Bimodal protein targeting through activation of cryptic mitochondrial targeting signals by an inducible cytosolic endoprotease

Abstract

Bimodal targeting of the endoplasmic reticular protein, cytochrome P4501A1 (CYP1A1), to mitochondria involves activation of a cryptic mitochondrial targeting signal through endoprotease processing of the protein. Here, we characterized the endoprotease that regulates mitochondrial targeting of CYP1A1. The endoprotease, which was induced by beta-naphthoflavone, was a dimer of 90 kDa and 40 kDa subunits, each containing Ser protease domains. The purified protease processed CYP1A1 in a sequence-specific manner, leading to its mitochondrial import. The glucocorticoid receptor, retinoid X receptor, and p53 underwent similar processing-coupled mitochondrial transport. The inducible 90 kDa subunit was a limiting factor in many cells and some tissues and, thus, regulates the mitochondrial levels of these proteins. A number of other mitochondria-associated proteins with noncanonical targeting signals may also be substrates of this endoprotease. Our results describe a new mechanism of mitochondrial protein import that requires an inducible cytoplasmic endoprotease for activation of cryptic mitochondrial targeting signals.

Figure 1. CYP1A1 Processing Activity of Rat Liver Cytosol

(A) The DHFR-1A1 fusion construct used as a substrate for processing assays. (B) DHFR-1A1 processing by liver cytosol from control and BNF-treated rats as well asby (NH₄)₂SO₄ (AMS)-fractionated liver cytosol from the BNF group. The 1A1 (51 kDa) and DHFR (23 kDa) processed fragments are indicated. “S” indicates substrate alone. (C) Far western analysis of cytosolic liver protein with aprotinin. (D and E) Immunoblot analysis of 1A1 in trypsin treated (150 μ/ml, 30 min) mitochondrial (D) and microsomal fractions (E) from C6 glioma cells treated with 0.1% DMSO (“C”) or exposed to BNF (50 μM) ± pefabloc (“I”, 300 μM) for the indicated time. (F) Relative distribution of mitochondrial and microsomal CYP1A1 in BNF treated C6 glioma cells based on a 2.5:1 ratio of microsomes and mitochondria recovered by cell fractionation.

Figure 2. Endoprotease Purification by Aprotinin-Agarose Affinity Chromatography

(A) Elution pattern of aprotinin-agarose column-bound proteins. The DEAE Sephacel-purified fraction (IV) was loaded onto the aprotinin-agarose column, and bound proteins were eluted using a NaCl step gradient. (B) Cypro Ruby-stained protein fractions separated by SDS-PAGE. (C) Proteolytic activity of protein fractions, as determined using ³⁵S-labeled DHFR-1A1 as substrate. “S” indicates substrate alone, and “I” indicates reactions performed in the presence of Pefabloc. (D) Far western blot analysis of fractions using aprotinin. (E) Polyacrylamide gel electrophoresis (12%) of fractions at each progressive purification stage. Proteins shown, from left to right, are total liver cytosolic protein (Con, 10 μg protein), the liver cytosolic fraction from BNF-treated animals (BNF, 10 μg), molecular weight markers (MW), the 50% (NH₄)₂SO₄ fraction (AMS, 10 μg), the peak IV DEAE sephacel-purified fraction (DEAE, 3 μg), and the aprotinin-agarose purified fraction (Affinity, 0.5 μg). (F) Peptide sequences for p90 and p40.

Figure 3. Size Exclusion Chromatography of the Processing Protease

(A) Rates of elution of alcohol dehydrogenase (Ald), bovine serum albumin (BSA), ovalbumin (Ova), and carbonic anhydrase (Can) from the Sephacryl-200 column, based on apparent size. (B) Resolution of ³⁵S-DHFR-1A1 processing activity by size. Fractions 18–27 corresponded to 140 – 150 kDa, fractions 33 – 39 to 90 kDa, and fractions 45 – 51 to 40 kDa. 5μg protein each was used for assaying processing activity. (C) Combined effects of proteins from fractions 33–39 and 45–51 in ³⁵S DHFR-1A1 processing. (D–F) Immunoblot analysis of Sephacryl S200-eluted fractions using p90 and p40 peptide antibodies.

Figure 4. Effect of Protease Inhibitors on DHFR-1A1 Processing In Vitro and In Vivo

(A–C) Processing of ³⁵S-DHFR-1A1 by DEAE column-purified enzyme (1 μg) in the absence or presence of aprotinin (0.01, 0.1, or 0.5 mg/ml), Pefabloc (0.001, 0.01, or 0.1 mM), antipain (0.01, 0.1, or 10 μM), Soybean trypsin inhibitor (0.01, 0.1, or 10 μM), benzamidine (0.01, 0.1 or 1mM), or calpain inhibitor I (5, 25, or 50 μM). The enzyme was preincubated with the indicated inhibitor for 15 min at 37°C prior to the final incubation (30 min, 37°C) with DHFR-1A1. “S” indicates substrate alone. (D and E) Immunoblot analysis of 1A1 in cytosolic (D) and trypsin-treated (150 μg/ml, 30 min) mitochondrial proteins (E) isolated from DHFR-1A1-expressing COS cells incubated without [I(−)] or with Pefabloc (1 – 300 μM).

Figure 5. Sequence Specificity of the Processing Protease

(A) CYP1A1 signal domains and processing site mutations. (B) Processing of wild type and mutant ³⁵S-DHFR-1A1 by DEAE-Sephacel column purified enzyme. (C) Processing of mutant DHFR-1A1 in COS cells, as shown by SDS-PAGE of trypsin-treated (150 μg/ml, 30 min) mitochondrial fractions (50 μg per lane).

Figure 6. Cell-Type Specific CYP1A1 Processing Activities

(A and B) Processing of ³⁵S-DHFR-1A1 by (NH₄)₂SO₄-fractionated cytosolic extracts (50% fraction, 25 – 75 μg) from COS-7, 293T, C2C12, and NIH 3T3 cells. “I” indicates that the reaction was performed in the presence of Pefabloc (100μM). (C and D) Immunoblot analysis of 1A1 in cytosolic and mitochondrial fractions isolated from AK 131261- and/or DHFR-1A1-overexpressing NIH3T3 cells. In (D), the mitochondrial fractions were subjected to trypsin digestion (150 μg/ml, 30 min) prior to immunoblot analysis.

Figure 7. Processing of Other Substrates by the Purified Endoprotease

(A) Putative protease processing sites on other mitochondrial-targeted proteins containing non-canonical targeting signals. (B, D, F) In vitro processing of ³⁵S-p53 (B), GR (D), or RXRα (F) by purified protease in the presence or absence of Pefabloc (100 μM). Processing was allowed to proceed for 30 min at 37°C. (C, E, G) Processing of transfected p53 (C), GR (E), or RXRα (G) in COS cells treated with or without Pefabloc (300 μM), as determined by immunoblot analysis of cytosolic and mitochondrial fractions.

Figure 8. Effect of p90 and p40 mRNA Depletion on DHFR1A1 Processing Activity and CYP1A1 targeting in COS Cells

(A) Immunoblot analysis of 1A1 in cytosolic and mitochondrial fractions (50 μg protein per lane) from COS cells expressing p90 and/or p40 siRNA and cotransfected with DHFR-1A1. (B) A duplicate blot was subjected to far western blotting using biotinylated aprotinin to determine the relative levels of p90 and p40. (C) Samples in Figure 8A were reanalyzed following treatment with trypsin (150 μg/ml, 30 min). (D) Immunoblot analysis of mitochondrial and microsomal proteins expressing p90 and or p40 siRNA, co-expressing CYP1A1 protein. (F) Mitochondrial samples from (A) were reanalyzed following treatment with 150 μg/ml trypsin (30 min). (E) Relative distribution of microsomal and mitochondrial CYP1A1 based on the 2.5:1 recovery of these membrane fractions by cell fractionation.