1. Volume 20, Issue 17, Pages R724-R734 (September 2010)
Evolution of Complex Gene Regulatory Circuits by Addition of Refinements 
John W. Little 
Current Biology 
Volume 20, Issue 17, Pages R724-R734 (September 2010)
DOI: /j.cub
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2. Figure 1 Wiring diagrams.
(A) Wiring diagram of λ, showing the actions of CI and Cro in regulating expression of cI and early lytic genes. Lines ending with arrowheads and straight bars represent positive and negative effects, respectively. Details are in the text and in Figure 2. Dashed lines represent incomplete repression. The diagram typifies common representations of regulatory circuits. This representation does not include subtle features such as cooperative binding or looping, and does not convey the response of the system to graded doses of CI or Cro. (B) Wiring diagram for synthetic versions of the λ circuit; CI and Cro have been replaced by Tet repressor (TetR) and Lac repressor (LacI), whose binding is weakened by anhydrotetracycline (aTc) and iso-propylthiogalactopyranoside (IPTG), respectively (see text for details). The wiring diagram differs from that of λ, both because regulation of PRM has been removed and because Lac repressor is required to maintain the lysogenic state. The latter feature is difficult to depict in a diagram of this type.
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3. Figure 2 Introduction to phage λ.
(A) Life cycle: two lifestyles and an epigenetic switch of regulatory state. Regulatory decisions, developmental pathways, and the stable lysogenic state are indicated in bold. The lysis–lysogeny decision is made ∼10–15 minutes after infection [5]. In the lytic pathway, early genes are expressed from the PL and PR promoters. In the lysogenic pathway, a site-specific recombination event physically inserts the λ genome into the host chromosome, where it is subsequently replicated as part of the host genome, affording another means of making new viral genomes. The host SOS response involves two host proteins, LexA repressor and RecA; RecA is activated by binding to single-stranded DNA, and this active form stimulates self-cleavage of LexA [22,23]. CI is cleaved by an analogous reaction. (B) Activities of CI (modified from [31]; see text for details). CI has two domains: an amino-terminal DNA-binding domain, and a carboxy-terminal domain that has contacts for dimerization and cooperativity, and carries out the specific cleavage reaction. In the tetramer, structural evidence suggests that both subunits of a dimer contact the other dimer [16]. Cooperativity is ‘alternate pairwise’; a CI dimer bound to OR2 can contact a dimer at OR1 or at OR3, but not both simultaneously [1,16]. The architecture of the octamer in the looped form is not known, and it may have several possible forms. In addition to effects described in the text, looping increases the occupancy of OL and OR, affording more complete repression of PL and PR (from [31], © American Society for Microbiology). (C) Genes and cis-acting sites in the immunity region. Map is to scale. The immunity region is defined by the CI and Cro genes and the sites to which Cro and CI bind. Narrow arrows represent transcripts (those from PL and PR extend beyond the map shown). In many lambdoid phages (including λ) there is genetic material between CI and the OL region [58]; in others, OL lies adjacent to CI. (D) Molecular basis for bistability in λ [4]. Occupancy patterns at moderate concentrations of CI or Cro are shown. The resulting pattern of gene expression at the PRM and PR promoters are indicated; in the top panel, the result is CI on/Cro off, while in the bottom panel it is CI off/Cro on. Both states are self-perpetuating. Cro is required during lytic growth to give partial repression of PR and PL, by binding relatively weakly to OR1, OR2, OL1 and OL2.
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4. Figure 3 Evolution of symmetrical variants of λ towards the wild type.
The top map indicates the OR region of λ; the next map is that of the symmetrical variant λOR323, created by site-directed mutagenesis (SDM) of OR1 [9]. Sequences below are those of the OR1 and OR3 operators, showing the three mutations that create λOR323. Below are the sequence changes in this operator found in two variants that arose from λOR323 by two different selective pressures (see text); in each case the change is to the wild-type counterpart. Changes in position 8 have little or no effect on the binding of CI and Cro [59,60]. λOR323∗ was isolated in an enrichment for variants of λOR323 with higher set points. Variants isolated in this enrichment also included ones with mutations in OL3, which weaken negative autoregulation of cI and presumably lead to a higher level of CI [18]; up-promoter mutations in PRM, presumably leading again to a higher level of CI; and mutations in CI that, at least in some cases, reduce the rate of cleavage; this is feasible in part because CI cleaves itself [23].
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5. Figure 4
Hypothetical pathway for evolution of positive autoregulation in λ.
(A) Modular organization of λ and related (‘lambdoid’) phages. Map is not to scale. Each label represents a functional ‘module’ of the viral genome, and it is believed that recombination between two different phages can occur between each of these modules (some crossover points are indicated by dashed lines), giving new combinations of modules. Head and tail regions, capsid and tail components; att, locus of site-specific integration into the host genome; ‘recomb’, general and site-specific recombination functions; immunity and regulation, genes involved in gene regulation, including N, cI, cro and cII; ‘DNA repl.’, DNA replication; Q, anti-terminator for late genes; (Shiga toxin), location of these genes in certain phages; lysis, cell lysis. (B) Evolutionary pathway. In each intermediate the new mutation or altered allele is shown in bold. The first panel shows a hypothetical ancestor to λ with a strong PRM and no positive autoregulation (see text). The open box depicts an allele that is inert for present purposes. Recombination between this phage and another one carrying Shiga toxin genes (not shown) occurs to the right of cI, joining the Shiga toxin gene to the λ immunity region. Subsequent selection for frequent switching (see text) results in a weak PRM (bold). A second recombination event removes the Shiga toxin cassette. The resulting phage is under selective pressure for a higher set point (see text), which is achieved in this case by a mutation in CI creating a new, weak interaction between CI and RNA polymerase, as in λ. Positive autoregulation could also be added by changing the spacing between PRM and OR2, allowing CI and RNA polymerase to touch [4,41,48].
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6. Figure 5 Two-stage pathway for evolution of regulatory circuits.
(A) Model of pathway. (B) Example of the pathway. In the top panel, two separate regulatory proteins are made and bind at cis-acting sites. Small boxes indicate regulatory regions; large boxes indicate genes. Thin arrows depict mRNAs for the two genes. X negatively autoregulates its own expression and represses one or more other genes (not shown), while Y is expressed constitutively and regulates another gene (not shown). In the first step, a non-homologous recombination event inserts the bracketed segment spanning the Y gene into the regulatory region of the X gene. The middle panel depicts the resulting arrangement. In this circuit, termed a ‘toggle switch’ [3], X and Y repress each others' expression (double-negative feedback). Hence, the system can have two relatively stable states — Y on/X off, or Y off/X on. In the second step, a mutation leads to positive autoregulation of Y, resulting in the circuit in the bottom panel. This change could occur in the Y protein (for example, a new protein–protein contact with RNA polymerase or a change in its DNA-binding specificity), or in a cis-acting site in the regulatory region (for example, a new binding site for Y or a change in location of a Y binding site relative to the promoter). In a later step, addition of positive feedback could stabilize the other branch of the circuit as well.
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7. Figure 6 Examples in other systems.
(A) Anaphase transition in yeast. Phosphorylation of securin inhibits its APC-mediated degradation; the level of phosphorylation is controlled by the opposing actions of Clb5–Cdk1 kinase and Cdc14 phosphatase. Once a small amount of separase is activated, it further activates Cdc14, leading to increased degradation of securin in a positive feedback loop — separase stimulates its own further production. Mutating the phosphorylation sites in securin breaks this loop, since securin degradation is no longer inhibited by phosphorylation. (Adapted from [44].) (B) Regulation of hb in Drosphila at the posterior border of the anterior Hb zone. The hb gene is controlled by Bcd [45] in an incoherent feed-forward loop as shown (adapted from [46]). This network motif [61] might allow more rapid synthesis of Hb earlier rather than later. One additional feature, not shown, is that Hb positively autoregulates its own expression, a feature that sharpens the border, but does not affect its position. Repressive action of Kr and Kni is somewhat redundant.
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