; the extent of this and of 3-hydroxyproline and lysine hydroxylation varies between tissues and collagen types (Kivirikko et al. 1972, 1992). Hydroxylysine molecules can form cross-links between collagen molecules in fibrils, and are sites for glycosyl- and galactosylation. Collagen peptides all have non-collagenous domains; collagens within the subclasses have common chain structures. These non-collagenous domains have regulatory functions; some are biologically active when cleaved from the main peptide chain. Fibrillar collagens all have a large triple helical domain (COL1) bordered by N and C terminal extensions, called the N and C propeptides, which are cleaved prior to forma-tion of the collagen fibril. The C propeptide, also called the NC1 domain, is highly conserved. It dir-ects chain association during intracellular assembly of the procollagen molecule from three colla-gen propeptide alpha chains (Hulmes 2002). The N-propeptide has a short linker (NC2) connecting the main triple helix to a short minor one (COL2) and a globular N-terminal region NC3. NC3 do-mains are variable both in size and the domains they contain.
Collagen propeptides typically undergo a number of post-translational modifications. Proline and lysine residues are hydroxylated by prolyl 3-, prolyl 4- and lysyl hydroxylases. 4-hydroxyproline is essential for intramolecular hydrogen bonding and stability of the triple helical collagenous do-main. Prolyl 4-hydroxylase may also have a role in alpha chain association as no association of the C-propeptides of type XII collagen was seen in the presence of prolyl 4-hydroxylase inhibitors (Mazzorana et al. 1993, 1996). In fibril forming collagens approximately 50% of prolines are 4-hy-droxylated; the extent of this is species dependent, lower hydroxylation correlating with lower am-bient temperature and thermal stability (Cohen-Solal et al. 1986, Notbohm et al. 1992). Similarly the extent of 3-hydroxyproline and lysine hydroxylation varies between tissues and collagen types (Kivirikko et al. 1992). Hydroxylysine molecules can form cross-links between collagen molecules in fibrils, and are sites for glycosyl- and galactosylation.
Collagen molecules fold and assemble through a series of distinct intermediates (Bulleid 1996). In-dividual collagen polypeptide chains are translocated co-translationally across the membrane of the endoplasmic reticulum (ER). Intra-chain disulfide bonds are formed within the N-propeptide, and hydroxylation of proline and lysine residues occurs within the triple helical domain (Kivirikko et al. 1992). When the peptide chain is fully translocated into the ER lumen the C-propeptide folds, the conformation being stabilized by intra-chain disulfide bonds (Doege and Fessler 1986). Pro al-pha-chains associate via the C-propeptides (Byers et al. 1975, Bachinger et al. 1978), or NC2 do-mains for FACIT family collagens (Boudko et al. 2008) to form an initial trimer which can be stabil-ized by the formation of inter-chain disulfide bonds (Schofield et al. 1974, Olsen et al. 1976), though these are not a prerequisite for further folding (Bulleid et al. 1996). The triple helix then nucleates and folds in a C- to N- direction. The association of the individual chains and subsequent triple helix formation are distinct steps (Bachinger et al. 1980). The N-propeptides associate and in some cases form inter-chain disulfide bonds (Bruckner et al., 1978). Procollagen is released via carriers into the exracellular space (Canty & Kadler 2005). Fibrillar procollagens undergo removal of the C- and N-propeptides by procollagen C and N proteinases respectively, both Zn2+ dependent metallopro-teinases. Propeptide processing is a required step for normal collagen I and III fibril formation, but collagens can retain some or all of their non-collagenous propeptides. Retained collagen type V and XI N-propeptides contribute to the control of fibril growth by sterically limiting lateral molecule ad-dition (Fichard et al. 1995). Processed fibrillar procollagen is termed tropocollagen, which is con-sidered to be the unit of higher order fibrils and fibres. Tropocollagens of the fibril forming colla-gens I, II, III, V and XI sponteneously aggregate in vitro in a manner that has been compared with crystallization, commencing with a nucleation event followed by subsequent organized aggregation (Silver et al. 1992, Prockop & Fertala 1998). Fibril formation is stabilized by lysyl oxidase catalyzed crosslinks between adjacent molecules (Siegel & Fu 1976).
References
Kadler KE, Baldock C, Bella J & Boot-Handford RP (2007). Collagens at a glance. J Cell Sci, 120, 1955-
8.
Myllyharju J & Kivirikko KI (2004). Collagens, modifying enzymes and their mutations in humans,
ub-hydroxyPro-HIF-alpha:VCB (with or withoutub-hydroxyPro-HIF-alpha:VCB (with or withoutub-hydroxyPro-HIF-alpha:VCB (with or withoutLIMD1)LIMD1)LIMD1)
VBC complex (with or withoutLIMD1)
26S proteasome
1.4E2
-1.96E1
Cellular compartments: nucleoplasm.
HIF-alpha (HIF1A, HIF2A (EPAS1), HIF3A) is translocated to the nucleus, possibly by two pathways: importin 4/7 (Chachami et al. 2009) and importin alpha/beta (Depping et al. 2008). Once in the nuc-leus HIF-alpha heterodimerizes with HIF-beta (ARNT) (Wang et al. 1995, Jiang et al. 1996, Tian et al. 1997, Gu et al. 1998, Erbel et al. 2003) and recruits CBP and p300 to promoters of target genes (Ebert and Bunn 1998, Kallio et al. 1998, Ema et al. 1999, Gu et al. 2001, Dames et al. 2002, Freedman et al. 2002).
References
Chachami G, Paraskeva E, Mingot JM, Braliou GG, Görlich D & Simos G (2009). Transport of hypox-ia-inducible factor HIF-1alpha into the nucleus involves importins 4 and 7. Biochem Biophys
Res Commun, 390, 235-40.
Kallio PJ, Okamoto K, O'Brien S, Carrero P, Makino Y, Tanaka H & Poellinger L (1998). Signal trans-duction in hypoxic cells: inducible nuclear translocation and recruitment of the CBP/p300 co-
activator by the hypoxia-inducible factor-1alpha. EMBO J, 17, 6573-86.
Depping R, Steinhoff A, Schindler SG, Friedrich B, Fagerlund R, Metzen E, ... Köhler M (2008). Nuc-lear translocation of hypoxia-inducible factors (HIFs): involvement of the classical importin al-
The L1 family of cell adhesion molecules (L1CAMs) are a subfamily of the immunoglobulin super-family of transmembrane receptors, comprised of four structurally related proteins: L1, Close Homolog of L1 (CHL1), NrCAM, and Neurofascin. These CAMs contain six Ig like domains, five or six fibronectin like repeats, a transmembrane region and a cytoplasmic domain. The L1CAM family has been implicated in processes integral to nervous system development, including neurite out-growth, neurite fasciculation and inter neuronal adhesion.
L1CAM members are predominately expressed by neuronal, as well as some nonneuronal cells, during development. Except CHL1 all the other members of L1 family contain an alternatively spliced 12-nclueotide exon, encoding the amino acid residues RSLE in the neuronal splice forms but missing in the non-neuronal cells. The extracellular regions of L1CAM members are divergent and differ in their abilities to interact with extracellular, heterophilic ligands. The L1 ligands in-clude other Ig-domain CAMs (such as NCAM, TAG-1/axonin and F11), proteoglycans type molecules (neurocan), beta1 integrins, and extra cellular matrix protein laminin, Neuropilin-1, FGF and EGF receptors. Some of these L1-interacting proteins also bind to other L1CAM members. For example TAG-1/axonin interact with L1 and NrCAM; L1, neurofascin and CHL1 binds to contactin family members. The cytoplasmic domains of L1CAM members are most highly conserved. Nevertheless, they have different cytoplasmic binding partners, and even those with similar binding partners may be involved in different signaling complexes and mechanisms. The most conserved feature of L1CAMs is their ability to interact with the actin cytoskeletal adapter protein ankyrin. The cytoplas-mic ankyrin-binding domain, exhibits the highest degree of amino acid conservation throughout the L1 family.
References
Kamiguchi H (2003). The mechanism of axon growth: what we have learned from the cell adhesion
molecule L1. Mol Neurobiol, 28, 219-28.
Kamiguchi H & Lemmon V (1997). Neural cell adhesion molecule L1: signaling pathways and
growth cone motility. J Neurosci Res, 49, 1-8.
Herron LR, Hill M, Davey F & Gunn-Moore FJ (2009). The intracellular interactions of the L1 family
of cell adhesion molecules. Biochem J, 419, 519-31.
Schmid RS & Maness PF (2008). L1 and NCAM adhesion molecules as signaling coreceptors in neur-
onal migration and process outgrowth. Curr Opin Neurobiol, 18, 245-50.
Maness PF & Schachner M (2007). Neural recognition molecules of the immunoglobulin superfam-
ily: signaling transducers of axon guidance and neuronal migration. Nat Neurosci, 10, 19-26.
ATF4 is a transcription factor and activates expression of IL-8, MCP1, IGFBP-1, CHOP, HERP1 and ATF3.
References
Yamaguchi Y, Larkin D, Lara-Lemus R, Ramos-Castañeda J, Liu M & Arvan P (2008). Endoplasmic reticulum (ER) chaperone regulation and survival of cells compensating for deficiency in the ER
Averous J, Bruhat A, Jousse C, Carraro V, Thiel G & Fafournoux P (2004). Induction of CHOP expres-sion by amino acid limitation requires both ATF4 expression and ATF2 phosphorylation. J Biol
Chem, 279, 5288-97.
Armstrong JL, Flockhart R, Veal GJ, Lovat PE & Redfern CP (2010). Regulation of Endoplasmic Re-ticulum Stress-induced Cell Death by ATF4 in Neuroectodermal Tumor Cells. J Biol Chem, 285,
6091-100.
Gargalovic PS, Imura M, Zhang B, Gharavi NM, Clark MJ, Pagnon J, ... Lusis AJ (2006). Identification of inflammatory gene modules based on variations of human endothelial cell responses to oxid-
ized lipids. Proc Natl Acad Sci U S A, 103, 12741-6.
Gargalovic PS, Gharavi NM, Clark MJ, Pagnon J, Yang WP, He A, ... Lusis AJ (2006). The unfolded protein response is an important regulator of inflammatory genes in endothelial cells. Arterio-
scler Thromb Vasc Biol, 26, 2490-6.
Edit history
Date Action Author
2008-11-19 Created May B
2008-12-02 Reviewed Matthews L, D'Eustachio P, Gillespie ME
At the center of the mammalian circadian clock is a negative transcription/translation-based feed-back loop: The BMAL1:CLOCK/NPAS2 (ARNTL:CLOCK/NPAS2) heterodimer transactivates CRY and PER genes by binding E-box elements in their promoters; the CRY and PER proteins then inhibit transactivation by BMAL1:CLOCK/NPAS2. BMAL1:CLOCK/NPAS2 activates transcription of CRY, PER, and several other genes in the morning. Levels of PER and CRY proteins rise during the day and inhibit expression of CRY, PER, and other BMAL1:CLOCK/NPAS2-activated genes in the after-noon and evening. During the night CRY and PER proteins are targeted for degradation by phos-phorylation and polyubiquitination, allowing the cycle to commence again in the morning.
Transcription of the BMAL1 (ARNTL) gene is controlled by ROR-alpha and REV-ERBA (NR1D1), both of which are targets of BMAL1:CLOCK/NPAS2 in mice and both of which compete for the same element (RORE) in the BMAL1 promoter. ROR-alpha (RORA) activates transcription of BMAL1; REV-ERBA represses transcription of BMAL1. This mutual control forms a secondary, reinforcing loop of the circadian clock. REV-ERBA shows strong circadian rhythmicity and confers circadian expression on BMAL1.
BMAL1 can form heterodimers with either CLOCK or NPAS2, which act redundantly but show dif-ferent tissue specificity. The BMAL1:CLOCK and BMAL1:NPAS2 heterodimers activate a set of genes that possess E-box elements (consensus CACGTG) in their promoters. This confers circadian expression on the genes. The PER genes (PER1, PER2, PER3) and CRY genes (CRY1, CRY2) are among those activated by BMAL1:CLOCK and BMAL1:NPAS2. PER and CRY mRNA accumulates during the morning and the proteins accumulate during the afternoon. PER and CRY proteins form complexes in the cytosol and these are bound by either CSNK1D or CSNK1E kinases which phos-phorylate PER and CRY. The phosphorylated PER:CRY:kinase complex is translocated into the nuc-leus due to the nuclear localization signal of PER and CRY. Within the nucleus the PER:CRY com-plexes bind BMAL1:CLOCK and BMAL1:NPAS2, inhibiting their transactivation activity and their phosphorylation. This reduces expression of the target genes of BMAL1:CLOCK and BMAL1:NPAS2 during the afternoon and evening.
PER:CRY complexes also traffic out of the nucleus into the cytosol due to the nuclear export signal of PER. During the night PER:CRY complexes are polyubiquitinated and degraded, allowing the cycle to begin again. Phosphorylated PER is bound by Beta-TrCP1, a cytosolic F-box type compon-ent of some SCF E3 ubiquitin ligases. CRY is bound by FBXL3, a nucleoplasmic F-box type compon-ent of some SCF E3 ubiquitin ligases. Phosphorylation of CRY1 by Adenosine monophosphate-activ-ated kinase (AMPK) enhances degradation of CRY1. PER and CRY are subsequently polyubiquitin-ated and proteolyzed by the 26S proteasome.
The circadian clock is cell-autonomous and some, but not all cells of the body exhibit circadian rhythms in metabolism, cell division, and gene transcription. The suprachiasmatic nucleus (SCN) in the hypothalamus is the major clock in the body and receives its major input from light (via ret-inal neurons) and a minor input from nutrient intake. The SCN and other brain tissues determine waking and feeding cycles and influence the clocks in other tissues by hormone secretion and nervous stimulation. Independently of the SCN, other tissues such as liver receive inputs from sig-nals from the brain and from nutrients.
References
Hastings MH, Maywood ES & O'Neill JS (2008). Cellular circadian pacemaking and the role of
cytosolic rhythms. Curr Biol, 18, R805-R815.
Ko CH & Takahashi JS (2006). Molecular components of the mammalian circadian clock. Hum Mol
Genet, 15, R271-7.
Takahashi JS, Hong HK, Ko CH & McDearmon EL (2008). The genetics of mammalian circadian or-
der and disorder: implications for physiology and disease. Nat Rev Genet, 9, 764-75.
Green CB, Takahashi JS & Bass J (2008). The meter of metabolism. Cell, 134, 728-42.
Edit history
Date Action Author
2009-03-24 Created May B
2009-05-18 Edited May B
2009-05-18 Authored May B
2009-05-27 Reviewed D'Eustachio P
2010-06-23 Reviewed Hirota T, Delaunay F, Kay SA, Albrecht U
Direct and indirect interactions of MET with integrins, focal adhesion kinase PTK2 (FAK1), tensin-4 (TNS4) and GTPases RAP1 and RAC1, induce morphological changes that promote cell motility and play an important role in HGF-induced invasiveness of cancer cells (Weidner et al. 1993, Beviglia et al. 1999, Sakkab et al. 2000, Parr et al. 2001, Trusolino et al. 2001, Lamorte et al. 2002, Chen and Chen 2006, Watanabe et al. 2006, Muharram et al. 2014, Murray et al. 2014).
References
Beviglia L & Kramer RH (1999). HGF induces FAK activation and integrin-mediated adhesion in
MTLn3 breast carcinoma cells. Int. J. Cancer, 83, 640-9.
Sakkab D, Lewitzky M, Posern G, Schaeper U, Sachs M, Birchmeier W & Feller SM (2000). Signaling of hepatocyte growth factor/scatter factor (HGF) to the small GTPase Rap1 via the large docking
protein Gab1 and the adapter protein CRKL. J. Biol. Chem., 275, 10772-8.
Parr C, Davies G, Nakamura T, Matsumoto K, Mason MD & Jiang WG (2001). The HGF/SF-induced phosphorylation of paxillin, matrix adhesion, and invasion of prostate cancer cells were sup-
pressed by NK4, an HGF/SF variant. Biochem. Biophys. Res. Commun., 285, 1330-7.
Lamorte L, Royal I, Naujokas M & Park M (2002). Crk adapter proteins promote an epithelial-mes-enchymal-like transition and are required for HGF-mediated cell spreading and breakdown of
Chen SY & Chen HC (2006). Direct interaction of focal adhesion kinase (FAK) with Met is required for FAK to promote hepatocyte growth factor-induced cell invasion. Mol. Cell. Biol., 26, 5155-67.
Metallothioneins are highly conserved, cysteine-rich proteins that bind metals via thiolate bonds (recent general reviews in Capdevila et al. 2012, Blindauer et al. 2014, reviews of mammalian metal-lothioneins in Miles et al. 2000, Maret 2011, Vasak and Meloni 2011, Thirumoorthy et al. 2001, Bab-ula et al. 2012). Mammals contain 4 general metallothionein isoforms (MT1,2,3,4). The MT1 isoform has radiated in primates to 8 or 9 functional proteins (depending on classification of MT1L). Each mammalian metallothionein binds a total of 7 divalent metal ions in two clusters, the alpha and beta clusters. Though the functions of metallothioneins have not been fully elucidated, they appear to participate in detoxifying heavy metals (reviewed in Sharma et al. 2013), storing and transporting zinc, and redox biochemistry. Metallothioneins interact with many other cellular proteins, with most interactions involving proteins of the central nervous system (reviewed in Atrian and Capdev-ila 2013).
References
Miles AT, Hawksworth GM, Beattie JH & Rodilla V (2000). Induction, regulation, degradation, and biological significance of mammalian metallothioneins. Crit. Rev. Biochem. Mol. Biol., 35, 35-70
.
Babula P, Masarik M, Adam V, Eckschlager T, Stiborova M, Trnkova L, ... Kizek R (2012). Mammali-
an metallothioneins: properties and functions. Metallomics, 4, 739-50.
Vašák M & Meloni G (2011). Chemistry and biology of mammalian metallothioneins. J. Biol. Inorg.
Chem., 16, 1067-78.
Thirumoorthy N, Shyam Sunder A, Manisenthil Kumar K, Senthil Kumar M, Ganesh G & Chatterjee M (2011). A review of metallothionein isoforms and their role in pathophysiology. World J Surg
Human beta-1,3-glucosyltransferase like protein (B3GALTL, HGNC Approved Gene Symbol: B3GLCT; MIM:610308; CAZy family GT31), localised on the ER membrane, glucosylates O-fucosylated proteins. The resultant glc-beta-1,3-fuc disaccharide modification on thrombospondin type 1 repeat (TSR1) domain-containing proteins is thought to assist in the secretion of many of these proteins from the ER lumen, and mediate an ER quality-control mechanism of folded TSRs (Vasudevan et al. 2015). Defects in B3GALTL can cause Peters plus syndrome (PpS; MIM:261540), an autosomal recessive disorder characterised by anterior eye chamber defects, short stature, delay in growth and mental developmental and cleft lip and/or palate (Heinonen & Maki 2009).
References
Heinonen TY & Maki M (2009). Peters'-plus syndrome is a congenital disorder of glycosylation caused by a defect in the beta1,3-glucosyltransferase that modifies thrombospondin type 1 re-
peats. Ann. Med., 41, 2-10.
Vasudevan D, Takeuchi H, Johar SS, Majerus E & Haltiwanger RS (2015). Peters plus syndrome
mutations disrupt a noncanonical ER quality-control mechanism. Curr. Biol., 25, 286-95.
Layers of smooth muscle cells can be found in the walls of numerous organs and tissues within the body. Smooth muscle tissue lacks the striated banding pattern characteristic of skeletal and cardiac muscle. Smooth muscle is triggered to contract by the autonomic nervous system, hormones, auto-crine/paracrine agents, local chemical signals, and changes in load or length.
Actin:myosin cross bridging is used to develop force with the influx of calcium ions (Ca2+) initiat-ing contraction. Two separate protein pathways, both triggered by calcium influx contribute to con-traction, a calmodulin driven kinase pathway, and a caldesmon driven pathway.
Recent evidence suggests that actin, myosin, and intermediate filaments may be far more volatile then previously suspected, and that changes in these cytoskeletal elements along with alterations of the focal adhesions that anchor these proteins may contribute to the contractile cycle.
Contraction in smooth muscle generally uses a variant of the same sliding filament model found in striated muscle, except in smooth muscle the actin and myosin filaments are anchored to focal ad-hesions, and dense bodies, spread over the surface of the smooth muscle cell. When actin and my-osin move across one another focal adhesions are drawn towards dense bodies, effectively squeez-ing the cell into a smaller conformation. The sliding is triggered by calcium:caldesmon binding, caldesmon acting in an analogous fashion to troponin in striated muscle. Phosphorylation of myos-in light chains also is involved in the initiation of an effective contraction.
WNT responsiveness is influenced by expression levels of FZD and LRP proteins. Levels of these receptors at the cell surface are regulated in part by endocytosis, but the mechanisms are not fully elucidated (Garliardi et al, 2008). A number of recent studies have identified a role for ubiquitina-tion in the localization and turnover of WNT receptors at the plasma membrane. ZNRF3 and RNF43 are E3 ligases that have been shown to ubiquitinate FZD proteins and promote their lyso-somal degradation, while the deubiquitinating enzyme USP8 promotes recycling of the receptor back to the plasma membrane (Hao et al, 2012; Mukai et al, 2010). This balance of ubiquitination and deubiquitination is in turn regulated by the R-spondin (RSPO) proteins, agonists of WNT signal-ing which appear to act by downregulating ZNRF3 and RNF43, thus potentiating both canonical and non-canonical pathways (Hao et al, 2012; reviewed in Abo and Clevers, 2012; Fearon and Spence, 2012, Papartriantafyllou, 2012).
References
Hao HX, Xie Y, Zhang Y, Charlat O, Oster E, Avello M, ... Cong F (2012). ZNRF3 promotes Wnt re-
ceptor turnover in an R-spondin-sensitive manner. Nature, 485, 195-200.
Mukai A, Yamamoto-Hino M, Awano W, Watanabe W, Komada M & Goto S (2010). Balanced ubi-quitylation and deubiquitylation of Frizzled regulate cellular responsiveness to Wg/Wnt. EMBO
J., 29, 2114-25.
Gagliardi M, Piddini E & Vincent JP (2008). Endocytosis: a positive or a negative influence on Wnt
signalling?. Traffic, 9, 1-9.
Abo A & Clevers HC (2012). Modulating WNT receptor turnover for tissue repair. Nat. Biotechnol.,
30, 835-6.
Fearon ER & Spence JR (2012). Cancer biology: a new RING to Wnt signaling. Curr. Biol., 22, R849-
Collagen is a family of at least 29 structural proteins derived from over 40 human genes (Myllyharju & Kivirikko 2004). It is the main component of connective tissue, and the most abundant protein in mammals making up about 25% to 35% of whole-body protein content. A defining feature of colla-gens is the formation of trimeric left-handed polyproline II-type helical collagenous regions. The packing within these regions is made possible by the presence of the smallest amino acid, glycine, at every third residue, resulting in a repeating motif Gly-X-Y where X is often proline (Pro) and Y of-ten 4-hydroxyproline (4Hyp). Gly-Pro-Hyp is the most common triplet in collagen (Ramshaw et al. 1998). Collagen peptide chains also have non-collagenous domains, with collagen subclasses having common chain structures. Collagen fibrils are mostly found in fibrous tissues such as tendon, liga-ment and skin. Other forms of collagen are abundant in cornea, cartilage, bone, blood vessels, the gut, and intervertebral disc. In muscle tissue, collagen is a major component of the endomysium, constituting up to 6% of muscle mass. Gelatin, used in food and industry, is collagen that has been irreversibly hydrolyzed. On the basis of their fibre architecture in tissues, the genetically distinct collagens have been di-vided into subgroups. Group 1 collagens have uninterrupted triple-helical domains of about 300 nm, forming large extracellular fibrils. They are referred to as the fibril-forming collagens, consist-ing of collagens types I, II, III, V, XI, XXIV and XXVII. Group 2 collagens are types IV and VII, which have extended triple helices (>350 nm) with imperfections in the Gly-X-Y repeat sequences. Group 3 are the short-chain collagens. These have two subgroups. Group 3A have continuous triple-helical domains (type VI, VIII and X). Group 3B have interrupted triple-helical domains, referred to as the fibril-associated collagens with interrupted triple helices (FACIT collagens, Shaw & Olsen 1991). FACITs include collagen IX, XII, XIV, XVI, XIX, XX, XXI, XXII and XXVI plus the transmem-brane collagens (XIII, XVII, XXIII and XXV) and the multiple triple helix domains and interruptions (Multiplexin) collagens XV and XVIII (Myllyharju & Kivirikko 2004). The non-collagenous domains of collagens have regulatory functions; several are biologically active when cleaved from the main peptide chain. Fibrillar collagen peptides all have a large triple helical domain (COL1) bordered by N and C terminal extensions, called the N- and C-propeptides, which are cleaved prior to formation of the collagen fibril. The intact form is referred to as a collagen propeptide, not procollagen, which is used to refer to the trimeric triple-helical precursor of collagen before the propeptides are removed. The C-propeptide, also called the NC1 domain, directs chain association during assembly of the procollagen molecule from its three constituent alpha chains (Hulmes 2002).
Fibril forming collagens are the most familiar and best studied subgroup. Collagen fibres are ag-gregates or bundles of collagen fibrils, which are themselves polymers of tropocollagen complexes, each consisting of three polypeptide chains known as alpha chains. Tropocollagens are considered the subunit of larger collagen structures. They are approximately 300 nm long and 1.5 nm in dia-meter, with a left-handed triple-helical structure, which becomes twisted into a right-handed coiled-coil 'super helix' in the collagen fibril. Tropocollagens in the extracellular space polymerize spontaneously with regularly staggered ends (Hulmes 2002). In fibrillar collagens the molecules are staggered by about 67 nm, a unit known as D that changes depending upon the hydration state. Each D-period contains slightly more than four collagen molecules so that every D-period repeat of the microfibril has a region containing five molecules in cross-section, called the 'overlap', and a re-gion containing only four molecules, called the 'gap'. The triple-helices are arranged in a hexagonal or quasi-hexagonal array in cross-section, in both the gap and overlap regions (Orgel et al. 2006). Collagen molecules cross-link covalently to each other via lysine and hydroxylysine side chains. These cross-links are unusual, occuring only in collagen and elastin, a related protein.
The macromolecular structures of collagen are diverse. Several group 3 collagens associate with larger collagen fibers, serving as molecular bridges which stabilize the organization of the extracel-lular matrix. Type IV collagen is arranged in an interlacing network within the dermal-epidermal junction and vascular basement membranes. Type VI collagen forms distinct microfibrils called beaded filaments. Type VII collagen forms anchoring fibrils. Type VIII and X collagens form hexagonal networks. Type XVII collagen is a component of hemidesmosomes where it is com-plexed wtih alpha6Beta4 integrin, plectin, and laminin-332 (de Pereda et al. 2009). Type XXIX colla-gen has been recently reported to be a putative epidermal collagen with highest expression in suprabasal layers (Soderhall et al. 2007). Collagen fibrils/aggregates arranged in varying combina-tions and concentrations in different tissues provide specific tissue properties. In bone, collagen triple helices lie in a parallel, staggered array with 40 nm gaps between the ends of the tropocolla-gen subunits, which probably serve as nucleation sites for the deposition of crystals of the mineral component, hydroxyapatite (Ca10(PO4)6(OH)2) with some phosphate. Collagen structure affects cell-cell and cell-matrix communication, tissue construction in growth and repair, and is changed in development and disease (Sweeney et al. 2006, Twardowski et al. 2007). A single collagen fibril can be heterogeneous along its axis, with significantly different mechanical properties in the gap and overlap regions, correlating with the different molecular organizations in these regions (Mi-nary-Jolandan & Yu 2009).
References
Prockop DJ & Kivirikko KI (1995). Collagens: molecular biology, diseases, and potentials for therapy
. Annu Rev Biochem, 64, 403-34.
Gordon MK & Hahn RA (2010). Collagens. Cell Tissue Res, 339, 247-57.