Differential effectiveness of yeast cytochrome c oxidase subunit genes results from differences in expression not function

Human Mitochondrial Pathologies of the Respiratory Chain and ATP Synthase: Contributions from Studies of Saccharomyces cerevisiae

The ease with which the unicellular yeast Saccharomyces cerevisiae can be manipulated genetically and biochemically has established this organism as a good model for the study of human mitochondrial diseases. The combined use of biochemical and molecular genetic tools has been instrumental in elucidating the functions of numerous yeast nuclear gene products with human homologs that affect a large number of metabolic and biological processes, including those housed in mitochondria. These include structural and catalytic subunits of enzymes and protein factors that impinge on the biogenesis of the respiratory chain. This article will review what is currently known about the genetics and clinical phenotypes of mitochondrial diseases of the respiratory chain and ATP synthase, with special emphasis on the contribution of information gained from pet mutants with mutations in nuclear genes that impair mitochondrial respiration. Our intent is to provide the yeast mitochondrial specialist with basic knowledge of human mitochondrial pathologies and the human specialist with information on how genes that directly and indirectly affect respiration were identified and characterized in yeast.

Mitochondrial Efficiency-Dependent Viability of Saccharomyces cerevisiae Mutants Carrying Individual Electron Transport Chain Component Deletions

Mitochondria play a crucial role in eukaryotic cells; the mitochondrial electron transport chain (ETC) generates adenosine triphosphate (ATP), which serves as an energy source for numerous critical cellular activities. However, the ETC also generates deleterious reactive oxygen species (ROS) as a natural byproduct of oxidative phosphorylation. ROS are considered the major cause of aging because they damage proteins, lipids, and DNA by oxidation. We analyzed the chronological life span, growth phenotype, mitochondrial membrane potential (MMP), and intracellular ATP and mitochondrial superoxide levels of 33 single ETC component-deleted strains during the chronological aging process. Among the ETC mutant strains, 14 (sdh1Δ, sdh2Δ, sdh4Δ, cor1Δ, cyt1Δ, qcr7Δ, qcr8Δ, rip1Δ, cox6Δ, cox7Δ, cox9Δ, atp4Δ, atp7Δ, and atp17Δ) showed a significantly shorter life span. The deleted genes encode important elements of the ETC components succinate dehydrogenase (complex II) and cytochrome c oxidase (complex IV), and some of the deletions lead to structural instability of the membrane-F1F0-ATP synthase due to mutations in the stator stalk (complex V). These short-lived strains generated higher superoxide levels and produced lower ATP levels without alteration of MMP. In summary, ETC mutations decreased the life span of yeast due to impaired mitochondrial efficiency.

Comparisons of subunit 5A and 5B isoenzymes of yeast cytochrome c oxidase

Subunit 5 of Saccharomyces cerevisiae cytochrome c oxidase (CcO) is essential for assembly and has two isoforms, 5A and 5B. 5A is expressed under normoxic conditions, whereas 5B is expressed at very low oxygen tensions. As a consequence, COX5A-deleted strains (Δcox5A) have no or only low levels of CcO under normoxic conditions rendering them respiratory deficient. Previous studies have reported that respiratory growth could be restored by combining Δcox5A with mutations of ROX1 that encodes a repressor of COX5B expression. In these mutants, 5B isoenzyme expression level was 30–50% of wild-type (5A isoenzyme) and exhibited a maximum catalytic activity up to 3-fold faster than that of 5A isoenzyme. To investigate the origin of this effect, we constructed a mutant strain in which COX5B replaced COX5A downstream of the COX5A promoter. This strain expressed wild-type levels of the 5B isoenzyme, without the complication of additional effects caused by mutation of ROX1. When produced this way, the isoenzymes displayed no significant differences in their maximum catalytic activities or in their affinities for oxygen or cytochrome c. Hence the elevated activity of the 5B isoenzyme in the rox1 mutant is not caused simply by exchange of isoforms and must arise from an additional effect that remains to be resolved.

Yeast cytochrome c oxidase isoenzymes with subunits 5A or 5B can exhibit different kinetic properties. We demonstrate that these differences are not induced by simple 5A/5B replacement and that the effect additionally requires expression level changes and/or undefined post-translational effects.

Hypermethylation of Cox5a promoter is associated with mitochondrial dysfunction in skeletal muscle of high fat diet-induced insulin resistant rats

High-fat diet (HFD) is an environmental factor that contributes to the pathogenesis of obesity and type 2 diabetes. A number of genes influencing oxidative phosphorylation (OXPHOS) were found to be downregulated in skeletal muscle of humans and rats treated with HFD and have been implicated in mitochondrial dysfunction, insulin resistance, and consequent type 2 diabetes. In this study, we hypothesized that DNA methylation plays a crucial role in the regulation of OXPHOS genes in skeletal muscle of rats exposed to HFD. Using whole genome promoter methylation analysis of skeletal muscle followed by qPCR and bisulfite sequencing analysis, we identified hypermethylation of Cox5a in HFD rats. Furthermore, we found that Cox5a hypermethylation was associated with downregulation of Cox5a expression at the mRNA and protein level, and a reduction in mitochondrial complex IV activity and ATP content in HFD-induced insulin resistant rats compared to controls. Moreover, we found that while exposure to palmitate resulted in hypermethylation of the Cox5a promoter in rat myotubes, demethylation with 5-aza-2′-deoxycytidine was associated with preserved Cox5a expression, as well as restoration of complex IV activity and cellular ATP content. These novel observations indicate that Cox5a hypermethylation is associated with mitochondrial dysfunction in skeletal muscle of HFD-induced insulin resistant rats.

Oxygen-regulated isoforms of cytochrome c oxidase have differential effects on its nitric oxide production and on hypoxic signaling

Recently, it has been reported that mitochondria possess a novel pathway for nitric oxide (NO) synthesis. This pathway is induced when cells experience hypoxia, is nitrite (NO(2)(-))-dependent, is independent of NO synthases, and is catalyzed by cytochrome c oxidase (Cco). It has been proposed that this mitochondrially produced NO is a component of hypoxic signaling and the induction of nuclear hypoxic genes. In this study, we examine the NO(2)(-)-dependent NO production in yeast engineered to contain alternative isoforms, Va or Vb, of Cco subunit V. Previous studies have shown that these isoforms have differential effects on oxygen reduction by Cco, and that their genes (COX5a and COX5b, respectively) are inversely regulated by oxygen. Here, we find that the Vb isozyme has a higher turnover rate for NO production than the Va isozyme and that the Vb isozyme produces NO at much higher oxygen concentrations than the Va isozyme. We have also found that the hypoxic genes CYC7 and OLE1 are induced to higher levels in a strain carrying the Vb isozyme than in a strain carrying the Va isozyme. Together, these results demonstrate that the subunit V isoforms have differential effects on NO(2)(-)-dependent NO production by Cco and provide further support for a role of Cco in hypoxic signaling. These findings also suggest a positive feedback mechanism in which mitochondrially produced NO induces expression of COX5b, whose protein product then functions to enhance the ability of Cco to produce NO in hypoxic/anoxic cells.

Cell cycle- and ribonucleotide reductase-driven changes in mtDNA copy number influence mtDNA Inheritance without compromising mitochondrial gene expression

Most eukaryotes maintain multiple copies of mtDNA, ranging from 20-50 in yeast to as many as 10,000 in mammalian cells. The mitochondrial genome encodes essential subunits of the respiratory chain, but the number of mtDNA molecules is apparently in excess of that needed to sustain adequate respiration, as evidenced by the "threshold effect" in mitochondrial diseases. Thus, other selective pressures apparently have contributed to the universal maintenance of multiple mtDNA molecules/cell. Here we analyzed the interplay between the two pathways proposed to regulate mtDNA copy number in Saccharomyces cerevisiae, and the requirement of normal mtDNA copy number for mitochondrial gene expression, respiration, and inheritance. We provide the first direct evidence that upregulation of mtDNA can be achieved by increasing ribonucleotide reductase (RNR) activity via derepression of nuclear RNR gene transcription or elimination of allosteric-feedback regulation. Analysis of rad53 mutant strains also revealed upregulation of mtDNA copy number independent of that resulting from elevated RNR activity. We present evidence that a prolonged cell cycle allows accumulation of mtDNA in these strains. Analysis of multiple strains with increased or decreased mtDNA revealed that mechanisms are in place to prevent significant changes in mitochondrial gene expression and respiration in the face of approximately two-fold alterations in mtDNA copy number. However, depletion of mtDNA in abf2 null strains leads to defective mtDNA inheritance that is partially rescued by replenishing mtDNA via overexpression of RNR1. These results indicate that one role for multiple mtDNA copies is to ensure optimal inheritance of mtDNA during cell division.

Oxygen sensing in yeast: evidence for the involvement of the respiratory chain in regulating the transcription of a subset of hypoxic genes

Oxygen availability affects the transcription of a number of genes in nearly all organisms. Although the molecular mechanisms for sensing oxygen are not precisely known, heme is thought to play a pivotal role. Here, we address the possibility that oxygen sensing in yeast, as in mammals, involves a redox-sensitive hemoprotein. We have found that carbon monoxide (CO) completely blocks the anoxia-induced expression of two hypoxic genes, OLE1 and CYC7, partially blocks the induction of a third gene, COX5b, and has no effect on the expression of other hypoxic or aerobic genes. In addition, transition metals (Co and Ni) induce the expression of OLE1 and CYC7 in a concentration-dependent manner under aerobic conditions. These findings suggest that the redox state of an oxygen-binding hemoprotein is involved in controlling the expression of at least two hypoxic yeast genes. By using mutants deficient in each of the two major yeast CO-binding hemoproteins (cytochrome c oxidase and flavohemoglobin), respiratory inhibitors, and cob1 and rho0 mutants, we have found that the respiratory chain is involved in the anoxic induction of these two genes and that cytochrome c oxidase is likely the hemoprotein "sensor." Our findings also indicate that there are at least two classes of hypoxic genes in yeast (CO sensitive and CO insensitive) and imply that multiple pathways/mechanisms are involved in modulating the expression of hypoxic yeast genes.

A fermentor system for regulating oxygen at low concentrations in cultures of Saccharomyces cerevisiae

The growth of yeast cells to high densities at low, but constant, oxygen concentrations is difficult because the cells themselves respire oxygen; hence, as cell mass increases, so does oxygen consumption. To circumvent this problem, we have designed a system consisting of a computer-controlled gas flow train that adjusts oxygen concentration in the gas flow to match cellular demand. It does this by using a proportional-integral-differential algorithm in conjunction with a three-way valve to mix two gases, adjusting their proportions to maintain the desired oxygen concentration. By modeling yeast cell yields at intermediate to low oxygen concentrations, we have found that cellular respiration declines with oxygen concentration, most likely because of a decrease in the expression of genes for respiratory proteins. These lowered rates of oxygen consumption, together with the gas flow system described here, allow the growth of yeast cells to high densities at low oxygen concentrations. This system can also be used to grow cells at any desired oxygen concentration and for regulated shifts between oxygen concentrations.

Upstream activation and repression elements control transcription of the yeast COX5b gene

The Saccharomyces cerevisiae COX5b gene is regulated at the level of transcription by both the carbon source and oxygen. To define the cis-acting elements that underlie this transcriptional control, deletion analysis of the upstream regulatory region of COX5b was performed. The results of the study suggest that at least four distinct regulatory sites are functional upstream of the COX5b transcriptional starts. One, which was precisely defined to a region of 20 base pairs, contains two TATA-like elements. Two upstream activating sequences (UAS15b and UAS2(5b)) and an upstream repression sequence (URS5b) were also found. Each of the latter three elements was able either to activate (UAS1(5b) and UAS2(5b)) or to repress URS5b) the transcription of a heterologous yeast gene. Further analysis revealed that UAS1(5b) is the site of carbon source control and may be composed of two distinct domains that act synergistically. URS5b mediates the aerobic repression of COX5b and contains two sequences that are highly conserved in other yeast genes negatively regulated by oxygen.

Upstream activation and repression elements control transcription of the yeast COX5b gene

The Saccharomyces cerevisiae COX5b gene is regulated at the level of transcription by both the carbon source and oxygen. To define the cis-acting elements that underlie this transcriptional control, deletion analysis of the upstream regulatory region of COX5b was performed. The results of the study suggest that at least four distinct regulatory sites are functional upstream of the COX5b transcriptional starts. One, which was precisely defined to a region of 20 base pairs, contains two TATA-like elements. Two upstream activating sequences (UAS15b and UAS2(5b)) and an upstream repression sequence (URS5b) were also found. Each of the latter three elements was able either to activate (UAS1(5b) and UAS2(5b)) or to repress URS5b) the transcription of a heterologous yeast gene. Further analysis revealed that UAS1(5b) is the site of carbon source control and may be composed of two distinct domains that act synergistically. URS5b mediates the aerobic repression of COX5b and contains two sequences that are highly conserved in other yeast genes negatively regulated by oxygen.

Overexpression of a leaderless form of yeast cytochrome c oxidase subunit Va circumvents the requirement for a leader peptide in mitochondrial import

Subunit Va of Saccharomyces cerevisiae cytochrome c oxidase is a nucleus-encoded mitochondrial protein that is derived from a precursor with a 20-residue leader peptide. We previously reported that this leader peptide is required for import of subunit Va into mitochondria in vivo (S. M. Glaser, C. E. Trueblood, L. K. Dircks, R. O. Poyton, and M. G. Cumsky, J. Cell. Biochem. 36:275-278, 1988). Here we show that overproduction of a leaderless form of subunit Va circumvents the leader peptide requirement for import into mitochondria in vivo.

Overexpression of a leaderless form of yeast cytochrome c oxidase subunit Va circumvents the requirement for a leader peptide in mitochondrial import

Subunit Va of Saccharomyces cerevisiae cytochrome c oxidase is a nucleus-encoded mitochondrial protein that is derived from a precursor with a 20-residue leader peptide. We previously reported that this leader peptide is required for import of subunit Va into mitochondria in vivo (S. M. Glaser, C. E. Trueblood, L. K. Dircks, R. O. Poyton, and M. G. Cumsky, J. Cell. Biochem. 36:275-278, 1988). Here we show that overproduction of a leaderless form of subunit Va circumvents the leader peptide requirement for import into mitochondria in vivo.

Removal of a hydrophobic domain within the mature portion of a mitochondrial inner membrane protein causes its mislocalization to the matrix

We have examined the import and intramitochondrial localization of the precursor to yeast cytochrome c oxidase subunit Va, a protein of the mitochondrial inner membrane. The results of studies on the import of subunit Va derivatives carrying altered presequences suggest that the uptake of this protein is highly efficient. We found that a presequence of only 5 amino acids (Met-Leu-Ser-Leu-Arg) could direct the import and localization of subunit Va with wild-type efficiency, as judged by several different assays. We also found that subunit Va could be effectively targeted to the mitochondrial inner membrane with a heterologous presequence that failed to direct import of its cognate protein. The results presented here confirmed those of an earlier study and showed clearly that the information required to "sort" subunit Va to the inner membrane resides in the mature protein sequence, not within the presequence per se. We present additional evidence that the aforementioned sorting information is contained, at least in part, in a hydrophobic stretch of 22 amino acids residing within the C-terminal third of the protein. Removal of this domain caused subunit Va to be mislocalized to the mitochondrial matrix.

Removal of a hydrophobic domain within the mature portion of a mitochondrial inner membrane protein causes its mislocalization to the matrix

We have examined the import and intramitochondrial localization of the precursor to yeast cytochrome c oxidase subunit Va, a protein of the mitochondrial inner membrane. The results of studies on the import of subunit Va derivatives carrying altered presequences suggest that the uptake of this protein is highly efficient. We found that a presequence of only 5 amino acids (Met-Leu-Ser-Leu-Arg) could direct the import and localization of subunit Va with wild-type efficiency, as judged by several different assays. We also found that subunit Va could be effectively targeted to the mitochondrial inner membrane with a heterologous presequence that failed to direct import of its cognate protein. The results presented here confirmed those of an earlier study and showed clearly that the information required to "sort" subunit Va to the inner membrane resides in the mature protein sequence, not within the presequence per se. We present additional evidence that the aforementioned sorting information is contained, at least in part, in a hydrophobic stretch of 22 amino acids residing within the C-terminal third of the protein. Removal of this domain caused subunit Va to be mislocalized to the mitochondrial matrix.

Splicing of a yeast intron containing an unusual 5' junction sequence

The Saccharomyces cerevisiae COX5b gene contains a small intron that is unique in two respects. First, it interrupts the ATG codon that initiates translation of the COX5b product. Second, it contains a sequence at the 5' splice junction (5'-GCATGT-3') that differs from the highly conserved yeast hexanucleotide (5'-GTAPyGT-3') and from the 5'-GT found at the corresponding position in nearly all introns of eucaryotic protein-coding genes. We have analyzed both the transcripts derived from the COX5b gene and the splicing of its intron. We show here that an unspliced mRNA precursor constituted a minor fraction of the total COX5b message, even when the gene was overexpressed. We also show that both major transcripts derived from COX5b had been spliced. Our results suggest that at least in the case of COX5b, a 5'-GC can function as efficiently as the highly conserved 5'-GT in the splicing reaction.

Inverse regulation of the yeast COX5 genes by oxygen and heme

The COX5a and COX5b genes encode divergent forms of yeast cytochrome c oxidase subunit V. Although the polypeptide products of the two genes are functionally interchangeable, it is the Va subunit that is normally found in preparations of yeast mitochondria and cytochrome c oxidase. We show here that the predominance of subunit Va stems in part from the differential response of the two genes to the presence of molecular oxygen. Our results indicate that during aerobic growth, COX5a levels were high, while COX5b levels were low. Anaerobically, the pattern was reversed; COX5a levels dropped sevenfold, while those of COX5b were elevated sevenfold. Oxygen appeared to act at the level of transcription through heme, since the addition of heme restored an aerobic pattern of transcription to anaerobically grown cells and the effect of anaerobiosis on COX5 transcription was reproduced in strains containing a mutation in the heme-biosynthetic pathway (hem1). In conjunction with the oxygen-heme response, we determined that the product of the ROX1 gene, a trans-acting regulator of several yeast genes controlled by oxygen, is also involved in COX5 expression. These results, as well as our observation that COX5b expression varied significantly in certain yeast strains, indicate that the COX5 genes undergo a complex pattern of regulation. This regulation, especially the increase in COX5b levels anaerobically, may reflect an attempt to modulate the activity of a key respiratory enzyme in response to varying environmental conditions. The results presented here, as well as those from other laboratories, suggest that the induction or derepression of certain metabolic enzymes during anaerobiosis may be a common and important physiological response in yeast cells.

Functional characterization of the two alcohol oxidase genes from the yeast Pichia pastoris

In Pichia pastoris, alcohol oxidase (AOX) is the first enzyme in the methanol utilization pathway and is encoded by two genes, AOX1 and AOX2. The DNA and predicted amino acid sequences of the protein-coding portions of the genes are closely homologous, whereas flanking sequences share no homology. The functional roles of AOX1 and AOX2 in the metabolism of methanol were examined. Studies of strains with disrupted AOX genes revealed that AOX1 was the major source of methanol-oxidizing activity in methanol-grown P. pastoris. The results of two types of experiments each suggested that the difference in AOX activity contributed by the two genes was a consequence of sequences located 5' of the protein-coding portions of the genes. First, the coding portion of AOX2 was able to functionally substitute for that of AOX1 when placed under the control of AOX1 regulatory sequences. Second, when labeled oligonucleotide probes specific for the 5' nontranslated region of each gene were used, it was apparent that the steady-state level of AOX1 mRNA was much higher than that of AOX2. Except for the difference in the amount of mRNA present, the two genes appeared to be regulated in the same manner. A physiological reason for the existence of AOX2 was sought but was not apparent.

Splicing of a yeast intron containing an unusual 5' junction sequence

The Saccharomyces cerevisiae COX5b gene contains a small intron that is unique in two respects. First, it interrupts the ATG codon that initiates translation of the COX5b product. Second, it contains a sequence at the 5' splice junction (5'-GCATGT-3') that differs from the highly conserved yeast hexanucleotide (5'-GTAPyGT-3') and from the 5'-GT found at the corresponding position in nearly all introns of eucaryotic protein-coding genes. We have analyzed both the transcripts derived from the COX5b gene and the splicing of its intron. We show here that an unspliced mRNA precursor constituted a minor fraction of the total COX5b message, even when the gene was overexpressed. We also show that both major transcripts derived from COX5b had been spliced. Our results suggest that at least in the case of COX5b, a 5'-GC can function as efficiently as the highly conserved 5'-GT in the splicing reaction.

Cytochrome oxidase subunit V gene of Neurospora crassa: DNA sequences, chromosomal mapping, and evidence that the cya-4 locus specifies the structural gene for subunit V

The sequences of cDNA and genomic DNA clones for Neurospora cytochrome oxidase subunit V show that the protein is synthesized as a 171-amino-acid precursor containing a 27-amino-acid N-terminal extension. The subunit V protein sequence is 34% identical to that of Saccharomyces cerevisiae subunit V; these proteins, as well as the corresponding bovine subunit, subunit IV, contain a single hydrophobic domain which most likely spans the inner mitochondrial membrane. The Neurospora crassa subunit V gene (cox5) contains two introns, 398 and 68 nucleotides long, which share the conserved intron boundaries 5'GTRNGT...CAG3' and the internal consensus sequence ACTRACA. Two short sequences, YGCCAG and YCCGTTY, are repeated four times each in the cox5 gene upstream of the mRNA 5' termini. The cox5 mRNA 5' ends are heterogeneous, with the major mRNA 5' end located 144 to 147 nucleotides upstream from the translational start site. The mRNA contains a 3'-untranslated region of 186 to 187 nucleotides. Using restriction-fragment-length polymorphism, we mapped the cox5 gene to linkage group IIR, close to the arg-5 locus. Since one of the mutations causing cytochrome oxidase deficiency in N. crassa, cya-4-23, also maps there, we transformed the cya-4-23 strain with the wild-type cox5 gene. In contrast to cya-4-23 cells, which grow slowly, cox5 transformants grew quickly, contained cytochrome oxidase, and had 8- to 11-fold-higher levels of subunit V in their mitochondria. These data suggest (i) that the cya-4 locus in N. crassa specifies structural information for cytochrome oxidase subunit V and (ii) that, in N. crassa, as in S. cerevisiae, deficiencies in the production of nuclearly encoded cytochrome oxidase subunits result in deficiency in cytochrome oxidase activity. Finally, we show that the lower levels of subunit V in cya-4-23 cells are most likely due to substantially reduced levels of translatable subunit V mRNA.

Inverse regulation of the yeast COX5 genes by oxygen and heme

The COX5a and COX5b genes encode divergent forms of yeast cytochrome c oxidase subunit V. Although the polypeptide products of the two genes are functionally interchangeable, it is the Va subunit that is normally found in preparations of yeast mitochondria and cytochrome c oxidase. We show here that the predominance of subunit Va stems in part from the differential response of the two genes to the presence of molecular oxygen. Our results indicate that during aerobic growth, COX5a levels were high, while COX5b levels were low. Anaerobically, the pattern was reversed; COX5a levels dropped sevenfold, while those of COX5b were elevated sevenfold. Oxygen appeared to act at the level of transcription through heme, since the addition of heme restored an aerobic pattern of transcription to anaerobically grown cells and the effect of anaerobiosis on COX5 transcription was reproduced in strains containing a mutation in the heme-biosynthetic pathway (hem1). In conjunction with the oxygen-heme response, we determined that the product of the ROX1 gene, a trans-acting regulator of several yeast genes controlled by oxygen, is also involved in COX5 expression. These results, as well as our observation that COX5b expression varied significantly in certain yeast strains, indicate that the COX5 genes undergo a complex pattern of regulation. This regulation, especially the increase in COX5b levels anaerobically, may reflect an attempt to modulate the activity of a key respiratory enzyme in response to varying environmental conditions. The results presented here, as well as those from other laboratories, suggest that the induction or derepression of certain metabolic enzymes during anaerobiosis may be a common and important physiological response in yeast cells.

Functional characterization of the two alcohol oxidase genes from the yeast Pichia pastoris

In Pichia pastoris, alcohol oxidase (AOX) is the first enzyme in the methanol utilization pathway and is encoded by two genes, AOX1 and AOX2. The DNA and predicted amino acid sequences of the protein-coding portions of the genes are closely homologous, whereas flanking sequences share no homology. The functional roles of AOX1 and AOX2 in the metabolism of methanol were examined. Studies of strains with disrupted AOX genes revealed that AOX1 was the major source of methanol-oxidizing activity in methanol-grown P. pastoris. The results of two types of experiments each suggested that the difference in AOX activity contributed by the two genes was a consequence of sequences located 5' of the protein-coding portions of the genes. First, the coding portion of AOX2 was able to functionally substitute for that of AOX1 when placed under the control of AOX1 regulatory sequences. Second, when labeled oligonucleotide probes specific for the 5' nontranslated region of each gene were used, it was apparent that the steady-state level of AOX1 mRNA was much higher than that of AOX2. Except for the difference in the amount of mRNA present, the two genes appeared to be regulated in the same manner. A physiological reason for the existence of AOX2 was sought but was not apparent.

Organization and expression of the COX6 genetic locus in Saccharomyces cerevisiae: multiple mRNAs with different 3' termini are transcribed from COX6 and regulated differentially

COX6 and its surrounding genetic locus have been characterized for the yeast Saccharomyces cerevisiae. Flanking genes are found closely spaced upstream and downstream of COX6. The upstream gene and COX6 are transcribed from opposite strands and are separated by no more than 300 bp. COX6 is transcribed into three different size classes of mRNA (1000b, 830b, and 700b) differing in length in their 3' untranslated regions. All three classes of mRNAs are found on polysomes and, hence, are most likely translated. The different COX6 mRNAs vary in abundance during growth in rich media and are affected differentially as cells are shifted into media containing high or low glucose concentrations. The largest mRNA is much more susceptible to glucose repression/derepression than are the two smaller mRNAs, whereas the smallest RNA is preferentially accumulated during growth in rich media. These findings demonstrate that COX6 mRNAs with different 3'-termini are either synthesized differentially or differ in stability and suggest the existence of a complex system regulating COX6 expression.

Cytochrome oxidase subunit V gene of Neurospora crassa: DNA sequences, chromosomal mapping, and evidence that the cya-4 locus specifies the structural gene for subunit V

The sequences of cDNA and genomic DNA clones for Neurospora cytochrome oxidase subunit V show that the protein is synthesized as a 171-amino-acid precursor containing a 27-amino-acid N-terminal extension. The subunit V protein sequence is 34% identical to that of Saccharomyces cerevisiae subunit V; these proteins, as well as the corresponding bovine subunit, subunit IV, contain a single hydrophobic domain which most likely spans the inner mitochondrial membrane. The Neurospora crassa subunit V gene (cox5) contains two introns, 398 and 68 nucleotides long, which share the conserved intron boundaries 5'GTRNGT...CAG3' and the internal consensus sequence ACTRACA. Two short sequences, YGCCAG and YCCGTTY, are repeated four times each in the cox5 gene upstream of the mRNA 5' termini. The cox5 mRNA 5' ends are heterogeneous, with the major mRNA 5' end located 144 to 147 nucleotides upstream from the translational start site. The mRNA contains a 3'-untranslated region of 186 to 187 nucleotides. Using restriction-fragment-length polymorphism, we mapped the cox5 gene to linkage group IIR, close to the arg-5 locus. Since one of the mutations causing cytochrome oxidase deficiency in N. crassa, cya-4-23, also maps there, we transformed the cya-4-23 strain with the wild-type cox5 gene. In contrast to cya-4-23 cells, which grow slowly, cox5 transformants grew quickly, contained cytochrome oxidase, and had 8- to 11-fold-higher levels of subunit V in their mitochondria. These data suggest (i) that the cya-4 locus in N. crassa specifies structural information for cytochrome oxidase subunit V and (ii) that, in N. crassa, as in S. cerevisiae, deficiencies in the production of nuclearly encoded cytochrome oxidase subunits result in deficiency in cytochrome oxidase activity. Finally, we show that the lower levels of subunit V in cya-4-23 cells are most likely due to substantially reduced levels of translatable subunit V mRNA.

Differential regulation of the two genes encoding Saccharomyces cerevisiae cytochrome c oxidase subunit V by heme and the HAP2 and REO1 genes

In Saccharomyces cerevisiae, the COX5a and COX5b genes encode two forms of cytochrome c oxidase subunit V, Va and Vb. We report here that heme increases COX5a expression and decreases COX5b expression and that the HAP2 and REO1 genes are involved in positive regulation of COX5a and negative regulation of COX5b, respectively. Heme regulation of COX5a and COX5b may dictate which subunit V isoform is available for assembly into cytochrome c oxidase under conditions of high- and low-oxygen tension.

Differential regulation of the two genes encoding Saccharomyces cerevisiae cytochrome c oxidase subunit V by heme and the HAP2 and REO1 genes

In Saccharomyces cerevisiae, the COX5a and COX5b genes encode two forms of cytochrome c oxidase subunit V, Va and Vb. We report here that heme increases COX5a expression and decreases COX5b expression and that the HAP2 and REO1 genes are involved in positive regulation of COX5a and negative regulation of COX5b, respectively. Heme regulation of COX5a and COX5b may dictate which subunit V isoform is available for assembly into cytochrome c oxidase under conditions of high- and low-oxygen tension.

Structural analysis of two genes encoding divergent forms of yeast cytochrome c oxidase subunit V

In Saccharomyces cerevisiae, subunit V of the inner mitochondrial membrane protein complex cytochrome c oxidase is encoded by two nonidentical genes, COX5a and COX5b. Both genes are present as single copies in S. cerevisiae and in several other Saccharomyces species. Nucleotide sequencing studies with the S. cerevisiae COX5 genes reveal that they encode proteins of 153 and 151 amino acids, respectively. Overall, the coding sequences of COX5a and COX5b have nucleotide and protein homologies of 67 and 66%, respectively. They are saturated for nucleotide substitutions that result in a synonomous codon, indicating a long divergence time between these two genes. Nucleotide sequences flanking the COX5a and COX5b coding regions exhibit no significant homology. The COX5a protein, pre-subunit Va, contains a 20-amino-acid leader peptide, whereas the COX5b protein, pre-subunit Vb, contains a 17-amino-acid leader peptide. These two leader peptides exhibit only 45% homology in the primary sequence, but have similar predicted secondary structures. By analyzing the RNA transcripts from both genes we have found that COX5a is a contiguous gene but that COX5b contains an intron. Surprisingly, the COX5b intron interrupts the AUG codon that initiates translation of the pre-subunit Vb polypeptide and contains a 5' donor splice sequence that differs from that normally found in yeast introns.

Structural analysis of two genes encoding divergent forms of yeast cytochrome c oxidase subunit V

In Saccharomyces cerevisiae, subunit V of the inner mitochondrial membrane protein complex cytochrome c oxidase is encoded by two nonidentical genes, COX5a and COX5b. Both genes are present as single copies in S. cerevisiae and in several other Saccharomyces species. Nucleotide sequencing studies with the S. cerevisiae COX5 genes reveal that they encode proteins of 153 and 151 amino acids, respectively. Overall, the coding sequences of COX5a and COX5b have nucleotide and protein homologies of 67 and 66%, respectively. They are saturated for nucleotide substitutions that result in a synonomous codon, indicating a long divergence time between these two genes. Nucleotide sequences flanking the COX5a and COX5b coding regions exhibit no significant homology. The COX5a protein, pre-subunit Va, contains a 20-amino-acid leader peptide, whereas the COX5b protein, pre-subunit Vb, contains a 17-amino-acid leader peptide. These two leader peptides exhibit only 45% homology in the primary sequence, but have similar predicted secondary structures. By analyzing the RNA transcripts from both genes we have found that COX5a is a contiguous gene but that COX5b contains an intron. Surprisingly, the COX5b intron interrupts the AUG codon that initiates translation of the pre-subunit Vb polypeptide and contains a 5' donor splice sequence that differs from that normally found in yeast introns.