A genetic network for the clock of Neurospora crassa

Abstract

A diverse array of organisms from bacteria to humans may have evolved the ability to tell time in the presence or absence of external environmental cues. In the lowly bread mould, Neurospora crassa, biomolecular reactions involving the white-collar-1 (wc-1), white-collar-2 (wc-2), and frequency (frq) genes and their products constitute building blocks of a biological clock. Here we use genetic network models to explain quantitatively, from a systems perspective, how these building blocks interact, and how a complex trait like clock oscillation emerges from these interactions. We use a recently developed method of genetic network identification to find an ensemble of oscillating network models quantitatively consistent with available RNA and protein profiling data on the N. crassa clock. Predicted key features of the N. crassa clock system are a dynamically frustrated closed feedback loop, cooperativity in frq gene activation, and/or WC-1/WC-2 protein complex deactivation and substantial posttranscriptional enhancement of wc-1 RNA lifetime. Measuring the wc-1 mRNA lifetime provides a critical test of the genetic networks. (1) and are at the heart of a new systems approach to biology (2). The biological clock (3) provides a prototypical and biologically ubiquitous example of how a complex trait can emerge from the interaction of even a small number of gene regulatory elements. In an experimentally well studied example, the filamentous fungus, Neurospora crassa, and the biomolecular reactions involving the white-collar-1, white-collar-2, and frequency genes and their products constitute building blocks of a biological clock (4). A central open question of systems biology is whether these building blocks are necessary and sufficient to define a circuit or genetic network that oscillates, and how, in quantitative detail, such oscillations emerge from the interactions among these building blocks. Here we use a recently developed method of genetic network identification (5) to find an ensemble of oscillating network models, constituted from wc-1, wc-2, and frq and their products, which is quantitatively consistent with available RNA and protein profiling data on the N. crassa biological clock. The use of genetic networks to integrate diverse experimental information and to predict the behavior of a complex trait, such as the biological clock, provides a new paradigm for quantitative genetics at the molecular level (6).Key features of the genetic network that permit oscillations are: (i) the presence of functional wc-1, wc-2, and frq genes, generating protein products WC-1, WC-2, and FRQ, and the white collar complex (WCC) formed by WC-1 and WC-2; (ii) a closed-feedback loop of the biomolecular reactions in the genetic network, with WCC activating the frq gene 3 the activated frq gene producing frq mRNA 3 frq mRNA producing FRQ protein and 3 FRQ protein deactivating WCC; (iii) dynamical frustration arising in the feedback loop because of WCC's stimulation of the production of FRQ, whereas FRQ induces the deactivation o...

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“…When the model in Eq. 3 is linearized, it then becomes similar to the repressilator43. This fact suggested that the coupling of cells might be taken to be similar to that of coupled repressilators42.…”

“…2B over time). They analyzed this measure in the context of a system of coupled repressilators related to our own working clock network43. What was missing from this measure is accounting for the between droplet variability in our experiment.…”

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