Functional expression of rat cytochrome c in Saccharomyces cerevisiae

Transcriptional paradigms in mammalian mitochondrial biogenesis and function

Mitochondria contain their own genetic system and undergo a unique mode of cytoplasmic inheritance. Each organelle has multiple copies of a covalently closed circular DNA genome (mtDNA). The entire protein coding capacity of mtDNA is devoted to the synthesis of 13 essential subunits of the inner membrane complexes of the respiratory apparatus. Thus the majority of respiratory proteins and all of the other gene products necessary for the myriad mitochondrial functions are derived from nuclear genes. Transcription of mtDNA requires a small number of nucleus-encoded proteins including a single RNA polymerase (POLRMT), auxiliary factors necessary for promoter recognition (TFB1M, TFB2M) and activation (Tfam), and a termination factor (mTERF). This relatively simple system can account for the bidirectional transcription of mtDNA from divergent promoters and key termination events controlling the rRNA/mRNA ratio. Nucleomitochondrial interactions depend on the interplay between transcription factors (NRF-1, NRF-2, PPARalpha, ERRalpha, Sp1, and others) and members of the PGC-1 family of regulated coactivators (PGC-1alpha, PGC-1beta, and PRC). The transcription factors target genes that specify the respiratory chain, the mitochondrial transcription, translation and replication machinery, and protein import and assembly apparatus among others. These factors are in turn activated directly or indirectly by PGC-1 family coactivators whose differential expression is controlled by an array of environmental signals including temperature, energy deprivation, and availability of nutrients and growth factors. These transcriptional paradigms provide a basic framework for understanding the integration of mitochondrial biogenesis and function with signaling events that dictate cell- and tissue-specific energetic properties.

Ca2+ transport in mitochondria from yeast expressing recombinant aequorin

We have expressed aequorin in mitochondria of the yeast Saccharomyces cerevisiae and characterized the resulting strain with respect to mitochondrial Ca(2+) transport in vivo and in vitro. When intact cells are suspended in water containing 1.4 mM ethanol and 14 mM CaCl(2), the matrix free Ca(2+) concentration is 200 nM, similar to the values expected in cytoplasm. Addition of ionophore ETH 129 allows an active accumulation of Ca(2+) and promptly increases the value to 1.2 microM. Elevated Ca(2+) concentrations are maintained for periods of 6 min or longer under these conditions. Isolated yeast mitochondria oxidizing ethanol also accumulate Ca(2+) when ETH 129 is present, but the cation is not retained depending on the medium conditions. This finding confirms the presence of a Ca(2+) release mechanism that requires free fatty acids as previously described [P.C. Bradshaw et al. (2001) J. Biol. Chem. 276, 40502-40509]. When a respiratory substrate is not present, Ca(2+) enters and leaves yeast mitochondria slowly, at a specific activity near 0.2 nmol/min/mg protein. Transport under these conditions equilibrates the internal and external concentrations of Ca(2+) and is not affected by ruthenium red, uncouplers, or ionophores that perturb transmembrane gradients of charge and pH. This activity displays sigmoid kinetics and a K(1/2) value for Ca(2+) that is near to 900 nM, in the absence of ethanol or when it is present. It is furthermore shown that the activity coefficient of Ca(2+) in yeast mitochondria is a function of the matrix Ca(2+) content and is substantially larger than that in mammalian mitochondria. Characteristics of the aequorin-expressing strain appear suitable for its use in expression-based methods directed at cloning Ca(2+) transporters from mammalian mitochondria and for further examining the interrelationships between mitochondrial and cytoplasmic Ca(2+) in yeast.

Cloning, nucleotide sequence and expression of the cytochrome c-552 gene from Hydrogenobacter thermophilus

A cytochrome c-552 gene from a thermophilic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus, was cloned by using two oligonucleotide probes, which had been synthesized based on the known amino acid sequence of the protein. A 780-bp PstI-SphI fragment of the cloned DNA was sequenced and found to contain the entire structural gene coding for cytochrome c-552 bracketed by apparent Escherichia coli consensus sequences for initiation and termination of transcription. Cytochrome c-552 is synthesized in vivo as a precursor having an N-terminal signal sequence consisting of 18 amino acid residues. The cloned cytochrome c-552 gene without its own signal sequence was introduced into the pKK223-3 vector and expressed in E. coli upon induction with isopropyl beta-D-thiogalactoside. An expressed cytochrome c-552 protein had a methionine residue at the N-terminus since an initiation signal was introduced before the first amino acid residue of the mature cytochrome c-552. The heme c was attached to apo-type cytochrome c-552 in the cytoplasm of E. coli and the holoprotein had spectral properties, similar to the authentic cytochrome c-552 from H. thermophilus.

Mitochondrial protein import

A dynamic picture of the mitochondrial protein import pathway is emerging, with conformational alteration a critical feature both preceding and following membrane translocation. The mediators of these steps of conformational alteration, as well as steps of recognition, translocation, and proteolytic cleavage, appear to be proteins. Using powerful tools of genetics and biochemistry, in years to come it should be possible to determine the precise molecular function of these proteins in mediating these novel reactions.

Mitochondrial targeting of yeast apoiso-1-cytochrome c is mediated through functionally independent structural domains

An iso-1-cytochrome c-chloramphenicol acetyltransferase fusion protein (iso-1/CAT) was expressed in Saccharomyces cerevisiae and used to delineate two stages in the cytochrome c import pathway in vivo (S. H. Nye and R. C. Scarpulla, Mol. Cell. Biol. 10:5753-5762, 1990 [this issue]). Fusion proteins with the CAT reporter domain in its native conformation were arrested at the initial stage of mitochondrial membrane recognition and insertion. In contrast, those with a deletional disruption of the CAT moiety were relieved of this block and allowed to translocate to the intermembrane space, where they functioned in respiratory electron transfer. In the present study, iso-1/CAT was used to map structural determinants in apoiso-1-cytochrome c involved in the initial step of targeting to the mitochondrial membrane. Carboxy-terminal deletions revealed that one of these determinants consisted of the amino-terminal 68 residues. Deletion mutations either within or at the ends of this determinant destroyed mitochondrial targeting activity, suggesting that functionally important information spans the length of this fragment. Disruption of an alpha-helix near the amino terminus by a helix-breaking proline substitution for leucine 14 also eliminated the targeting activity of the 1 to 68 determinant, suggesting a contribution from this structure. A second, functionally independent targeting determinant was found in the carboxy half of the apoprotein between residues 68 and 85. This determinant coincided with a stretch of 11 residues that are invariant in nearly 100 eucaryotic cytochromes c. Therefore, in lieu of an amino-terminal presequence, apocytochrome c has redundant structural information located in both the amino and carboxy halves of the molecule that can function independently to specify mitochondrial targeting and membrane insertion in vivo.

In vivo expression and mitochondrial targeting of yeast apoiso-1-cytochrome c fusion proteins

To define the import pathway for apoiso-1-cytochrome c in vivo, the coding region for bacterial chloramphenicol acetyltransferase (CAT) or yeast copper metallothionein (CuMT) was fused to the carboxy terminus of the apoiso-1-cytochrome c (iso-1) coding region. When the resulting iso-1/CAT and iso-1/CuMT fusion proteins were individually expressed in Saccharomyces cerevisiae, they were specifically targeted to the mitochondria and protected from trypsin digestion. Although iso-1/CAT was accessible to heme modification, it remained membrane associated because of the folded conformation of the CAT domain. A small deletion disrupting CAT structure resulted in the translocation of the resulting fusion protein, iso-1/CAT delta, to the intermembrane space, where it functioned efficiently in respiratory electron transfer. Similarly, iso-1/CuMT was heme modified and nearly identical to iso-1 in its ability to support respiratory growth, indicating that the CuMT domain was compatible with translocation to the IMS. Inclusion of copper in the growth medium, which converts the loosely structured apo-CuMT to a tightly folded holo-CuMT, inhibited both heme attachment and respiratory growth without affecting mitochondrial targeting. Thus, by altering the folded conformation of the reporter moiety of these fusion proteins, it was possible to differentiate between those molecules arrested at the mitochondrial targeting step of the cytochrome c import pathway and those translocated to the intermembrane space. By replacing the heme-binding cysteine residues with serines, this system was used to demonstrate that the import requirement for heme attachment operated at the level of membrane translocation and not on mitochondrial targeting in vivo.

In vivo expression and mitochondrial targeting of yeast apoiso-1-cytochrome c fusion proteins

To define the import pathway for apoiso-1-cytochrome c in vivo, the coding region for bacterial chloramphenicol acetyltransferase (CAT) or yeast copper metallothionein (CuMT) was fused to the carboxy terminus of the apoiso-1-cytochrome c (iso-1) coding region. When the resulting iso-1/CAT and iso-1/CuMT fusion proteins were individually expressed in Saccharomyces cerevisiae, they were specifically targeted to the mitochondria and protected from trypsin digestion. Although iso-1/CAT was accessible to heme modification, it remained membrane associated because of the folded conformation of the CAT domain. A small deletion disrupting CAT structure resulted in the translocation of the resulting fusion protein, iso-1/CAT delta, to the intermembrane space, where it functioned efficiently in respiratory electron transfer. Similarly, iso-1/CuMT was heme modified and nearly identical to iso-1 in its ability to support respiratory growth, indicating that the CuMT domain was compatible with translocation to the IMS. Inclusion of copper in the growth medium, which converts the loosely structured apo-CuMT to a tightly folded holo-CuMT, inhibited both heme attachment and respiratory growth without affecting mitochondrial targeting. Thus, by altering the folded conformation of the reporter moiety of these fusion proteins, it was possible to differentiate between those molecules arrested at the mitochondrial targeting step of the cytochrome c import pathway and those translocated to the intermembrane space. By replacing the heme-binding cysteine residues with serines, this system was used to demonstrate that the import requirement for heme attachment operated at the level of membrane translocation and not on mitochondrial targeting in vivo.

Mitochondrial targeting of yeast apoiso-1-cytochrome c is mediated through functionally independent structural domains

An iso-1-cytochrome c-chloramphenicol acetyltransferase fusion protein (iso-1/CAT) was expressed in Saccharomyces cerevisiae and used to delineate two stages in the cytochrome c import pathway in vivo (S. H. Nye and R. C. Scarpulla, Mol. Cell. Biol. 10:5753-5762, 1990 [this issue]). Fusion proteins with the CAT reporter domain in its native conformation were arrested at the initial stage of mitochondrial membrane recognition and insertion. In contrast, those with a deletional disruption of the CAT moiety were relieved of this block and allowed to translocate to the intermembrane space, where they functioned in respiratory electron transfer. In the present study, iso-1/CAT was used to map structural determinants in apoiso-1-cytochrome c involved in the initial step of targeting to the mitochondrial membrane. Carboxy-terminal deletions revealed that one of these determinants consisted of the amino-terminal 68 residues. Deletion mutations either within or at the ends of this determinant destroyed mitochondrial targeting activity, suggesting that functionally important information spans the length of this fragment. Disruption of an alpha-helix near the amino terminus by a helix-breaking proline substitution for leucine 14 also eliminated the targeting activity of the 1 to 68 determinant, suggesting a contribution from this structure. A second, functionally independent targeting determinant was found in the carboxy half of the apoprotein between residues 68 and 85. This determinant coincided with a stretch of 11 residues that are invariant in nearly 100 eucaryotic cytochromes c. Therefore, in lieu of an amino-terminal presequence, apocytochrome c has redundant structural information located in both the amino and carboxy halves of the molecule that can function independently to specify mitochondrial targeting and membrane insertion in vivo.

Cloning by function: an alternative approach for identifying yeast homologs of genes from other organisms

Studies of cell physiology and structure have identified many intriguing proteins that could be analyzed for function by using the power of yeast genetics. Unfortunately, identifying the homologous yeast gene with the two most commonly used approaches--DNA hybridization and antibody cross-reaction--is often difficult. We describe a strategy to identify yeast homologs based on protein function itself. This cloning-by-function strategy involves first identifying a yeast mutant that depends on a plasmid expressing a cloned foreign gene. The corresponding yeast gene is then cloned by complementation of the mutant defect. To detect plasmid dependence, the colony color assay of Koshland et al. [Koshland, D., Kent, J. C. & Hartwell, L. H. (1985) Cell 40, 393-403] is used. In this paper, we test the feasibility of this approach using the well-characterized system of DNA topoisomerase II in yeast. We show that (i) plasmid dependence is easily recognized; (ii) the screen efficiently isolates mutations in the desired gene; and (iii) the wild-type yeast homolog of the gene can be cloned by screening for reversal of the plasmid-dependent phenotype. We conclude that cloning by function can be used to isolate the yeast homologs of essential genes identified in other organisms.

Functional expression of a Drosophila gene in yeast: genetic complementation of DNA topoisomerase II

Since DNA topoisomerase II (EC 5.99.1.3) is an essential enzyme in yeast, heterologous topoisomerase II gene expression in yeast cells can provide a system for analyzing the structure and function of topoisomerase II genes from other species. A series of yeast expression plasmids was constructed in which segments of the cDNA sequences encoding Drosophila DNA topoisomerase II were inserted under the transcriptional control of yeast GAL1 promoter. Expression of the functional form of Drosophila topoisomerase II cDNA can complement conditionally lethal, temperature-sensitive mutations in the yeast topoisomerase II gene (TOP2), as well as mutations in which the TOP2 locus was disrupted. The survival of these yeast cells depends upon the continuous expression of Drosophila topoisomerase II. Repression of Drosophila gene expression by glucose causes these yeast cells to cease dividing after a few generations. In addition to these genetic complementation data, the expression of the Drosophila topoisomerase II gene in yeast cells with a disruption in TOP2 can also be detected by immunochemical methods with an antibody specific for Drosophila topoisomerase II.

Import and processing of human ornithine transcarbamoylase precursor by mitochondria from Saccharomyces cerevisiae

Expression of the subunit precursor of the human mitochondrial matrix enzyme ornithine transcarbamoylase (OTCase; EC 2.1.3.3) was programmed in Saccharomyces cerevisiae from a 2-micron plasmid by using an inducible galactose operon promoter. In the presence of the inducing sugar (galactose), two polypeptides were specifically precipitable with anti-OTCase antiserum: the human OTCase precursor (40 kDa); and the mature OTCase subunit (36 kDa). When yeast cells containing these species were lysed and fractionated, the OTCase precursor was found to be associated with mitochondrial membranes, while the mature subunit was found partly with mitochondrial membranes and partly in the soluble mitochondrial matrix-containing fraction. When OTCase enzymatic activity was assayed in fractions similarly derived from an S. cerevisiae strain devoid of yeast OTCase activity (an arg3 mutant) but expressing human OTCase, activity was detected specifically in the mitochondrial matrix fraction. A mutant human OTCase precursor containing an artificial mutation in the NH2-terminal leader peptide (arginine-23 to glycine) was similarly examined. As was previously observed with mammalian mitochondria, this precursor failed both to reach the matrix compartment and to be proteolytically processed; it also failed to exhibit OTCase enzymatic activity. Presence of OTCase enzymatic activity in an arg3 strain expressing wild-type precursor was utilized to obtain selective growth in a medium devoid of arginine but supplemented with the OTCase substrate ornithine. We conclude that, during evolution, the pathway of mitochondrial import utilized by the human OTCase precursor is conserved between yeast and humans, and that, by using selective growth conditions, it may be possible to examine genetically this pathway in S. cerevisiae.