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. 2011 Apr 13;19(4):503-14.
doi: 10.1016/j.str.2011.01.017.

The Hypoxic Regulator of Sterol Synthesis nro1 Is a Nuclear Import Adaptor

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The Hypoxic Regulator of Sterol Synthesis nro1 Is a Nuclear Import Adaptor

Tzu-Lan Yeh et al. Structure. .
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Abstract

Fission yeast protein Sre1, the homolog of the mammalian sterol regulatory element-binding protein (SREBP), is a hypoxic transcription factor required for sterol homeostasis and low-oxygen growth. Nro1 regulates the stability of the N-terminal transcription factor domain of Sre1 (Sre1N) by inhibiting the action of the prolyl 4-hydroxylase-like Ofd1 in an oxygen-dependent manner. The crystal structure of Nro1 determined at 2.2 Å resolution shows an all-α-helical fold that can be divided into two domains: a small N-terminal domain, and a larger C-terminal HEAT-repeat domain. Follow-up studies showed that Nro1 defines a new class of nuclear import adaptor that functions both in Ofd1 nuclear localization and in the oxygen-dependent inhibition of Ofd1 to control the hypoxic response.

Figures

Figure 1
Figure 1. The crystal structure of Nro1 shows an all-helical HEAT-repeat protein
(A) Cartoon of the Nro1 crystal structure. Residues not detected in the crystal structure are represented as a dashed line. (B and C) Molecular surface of Nro1 colored for the electrostatic potential on the surface. Color ramps from red (negative potentials) to blue (positive potentials). The α0 helix (from the other monomer in the asymmetric unit) is shown contacting the CTD as observed in the crystal structure. (D) Overlap between Nro1 CTD (green) and Imp-α C-terminal domain (pink). (E) Overlap between the C-terminal subdomain α7–α14 of Nro1 (green) and the C-terminus of Imp-β (tan) viewed across the axis of the Imp-β superhelix. The electrostatic potential was calculated using the Adaptive Poisson-Boltzmann Solver (APBS) (Baker et al., 2001). Figure was made using the molecular graphic program PyMOL (Schrödinger, LLC). See also Figure S1.
Figure 2
Figure 2. Amino acid conservation of Nro1 yeast orthologs
(A) Sequence alignment between S. pombe Nro1 and S. cerevisiae Yor051c. Six sequences of yeast Nro1 orthologs in the NCBI non-redundant protein database were selected using the program BLAST (Altschul et al., 1997) and were aligned using ClustalW2 (Larkin et al., 2007). In the figure, only Nro1 and Yor051c sequences are shown (see Figure S2 for the full alignment). Yellow boxes represent a degree of conservation higher than 75% among the six sequences, and red boxes denote identical residues. Nro1 secondary structure (Nro1-SS) is indicated. (B) Cartoon representation of Nro1 organization. The putative nuclear localization sequence (NLS) assigned by inspection is indicated. (C) Two views of Nro1 molecular surface showing in red amino acids with strict conservation across the yeast family. Nro1 domains are colored blue (NTD) and green (CTD). Numbered amino acids indicate the position of residues targeted by our mutational analysis; the dark green color marks Asp-295 the only non-conserved residue mutated. The molecular graphics programs PyMol and ESPript (Gouet et al., 2003) (for the alignment graphic) were used for the figure. See also Figure S2.
Figure 3
Figure 3. Ofd1 requires Nro1 and an Imp-β receptor to localize in the nucleus
(A) Ofd1 localization in sre1N, sre1N ofd1Δ and sre1N nro1Δ cells was assayed by indirect immunofluorescence using anti-Ofd1 antibody (upper panels). In each case, cells were incubated with 4′,6-diamidino-2-phenylindole (DAPI) to label DNA (lower panels). (B) Ofd1 localization in sre1N, sre1N ofd1Δ and sre1N kap123Δ cells was assayed by indirect immunofluorescence using anti-Ofd1 antibody (upper panels). (C) Nro1 localization in sre1N, sre1N nro1Δ and sre1N kap123Δ cells, was assayed by indirect immunofluorescence using purified anti-Nro1 antibody (upper panels). See also Table S1.
Figure 4
Figure 4. Nuclear localization of Ofd1 is not required for Sre1 destabilization
(A) Restoring Ofd1 localization. sre1N and sre1N NLS-ofd1 nro1Δ cells were analyzed by indirect immunofluorescence using anti-Ofd1 antibody (upper panels) and 4′,6-diamidino-2-phenylindole (DAPI) to stain DNA (lower panels). (B) sre1N, sre1N ofd1Δ, sre1N nro1Δ and sre1N NLS-ofd1 nro1Δ were grown in the absence of oxygen for indicated times. Whole-cell extracts (40 µg) were subjected to immunoblot analysis using anti-Sre1 or anti-Ofd1 antibodies.
Figure 5
Figure 5. Structural mapping of Nro1 function
(A) sre1N ofd1Δ and sre1N nro1Δ cells containing empty vector or a plasmid expressing either wild-type Nro1, Nro1(Y120H, D383A), Nro1(E295Q, D299N, D302N) or Nro1(Δ10–29) from CaMV promoter were cultured in minimal medium. Cells were treated with crosslinker, and detergent-solubilized, whole cell extracts were subjected to immunoprecipitation with anti-Ofd1 antibody. Bound (10-fold overloaded) and unbound fractions were analyzed by western blot analysis with anti-Ofd1-HRP and anti-Nro1 antibodies. (B) sre1N and sre1N nro1Δ cells containing empty vector or a plasmid expressing either wild-type Nro1, Nro1(D299N), Nro1(Y120H, D383A), Nro1(E295Q, D299N, D302N) or Nro1(Δ10–29) from CaMV promoter were cultured in minimum medium with or without oxygen for 2 hours. Whole-cell extracts (40 µg) were subjected to western blot analysis using anti-Sre1, anti-Ofd1 or anti-Nro1 antibodies as indicated. (C) sre1N nro1Δ cells and sre1N ofd1Δ cells containing empty vector of a plasmid expressing either wild-type Nro1, Nro1(Y120H, D383A), Nro1(E295Q, D299N, D302N) or Nro1(Δ10–29) from CaMV promoter were cultured in minimal medium. Cells were analyzed by indirect immunofluorescence using anti-Ofd1 antibody (upper panels) and 4′,6-diamidino-2-phenylindole (DAPI) to stain DNA (lower panels). See also Figure S3.
Figure 6
Figure 6. In vitro and in vivo characterization of Nro1-Ofd1CTDD binding
(A) Isothermal titration calorimetry of complex formation between Nro1 and Ofd1CTDD. (B) Nro1 and Ofd1 migrate as a heterodimer by size exclusion chromatography (SEC). (C) The NTD shows a stronger interaction with Ofd1CTDD than the CTD. Yeast two-hybrid showing the in vivo interaction between Nro1 and Ofd1CTDD. Cells containing an Ofd1CTDD plasmid were transformed either with wild-type Nro1, NTD, CTD or empty vector. Cells were plated on non-selection or selection medium. (D) GFP-NTD fusion protein stabilizes Sre1N. sre1N, sre1N ofd1Δ and sre1N nro1Δ cells containing an empty vector or a plasmid expressing GFP or GFP-NTD from the thiamine-repressible nmt* promoter were cultured in minimal medium for 20 hours. Samples were processed as in Figure 5B.
Figure 7
Figure 7. Model for mechanism of Sre1N regulation by Nro1-Ofd1
Ofd1-Nro1 complex enters the nucleus through a Kap123-dependent pathway. Oxygen destabilizes the Nro1-Ofd1 interaction (represented by the orange star) allowing Ofd1 to interact with the Sre1N transcription factor. Nro1 helix α0 is represented as a coil.

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