Saccharomyces cerevisiae contains an RNase MRP that cleaves at a conserved mitochondrial RNA sequence implicated in replication priming

Cytosolic Ribosomal Protein Haploinsufficiency affects Mitochondrial Morphology and Respiration

The interplay between ribosomal protein composition and mitochondrial function is essential for sustaining energy homeostasis. Precise stoichiometric production of ribosomal proteins is crucial to maximize protein synthesis efficiency while reducing the energy costs to the cell. However, the impact of this balance on mitochondrial ATP generation, morphology and function remains unclear. Particularly, the loss of a single copy ribosomal protein gene is observed in Mendelian disorders like Diamond Blackfan Anemia and is common in somatic tumors, yet the implications of this imbalance on mitochondrial function and energy dynamics are still unclear. In this study, we investigated the impact of haploinsufficiency for four ribosomal protein genes implicated in ribosomopathy disorders (rps-10, rpl-5, rpl-33, rps-23) in Caenorhabditis elegans and corresponding reductions in human lymphoblast cells. Our findings uncover significant, albeit variably penetrant, mitochondrial morphological differences across these mutants, alongside an upregulation of glutathione transferases, and SKN-1 dependent increase in oxidative stress resistance, indicative of increased ROS production. Specifically, loss of a single copy of rps-10 in C. elegans led to decreased mitochondrial activity, characterized by lower energy levels and reduced oxygen consumption. A similar reduction in mitochondrial activity and energy levels was observed in human leukemia cells with a 50% reduction in RPS10 transcript levels. Importantly, we also observed alterations in the translation efficiency of nuclear and mitochondrial electron transport chain components in response to reductions in ribosomal protein genes' expression in both C. elegans and human cells. This suggests a conserved mechanism whereby the synthesis of components vital for mitochondrial function are adjusted in the face of compromised ribosomal machinery. Finally, mitochondrial membrane and cytosolic ribosomal components exhibited significant covariation at the RNA and translation efficiency level in lymphoblastoid cells across a diverse group of individuals, emphasizing the interplay between the protein synthesis machinery and mitochondrial energy production. By uncovering the impact of ribosomal protein haploinsufficiency on the translation efficiency of electron transport chain components, mitochondrial physiology, and the adaptive stress responses, we provide evidence for an evolutionarily conserved strategy to safeguard cellular functionality under genetic stress.

Identification of host RNAs that interact with EBV noncoding RNA EBER2

Epstein-Barr virus (EBV) expresses an abundant nuclear noncoding RNA called EBER2, which interacts with and acts as a guide RNA for the host transcription factor PAX5. This ribonucleoprotein complex localizes to the terminal repeat (TR) regions of the EBV genome via RNA-RNA interactions between EBER2 and nascent transcripts originating from these target sites. Given the fact that EBER2 base pairs with a viral RNA, we developed a protocol to identify EBER2-interacting RNAs in a transcriptome-wide manner. Our approach entails psoralen-mediated crosslinking, selection with antisense oligonucleotides targeting EBER2, and RNase V1 digestion coupled to next-generation sequencing. The use of RNase V1 circumvents the need of extensive computational analysis post data acquisition to search for predicted RNA hybrids, as the RNase V1 cleavage site marks the region of RNA duplex formation. As proof of principle, we show that our approach correctly identifies the known EBER2 interaction with TR RNAs. Moreover, we identify the host functional noncoding RNAs MRP, H1, and 7SL RNAs as well as three putative enhancer RNAs as candidate EBER2-interacting RNAs. As all of these gene loci exhibit PAX5 occupancy, we propose that EBER2 is recruited to these sites through its binding partner PAX5 and forms RNA-RNA interactions with nascent transcripts on chromatin. Thus, our novel approach facilitates the identification of targeted RNA-RNA-interactions and minimizes the need of downstream computational analyses to predict RNA duplexes.

Of Wnts and Ribosomes

Wnt proteins are secreted glycoproteins that activate different intracellular signal transduction pathways. They regulate cell proliferation and are required for proper embryonic development. Misregulation of Wnt signaling can result in various diseases including cancer. In most circumstances, cell growth is essential for cell division and thus cell proliferation. Therefore, several reports have highlighted the key role of Wnt proteins for cell growth. Ribosomes represent the cellular protein synthesis machinery and cells need to be equipped with an appropriate number of ribosomes to allow cell growth. Recent findings suggest a role for Wnt proteins in regulating ribosome biogenesis and we here summarize these findings representing a previously unknown function of Wnt proteins. Understanding this role of Wnt signaling might open new avenues to slow down proliferation by drugs for instance in cancer therapy.

RNase MRP cleaves pre-tRNASer-Met in the tRNA maturation pathway

Ribonuclease mitochondrial RNA processing (RNase MRP) is a multifunctional ribonucleoprotein (RNP) complex that is involved in the maturation of various types of RNA including ribosomal RNA. RNase MRP consists of a potential catalytic RNA and several protein components, all of which are required for cell viability. We show here that the temperature-sensitive mutant of rmp1, the gene for a unique protein component of RNase MRP, accumulates the dimeric tRNA precursor, pre-tRNA^Ser-Met. To examine whether RNase MRP mediates tRNA maturation, we purified the RNase MRP holoenzyme from the fission yeast Schizosaccharomyces pombe and found that the enzyme directly and selectively cleaves pre-tRNA^Ser-Met, suggesting that RNase MRP participates in the maturation of specific tRNA in vivo. In addition, mass spectrometry–based ribonucleoproteomic analysis demonstrated that this RNase MRP consists of one RNA molecule and 11 protein components, including a previously unknown component Rpl701. Notably, limited nucleolysis of RNase MRP generated an active catalytic core consisting of partial mrp1 RNA fragments, which constitute “Domain 1” in the secondary structure of RNase MRP, and 8 proteins. Thus, the present study provides new insight into the structure and function of RNase MRP.

Ribonucleases P/MRP and the expanding ribonucleoprotein world

One of the hallmarks of life is the widespread use of certain essential ribozymes. The ubiquitous ribonuclease P (RNase P) and eukaryotic RNase MRP are essential complexes where a structured, noncoding RNA acts in catalysis. Recent discoveries have elucidated the three-dimensional structure of the ancestral ribonucleoprotein complex, suggested the possibility of a protein-only composition in organelles, and even noted the absence of RNase P in a non-free-living organism. With respect to these last two findings, import mechanisms for RNases P/MRP into mitochondria have been demonstrated, and RNase P is present in organisms with some of the smallest known genomes. Together, these results have led to an ongoing debate regarding the precise definition of how "essential" these ribozymes truly are.

Of proteins and RNA: the RNase P/MRP family

Nuclear ribonuclease (RNase) P is a ubiquitous essential ribonucleoprotein complex, one of only two known RNA-based enzymes found in all three domains of life. The RNA component is the catalytic moiety of RNases P across all phylogenetic domains; it contains a well-conserved core, whereas peripheral structural elements are diverse. RNA components of eukaryotic RNases P tend to be less complex than their bacterial counterparts, a simplification that is accompanied by a dramatic reduction of their catalytic ability in the absence of protein. The size and complexity of the protein moieties increase dramatically from bacterial to archaeal to eukaryotic enzymes, apparently reflecting the delegation of some structural functions from RNA to proteins and, perhaps, in response to the increased complexity of the cellular environment in the more evolutionarily advanced organisms; the reasons for the increased dependence on proteins are not clear. We review current information on RNase P and the closely related universal eukaryotic enzyme RNase MRP, focusing on their functions and structural organization.

Comparison of mitochondrial and nucleolar RNase MRP reveals identical RNA components with distinct enzymatic activities and protein components

RNase MRP is a ribonucleoprotein endoribonuclease found in three cellular locations where distinct substrates are processed: the mitochondria, the nucleolus, and the cytoplasm. Cytoplasmic RNase MRP is the nucleolar enzyme that is transiently relocalized during mitosis. Nucleolar RNase MRP (NuMRP) was purified to homogeneity, and we extensively purified the mitochondrial RNase MRP (MtMRP) to a single RNA component identical to the NuMRP RNA. Although the protein components of the NuMRP were identified by mass spectrometry successfully, none of the known NuMRP proteins were found in the MtMRP preparation. Only trace amounts of the core NuMRP protein, Pop4, were detected in MtMRP by Western blot. In vitro activity of the two enzymes was compared. MtMRP cleaved only mitochondrial ORI5 substrate, while NuMRP cleaved all three substrates. However, the NuMRP enzyme cleaved the ORI5 substrate at sites different than the MtMRP enzyme. In addition, enzymatic differences in preferred ionic strength confirm these enzymes as distinct entities. Magnesium was found to be essential to both enzymes. We tested a number of reported inhibitors including puromycin, pentamidine, lithium, and pAp. Puromycin inhibition suggested that it binds directly to the MRP RNA, reaffirming the role of the RNA component in catalysis. In conclusion, our study confirms that the NuMRP and MtMRP enzymes are distinct entities with differing activities and protein components but a common RNA subunit, suggesting that the RNA must be playing a crucial role in catalytic activity.

In vitro analysis of the yeast mitochondrial RNA polymerase

Understanding the details of how genetic information is expressed from the separate mitochondrial genome requires a detailed description of the properties of the mitochondrial RNA polymerase. This nuclear-encoded enzyme is necessary and sufficient for the transcription of all mitochondrially encoded genes. Mitochondria from yeast to humans use a single-polypeptide catalytic RNA polymerase related to enzymes from bacteriophage. They also require separable transcription factors necessary for initiation at promoter sequences on the mitochondrial DNA template. It has recently become possible to work with highly purified, recombinant forms of the mitochondrial RNA polymerase subunits from yeast. This chapter describes detailed protocols for working in vitro with this purified enzyme in transcription reactions. These assays are critical for elucidating the nature of a mitochondrial promoter and for understanding how the mitochondrial RNA polymerase recognizes these DNA sequences and selectively initiates the transcription cycle, resulting in discrete transcripts.

RNA-modifying machines in archaea

It has been known for nearly half a century that coding and non-coding RNAs (mRNA, and tRNAs and rRNAs respectively) play critical roles in the process of information transfer from DNA to protein. What is both surprising and exciting, are the discoveries in the last decade that cells, particularly eukaryotic cells, contain a plethora of non-coding RNAs and that these RNAs can either possess catalytic activity or can function as integral components of dynamic ribonucleoprotein machines. These machines appear to mediate diverse, complex and essential processes such as intron excision, RNA modification and editing, protein targeting, DNA packaging, etc. Archaea have been shown to possess RNP complexes; some of these are authentic homologues of the eukaryotic complexes that function as machines in the processing, modification and assembly of rRNA into ribosomal subunits. Deciphering how these RNA-containing machines function will require a dissection and analysis of the component parts, an understanding of how the parts fit together and an ability to reassemble the parts into complexes that can function in vitro. This article summarizes our current knowledge about small-non-coding RNAs in Archaea, their roles in ribosome biogenesis and their relationships to the complexes that have been identified in eukaryotic cells.

New features of mitochondrial DNA replication system in yeast and man

In this review, we sum up the research carried out over two decades on mitochondrial DNA (mtDNA) replication, primarily by comparing this system in Saccharomyces cerevisiae and Homo sapiens. Brief incursions into systems of other organisms have also been achieved when they provide new information.S. cerevisiae and H. sapiens mitochondrial DNA (mtDNA) have been thought for a long time to share closely related architecture and replication mechanisms. However, recent studies suggest that mitochondrial genome of S. cerevisiae may be formed, at least partially, from linear multimeric molecules, while human mtDNA is circular. Although several proteins involved in the replication of these two genomes are very similar, divergences are also now increasingly evident. As an example, the recently cloned human mitochondrial DNA polymerase beta-subunit has no counterpart in yeast. Yet, yeast Abf2p and human mtTFA are probably not as closely functionally related as thought previously. Some mtDNA metabolism factors, like DNA ligases, were until recently largely uncharacterized, and have been found to be derived from alternative nuclear products. Many factors involved in the metabolism of mitochondrial DNA are linked through genetic or biochemical interconnections. These links are presented on a map. Finally, we discuss recent studies suggesting that the yeast mtDNA replication system diverges from that observed in man, and may involve recombination, possibly coupled to alternative replication mechanisms like rolling circle replication.

Expression of mitochondrial protein-coding genes in Tetrahymena pyriformis

In the ciliate protozoon, Tetrahymena pyriformis, mitochondrial protein-coding genes are highly divergent in sequence, and in a number of cases they lack AUG initiation codons. We asked whether RNA editing might be acting to generate protein sequences that are more conventional than those inferred from the corresponding gene sequences, and/or to create standard AUG initiation codons where these are absent. However, comparison of genomic and cDNA sequences (the latter generated by reverse transcriptase sequencing of T. pyriformis mitochondrial mRNAs) yielded no evidence of mitochondrial RNA editing in this organism. To delineate the 5' ends of mitochondrial protein-coding transcripts, primer extension experiments were conducted. In all cases, 5' termini were found to map within a few nucleotides of potential initiation codons, indicating that T. pyriformis mitochondrial mRNAs have little or no 5' untranslated leader sequence. The pattern of strong primer extension stops suggested that both standard (AUG) and non-standard (AUU, AUA, GUG, UUG) initiation codons are utilized by the Tetrahymena mitochondrial translation system. We also investigated expression of the nad1 gene, which in both T. pyriformis and Paramecium aurelia is split into two portions that are encoded by and transcribed from different DNA strands. Northern hybridization analysis showed that the corresponding transcripts are not trans-spliced, implying that separate N-terminal and C-terminal portions of Nad1 are made in this system. Finally, in a search for primary transcripts, we isolated from a T. pyriformis mitochondrial fraction several small RNAs that were reproducibly labeled by incubation in the presence of [alpha-(32)P]GTP and guanylyltransferase. Partial sequence information revealed that none of these cappable RNAs is encoded in the T. pyriformis mitochondrial genome.

The maize mitochondrial cox2 gene has five promoters in two genomic regions, including a complex promoter consisting of seven overlapping units

Plant mitochondrial genes are often transcribed into complex sets of RNAs, resulting from multiple initiation sites and processing steps. To elucidate the role of initiation in generating the more than 10 cox2 transcripts found in maize mitochondria, we surveyed sequences upstream of cox2 for active promoters. Because the cox2 coding region is immediately downstream of a 0.7-kb recombination repeat, cox2 is under the control of two different sets of potential expression signals. Using an in vitro transcription assay, we localized four promoters upstream of the coding region in the so-called master chromosome, and two promoters upstream of the coding region in the recombinant subgenome. Ribonuclease protection analysis of labeled primary transcripts confirmed that all but one of these promoters is active in vivo. Primer extension was used to identify the promoter sequences and initiation sites, which agree with the consensus established earlier for maize mitochondria. This study identified two unusual promoters, the core sequences of which were composed entirely of adenines and thymines, and one of which was a complex promoter consisting of seven overlapping units. Deletion mutagenesis of the complex promoter suggested that each of its units was recognized independently by RNA polymerase. While each active promoter fit the maize core consensus sequence YRTAT, not all such sequences surveyed supported initiation. We conclude that in vitro transcription is a powerful tool for locating mitochondrial promoters and that, in the case of cox2, promoter multiplicity contributes strongly to transcript complexity.

Towards a new concept of gene inactivation: specific RNA cleavage by endogenous ribonuclease P

In the first part of this chapter, general concepts for gene inactivation, antisense techniques and catalytic RNAs (ribozymes) are presented. The requirements for modified oligonucleotides are discussed with their effects on the stability of base-paired hybrids and on resistance against nuclease attack. This also includes the problems in the choice of an optimal target sequence within the inactivated RNA and the options of cellular delivery systems. The second part describes the recently introduced antisense concept based on the ubiquitous cellular enzyme ribonuclease P. This system is unique, since the substrate recognition requires the proper tertiary structure of the cleaved RNA. General properties and possible advantages of this approach are discussed.

RNA-DNA hybrid formation at the human mitochondrial heavy-strand origin ceases at replication start sites: an implication for RNA-DNA hybrids serving as primers

Critical elements of a mammalian mitochondrial DNA heavy-strand replication origin include a promoter and three downstream conserved sequence blocks (CSBIII, CSBII and CSBI). We found recently that a stable and persistent RNA-DNA hybrid forms during in vitro transcription at Saccharomyces cerevisiae mitochondrial origins; hybrid formation was dependent on the conserved CSBII element. We report here that during in vitro transcription with human mitochondrial RNA polymerase, stable and persistent RNA-DNA hybrid formation is also evident at the human mitochondrial heavy-strand origin. As predicted, hybrid formation was dependent on the GC-rich CSBII element. The human RNA-DNA hybrids terminate within or downstream of CSBI at locations implicated in initiation of mitochondrial DNA replication. Interestingly, efficient hybrid formation in the human system is influenced by sequence 5' to the RNA-DNA hybrid, including the CSBIII element. These results suggest that the RNA-DNA hybrids formed during transcription across the mitochondrial DNA heavy-strand origin provide RNA primers for initiation of mitochondrial DNA replication.

The yeast, Saccharomyces cerevisiae, RNase P/MRP ribonucleoprotein endoribonuclease family

Ribonuclease P (RNase P) is a ribonucleoprotein responsible for the endonucleolytic cleavage of the 5'-termini of tRNAs. Ribonuclease MRP (RNase MRP) is a ribonucleoprotein that has the ability to cleave both mitochondrial RNA primers presumed to be involved in mitochondrial DNA replication and rRNA precursors for the production of mature rRNAs. Several lines of evidence suggest that these two ribonucleoproteins are related to each other, both functionally and evolutionarily. Both of these enzymes have activity in the nucleus and mitochondria. Each cleave their RNA substrates in a divalent cation dependent manner to generate 5'-phosphate and 3'-OH termini. In addition, the RNA subunits of both complexes can be folded into a similar secondary structure. Each can be immunoprecipitated from mammalian cells with Th antibodies. In yeast, both have been found to share at least one common protein. This review will discuss some of the recent advances in our understanding of the structure, function and evolutionary relationship of these two enzymes in the yeast, Saccharomyces cerevisiae.

Processing of pre-ribosomal RNA in Saccharomyces cerevisiae

Post-transcriptional processing of precursor-ribosomal RNA comprises a complex pathway of endonucleolytic cleavages, exonucleolytic digestion and covalent modifications. The general order of the various processing steps is well conserved in eukaryotic cells, but the underlying mechanisms are largely unknown. Recent analysis of pre-rRNA processing, mainly in the yeast Saccharomyces cerevisiae, has significantly improved our understanding of this important cellular activity. Here we will review the data that have led to our current picture of yeast pre-rRNA processing.

Schizosaccharomyces pombe RNase MRP RNA is homologous to metazoan RNase MRP RNAs and may provide clues to interrelationships between RNase MRP and RNase P

RNase MRP and RNase P ribonucleoproteins are structurally and functionally similar across a large evolutionary distance. To better characterize possible complex interrelationships between these two enzymes, we have employed the fission yeast Schizosaccharomyces pombe. Unlike Saccharomyces cerevisiae, S. pombe is believed to harbour only one genetic locus for the RNA component of RNase P and does not contain a known mitochondrially encoded RNase P RNA. We have identified the single nuclear gene for the RNA component of RNase MRP in S. pombe, mrp-1, by homology to vertebrate RNase MRP RNAs. The mrp-1 gene encodes an RNA of maximum mature length 400 nucleotides that shares a high degree of identity, in evolutionarily conserved regions, to both vertebrate RNase MRP RNAs and S. pombe RNase P RNA. Disruption of mrp-1 in the diploid strain SP826 and sporulation of tetrads resulted in a 2 dead:2 viable segregation, consistent with the gene being essential. Lethality is rescued by a plasmid-borne copy of mrp-1. Partially purified ribonucleoprotein RNase MRP activity correctly and efficiently processed all previously characterized heterologous mitochondrial RNA substrates. The compact mitochondrial genome of S. pombe contains sequence elements with > 50% identity to mammalian D-loop CSBI and CSBII elements. The identification of mrp-1 in S. pombe should facilitate not only comparisons between the related ribonucleoproteins RNase MRP and RNase P, but should also provide an opportunity for genetic elucidation of RNase MRP function in a situation reflective of the animal kingdom.

RNase mitochondrial RNA processing cleaves RNA from the rat mitochondrial displacement loop at the origin of heavy-strand DNA replication

Ribonuclease mitochondrial RNA processing cleaves RNAs from the mammalian mitochondrial main non-coding regulatory region, called the displacement loop. Our data demonstrate that rat cells contain a site-specific ribonuclease mitochondrial RNA processing activity. We found that this enzyme processes the rat mitochondrial displacement-loop RNA substrate at the level of the conserved sequence block 1, a result which is different from that for mouse. This finding correlates with the in-vivo transcriptional analysis of the rat displacement-loop region. Processing by homologous and heterologous ribonuclease mitochondrial RNA enzymes occurs in the same manner, suggesting a conserved mode of substrate recognition.

Characterization of a unique protein component of yeast RNase MRP: an RNA-binding protein with a zinc-cluster domain

RNase MRP is a ribonucleoprotein endoribonuclease that has been shown to cleave mitochondrial primer RNA sequences from a variety of sources. Most of the RNase MRP activity is found in the nucleus where it plays a role in the processing of 5.8S rRNA. A temperature-conditional point mutation in the yeast RNA component of the enzyme has been identified. This mutation results in a loss of normal rRNA processing at the nonpermissive temperature while cellular levels of the RNA component of RNase MRP remain stable. High-copy suppressor analysis of this point mutation was employed to identify interacting proteins. A unique suppressor, termed SNM1 (suppressor of nuclear mitochondrial endoribonuclease 1), was identified repeatedly. The SNM1 gene was localized to the right arm of chromosome IV, directly adjacent to the SNF1 gene, and it contains an open reading frame encoding a protein of 198 amino acids. The protein contains a leucine zipper motif, a zinc-cluster motif, and a serine/lysine-rich tail. The gene was found to be essential for viability in a yeast cell, consistent with it being a protein component of the RNase MRP ribonucleoprotein complex. Recombinant SNM1 protein binds RNA in both gel retardation and Northwestern assays. Antibodies raised against bacterially expressed proteins identified four separate species in yeast whole cell extracts. Antibodies directed against the SNM1 protein immunoprecipitated RNase MRP RNA from whole-cell extracts without precipitating the structurally and functionally related RNase P RNA. We propose that the SNM1 protein is an essential and specific component of the RNase MRP ribonucleoprotein complex, the first unique protein of this complex to be identified.

Conserved features of yeast and mammalian mitochondrial DNA replication

Mammalian mitochondrial DNA replication is initiated by the processing of RNA transcripts derived from an upstream promoter to create RNA primers for DNA replication. In the yeast Saccharomyces cerevisiae, mitochondrial ori/rep sequences contain a transcription promoter upstream of the site of transition from RNA to DNA synthesis, suggesting a common mode of replication initiation. Recent research has identified features in the mode and machinery of DNA replication conserved from yeast to mammals.

RNase MRP/RNase P: a structure-function relation conserved in evolution?

RNase P and RNase MRP are related ribonucleoproteins. RNase MRP processes mitochondrial precursor- (primer) RNAs, whereas RNase P cleaves precursor-tRNAs to produce their mature 5'-ends. Both RNase P and RNase MRP are associated with the Th/To ribonucleoprotein suggesting possible interrelated pathways and/or functions. All known RNase P and RNase MRP RNAs contain conserved structural elements possibly involved in catalysis/substrate binding, but these elements do not predict all cellular functions of the RNPs.

Transcription and replication of animal mitochondrial DNAs

The development of in vitro transcription and replication systems has allowed the identification of promoter sequences and origins of replication for several animal mtDNAs. As a consequence, the necessary reagents and basic information are available to permit the characterization of transacting factors that are required for transcription and replication. All of the animal trans-acting species purified at this time are known or reasoned to be nuclear gene products. There is now the opportunity to learn how these nuclear genes are regulated and the mechanisms that are utilized for the import of their products into the organelle. With regard to import, the human transcription factor mtTF1 appears to have an amino-terminal sequence characteristic of other imported mitochondrial proteins (Parisi and Clayton, 1991). An interesting issue is the degree to which fundamental features of mtDNA replication and transcription are conserved between species. With regard to animal mtDNAs, there is very little in the way of conservation of DNA sequence at the promoters and origins of replication. The exceptions to this are the presence of a characteristic stem-loop L-strand origin of replication sequence in vertebrates [except for chicken mtDNA (Desjardins and Morais, 1990)] and the general presence of CSBs II and III (and to a lesser extent CSB I) in most higher animal mtDNAs. Because mtDNA promoters are not highly conserved, it is perhaps not surprising that general cross-species transcription does not occur, except for very limited examples of closely related species and sequences (Chang et al., 1985b). Using crude mtRNA polymerase holoenzyme preparations, there is no specific transcriptional initiation when proteins from human mitochondria are used with mouse mtDNA promoter templates, and vice versa. However, in contrast to this overall observation, purified fractions of human or mouse mtTF1 can be exchanged and shown to function across species boundaries (Fisher et al., 1989). The ability of mitochondrial mtTF1-type proteins to operate across even greater evolutionary distances was suggested by the ability of human and yeast proteins to recognize some mitochondrial promoter sequences in common (Fisher et al., 1992). More recent studies suggest that human mtTF1 can substitute for its yeast homolog in vivo, and thereby perform at least the most critical functions required to maintain yeast mtDNA in the cell (M.A. Parisi, B. Xu, and D.A. Clayton, submitted for publication). The other sites of conserved macromolecular interactions are related to the two origins of DNA replication.(ABSTRACT TRUNCATED AT 400 WORDS)