Molecular interaction map of the mammalian cell cycle control and DNA repair systems

Abstract

Eventually to understand the integrated function of the cell cycle regulatory network, we must organize the known interactions in the form of a diagram, map, and/or database. A diagram convention was designed capable of unambiguous representation of networks containing multiprotein complexes, protein modifications, and enzymes that are substrates of other enzymes. To facilitate linkage to a database, each molecular species is symbolically represented only once in each diagram. Molecular species can be located on the map by means of indexed grid coordinates. Each interaction is referenced to an annotation list where pertinent information and references can be found. Parts of the network are grouped into functional subsystems. The map shows how multiprotein complexes could assemble and function at gene promoter sites and at sites of DNA damage. It also portrays the richness of connections between the p53-Mdm2 subsystem and other parts of the network.

Figure 1

Summary of symbols.

Figure 2

Concise representation of alternative binding modes. Example: heterodimers formed by Cyclins E, A, and B binding to Cdk1 or 2. (a) CycE:Cdk2; (b) Cdk2 complexed with either CycE or CycA; (c) CycA:Cdk2; (d) CycA complexed with either Cdk2 or Cdk1; (e) CycA:Cdk1; (f) Cdk1 complexed with either CycA or CycB. Note that a, c, d, e, and g each lie on a unique connector line, and each represents a unique heterodimer. Nodes b, d, and f, on the other hand, represent dimer combinations. This notation greatly simplifies the representation of multiple alternative interactions: for example, the interactions of p21, p27, or p57 with various Cyclin:Cdk dimers in Figure 6A. A formal rule, required to avoid ambiguity, is that lines representing alternative interactions must join at an acute angle.

Figure 3

Representation of multimolecular complexes: stimulatory and inhibitory complexes of E2F1, DP1, and pRb. (a) E2F1:DP1 dimer; (b) E2F1:DP1:pRb trimer; (c) E2F1:DP1 bound to promoter element E2 (transcriptional activation shown); (d) E2F1:DP1:pRb bound to E2 (transcriptional inhibition shown). Note that the promoter element can be occupied either by E2F1:DP1 or by E2F1:DP1:pRb (alternative binding represented by interaction lines joined at an acute angle).

Figure 4

Concise representation of homopolymers: formation and effects of p53 homotetramer. (1) The three additional copies of p53 monomer required to make up the tetramer are represented by three nodes placed side by side and linked to the identified p53 monomer; a node placed internally on this line represents the homotetramer itself. (2) p53 tetramer can bind to promoter element. (3) Tetramerization stimulates (or is required for) phosphorylation of p53 Ser15 by DNA-PK.

Figure 5

Phosphorylation control of pRb: illustration of the use of conjunction symbols to denote protein modification combinations. (1) Cyclin D binds Cdk4; the filled circle (node) on the line represents the CycD:Cdk4 complex itself. (2) Similarly for Cyclin E and Cdk2. (3) The single-arrowed line linking P^(D) to pRb represents phosphorylation of pRb at sites kinased by CycD:Cdk4; a node on this line represents pRb-P^(D) [the P^(D)-phosphorylated form of pRb]. (4) Similarly for pRb phosphorylated at sites, P^(E), kinased by CycE:Cdk2. (5) CycD:Cdk4 phosphorylates pRb at sites P^(D). (6) CycE:Cdk2 acts on pRb-P^(D), generating fully phosphorylated pRb; the line with the filled arrowhead indicates stoichiometric conversion of pRb-P^(D) to the fully phosphorylated form, which is represented by the node on the nonarrowed line connecting the pRb-P^(E) and pRb-P^(E) nodes. (7) E2F1 binds DP1. (8) pRb binds to E2F1:DP1. (9) Fully phosphorylated pRb can-not bind to E2F1:DP1. Thus dissociation of pRb from E2F1:DP1 requires hyperphosphorylation by Cyclin E:Cdk2, which in turn requires previous phosphorylation by Cyclin D:Cdk4/6 (Zarakowska and Mittnacht, 1997; Lundberg and Weinberg, 1998).

Figure 6

Molecular interaction map of the regulatory network that controls the mammalian cell cycle and DNA repair systems. The map is presented in two parts: A focuses on the E2F-pRb and Cyclin:Cdk subsystems and functionally related interactions; B focuses on the p53-Mdm2 and DNA repair subsystem and functionally related interactions. Some duplication between the two parts of the maps was unavoidable but was noted by using italicized species or subsystem names to indicate that their interactions are shown in greater detail on the other part of the map. Although interaction symbols are fully defined by the conventions listed in Figure 1, the following colors were used to enhance readability: black, binding interactions and stoichiometric conversions; red, covalent modifications and gene expression; green, enzyme actions; blue, stimulations and inhibitions. See Appendix for annotations.

Figure 6

Molecular interaction map of the regulatory network that controls the mammalian cell cycle and DNA repair systems. The map is presented in two parts: A focuses on the E2F-pRb and Cyclin:Cdk subsystems and functionally related interactions; B focuses on the p53-Mdm2 and DNA repair subsystem and functionally related interactions. Some duplication between the two parts of the maps was unavoidable but was noted by using italicized species or subsystem names to indicate that their interactions are shown in greater detail on the other part of the map. Although interaction symbols are fully defined by the conventions listed in Figure 1, the following colors were used to enhance readability: black, binding interactions and stoichiometric conversions; red, covalent modifications and gene expression; green, enzyme actions; blue, stimulations and inhibitions. See Appendix for annotations.

Figure 6

Molecular interaction map of the regulatory network that controls the mammalian cell cycle and DNA repair systems. The map is presented in two parts: A focuses on the E2F-pRb and Cyclin:Cdk subsystems and functionally related interactions; B focuses on the p53-Mdm2 and DNA repair subsystem and functionally related interactions. Some duplication between the two parts of the maps was unavoidable but was noted by using italicized species or subsystem names to indicate that their interactions are shown in greater detail on the other part of the map. Although interaction symbols are fully defined by the conventions listed in Figure 1, the following colors were used to enhance readability: black, binding interactions and stoichiometric conversions; red, covalent modifications and gene expression; green, enzyme actions; blue, stimulations and inhibitions. See Appendix for annotations.

Figure 6

Molecular interaction map of the regulatory network that controls the mammalian cell cycle and DNA repair systems. The map is presented in two parts: A focuses on the E2F-pRb and Cyclin:Cdk subsystems and functionally related interactions; B focuses on the p53-Mdm2 and DNA repair subsystem and functionally related interactions. Some duplication between the two parts of the maps was unavoidable but was noted by using italicized species or subsystem names to indicate that their interactions are shown in greater detail on the other part of the map. Although interaction symbols are fully defined by the conventions listed in Figure 1, the following colors were used to enhance readability: black, binding interactions and stoichiometric conversions; red, covalent modifications and gene expression; green, enzyme actions; blue, stimulations and inhibitions. See Appendix for annotations.