Conserved RNA helicase FRH acts nonenzymatically to support the intrinsically disordered neurospora clock protein FRQ

Abstract

Protein conformation dictates a great deal of protein function. A class of naturally unstructured proteins, termed intrinsically disordered proteins (IDPs), demonstrates that flexibility in structure can be as important mechanistically as rigid structure. At the core of the circadian transcription/translation feedback loop in Neurospora crassa is the protein FREQUENCY (FRQ), shown here shown to share many characteristics of IDPs. FRQ in turn binds to FREQUENCY-Interacting RNA Helicase (FRH), whose clock function has been assumed to relate to its predicted helicase function. However, mutational analyses reveal that the helicase function of FRH is not essential for the clock, and a region of FRH distinct from the helicase region is essential for stabilizing FRQ against rapid degradation via a pathway distinct from its typical ubiquitin-mediated turnover. These data lead to the hypothesis that FRQ is an IDP and that FRH acts nonenzymatically, stabilizing FRQ to enable proper clock circuitry/function.

Figure 1

Helicase/ATPase activity is not required for the circadian oscillator-specific function of FRH. (A) Strain genotypes: Linkage group 1; at the csr-1 locus: mutant versions of frh driven by the frh promoter. Linkage group 2; at the frh native locus: frh^R806H driven by its native promoter. (B) Colored blocks represent the basic structural domains of FRH as predicted from homology with Mtr4p (Jackson et al., 2010; Weir et al., 2010) as well as the core helicase motifs of eIF4A and other members of the DSHCT helicase family. The location of individual point mutations engineered to cripple the enzymatic functions of FRH are shown schematically at the top and the actual sequence context is provided at the bottom. (C) Race tube assay of wild type (rhythmic, top), frh^R806H (arrhythmic, next to last) and the frh mutants knocked into the csr-1 locus (τ = period in hours, σ = standard deviation, n = number of race tubes).

Figure 2

The helicase regions provide the FRH functions that are essential for growth. (A) Race tube assay of wild type and FRH^R806H shown as three representative race tubes grown with the three concentrations of inducer (QA). (B) Strain genotypes of experimental strains (bottom eight groups of three): Linkage group 1; at the csr-1 locus: mutant versions of frh driven by the frh promoter. Linkage group 2; at the frh native locus: frh driven by the QA-inducible qa-2 promoter. (C) Race tube assay of qa-2 driven FRH and the mutant knock-ins at the csr-1 locus. Each strain contains an inducible copy of wt frh as well as a native promoter-driven but mutated copy of frh at the csr-1 locus and is shown as three representative race tubes grown with the three concentrations of inducer (QA). Less than wild type growth rate indicates a level of functional FRH inadequate for full rescue of essential functions. Restoration of growth indicates that the induced wt FRH was able to supply the essential functions (QA[] = concentration of QA, τ= period in hours, σ = standard deviation, n = number of race tubes, GR = growth rate in mm/day).

Figure 3

A single FRH interacts with the FRQ homodimer. (A) Strain genotypes: Linkage group 1; at the csr-1 locus: native csr-1 or 3XFlag tagged frh driven by the frh native promoter. Linkage group 2; at the frh native locus: frh^V5H6 or untagged frh, driven by the frh promoter. Linkage group 7; at the frq locus: native frq, or hph driven by the trpC promoter. (B) IP demonstrating that FRH does not form a dimer in it’s interaction with the FRQ homodimer. V5 and 3Flag antibody were used to pull down tagged FRH. Proteins were western blotted and detected with V5, FRH or FRQ antibody.

Figure 4

FRQ demonstrates characteristics of a classic IDP. (A) PONDR analysis of FRH and FRQ from N. crassa. Basic structural domains of each are shown as predicted. Black lines represent distinct and probable regions of low structural complexity (B) Solubility of FRQ and FRH were analyzed after a mock or heat treatment to determine the stability of each protein following heat-induced unfolding. The lack of the protein demonstrates precipitation after heat treatment. (C) Protease sensitivity assay. Comparable levels of FRQ, FRH, and tubulin (see Experimental procedures) were exposed to low levels of the non-specific protease Proteinase K; the globular structured FRH and tubulin proteins were much more stable than FRQ which was rapidly degraded. (D) Far-UV spectra of short-FRQ and FRH. The spectra is an average of three independent acquisitions.

Figure 5

FRQ stability is independently determined by interactions with FRH and FWD-1. (A) Strain genotypes: Linkage group 7; at the frq locus: V5H6 tagged frq with the FFD (FRQ-FRH Interaction domain) intact or deleted; at the fwd-1 locus: fwd-1 or hph. (B) Total levels of FRQ during its degradation were followed in epitope tagged strains with or without the FRQ FFD (frq and frq ^{Δ FFD}) and/or with or without FWD-1 (frq, Δ fwd-1 and frq ^{Δ FFD}, Δ fwd-1) after addition of CHX (to inhibit translation). 10μg of total protein was loaded per lane and membranes (mem) stained with Amido Black were used as loading control. (C) Densitometric analysis of data shown in (B) was used to calculate half-life. For each strain, time zero was set to 100%, allowing degradation rate to be analyzed relative to the other strains. Half-life was calculated by least squares regression of the line through the data points with the resulting equation and goodness of fit (R²) shown. Data are means ± S.E., n = 3.

Figure 6

An N-terminal region of FRH is essential for interaction with FRQ and for FRQ stability, distinguishing oscillator function from essential functions. (A) IP demonstrating that deletions of amino acids 100-150 from FRH eliminated interaction with FRQ. For input, 10ug of protein lysate was loaded and after western blotting proteins were visualized with antisera to V5 or FRQ. For IP, V5 antibody was used to pull down FRH and co-immunoprecipitated FRQ monitored. Proteins were western blotted with V5 and FRQ antibody. (B) Race tube assay of the frh domain deletion mutants at the csr-1 locus in the frh^R806H background. (C) Race tube assay of the frh domain-deletion mutants at the csr-1 locus in the qa-2 driven frh background. Each strain contains an inducible copy of frh as well as a native promoter-driven but truncated copy of the gene at the csr-1 locus and is shown as three respective race tubes grown with three concentrations of inducer (QA). Rhythmicity in frh^Δ100-150 is not restored until adequate wt frh is expressed from the qa-2 promoter driven copy. (QA[ ] = concentration of QA, τ= period in hours, σ= standard deviation, n = number of race tubes, GR = growth rate in mm/day). (D) Strain genotypes: Linkage group 2; at the frh locus: qa-2 driven frh either wild type or with amino acids 100-150 deleted. (E) Assay of FRQ stability in wt or frh-mutant strains. CHX was added at time 0 and total levels of FRQ were monitored during its degradation in WT and frh^Δ100-150 strains. Membranes (mem) stained with Amido Black were used as loading control. (F) Densitometric analysis of data shown in (E) used to calculate half-life. For each strain, time zero was set to 100%, allowing degradation rate to be analyzed relative to the other strains. Half-life was calculated by least squares regression of the line through the data points with the resulting equation and goodness of fit (R²) shown. Data are means ± S.E., n = 3.

Figure 7

FRH stabilizes the IDP FRQ thereby supporting the normal oscillator cycle. Schematic representation of the role of FRH: If FRQ can bind to FRH, FRH is able to stabilize FRQ throughout its functional cycle of interactions and progressive phosphorylations until it is targeted by FWD-1 for the ubiquitylations that will lead to its degradation in the proteasome. If FRQ cannot bind to FRH, FRQ remains highly unstable and is targeted for degradation as soon as translation is complete.