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Trm1 is a tRNA specific m(2)(2)G methyltransferase shared by nuclei and mitochondria in Saccharomyces cerevisiae. In nuclei, Trm1 is peripherally associated with the inner nuclear membrane (INM). We investigated the mechanism delivering/tethering Trm1 to the INM. Analyses of mutations of the Ran pathway and nuclear pore components showed that Trm1 accesses the nucleoplasm via the classical nuclear import pathway. We identified a Trm1 cis-acting sequence sufficient to target passenger proteins to the INM. Detailed mutagenesis of this region uncovered specific amino acids necessary for authentic Trm1 to locate at the INM. The INM information is contained within a sequence of less than 20 amino acids, defining the first motif for addressing a peripheral protein to this important subnuclear location. The combined studies provide a multi-step process to direct Trm1 to the INM: (i) translation in the cytoplasm; (ii) Ran-dependent import into the nucleoplasm; and (iii) redistribution from the nucleoplasm to the INM via the INM motif. Furthermore, we demonstrate that the Trm1 mitochondrial targeting and nuclear localization signals are in competition with each other, as Trm1 becomes mitochondrial if prevented from entering the nucleus.

The integrated stress response (ISR) controls cellular adaptations to nutrient deprivation, redox imbalances, and endoplasmic reticulum (ER) stress. ISR genes are upregulated in stressed cells, primarily by the bZIP transcription factor ATF4 through its recruitment to cis-regulatory C/EBP:ATF response elements (CAREs) together with a dimeric partner of uncertain identity. Here, we show that C/EBPγ:ATF4 heterodimers, but not C/EBPβ:ATF4 dimers, are the predominant CARE-binding species in stressed cells. C/EBPγ and ATF4 associate with genomic CAREs in a mutually dependent manner and coregulate many ISR genes. In contrast, the C/EBP family members C/EBPβ and C/EBP homologous protein (CHOP) were largely dispensable for induction of stress genes. Cebpg(-/-) mouse embryonic fibroblasts (MEFs) proliferate poorly and exhibit oxidative stress due to reduced glutathione levels and impaired expression of several glutathione biosynthesis pathway genes. Cebpg(-/-) mice (C57BL/6 background) display reduced body size and microphthalmia, similar to ATF4-null animals. In addition, C/EBPγ-deficient newborns die from atelectasis and respiratory failure, which can be mitigated by in utero exposure to the antioxidant, N-acetyl-cysteine. Cebpg(-/-) mice on a mixed strain background showed improved viability but, upon aging, developed significantly fewer malignant solid tumors than WT animals. Our findings identify C/EBPγ as a novel antioxidant regulator and an obligatory ATF4 partner that controls redox homeostasis in normal and cancerous cells.

The RNA subunit of mitochondrial RNase P (mtP-RNA) is encoded by a mitochondrial gene (rnpB) in several ascomycete fungi and in the protists Reclinomonas americana and Nephroselmis olivacea. By searching for universally conserved structural elements, we have identified previously unknown rnpB genes in the mitochondrial DNAs (mtDNAs) of two fission yeasts, Schizosaccharomyces pombe and Schizosaccharomyces octosporus; in the budding yeast Pichia canadensis; and in the archiascomycete Taphrina deformans. The expression of mtP-RNAs of the predicted size was experimentally confirmed in the two fission yeasts, and their precise 5′ and 3′ ends were determined by sequencing of cDNAs generated from circularized mtP-RNAs. Comparative RNA secondary structure modeling shows that in contrast to mtP-RNAs of the two protists R. americana and N. olivacea, those of ascomycete fungi all have highly reduced secondary structures. In certain budding yeasts, such as Saccharomycopsis fibuligera, we find only the two most conserved pairings, P1 and P4. A P18 pairing is conserved in Saccharomyces cerevisiae and its close relatives, whereas nearly half of the minimum bacterial consensus structure is retained in the RNAs of fission yeasts, Aspergillus nidulans and Taphrina deformans. The evolutionary implications of the reduction of mtP-RNA structures in ascomycetes will be discussed.

Mitochondria and chloroplasts contain their own systems for the biosynthesis of proteins coded by the organelle genome. It had generally been thought that tRNAs participating in organelle protein synthesis were coded by the organelle genome. This genetic diversity of tRNAs makes the subject of organelle tRNA biosynthesis more complex than it would be if all tRNAs were made in the organelle. tRNA genes in organelle DNAs are scattered around the genome and intermixed with mRNA and rRNA genes. tRNAs are transcribed with rRNAs and mRNAs. In mammalian mitochondria, the entire genome is transcribed and, subsequently, the tRNAs are processed out of the large primary transcript. This review focuses on the organelle tRNAs that are coded by mitochondrial or chloroplast DNA and on the structure of precursor tRNAs and the enzymes necessary for their processing. In addition, it considers organelle aminoacyl-tRNA synthetases as well as mutant organelle tRNAs.

RPM2 is a Saccharomyces cerevisiae nuclear gene that encodes the protein subunit of mitochondrial RNase P and has an unknown function essential for fermentative growth. Cells lacking mitochondrial RNase P cannot respire and accumulate lesions in their mitochondrial DNA. The effects of a new RPM2 allele, rpm2-100, reveal a novel function of RPM2 in mitochondrial biogenesis. Cells with rpm2-100 as their only source of Rpm2p have correctly processed mitochondrial tRNAs but are still respiratory deficient. Mitochondrial mRNA and rRNA levels are reduced in rpm2-100 cells compared to wild type. The general reduction in mRNA is not reflected in a similar reduction in mitochondrial protein synthesis. Incorporation of labeled precursors into mitochondrially encoded Atp6, Atp8, Atp9, and Cytb protein was enhanced in the mutant relative to wild type, while incorporation into Cox1p, Cox2p, Cox3p, and Var1p was reduced. Pulse-chase analysis of mitochondrial translation revealed decreased rates of translation of COX1, COX2, and COX3 mRNAs. This decrease leads to low steady-state levels of Cox1p, Cox2p, and Cox3p, loss of visible spectra of aa3 cytochromes, and low cytochrome c oxidase activity in mutant mitochondria. Thus, RPM2 has a previously unrecognized role in mitochondrial biogenesis, in addition to its role as a subunit of mitochondrial RNase P. Moreover, there is a synthetic lethal interaction between the disruption of this novel respiratory function and the loss of wild-type mtDNA. This synthetic interaction explains why a complete deletion of RPM2 is lethal.

The Saccharomyces cerevisiae nuclear gene RPM2 encodes a component of the mitochondrial tRNA-processing enzyme RNase P. Cells grown on fermentable carbon sources do not require mitochondrial tRNA processing activity, but still require RPM2, indicating an additional function for the Rpm2 protein. RPM2-null cells arrest after 25 generations on fermentable media. Spontaneous mutations that suppress arrest occur with a frequency of ~9 × 10−6. The resultant mutants do not grow on nonfermentable carbon sources. We identified two loci responsible for this suppression, which encode proteins that influence proteasome function or assembly. PRE4 is an essential gene encoding the β-7 subunit of the 20S proteasome core. A Val-to-Phe substitution within a highly conserved region of Pre4p that disrupts proteasome function suppresses the growth arrest of RPM2-null cells on fermentable media. The other locus, UMP1, encodes a chaperone involved in 20S proteasome assembly. A nonsense mutation in UMP1 also disrupts proteasome function and suppresses Δrpm2 growth arrest. In an RPM2 wild-type background, pre4-2 and ump1-2 strains fail to grow at restrictive temperatures on nonfermentable carbon sources. These data link proteasome activity with Rpm2p and mitochondrial function.

Sorting isozymes are encoded by single genes, but the encoded proteins are distributed to multiple subcellular compartments. We surveyed the predicted protein sequences of several nucleic acid interacting sorting isozymes from the eukaryotic taxonomic domain and compared them with their homologs in the archaeal and eubacterial domains. Here, we summarize the data showing that the eukaryotic sorting isozymes often possess sequences not present in the archaeal and eubacterial counterparts and that the additional sequences can act to target the eukaryotic proteins to their appropriate subcellular locations. Therefore, we have named these protein domains ADEPTs (Additional Domains for Eukaryotic Protein Targeting). Identification of additional domains by phylogenetic comparisons should be generally useful for locating candidate sequences important for subcellular distribution of eukaryotic proteins.

WIP, the Wiskott-Aldrich syndrome protein-interacting protein, is a human protein involved in actin polymerization and redistribution in lymphoid cells. The mechanism by which WIP reorganizes actin cytoskeleton is unknown. WIP is similar to yeast verprolin, an actin- and myosin-interacting protein required for polarized morphogenesis. To determine whether WIP and verprolin are functional homologues, we analyzed the function of WIP in yeast. WIP suppresses the growth defects of VRP1 missense and null mutations as well as the defects in cytoskeletal organization and endocytosis observed in vrp1-1 cells. The ability of WIP to replace verprolin is dependent on its WH2 actin binding domain and a putative profilin binding domain. Immunofluorescence localization of WIP in yeast cells reveals a pattern consistent with its function at the cortical sites of growth. Thus, like verprolin, WIP functions in yeast to link the polarity development pathway and the actin cytoskeleton to generate cytoskeletal asymmetry. A role for WIP in cell polarity provides a framework for unifying, under a common paradigm, distinct molecular defects associated with immunodeficiencies like Wiskott-Aldrich syndrome.

MOD5 encodes a tRNA modification activity located in three subcellular compartments. Alternative translation initiation generates Mod5p-I, located in the mitochondria and the cytosol, and Mod5p-II, located in the cytosol and nucleus. Here we study the nucleus/cytosol distribution of overexpressed Mod5p-II. Nuclear Mod5p-II appears concentrated in the nucleolus, perhaps indicating that the nuclear pool may have a different biological role than the cytoplasmic and mitochondrial pools. Mod5p contains three motifs resembling bipartite-like nuclear localization sequences (NLSs), but only one is sufficient to locate a passenger protein to the nucleus. Mutations of basic residues of this motif cumulatively contribute to a cytosolic location for the fusion proteins. These alterations also cause decreased nuclear pools of endogenous Mod5p-II. Depletion of nuclear Mod5p-II does not affect tRNATyr function. Despite the NLS, most Mod5p is cytosolic. We assessed whether Mod5p sequences cause a karyophilic reporter to be located in the cytosol. By this assay, Mod5p may contain more than one region that functions as cytoplasmic retention and/or nuclear export sequences. Thus, distribution of Mod5p results from the presence/absence of mitochondrial targeting information and sequences antagonistic for nuclear and cytosolic locations. Mod5p is highly conserved; sequences responsible for subcellular distribution appear to reside in “accessory” motifs missing from prokaryotic counterparts.

This article present the collaborative process for conducting research among a state home care foundation, its associated membership, and a university. Research collaboration allowed the merging of talents and resources from persons, home care agencies, and a university. The history and development of the project, sampling procedure, and data collection and analysis are discussed. The project increased the appreciation for research, allowed an opportunity for scholarly exchange, and accented the positive use of resources in all settings.

RPM2 is a Saccharomyces cerevisiae nuclear gene required for normal cell growth yet the only known function of Rpm2p is as a protein subunit of yeast mitochondrial RNase P, an enzyme responsible for the 5′ maturation of mitochondrial tRNAs. Since mitochondrial protein synthesis in S. cerevisiae is not essential for viability, RPM2 must provide another function in addition to its known role as a mitochondrial tRNA processing enzyme. During a search for RPM2 homologues from Kluyveromyces lactis, we recovered a K. lactis gene that compensates for the essential function but not the RNase P function of RPM2. We have named this gene SEF1 (Suppressor of the Essential Function). DNA sequence analysis of SEF1 reveals it contains a Zn(2)-Cys(6) binuclear cluster motif found in a growing number of yeast transcription factors. The SEF1 homologue of S. cerevisiae also compensates for the essential function of RPM2. The two proteins share 49% identity and 72% amino acid sequence similarity. The SEF1 sequence has been deposited in the GenBank data library under accession number U92898. © 1998 John Wiley & Sons, Ltd.

Yeast verprolin, encoded by VRP1, is implicated in cell growth, cytoskeletal organization, endocytosis and mitochondrial protein distribution and function. We show that verprolin is also required for bipolar bud-site selection. Previously we reported that additional actin suppresses the temperature-dependent growth defect caused by a mutation in VRP1. Here we show that additional actin suppresses all known defects caused by vrp1-1 and conclude that the defects relate to an abnormal cytoskeleton. Using the two-hybrid system, we show that verprolin binds actin. An actin-binding domain maps to the LKKAET hexapeptide located in the first 70 amino acids. A similar hexapeptide in other acting-binding proteins was previously shown to be necessary for actin-binding activity. The entire 70– amino acid motif is conserved in novel higher eukaryotic proteins that we predict to be actin-binding, and also in the actin-binding proteins, WASP and N-WASP. Verprolin-GFP in live cells has a cell cycle-dependent distribution similar to the actin cortical cytoskeleton. In fixed cells hemagglutinin-tagged Vrp1p often co-localizes with actin in cortical patches. However, disassembly of the actin cytoskeleton using Latrunculin-A does not alter verprolin's location, indicating that verprolin establishes and maintains its location independent of the actin cytoskeleton. Verprolin is a new member of the actin-binding protein family that serves as a polarity development protein, perhaps by anchoring actin. We speculate that the effects of verprolin upon the actin cytoskeleton might influence mitochondrial protein sorting/function via mRNA distribution.

Rpm2p is a protein subunit of Saccharomyces cerevisiae yeast mitochondrial RNase P, an enzyme which removes 5' leader sequences from mitochondrial tRNA precursors. Precursor tRNAs accumulate in strains carrying a disrupted allele of RPM2. The resulting defect in mitochondrial protein synthesis causes petite mutants to form. We report here that alteration in the biogenesis of Rpm1r, the RNase P RNA subunit, is another consequence of disrupting RPM2. High-molecular-weight transcripts accumulate, and no mature Rpm1r is produced. Transcript mapping reveals that the smallest RNA accumulated is extended on both the 5' and 3' ends relative to mature Rpm1r. This intermediate and other longer transcripts which accumulate are also found as low-abundance RNAs in wild-type cells, allowing identification of processing events necessary for conversion of the primary transcript to final products. Our data demonstrate directly that Rpm1r is transcribed with its substrates, tRNA met f and tRNAPro, from a promoter located upstream of the tRNA met f gene and suggest that a portion also originates from a second promoter, located between the tRNA met f gene and RPM1. We tested the possibility that precursors accumulate because the RNase P deficiency prevents the removal of the downstream tRNAPro. Large RPM1 transcripts still accumulate in strains missing this tRNA. Thus, an inability to process cotranscribed tRNAs does not explain the precursor accumulation phenotype. Furthermore, strains with mutant RPM1 genes also accumulate precursor Rpm1r, suggesting that mutations in either gene can lead to similar biogenesis defects. Several models to explain precursor accumulation are presented.

CCA1 codes for mitochondrial, cytosolic, and nuclear ATP(CTP):tRNA nucleotidyltransferase. Studies reported here examine the mechanisms leading to and the consequences of altering the distribution of this important tRNA processing enzyme. We show that the majority of Cca1p-I, translated from the first in-frame ATG, is in mitochondria but surprisingly, there is a small contribution to nuclear and cytosolic tRNA processing by this form as well. The majority of Cca1p-II and Cca1p-III, translated from ATG2 and ATG3, respectively, is in the cytosol but both are also located in the nucleus for processing precursors. Altering the cytosolic/nuclear distribution of Cca1p by fusing the SV40 nuclear localization signal to the 5′ end of CCA1 causes a growth defect and results in the accumulation of end-shortened tRNAs in the cytosol. These results suggest an important role for Cca1p in the cytosol of eukaryotes, presumably in the repair of 3′ CCA termini. These experiments also demonstrate that individual tRNAs are affected differently by reduced cytosolic nucleotidyltransferase and that cells resuming exponential growth are more severely affected than those continuing exponential growth.

The Saccharomyces cerevisiae MOD5 gene encodes proteins that function in three subcellular locations: mitochondria, the cytoplasm, and nuclei (M. Boguta, L.A. Hunter, W.-C. Shen, E. C. Gillman, N. C. Martin, and A. K. Hopper, Mol. Cell. Biol. 14:2298-2306, 1994; E. C. Gillman, L. B. Slusher, N. C. Martin, and A. K. Hopper, Mol. Cell. Biol. 11:2382-2390, 1991). A mutant allele of MOD5 encoding a protein (Mod5p-I,KR6) located predominantly in mitochondria was constructed. Mutants defective in delivering Mod5p-I,KR6 to mitochondria were sought by selecting cells with increased cytosolic activity of this protein. Twenty-five mutants defining four complementation groups, mdp1, mdp2, mdp3, and mdp4, were found. They are unable to respire at 34 degrees C or to grow on glucose medium at 38 degrees C. Cell fractionation studies showed that mdp1, mdp2, and mdp3 mutants have an altered mitochondrial-cytoplasmic distribution of Mod5p. mdp2 can be suppressed by ACT1, the actin-encoding gene. The actin cytoskeleton organization is also aberrant in mdp2 cells. MDP2 is the same as VRP1 (S. F. H. Donnelly, M. J. Picklington, D. Pallotta, and E. Orr, Mol. Microbiol. 10:585-596, 1993). MDP3 is identical to PAN1, which encodes a protein that interacts with mRNA 3' ends and affects initiation of protein synthesis (A. B. Sachs and J. A. Deardoff, Cell 70:961-973, 1992). These results implicate the actin cytoskeleton and mRNA 3' ends and/or protein synthesis as being as important for protein distribution in S. cerevisiae as they are for distribution of cytosolic proteins in higher eukaryotes. This provides the potential to apply genetic and molecular approaches to study gene products and mechanisms involved in this type of protein distribution. The selection strategy also offers a new approach for identifying gene products involved in the distribution of proteins to their subscellular destinations.

Mitochondrial RNase P RNA (Rpm1r) is coded by the RPM1 gene of mitochondrial DNA in many yeasts. As an initial step to developing a genetic approach to the structure and biogenesis of yeast mitochondrial RNase P, biolistic transformation has been used to introduce wild type and altered RPM1 genes into strains containing no mitochondrial DNA. The introduced wild type gene does support RNase P activity demonstrating that pre-existing RNase P activity is not necessary for the biosynthesis of the enzyme. Mutations introduced into RPM1 in vitro result in reduced accumulation of mature tRNA and in an alteration of the processing of Rpm1r in vivo.

Two forms of Mod5p, a tRNA modification enzyme, are found in three intracellular compartments, mitochondria, cytoplasm and nucleus, but are encoded by a single MOD5 gene. The two forms of the enzyme, Mod5p-I and Mod5p-II differ at the N-termini and are produced by initiation of translation at different start codons. Mod5p-I does contain a mitochondrial targeting signal and is distributed between mitochondria and cytoplasm, whereas Mod5p-II is found in the cytosol and nucleus (Boguta, M., et al. 1994, Mol. Cell. Biol. 14, 2298-2306). In the present work mutants which mislocalize the Mod5p-I enzyme were isolated. The screen was based on a correlation between the amount of cytosolic protein and the efficiency of tRNA mediated suppression. Identification of mutants is possible because a red pigment accumulates in the cells unable to suppress an ade2-1 nonsense allele. The maf1 mutant, with an altered intracellular localization of the Mod5p-I protein, was isolated. Immunofluorescence data suggest that the mutation causes mislocalization of the Mod5p-I to the nucleus.

ATP (CTP):tRNA nucleotidyltransferase catalyzes the addition of the CCA end to tRNAs. In yeast, nucleotidyltransferase is encoded by the CCA1 gene and is localized to three cellular compartments: mitochondria, nucleus, and cytosol. There are three in-frame ATGs near the 5‘ end of the CCA1 open reading frame. Primer extension experiments show multiple transcription initiation sites upstream of ATG1 and between ATG1 and ATG2. Fractionation of cells carrying a CCA1-COXIV fusion gene demonstrates that all three in-frame AUGs are used as sites of initiation of translation. Therefore, both transcription of CCA1 mRNA with heterogeneous 5‘ ends and translation from downstream AUGs in CCA1 mRNAs play a role in the synthesis of three nucleotidyltransferase isozymes. Protein initiating from AUG1 is required for mitochondrial protein synthesis and, like many other proteins targeted to mitochondria, it is processed at the amino terminus upon import into the organelle. The shorter proteins arising from AUG2 and AUG3 provide nuclear/cytosol activity.

MOD5, a gene responsible for the modification of A37 to isopentenyl A37 of both cytosolic and mitochondrial tRNAs, encodes two isozymes. Initiation of translation at the first AUG of the MOD5 open reading frame generates delta 2-isopentenyl pyrophosphate:tRNA isopentanyl transferase I (IPPT-I), which is located predominantly, but not exclusively, in the mitochondria. Initiation of translation at a second AUG generates IPPT-II, which modifies cytoplasmic tRNA. IPPT-II is unable to target to mitochondria. The N-terminal sequence present in IPPT-I and absent in IPPT-II is therefore necessary for mitochondrial targeting. In these studies, we fused MOD5 sequences encoding N-terminal regions to genes encoding passenger proteins, pseudomature COXIV and dihydrofolate reductase, and studied the ability of these chimeric proteins to be imported into mitochondria both in vivo and in vitro. We found that the sequences necessary for mitochondrial import, amino acids 1 to 11, are not sufficient for efficient mitochondrial targeting and that at least some of the amino acids shared by IPPT-I and IPPT-II comprise part of the mitochondrial targeting information. We used indirect immunofluorescence and cell fractionation to locate the MOD5 isozymes in yeast. IPPT-I was found in two subcellular compartments: mitochondria and the cytosol. We also found that IPPT-II had two subcellular locations: nuclei and the cytosol. The nuclear location of this protein is surprising because the A37-->isopentenyl A37 modification had been predicted to occur in the cytoplasm. MOD5 is one of the first genes reported to encode isozymes found in three subcellular compartments.

As a rule, protein synthesis is initiated with methionine or formyl methionine from the first AUG codon in an ORF and that AUG is recognized by an initiator tRNAMet-i. Internal AUG codons are then translated by a second tRNA, the elongator tRNAMet-e (1). In eubacteria, mitochondria, and chloroplasts, the tRNAMet-i is charged with methionine, and subsequently the methionine is formylated by a methionyl-tRNA transformylase, whereas in the eukaryotic cytosol and archea, the methionine on the tRNAMet-i is not formylated (2). Until now, the one known exception to the tRNAMet-i/tRNAMet-e paradigm occurred in animal mitochondria where a single mtDNA-coded tRNA is thought to serve for both initiation and elongation (3). The work of Tan et al. (4) in this issue of PNAS provides a second exception with several different twists as they show that the function of a tRNA in initiation and/or elongation depends on its location.

We report here the sequence of the RPM2 gene which codes for the 105-kDa protein previously purified from the mitochondria of Saccharomyces cerevisiae and shown by genetic techniques to be required for mitochondrial RNase P activity. The sequence predicts a primary translation product of 1202 residues with a molecular mass of 139 kDa and no obvious sequence similarity to any known protein in the data bases. There are 122 amino-terminal amino acids predicted by the gene that are not found in the purified protein, some of which may play a role in mitochondrial targeting of the protein. Antibodies raised against a trpE-105-kDa fusion protein recognize a 105-kDa protein in wild-type cells but not in cells carrying a disruption of the RMP2 gene. Immune, but not preimmune serum, immunoprecipitates the RNase P RNA and the mitochondrial RNase P activity. Thus, the 105-kDa protein forms a complex with RNase P RNA and is required for RNase P activity as predicted for a bona fide subunit of the enzyme.

A number of mutants with pleiotropic effects on mitochondrial metabolism have been isolated in yeast Saccharomyces cerevisiae, and for many the biochemical function that is impaired is not yet known. We report here the isolation and characterization of the LIP5 gene involved in lipoic acid metabolism which complements the g189 mutant (Tzagoloff, A., and Dieckmann, C. L. (1990) Microbiol. Rev. 54, 211-225). DNA sequence analysis of complementing yeast genomic DNA revealed an open reading frame predicting a protein of 414 amino acids. The protein sequence deduced from the gene shares 43% identical residues with the product of the Escherichia coli lip gene, which codes an enzyme involved in lipoic acid synthesis. The LIP5 mutant is not capable of synthesizing lipoic acid but still possesses the activity necessary for attachment of lipoic acid to protein. Relative to the E. coli lip gene product, the LIP5 protein has an amino-terminal extension with characteristics of mitochondrial targeting signals. Cells carrying a disrupted copy of the LIP5 gene show slow growth on ethanol-rich media and barely detectable growth on glycerol-rich media. Unlike other strains with defects in the tricarboxylic acid cycle, LIP5 mutants undergo a high frequency of mitochondrial DNA deletions.

The TRM1 gene of Saccharomyces cerevisiae codes for a tRNA modification enzyme, N2,N2-dimethylguanosine-specific tRNA methyltransferase (m2(2)Gtase), shared by mitochondria and nuclei. Immunofluorescent staining at the nuclear periphery demonstrates that m2(2)Gtase localizes at or near the nuclear membrane. In determining sequences necessary for targeting the enzyme to nuclei and mitochondria, we found that information required to deliver the enzyme to the nucleus is not sufficient for its correct subnuclear localization. We also determined that mislocalizing the enzyme from the nucleus to the cytoplasm does not destroy its biological function. This change in location was caused by altering a sequence similar to other known nuclear targeting signals (KKSKKKRC), suggesting that shared enzymes are likely to use the same import pathway as proteins that localize only to the nucleus. As with other well-characterized mitochondrial proteins, the mitochondrial import of the shared methyltransferase depends on amino-terminal amino acids, and removal of the first 48 amino acids prevents its import into mitochondria. While this truncated protein is still imported into nuclei, the immunofluorescent staining is uniform throughout rather than at the nuclear periphery, a staining pattern identical to that described for a fusion protein consisting of the first 213 amino acids of m2(2)Gtase in frame with beta-galactosidase. As both of these proteins together contain the entire m2(2)Gtase coding region, the information necessary for association with the nuclear periphery must be more complex than the short linear sequence necessary for nuclear localization.

RNase P from the mitochondria of Saccharomyces cerevisiae was purified to near homogeneity > 1800-fold with a yield of 1.6% from mitochondrial extracts. The most abundant protein in the purified fractions is, at 105 kDa, considerably larger than the 14-kDa bacterial RNase P protein subunits. Oligonucleotides designed from the amino-terminal sequence of the 105-kDa protein were used to identify and isolate the 105-kDa protein-encoding gene. Strains carrying a disruption of the gene for the 105-kDa protein are viable but respiratory deficient and accumulate mitochondrial tRNA precursors with 5' extensions. As this is the second gene known to be necessary for yeast mitochondrial RNase P activity, we have named it RPM2 (for RNase P mitochondrial).

ATP (CTP):tRNA-specific tRNA nucleotidyltransferase is an enzyme required for the synthesis of functional tRNAs in eukaryotic cells. Neither the tRNA genes in the nucleus nor in organelles encode the CCA end, so it must be added post-transcriptionally. The gene that codes for the enzyme that adds the CCA end to nuclear coded tRNAs in Saccharomyces cerevisiae has been isolated (Aebi, M., Kirchner, G., Chen, J.-Y., Vijayraghavan, U., Jacobson, A., Martin, N. C., and Abelson, J. (1990) J. Biol. Chem. 265, 16216-16220). We now demonstrate that there is a mitochondrial tRNA nucleotidyltransferase activity in yeast and that it is a matrix enzyme. A comparison of purified mitochondrial enzyme with its cytoplasmic counterpart revealed no differences. These results suggest that proteins responsible for this step in the maturation of tRNAs in the nucleus and mitochondria might be identical and coded by the same nuclear gene. Accumulation of shortened mitochondrial as well as cytoplasmic tRNAs in a strain with a temperature-sensitive tRNA nucleotidyltransferase is consistent with this hypothesis. Alteration of the wild type gene such that amino-terminal truncated proteins are produced leads to a defect in mitochondrial function and a decrease in mitochondrial nucleotidyltransferase activity. This provides a direct demonstration that one gene provides this enzyme activity for the biosynthesis of tRNAs in both the nuclear/cytoplasmic and mitochondrial compartments in yeast.

MOD5, a nuclear gene of Saccharomyces cerevisiae, encodes two isozymic forms of a tRNA-modification enzyme. These enzymes modify both cytoplasmic and mitochondrial tRNAs. Two inframe ATGs of the MOD5 gene are used for initiation of translation, and the form of the protein translated from the first AUG is imported into mitochondria. Protein translated from the second AUG functions in the cytoplasm. Since all transcripts contain both of these translational start sites and two proteins are made, the question arises as to the factors that influence the translation start-site choice. Extending the 5' ends of the MOD5 mRNA to include leader sequences of the ADH1 (alcohol dehydrogenase defective) transcript produces significant changes in the choice of AUGs. This suggests that for wild-type MOD5 transcripts, the length or structure of the leader sequence plays a role in AUG choice. The nucleotides surrounding the first ATG of MOD5 also have an effect on translation initiation. Altering these nucleotides changes initiation choice and suggests that ribosomal bypass of a suboptimal AUG is another mechanism controlling the alternate use of two initiation codons. Our data support the model that at least one MOD5 transcript is able to produce two proteins with different N-terminal sequences.

MOD5 is one of several genes that code for enzymes found in mitochondria and another cellular compartment. Like other such genes, it contains two in-frame ATGs that could be used to produce two proteins, differing from each other by an amino-terminal extension. Certain other genes produce heterogeneous mRNAs with some 5' ends falling upstream of the longest open reading frame and some 5' ends falling between the first and second ATGs. In these cases, selection of transcription start sites appears to play a significant role in translation start site selection. MOD5, in contrast, produces mRNAs with 5' ends that all fall upstream of both ATGs. To determine how MOD5 encodes isozymes that are located in different cellular compartments and to determine whether they differ in structure, we constructed MOD5 and MOD5-COXIV fusions with mutations of the first, second, or both ATGs. The effect of these alterations on protein production, tRNA modification, and cellular location was assessed. Both the first and second ATGs are used to produce MOD5 protein in vivo, but only the long form of the protein is imported into mitochondria. Thus, the first 11 amino acids present on the amino-terminal extended protein are necessary for mitochondrial import. Surprisingly, this extension does not promote complete import of the long form of the protein, but rather a functional pool of the extended protein remains in the cytoplasm. The amino-terminal extension is also unusual because it is probably not proteolytically removed upon import and therefore does not constitute part of a mitochondrial presequence.

We have mapped a gene in the mitochondrial DNA of Candida (Torulopsis) glabrata and shown that it is required for 5' end maturation of mitochondrial tRNAs. It is located between the tRNAfMet and tRNAPro genes, the same tRNA genes that flank the mitochondrial RNase P RNA gene in the yeast Saccharomyces cerevisiae. The gene is extremely AT rich and codes for AU-rich RNAs that display some sequence homology with the mitochondrial RNase P RNA from S. cerevisiae, including two regions of striking sequence homology between the mitochondrial RNAs and the bacterial RNase P RNAs. RNase P activity that is sensitive to micrococcal nuclease has been detected in mitochondrial extracts of C. glabrata. An RNA of 227 nucleotides that is one of the RNAs encoded by the gene that we mapped cofractionated with this mitochondrial RNase P activity on glycerol gradients. The nuclease sensitivity of the activity, the cofractionation of the RNA with activity, and the homology of the RNA with known RNase P RNAs lead us to propose that the 227-nucleotide RNA is the RNA subunit of the C. glabrata mitochondrial RNase P enzyme.

The biosynthesis of some mitochondrial enzymes requires contributions of both the mitochondrial and nuclear genomes. The ribonucleoprotein enzyme Ribonuclease P (RNase P) is composed of a mitochondrial encoded RNA and nuclear coded protein in many yeasts, including C. glabrata. We have determined that there are at least two sites of transcription initiation that contribute to the expression of the mitochondrial RNase P RNA. A nonanucleotide promoter sequence is located upstream of the initiator tRNA while the other site of initiation of transcription is at an undetermined upstream site. An analysis of the transcripts from the region of the RNase P gene demonstrates directly that the RNase P RNA is present in large primary transcripts and located between the precursors to the initiator tRNAf(Met) and tRNA(Pro) genes. Thus this enzyme subunit is synthesized with some of its substrate tRNAs. An activity with cleavage site specificity like a previously described endonuclease that cleaves near the 3' end of tRNAs, RNase P activity and one or more additional endonucleases or exonucleases not described previously are required to convert the primary transcript to its final functional RNAs.

In the decade beginning in 1996, the National Institutes of Health (NIH) budget doubled, whereas NIH funding at the University of Louisville School of Medicine increased nearly sevenfold. The schools of nursing and dentistry, the other Health Science Center schools at Louisville, experienced comparable growth. The University of Louisville was thus one of the fastest growing research enterprises in the country during this period. While there was an infusion of state funds, the authors believe that the magnitude of the research growth depended more critically on development of an effective strategic plan with closely monitored outcomes. This process included first the identification of programs of distinction deserving of investment and then the reallocation of resources from units that were not research-intensive to those that were. The strategy focused on (1) the recruitment of endowed chairs and their teams (thus the popular name for the program "Bucks for Brains"), (2) the implementation of new promotion and tenure standards, (3) the creation of research-productivity linked salary incentives, (4) the implementation of posttenure review, and (5) an effort to improve research infrastructure, including core facilities, and physical plant. The authors describe how the investment by the Commonwealth of Kentucky was structured and how accountability to the state facilitated this growth. This description of how postsecondary education reform and the infusion of modest resources through the Research Challenge Trust Fund were leveraged into a substantial return-on-investment at Louisville could serve as a guide to schools during this time of NIH budgetary constraint.

Stress signals such as amino acid deprivation and redox imbalances activate the integrated stress response (ISR), which allows cells to alleviate the stress or to undergo apoptosis if the stress is unresolved. The ISR is also important for the survival of cancer cells, since they experience stress in the form of nutrient and oxygen deprivation and hence frequently activate stress-response pathways. Cellular stresses trigger up-regulation of the transcription factor ATF4, which subsequently activates stress response genes through recruitment to cis-regulatory sites known as C/EBP:ATF response elements (CAREs). Although the role of ATF4 in regulating stress response is well established, the identity of the C/EBP partner that heterodimerizes with ATF4 to execute this crucial function remains obscure. Here we show that the transcription factor C/EBPG is a critical partner of ATF4 and that C/EBPG:ATF4 heterodimers are the predominant CARE-binding species in stressed cells. Similar to ATF4, C/EBPG is necessary for resistance of MEFs to oxidative stress. MEFs lacking C/EBPG show increased levels of reactive oxygen species (ROS) as a consequence of impaired glutathione biosynthesis, as was also seen in ATF4-deficient MEFs. C/EBPG is required for stress-induced association of ATF4 with CAREs and the subsequent activation of several critical stress-responsive genes, including those with known pro-oncogenic functions. Accordingly, resistance to stress conferred by C/EBPG also facilitates the growth of cancer cells. Depletion of C/EBPG impairs the proliferation of cancer cells in vitro and elevates ROS levels. These effects can be suppressed by addition of the antioxidant, N-acetylcysteine. Mice lacking C/EBPG are smaller in size and show defective eye lens formation, similar to ATF4-deficient mice. The absence of C/EBPG also causes perinatal mortality due to pulmonary atelectasis and respiratory failure. This mortality can be rescued by in utero exposure to N-acetylcysteine. Accordingly, gene expression analysis suggests the presence of increased oxidative stress and impaired expression of stress-responsive genes in the lungs of Cebpg-/- newborn mice. Interestingly, Cebpg-/- mice on a mixed strain background, which do not show perinatal lethality, are resistant to the development of solid malignant tumors. These findings suggest that the role of C/EBPG as a stress response regulator may be important for tumor development/progression. A pro-oncogenic function for C/EBPG is also suggested by the observation that elevated C/EBPG levels are associated with poor patient prognosis in several clinical cancer studies. Activation of stress-responsive genes through upregulation of C/EBPG could be a mechanism deployed by cancer cells to mitigate the high levels of ROS and metabolic stresses that they experience. The importance of C/EBPG and its targets in tumor cells could potentially be exploited to devise novel anti-cancer therapies. Citation Format: Manasi K. Mayekar, Christopher J. Huggins, Nancy Martin, Karen L. Saylor, Mesfin Gonit, Parthav Jailwala, Manjula Kasoji, Diana C. Haines, Octavio A. Quinones, Peter F. Johnson. C/EBPG: A critical stress response regulator with a pro-oncogenic role. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr PR02.

ATP (CTP):tRNA nucleotidyltransferase (EC 2.7.7.25) has been purified from wild type cells of the yeast Saccharomyces cerevisiae, as well as from a strain that overproduces the activity. Purification from the wild type strain was accomplished with a multistep protocol including ammonium sulfate fractionation, anion exchange chromatography, gel filtration, and affinity chromatography. The purified enzyme is near homogeneity as evidenced by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and at 59,000 Da is smaller than reported previously. A similar molecular mass is obtained by gel filtration demonstrating that the enzyme is active as a monomer. The pH optimum for the enzyme is around 9.5. The apparent KM values for ATP and CTP were determined to be 5.6 x 10(-4) M and 1.8 x 10(-4) M, respectively. Purification of the enzyme from the overproducing cells was accomplished by a three step protocol with high yield. The nucleotidyltransferase activity from the overproducing cells had a KM for CTP indistinguishable from that of the wild type enzyme, and the mobility of the protein on sodium dodecyl sulfate gels was the same regardless of the source. Thus, the overproducing strain appears to be a good source for large amounts of yeast nucleotidyltransferase for further biochemical and structural studies.

Rpm2p, a protein subunit of yeast mitochondrial RNase P, has another function that is essential in cells lacking the wild-type mitochondrial genome. This function does not require the mitochondrial leader sequence and appears to affect transcription of nuclear genes. Rpm2p expressed as a fusion protein with green fluorescent protein localizes to the nucleus and activates transcription from promoters containing lexA-binding sites when fused to a heterologous DNA binding domain, lexA. The transcriptional activation region of Rpm2p contains two leucine zippers that are required for transcriptional activation and are conserved in the distantly related yeast Candida glabrata. The presence of a mitochondrial leader sequence does not prevent a portion of Rpm2p from locating to the nucleus, and several observations suggest that the nuclear location and transcriptional activation ability of Rpm2p are physiologically significant. The ability of RPM2 alleles to suppress tom40-3, a temperature-sensitive mutant of a component of the mitochondrial import apparatus, correlates with their ability to transactivate the reporter genes with lexA-binding sites. In cells lacking mitochondrial DNA, Rpm2p influences the levels of TOM40, TOM6, TOM20, TOM22, and TOM37 mRNAs, which encode components of the mitochondrial import apparatus, but not that of TOM70 mRNA. It also affects HSP60 and HSP10 mRNAs that encode essential mitochondrial chaperones. Rpm2p also increases the level of Tom40p, as well as Hsp60p, but not Atp2p, suggesting that some, but not all, nucleus-encoded mitochondrial components are affected.

Rpm2p is a protein subunit of yeast mitochondrial RNase P and is also required for the maturation of Rpm1r, the mitochondrially-encoded RNA subunit of the enzyme. Previous work demonstrated that an insertional disruption of RPM2, which produces the C-terminally truncated protein Rpm2-DeltaCp, supports growth on glucose but cells lose some or all of their mitochondrial genome and become petite. These petites, even if they retain the RPM1 locus, lose their ability to process the 5'-ends of mitochondrial tRNA. We report here that if strains containing the truncated RPM2 allele are created and maintained on respiratory carbon sources they have wild-type mitochondrial genomes, and a significant portion of tRNA transcripts are processed. In contrast, precursor Rpm1r transcripts accumulate and mature Rpm1r is not made. These data show that one function of the deleted C-terminal region is in the maturation of Rpm1r, and that this region and mature Rpm1r are not absolutely required for RNase P activity. Finally, we demonstrate that full activity can be restored if the N-terminal and C-terminal domains of Rpm2p are supplied in trans.

The yeast RNA polymerase III (Pol III) transcription system is well characterized. Small untranslated RNAs with essential housekeeping functions, such as tRNAs, 5S rRNA, or the U6 small nuclear RNA (snRNA) that is required for mRNA splicing, are synthesized by Pol III with the help of two general auxiliary factors, TFIIIC and TFIIIB. The large TFIIIC factor (six subunits) binds to the DNA promoter elements and assembles the initiation factor TFIIIB (three components) upstream of the start site. Once TFIIIB is in position, it recruits the Pol III enzyme (17 subunits) and directs accurate and multiple rounds of transcription. All of the polypeptide components of the Pol III apparatus (∼1,500 kDa) have been characterized and found to be essential for cell viability (8, 23). The identification of the components of the Pol III system has facilitated the description of a cascade of protein-protein interactions that leads to the recruitment of the Pol III enzyme (reviewed in reference 55). Detailed knowledge of the yeast Pol III transcription system contrasts with the limited information available on the control of class III gene expression in yeast. Cellular tRNA levels respond to cell growth rate (48, 49), to a nutritional upshift (27, 48) or to nitrogen starvation (36) but only modestly to amino acid starvation (41). Finally, Pol III transcription is repressed in secretion-defective cells (30). Although the mechanism of repression is not clear, it does involve activation of the cell integrity pathway (30). The effect of growth conditions on Pol III transcription is well mimicked in vitro with whole-cell extracts (11, 39). tRNA synthesis is downregulated in dense cell cultures approaching stationary phase, a result due essentially to reduced TFIIIB activity. The TFIIIB component Brf/TFIIIB70 was found to be the limiting factor in extracts from such cells (39). However, the occupancy of the TFIIIB binding site on the SUP53 gene encoding tRNALeu does not decrease in stationary-phase cells. Rather, in vivo footprinting data suggest reduced promoter occupancy by Pol III (25). In higher eukaryotic cells, Pol III transcription responds to growth rate, developmental phase, cell cycle position, and a number of pathological conditions (reviewed in reference 55). The regulation operates principally at the level of TFIIIB and TFIIIC (17, 20, 42, 46, 52). The tumor suppressors Rb and p53 inhibit TFIIIB (9, 10, 28, 53). Therefore, it is likely that the control of Pol III transcription rate is important in restraining tumor cell proliferation (54). No equivalent negative regulator of Pol III transcription has been found in yeast. Genes controlling tRNA synthesis in yeast can be identified by nonsense suppression approaches (22). One candidate for such a gene is Saccharomyces cerevisiae MAF1. It was originally identified by the isolation of maf1-1 as a temperature-sensitive mutation that decreases the efficiency of SUP11 (tRNA Tyr/UAA) suppression (34). A search for multicopy suppressors of maf1-1 revealed an intriguing genetic interaction between MAF1 and RPC160, the gene encoding the largest subunit of the RNA Pol III, C160. RPC160 genes with 3′ deletions in their open reading frame suppress the maf1-1 phenotypes when overexpressed (6). In the present work, we show that tRNA levels are elevated in maf1-1 cells and that spontaneous mutations in RPC160 which reduce tRNA levels also suppress the growth phenotype associated with maf1-1. maf1-1 cell extracts support increased levels of Pol III transcription in vitro compared to wild-type cells. Further, we show that Maf1p is a nuclear protein that physically interacts with RNA Pol III. Therefore, Maf1p appears to be a negative effector of Pol III activity, potentially regulating the level of cellular tRNA in response to external signals. A database search revealed that a variety of organisms have sequences similar to Maf1p, suggesting that this type of Pol III regulation may not be limited to yeast.

The Saccharomyces cerevisiae Mod5 protein catalyzes isopentenylation of A to i 6 A on tRNAs in the nucleus, cytosol, and mitochondria. The substrate for Mod5p, dimethylallyl pyrophosphate, is also a substrate for Erg20p that catalyzes an essential step in sterol biosynthesis. Changing the distribution of Mod5p so that less Mod5p is present in the cytosol decreases i 6 A on cytosolic tRNAs and alters tRNA-mediated nonsense suppression. We devised a colony color/growth assay to assess tRNA-mediated nonsense suppression and used it to search for genes, which, when overexpressed, affect nonsense suppression. We identified SAL6 , TEF4 , and YDL219w, all of which likely affect nonsense suppression via alteration of the protein synthesis machinery. We also identified ARC1 , whose product interacts with aminoacyl synthetases. Interestingly, we identified ERG20 . Midwestern analysis showed that yeast cells overproducing Erg20p have reduced levels of i 6 A on tRNAs. Thus, Erg20p appears to affect nonsense suppression by competing with Mod5p for substrate. Identification of ERG20 reveals that yeast have a limited pool of dimethylallyl pyrophosphate. It also demonstrates that disrupting the balance between enzymes that use dimethylallyl pyrophosphate as substrate affects translation.

In vitro cultured “activated” peripheral blood lymphocytes and T-cell lines synthesized a high-molecular-weight gelatin binding molecule (MW 500 kDa), whereas resting lymphocytes showed poor or negligible synthesis of the same component. Concanavalin A-mediated anchorage of the lymphocytes to a substratum potentiated synthesis of the high-molecular-weight molecule. Western blotting of the gelatin-binding lymphocyte molecule demonstrated reactivity with antibodies specific for human fibronectin. Furthermore, immunocytochemistry showed reactivity of anti-fibronectin antibodies with T-lymphocytes at the single-cell level. The lymphocyte-derived fibronectin was preferentially cell associated and relatively small amounts were present in the culture medium. RT-PCR of total RNA from CD4 + T-cells and the lymphoid T-cell line MOLT-4 showed that the most abundant species of fibronectin mRNA lacked the entire III CS exon encoding the α 4 β 1 binding region LDV. Amplification of the III CS region from other T-cell lines revealed that these cells expressed several fibronectin mRNA isoforms most of which were lacking the LDV coding sequence. In conclusion, synthesis of fibronectin is demonstrated to occur in T-lymphocytes and to be regulated by signals which activate the cells.

Publisher Summary Yeast mitochondrial RNase P is the endonuclease, which is is composed of both RNA and protein subunits coded by the mitochondrial and nuclear genomes, respectively. This chapter describes the in vivo and in vitro approaches used to understand the nucleocytoplasmic interactions necessary for the biosynthesis of this dually derived complex of yeast mitochondria and to gain insight into RNase P structure and function. Many questions about this enzyme and its biosynthesis remain despite the identification and current characterization of Rpm1r and Rpm2p. First, none of the experiments eliminates the possible presence of a nuclear encoded RNA in this enzyme. Second, although Rpm2p clearly fills all the criteria expected of a protein subunit of the enzyme and is the most abundant protein in near homogeneous preparations, it is possible that other proteins play either essential or stimulatory roles. Successful production of sufficient Rpm2p for in vitro reconstitution studies should determine if Rpm1r and Rpm2p are the only components necessary to support full activity in vitro. If they are, studies on the biochemistry and biogenesis of a well-defined yeast mitochondrial RNase P can be initiated. Immunoprecipitation of complexes or cross-linking between the known RNA and proteins offer other approaches to identify additional components that can be required for in vitro reconstitution or be associated with the enzyme in vivo.

Most steps in the maturation of nuclear coded tRNAs occur in the nucleus in eukaryotic cells, but little is known as to the intranuclear location of this RNA maturation pathway. Indirect immunofluorescence experiments using antibody to N2,N2 dimethylguanosine-specific tRNA methyltransferase, a tRNA processing enzyme, and to Nup1p, a nuclear pore protein, show that both locate to the nuclear periphery in wild type cells. Staining of the nuclear membrane is more uniform with anti-Trm1p than the punctate staining observed with antibodies recognizing Nup1p. Biochemical fractionation experiments comparing fractionation of Trm1p with Nup1p, tRNA splicing ligase, and tRNA splicing endonuclease show that Trm1p behaves more like the known peripheral nuclear membrane proteins, Nup1p and tRNA splicing ligase, than like the integral membrane protein, tRNA splicing endonuclease. Cells overproducing Trm1p also concentrate it to the nuclear periphery. Thus, the site(s) of interaction of Trm1p are not easily saturable and are likely to be in excess to Trm1p. Trm1p is shared by mitochondria and the nucleus. Cells transformed with a gene coding Trm1p with a mutant nuclear targeting signal display cytoplasmic staining and an enzyme with increased solubility when compared to the solubility of wild type enzyme. Thus, mutations that prevent the enzyme from entering the nucleus result in an increase in its cytosolic but not mitochondrial concentration suggesting that the mitochondrial/nuclear distribution of Trm1p is not due solely to competition of mitochondrial and nuclear targeting information.

We review here our studies of the tRNA processing enzyme, RNase P. Yeast mitochondrial RNase P contains an AU-rich mitochondrial coded RNA which varies in size in different yeasts. All of these RNAs contain two short sequences with similarity to two sequences found in all RNase P RNAs. The only identified protein subunit, coded by the RPM2 gene, is much larger than and displays little similarity to the bacterial protein subunits. Progress to date and issues for future research are discussed.

TRM1, MOD5 and CCA1 are yeast genes that provide tRNA processing enzymes to mitochondria and the nuclear/cytosolic compartments. The product of the TRM1 gene is N2,N2 dimethylguanosine tRNA methyltransferase. The product of the MOD5 gene is isopentenyl pyrophosphate: tRNA isopentenyl transferase and the product of the CCA1 gene is ATP (CTP): tRNA nucleotidyltransferase. N2,N2 dimethylguanosine tRNA methyltransferase is found in the mitochondria and the nucleus. The tRNA isopentenyl transferase and tRNA nucleotidyltransferase are found in mitochondria, nuclei and the cytosol. Genes coding for these three enzymes contain more than one in-frame ATG. Where translation begins dictates the efficiency with which these gene products reach mitochondria. Depending on the gene, ATGs choice is by transcription start site selection, by translational selection or by an interplay between these two processes. A short amino acid sequence is necessary and sufficient for the nuclear targeting of the dimethylguanosine transferase. There is a good candidate sequence for a nuclear targeting signal (NTS) for the isopentenyl pyrophosphate: tRNA isopentenyl transferase. There are no obvious candidate sequences for a NTS in the CCA1 sequence.

Protein disulfide bond formation in Escherichia coli requires the periplasmic protein DsbA. We describe here mutations in the gene for a second protein, DsbB, which is also necessary for disulfide bond formation. Evidence suggests that DsbB may act by reoxidizing DsbA, thereby regenerating its ability to donate its disulfide bond to target proteins. We propose that DsbB, an integral membrane protein, may be involved in transducing redox potential across the cytoplasmic membrane.

MOD5 is one of several genes that code for enzymes found in mitochondria and another cellular compartment. Like other such genes, it contains two in-frame ATGs that could be used to produce two proteins, differing from each other by an amino-terminal extension. Certain other genes produce heterogeneous mRNAs with some 5' ends falling upstream of the longest open reading frame and some 5' ends falling between the first and second ATGs. In these cases, selection of transcription start sites appears to play a significant role in translation start site selection. MOD5, in contrast, produces mRNAs with 5' ends that all fall upstream of both ATGs. To determine how MOD5 encodes isozymes that are located in different cellular compartments and to determine whether they differ in structure, we constructed MOD5 and MOD5-COXIV fusions with mutations of the first, second, or both ATGs. The effect of these alterations on protein production, tRNA modification, and cellular location was assessed. Both the first and second ATGs are used to produce MOD5 protein in vivo, but only the long form of the protein is imported into mitochondria. Thus, the first 11 amino acids present on the amino-terminal extended protein are necessary for mitochondrial import. Surprisingly, this extension does not promote complete import of the long form of the protein, but rather a functional pool of the extended protein remains in the cytoplasm. The amino-terminal extension is also unusual because it is probably not proteolytically removed upon import and therefore does not constitute part of a mitochondrial presequence.

To study the mechanism involved in the 3'-processing of mitochondrial tRNA precursors, we examined tRNA processing in a reconstituted system with a yeast mitochondrial extract. Two mitochondrial tRNA(Glu) precursors synthesized from SP6 RNA polymerase-directed transcription system were used as substrates. One contained a 214-nucleotide 5' terminus and 115-123-nucleotide 3' trailer. The other had the same sized 3' trailer, but contained a mature 5' terminus. An endonucleolytic activity was identified in a mitochondrial S30 fraction which cleaves the 3' terminus of the latter tRNA precursor precisely at the in vivo CCA addition site. No cleavage of the 5'-extended precursor was observed in vitro. This mitochondrial 3'-processing activity was partially purified using DEAE-CL-6B chromatography. It removes the 3' trailer sequence from the 5'-matured precursor leaving a 3'-hydroxyl group on the processed tRNA and a 5'-phosphate group on the trailer. The resulting tRNA product serves as a substrate for tRNA nucleotidyltransferase which catalyzes the addition of CCA residues to the tRNA to complete its 3' maturation. Thus, yeast mitochondrial 3'-tRNA processing events resemble those found in eucaryotic cytoplasmic/nuclear systems where a single endonucleolytic cleavage is responsible for the formation of the 3' end of the tRNAs. This is in contrast to the multistep 3'-processing events known to occur in procaryotes.

The mitochondrial genome of the yeast Saccharomyces cerevisiae codes for tRNAs and rRNAs used in mitochondrial protein synthesis. In addition, mRNAs for some respiratory enzyme components are also gene products of yeast mitochondrial DNA. To begin studies on the transcription of this genome, we have analyzed RNA synthesis in isolated mitochondria from both wild-type and petite strains of yeast and find that discrete RNA species are labeled by incorporation of radioactive precursors. Some of these RNAs correspond to abundant and fully processed RNAs while others appear to be unprocessed precursor RNAs. These findings suggest that this system can be used to study the synthesis of specific RNAs in vitro and to provide substrates for the dissection of RNA processing events in yeast mitochondrial extracts.

Cytoplasmic rRNA from the yeast mutant, mod5-1 is deficient in the modified base isopentenyladenosine and consequently migrates differently from isopentenylated wild type tRNAs on certain chromatographic systems. To determine if the mod5-1 mutation affects mitochondrial tRNA structure, the migration of mitochondrial tRNA from mod5-1 and wild type cells has been compared by reverse-phase chromatography. We conclude from this analysis that the single nuclear mutation that affects the isopentenylation of cytoplasmic tRNA also affects the isopentenylation of mitochondrial tRNA.