MOLECULAR AND CELLULAR BIOLOGY, Aug. 1987, p. 2728-2734 Vol. 7, No. 8 0270-7306/87/082728-07$02.00/0 Copyright C) 1987, American Society for Microbiology Saccharomyces cerevisiae Positive Regulatory Gene PET]]] Encodes a Mitochondrial Protein That.. Is Translated from an mRNA with a Long 5' Leader CHRISTINE A. STRICKl* AND THOMAS D. FOX2 Section ofBiochemistry, Molecular and Cell Biology,' and Section of Genetics and Development,2 Cornell University, Ithaca, New York 14853 Received 17 February 1987/Accepted 28 April 1987 The yeast nuclear gene PETI)I is required specifically for translation of the mitochondrion-coded mRNA for cytochrome c oxidase subunit II. We have determined the nucleotide sequence of a 3-kilobase segment of DNA that carries PET))). The sequence contains a single long open reading frame that predicts a basic protein of 718 amino acids. The PETIHl gene product is a mitochondrial protein, since a hybrid protein which includes the amino-terminal 154 amino acids of PETlll fused to 0-galactosidase is specifically associated with mitochondria. PETll is translated from a 2.9-kilobase mRNA which, interestingly, has an extended 5'-leader sequence containing four short open reading frames upstream of the long open reading frame. These open reading frames exhibit an interesting pattern of overlap with each other and with the PET))) reading frame. The yeast mitochondrial genetic system depends on a MATERIALS AND METHODS great number of nuclear gene products to express the few genes essential for respiration that are encoded in mitochon- Yeast strains and media. The wild-type Saccharomyces drial DNA (18). Many of these nuclear genes are required at cerevisiae strain was D273-1OB (ATCC 25657). PTE12 and posttranscriptional steps in the expression of specific mito- PTE14A strains both carry the pet)))-) mutation (19) and chondrial genes. These steps include 5'-end processing (14, have been described previously (50). YPEG medium con- 15, 17) and intron splicing (20, 41, 49) of mitochondrial tains 1% (wt/vol) yeast extract, 2% (wt/vol) peptone, 3% pre-mRNAs as well as mRNA translation (reviewed in (vol/vol) ethanol, and 3% (vol/vol) glycerol. SD is a minimal reference 22). For example, at least two proteins coded in medium containing glucose (60). the nucleus are required specifically to translate the mito- Plasmids and transformation procedures. DNA manipula- chondrial mRNA for cytochrome c oxidase subunit III (11, tions and transformation of Escherichia coli strains were 12, 47). Similarly, the translation of the mitochondrial performed as described elsewhere (39). Yeast were trans- mRNA for cytochrome b also depends on at least two formed by lithium acetate treatment of intact cells (32). nuclear gene products (16, 53-55). YpA35 is a yeast replicating vector carrying a 13.5-kilobase In this paper we describe the nuclear gene PETI)I (for- (kb) insert of yeast genomic DNA that complements pet))) merly PETE))), which is required for accumulation of mutations and has been described previously (50). pSP65-2.2 cytochrome c oxidase subunit II (coxII) (7, 19). CoxIl is and pSP64-XS were constructed by inserting a 2.2-kb BglII- encoded by the uninterrupted mitochondrial gene oxil (8, 10, HindIII fragment and a 1.8-kb SalI-XbaI fragment, respec- 21). Its mRNA is translated to yield a precursor protein that tively, from YpA35 into Riboprobe vectors (Promega is processed to coxIl by removal of the 15 amino-terminal Biotec; 43). YEp13-2.7L was constructed as follows. amino acid residues (51, 58). PETJ)) activity appears to be pMC1871 (9) was digested with BamHI and treated with required specifically for translation of coxll since pet))) Klenow fragment of DNA polymerase I to fill in recessed 3' mutants lack the protein but contain substantial amounts of ends. A 3-kb fragment carrying the lacZ gene was ligated its mRNA (50). Furthermore, pet))) mutations are sup- into pSP64-2.7 (a Riboprobe vector carrying a 2.76-kb pressed by mitochondrial gene rearrangements that fuse the HindIII fragment from YpA35 which contains the PET))) 5' portions of other mitochondrial genes to oxil (50). gene) which had been prepared by digestion with NdeI, Si In this paper we present the nucleotide sequence of nuclease digestion to remove 5' overhanging ends, and PETIJ) and the predicted amino acid sequence of its prod- dephosphorylation. The resulting plasmid (pSP64-2.7L) car- uct. We provide evidence that the PET) I) protein is located ried a 5.76-kb HindIll fragment containing a fusion of the in mitochondria and therefore probably acts directly to first 154 codons of PET))) in frame with codon 8 of lacZ. promote coxII translation. Interestingly, the PET I)I mRNA has an unusually long 5' leader that contains four short open YEp13-2.7L contains this Hindlll fragment ligated to reading frames. The results of recent studies on the expres- HindIII-cleaved YEp13 (6). sion of another yeast gene whose transcript also has a long 5' DNA sequence analysis. Sau3A, TaqI, AluI, and XbaI leader with short open reading frames (24, 27, 28, 46, 65) fragments of the 2.76-kb HindIII fragment that complements suggest that the expression of PET))) itself may be regu- pet))) (50) were subcloned into the M13 vectors mplO and lated at the level of translation. mpll (44). A 1.3-kb HindIII fragment from the 5' flank of the structural gene was cloned into M13 mpl8 and mpl9, and appropriate deletions were made by exonuclease III-Si * Corresponding author. digestion (26). These clones were used as templates for the 2728 VOL. 7, 1987 PETHII CODES FOR A MITOCHONDRIAL PROTEIN 2729 4 - . A S . H i .~~~~~~~. !. t X SA^ N 00 bp FIG. 1. Restriction map and sequencing strategy of PETJJJ. Restriction sites shown are as follows: A, AluI; B, BglII, H, Hindlll; N, NdeI; R, EcoRI; S, Sau3A; T, TaqI; V, EcoRV; and X, XbaI. , Position and orientation of N and C termini of the open reading frame. Arrows show the extent and direction of each sequence determined by the dideoxynucleotide chain termination method (55) (-k) or by chemical degradation of end-labeled fragments (40) (-*). All restriction sites were crossed; both strands were sequenced. bp, Base pairs. dideoxynucleotide chain termination sequencing reaction Fractions were assayed for ,-galactosidase activity by the (56). Some regions were also sequenced by chemical degra- method of Miller (45) and for fumarase by the method of dation of end-labeled fragments (40). Racker (52). Isolation of RNA. Total yeast nucleic acids (primarily RNA) were prepared from cells grown on YPEG medium to RESULTS early logarithmic stage by vortexing with glass beads in the presence of phenol as described elsewhere (63). Poly(A)- Primary sequence analysis of PET])). DNA that comple- containing RNA was selected by hybridization to oligo(dT)- ments petlll mutations is carried on a 2.76-kb HindIII cellulose (3) according to the procedure of the manufacturer fragment (50). The nucleotide sequence of this fragment and (Bethesda Research Laboratories, Inc., Gaithersburg, Md.). that of a portion of a flanking HindlIl fragment was deter- Northern hybridization (RNA blot) analysis. RNA was mined by subcloning restriction fragments into M13 vectors denatured with glyoxal, fractionated by electrophoresis in and using these as templates in dideoxynucleotide chain 1.1% agarose in 10 mM phosphate buffer (pH 7.0; 42), and termination reactions (56). Some restriction fragments were transferred to a nylon membrane (Biodyne A; 66). A uni- end labeled and subjected to chemical degradation (40). The formly radioactively labeled RNA probe was prepared by exact strategy used in described in the legend to Fig. 1. SP6 polymerase transcription (43) from pSP65-2.2, a The PETJIIJ sequence (Fig. 2) contains a single long open Riboprobe vector which contained a fragment from the reading frame which extends over 2.15 kb. If translation structural gene for PET]JJ in the antisense orientation. were to begin at the first ATG in this open reading frame, Hybridization was done at 65°C in a buffer containing 50% PETIII would encode a basic protein of 718 amino acids. formamide (62). Genetic evidence indicates that this open reading frame Si nuclease protection. A probe uniquely labeled at the codes for the PET] ]I product. A DNA fragment that carries BglIH site within PETJI] (Fig. 1) was generated as follows. just the long open reading frame and 57 upstream nucleotides YpA35 was restricted with BglII, and an 8-kb band was under the transcriptional direction of the ADCJ promoter (2) isolated from an agarose gel. This fragment was treated with complemented petlII mutations (data not shown). In addi- alkaline phosphatase and labeled by using T4 polynucleotide tion, the pet]I l-I mutation was mapped to a DNA fragment kinase as described elsewhere (39). The DNA was recut with which is delineated by two XbaI sites (Fig. 1) and includes Sall, and the appropriate 4-kb fragment was isolated from an primarily open reading frame (774 nucleotides of the open agarose gel. A probe uniquely labeled at the HindIII site reading frame and 219 upstream nucleotides). Also, insertion upstream of the PETJIJI coding region (Fig. 1) was generated of foreign DNA at the BglII site in the open reading frame as follows. pSP64-XS was digested with HindIII, and a destroyed the ability of the 2.76-kb HindIII fragment to 1.3-kb fragment was isolated from an agarose gel. This complement pet]ll mutations (50). fragment was labeled as described above and recut with The predicted amino acid sequence of PET] II was used in EcoRI, and the appropriate 500-base-pair fragment was a computer search of sequences contained in the National isolated from an agarose gel.